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https://openalex.org/W2274817238
https://equityhealthj.biomedcentral.com/counter/pdf/10.1186/s12939-016-0304-1
English
null
Evidence and knowledge gaps on the disease burden in sexual and gender minorities: a review of systematic reviews
International journal for equity in health
2,016
cc-by
8,496
REVIEW Open Access Open Access © 2016 Blondeel 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. Evidence and knowledge gaps on the disease burden in sexual and gender minorities: a review of systematic reviews Karel Blondeel1*, Lale Say2, Doris Chou2, Igor Toskin2,3, Rajat Khosla2, Elisa Scolaro2 and Marleen Temmerman1,2 Blondeel et al. International Journal for Equity in Health (2016) 15:16 DOI 10.1186/s12939-016-0304-1 Blondeel et al. International Journal for Equity in Health (2016) 15:16 DOI 10.1186/s12939-016-0304-1 Blondeel et al. International Journal for Equity in Health (2016) 15:16 DOI 10.1186/s12939-016-0304-1 Abstract Sexual and gender minorities (SGM) include individuals with a wide range of sexual orientations, physical characteristics, and gender identities and expressions. Data suggest that people in this group face a significant and poorly understood set of additional health risks and bear a higher burden of some diseases compared to the general population. A large amount of data is available on HIV/AIDS, but far less on other health problems. In this review we aimed to synthesize the knowledge on the burden of communicable and non-communicable diseases, mental health conditions and violence experienced by SGM, based on available systematic reviews. We conducted a global review of systematic reviews, including searching the Cochrane and the Campbell Collaboration libraries, as well as PubMed, using a range of search terms describing the populations of interest, without time or language restrictions. Google Scholar was also scanned for unpublished literature, and references of all selected reviews were checked to identify further relevant articles. We found 30 systematic reviews, all originally written in English. Nine reviews provided data on HIV, 12 on other sexually transmitted infections (STIs), 4 on cancer, 4 on violence and 3 on mental health and substance use. A quantitative meta-analysis was not possible. The findings are presented in a narrative format. Our review primarily showed that there is a high burden of disease for certain subpopulations of SGM in HIV, STIs, STI-related cancers and mental health conditions, and that they also face high rates of violence. Secondly, our review revealed many knowledge gaps. Those gaps partly stem from a lack of original research, but there is an equally urgent need to conduct systematic and literature reviews to assess what we already know on the disease burden in SGM. Additional reviews are needed on the non-biological factors that could contribute to the higher disease burden. In addition, to provide universal access to health-care for all, more information is needed on the barriers that SGM face in accessing health services, including the attitudes of health-care providers. Understanding these barriers and the additional health risks they impose is crucial to improving the health status of SGM. Keywords: Sexual and gender minorities, Disease burden, LGBT, Health difficulties than others in reaching this standard of health [2]. Those populations can be defined by age, gender, race or ethnicity, geography, wealth, disability, and also by sexual orientation and gender identity. * Correspondence: karel.blondeel@ugent.be 1Ghent University, Ghent, Belgium Full list of author information is available at the end of the article g p p of this article we have grouped men who have sex w men (MSM), women who have sex with women (WSW * Correspondence: karel.blondeel@ugent.be Ghent University, Ghent, Belgium Full list of author information is available at the end of the article © 2016 Blondeel 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. Review Background The Constitution of the World Health Organization (WHO) states that the “enjoyment of the highest attain- able standard of health is one of the fundamental rights of every human being without distinction of race, reli- gion, political belief, economic or social condition” [1]. Although medical ethics require health services to be in- clusive of all people, some populations have more Populations defined by sexual orientation and gender identity include individuals with a wide range of sexual orientations, physical characteristics (as in intersex per- sons), gender identities and expressions, all of which they may experience differently depending on societal gender norms and cultural traditions. For the purposes of this article we have grouped men who have sex with men (MSM), women who have sex with women (WSW), * Correspondence: karel.blondeel@ugent.be 1Ghent University, Ghent, Belgium Full list of author information is available at the end of the article Blondeel et al. International Journal for Equity in Health (2016) 15:16 Page 2 of 9 Page 2 of 9 ‘homosexuality’. We searched PubMed for the terms ‘sys- tematic’ AND ‘review’ combined with a search strategy (see Additional file 1) for sexual and gender minorities (SGM). No language, time or geographical restrictions were applied. The concept of ‘burden of disease’ was not specified in search strategies. Google Scholar was searched in English and references of the included reviews were checked to identify further relevant articles. transgender and intersex persons, all defined by the Joint United Nations Programme on HIV and AIDS (UNAIDS), together under the name of ‘sexual and gen- der minorities’ or SGM [3]. For research, health policy and advocacy reasons, estimating the size of populations of interest is important [4]. Due to stigma associated with homosexuality and non-gender-normative behav- iours, estimates of SGM populations are scarce, but studies show that SGM comprise substantial proportions of the population in countries worldwide [5–7]. transgender and intersex persons, all defined by the Joint United Nations Programme on HIV and AIDS (UNAIDS), together under the name of ‘sexual and gen- der minorities’ or SGM [3]. For research, health policy and advocacy reasons, estimating the size of populations of interest is important [4]. Due to stigma associated with homosexuality and non-gender-normative behav- iours, estimates of SGM populations are scarce, but studies show that SGM comprise substantial proportions of the population in countries worldwide [5–7]. Inclusion and exclusion criteria Data suggest that SGM face a significant and poorly understood set of additional health risks and bear a higher burden of some diseases compared to the general population [8, 9]. There have been international calls to answer the unique health-care needs of SGM [10, 11]. It is therefore indispensable to understand where we are with the knowledge on the health burden of SGM. In 2002 Boehmer showed that research was limited in scope, concentrating mostly on HIV and STIs and MSM [12]. In high-income countries the research scope has been broadening since, but the situation in middle- and low-income countries is less clear [13]. In this review we aimed to collate the knowledge and identify the know- ledge gaps on the burden of communicable and non- communicable diseases, mental health conditions and violence experienced by SGM globally, based on avail- able systematic reviews. Figure 1 shows how publications were selected for re- view. Our initial search generated 399 publications. Based on a review of the abstracts, the following exclu- sions were made: duplicates, one publication lacking an abstract, one protocol of a systematic review, publica- tions that were not systematic reviews, publications without data on disease burden, and publications with- out data on SGM or with data on only a very specific subset of SGM. We then retrieved and read the full text of 50 retained publications. Those were all publications we found on PubMed, the search on the Cochrane Data- base of Systematic Reviews and the Campbell Collabor- ation Library of Systematic Reviews did not generate reviews of interest. Next, we further excluded national reviews if they were included in larger reviews, and re- views that were redundant due to newer published re- views on the same subject and population. Twenty-five articles were retained. An additional five eligible reviews were identified from references and Google Scholar, bringing the total to 30. Search strategy d d y We conducted a review of systematic reviews in con- cordance with the PRISMA statement [16]. The Cochrane Database of Systematic Reviews and the Campbell Collaboration Library of Systematic Reviews were searched using the following terms to identify re- views on the populations of interest: ‘gay’, ‘lesbian’, ‘trans- gender’, ‘WSW’, ‘women who have sex with women’, ‘MSM’, ‘men who have sex with men’, ‘same sex’, ‘sexual orientation’, ‘gender identity’, ‘sexual minority’, ‘intersex’ and Methods A review of systematic reviews can aim to bring together a series of reviews on an important topic or summarize re- views on a variety of topics with a common main theme [14]. This review is of the latter type and while it is un- likely to be of interest to clinicians and patients deciding how best to address a specific problem, it may be relevant to policy makers or to addressing questions that cut across the different reviews [15]. The outcome of a review of re- views is typically a summary of review results. Conducting additional meta-analysis in a review of systematic reviews is a major challenge due to the heterogeneity of the methods, analyses and results of the original reviews. Therefore meta-analysis is not a relevant method to this review of systematic reviews and is descriptive in nature. Quality assessment y The quality of the systematic reviews was assessed with the AMSTAR scale (see Additional file 2) (http:// amstar.ca/). AMSTAR stands for A Measurement Tool to Assess Systematic Reviews and was initially developed to assess systematic reviews of randomised controlled trials [17]. However, it is increasingly being used to as- sess those that include observational studies as well. The scale consists of 11 items. We considered systematic re- views with a score from 0 to 3 as low quality, from 4 to 6 as medium quality, and from 7 up as high quality. The AMSTAR score was not used as an exclusion criterium, but used as an analytic tool. Regardless of the quality, we did not find inconsistencies in the conclusions of the included individual reviews. Data extraction We created a master table in Microsoft Excel containing key information from each of the included reviews (see Additional file 2): health topic, time range of the search, year published, geographical scope, databases searched, the SGM subpopulation, number of studies included, measures, comparison groups, a summary of the Blondeel et al. International Journal for Equity in Health (2016) 15:16 Page 3 of 9 Potentially relevant publications identified through search in PubMed (n=361) Potentially relevant publications identified through search in the Cochrane Database of Systematic Reviews (n=13) Potentially relevant publications identified through search in the Campbell Collaboration Library of Systematic Reviews (n=25) Publications retained for further analysis, full text retrieved (n=50) Publications excluded by title or abstract: – duplicates (n=6) – not a systematic review (n=94) – no SGM population (n=77) – very specific SGM population (n=7) – no data on disease burden (n=163) – protocol of systematic review (n=1) – no abstract available (n=1) Publications excluded because of geographical scale, no new data or insufficient data (n=25) Publications identified and included from lists of references and Google Scholar (n=5) Publications included in the review (n=30) Fig. 1 Flowchart of inclusion criteria for reviews Potentially relevant publications identified through search in the Cochrane Database of Systematic Reviews (n=13) Potentially relevant publications identified through search in the Cochrane Database of Systematic Reviews (n=13) Potentially relevant publications identified through search in PubMed (n=361) Potentially relevant publications identified through search in the Campbell Collaboration Library of Systematic Reviews (n=25) Potentially relevant publications identified through search in the Campbell Collaboration Library of Systematic Reviews (n=25) Publications excluded by title or abstract: – duplicates (n=6) – not a systematic review (n=94) – no SGM population (n=77) – very specific SGM population (n=7) – no data on disease burden (n=163) – protocol of systematic review (n=1) – no abstract available (n=1) Publications retained for further analysis, full text retrieved (n=50) Publications excluded because of geographical scale, no new data or insufficient data (n=25) Publications identified and included from lists of references and Google Scholar (n=5) Publications included in the review (n=30) quantitative and/or qualitative data on disease burden and quality assessment score. on violence [37–40], 4 on cancer [32, 41–43] and 3 on mental health and substance use [44–46]. One review pro- vided data on both HIV and STIs [21]; another yielded data on STIs as well as cancer [32]. Data extraction Twenty-five reviews provided data on MSM, 8 on WSW and 5 on transgender persons (some reviews included more than one subpopu- lation). Twenty-four studies compared data to the general population or other groups, of which one half on the basis of meta-analysis and the other half based on qualitative observations. Fourteen reviews were considered high Sexually transmitted infections y Twelve systematic reviews included data on STIs other than HIV in SGM, including 6 global, 4 regional and 2 national-level reviews [21, 26–36]. Nine of these reviews were on MSM, 2 on WSW and 1 on MSM and trans- gender persons. Men who have sex with men (MSM) Among the 6 re- views that provided data on MSM, 3 were exclusively on MSM. One review was global [24] and 5 were regional [6, 18, 19, 23, 25], of which 4 were mainly on low- and middle-income countries (LMICs). Except for one re- view from 2007, all were published in 2010 or later. All reviews showed a high burden of HIV in MSM. The re- gion with the highest HIV prevalence in MSM was the Caribbean with 25.4 %, followed by sub-Saharan Africa with 17.9 % [24]. In contrast, some countries in the Mid- dle East and North Africa show very low HIV prevalence in MSM [6]. In Asia, high rates of incident HIV- infections in MSM were observed wherever studied [18], and across the region of Latin America and the Carib- bean MSM was the population most affected by HIV [19]. MSM in LMICs have on average a 19.3 times higher chance of being infected with HIV compared with the general population [23]. In high-income countries, Sullivan et al. showed that among new HIV cases, the proportion attributed to male–male sex increased in all the included countries between 2006 and 2011 [25]. MSM Three reviews reported on syphilis in MSM. Zoni et al. showed high rates of active syphilis prevalence in MSM in Latin America, with rates of 7.5 % or more in half of the included studies [27]. In China, the median syphilis prevalence, based on a review of four studies in MSM, was 14.5 %, making MSM the group at highest risk for syphilis in China [28]. Caceres et al. found that syphilis prevalence among MSM in 16 LMICs ranged from 1.5 % in Bangladesh to 29 % in Peru [35]. Hepatitis prevalence was reported in four reviews. A 2003 low quality global systematic review on hepatitis A virus (HAV) did not find an important difference in anti-HAV positivity between MSM and control groups [29]. Two reviews on hepatitis B and C viruses (HBV and HCV) in Europe presented disaggregated data for MSM [30, 31]. Results All 30 reviews were originally written in English. Fifteen reviews were global in scope, while 11 were regional and 5 were national. Nineteen reviews were exclusively or pre- dominantly based on data from high-income countries. Nine reviews provided data on HIV [6, 18–25], 12 on other sexually transmitted infections (STIs) [21, 26–36], 4 Page 4 of 9 Blondeel et al. International Journal for Equity in Health (2016) 15:16 quality [6, 19, 20, 22, 23, 26, 27, 32, 36, 38, 42, 44–47], 9 medium quality [18, 24, 30, 31, 34, 35, 37, 39, 40] and 7 low quality [21, 25, 28, 29, 33, 41, 43]. We found no re- views on intersex people. Detailed results are presented in narrative form under five health topic sub-sections, by SGM subpopulation, as shown in Table 1. estimated a prevalence of 19.1 % and reported that this population has a 48.8 times higher chance of being in- fected with HIV than the general population of adults aged between 15 and 49 [22]. We found no reviews on HIV infection in female-to-male transgender persons. Women who have sex with women (WSW) A low quality systematic review on STIs in WSW globally did not generate any HIV prevalence data in this population [21]. HIV/AIDS Nine systematic reviews assessed the burden of HIV in SGM, including 5 global and 4 regional reviews [6, 18–25]. Six of these reviews were on MSM, 2 were on male-to- female transgender persons and 1 was on WSW. Sexually transmitted infections One showed higher hepatitis C virus anti- bodies and hepatitis B surface antigen prevalence than in the general population, based on three country estimates [30]. In LMICs, data on HBV prevalence was even sparser. With rates of HBV up to 38 % in Argentina and 31 % in Vietnam, MSM seem to be a high-risk group [35]. A global review comparing incidence of acute HCV in HIV-negative versus HIV-positive MSM found that the incidence in the latter group was four times higher; the incidence rates in HIV-negative MSM were similar Transgender persons Two systematic reviews, both of high quality, provided data on HIV infection in male-to- female transgender persons [20, 22]. The reviews were global, collectively including studies from 20 countries. One publication calculated an HIV prevalence of 14.7 % in transgender persons who did not engage in sex work and 27.3 % in those who did [20]. The second review Table 1 Number of reviews selected, by health topic and subpopulation Health topic Men who have sex with men (MSM) Women who have sex with women (WSW) Transgender persons Total number of reviews HIV/AIDS 6 1 2 9 STI 10 2 1 12 Cancer 3 1 0 4 Mental health and substance use 2 2 1 3 Violence 4 2 0 4 Total 25 8 5 30 Table 1 Number of reviews selected, by health topic and subpopulation Blondeel et al. International Journal for Equity in Health (2016) 15:16 Page 5 of 9 Page 5 of 9 to heterosexual populations [36]. The Pan American Health Organization (PAHO) is currently conducting a review of hepatitis B and C in the countries of the Americas; so far the findings point to a higher burden for MSM (personal communication, Rafael Mazin, focal point for HIV/STIs and hepatitis in key populations, PAHO, 30 May 2014). MSM Anal HPV is common in MSM, as are HBV and human herpesvirus 8 (HHV-8) infections. These viruses can lead to anal cancer, liver cancer and Kaposi sarcoma, respectively. One review considered MSM at high risk for anal cancer, and found that HIV-positive MSM were at highest risk [43]. Systematic reviews on HPV and on cancer in general in MSM found that HIV-positive MSM had a high incidence of anal cancer, similar to the incidence of cervical cancer in the general female popu- lation before the introduction of national cervical screening programmes [32, 41]. Boehmer et al. Sexually transmitted infections found that only 1 of the 47 studies included in their review on cancer in MSM was not linked to STIs [41]. In one low quality global review, prevalence of herpes simplex virus 2 (HSV-2) was demonstrated to be higher among male homosexual than among male heterosexual populations [33]. Chlamydia trachomatis and Neisseria gonorrhoeae have not been the subject of global systematic reviews in SGM. One review reported data from nine LMICs with prevalence rates ranging from 0 % (Peru) and 2.1 % (Nepal) up to 14.9 % and 16.1 % (both in Timor-Leste) [35]. A national review on C. trachomatis in Australia designated MSM amongst the populations with the greatest burden, calculating a pooled prevalence for rec- tal C. trachomatis of 5.6 % [34]. WSW Meads & Moore systematically reviewed studies on breast cancer in lesbian and bisexual women. This re- view included nine studies with prevalence estimates, of which two showed higher prevalence of breast cancer in lesbian and bisexual women then in heterosexual women, four showed no difference, one showed mixed results and two could not be compared. Though the re- view was of high quality, all the included studies were small and of poor quality. The reviewers concluded that there was no convincing evidence of a higher disease burden of breast cancer in WSW [42]. In a high quality global systematic review, Machalek et al. showed a pooled prevalence of any type of anal hu- man papillomavirus (HPV) of 53.6 % in HIV-negative MSM and 89.0 % in HIV-positive MSM [32]. High-grade anal intraepithelial neoplasia was present in 20–30 % of all MSM [32]. Mental health and substance use Three high quality reviews – 2 global and 1 national – provided data on mental health and substance use in SGM [44–46]. Two of these were in MSM and WSW while 1 was in transgender persons. WSW Two global systematic reviews on bacterial vagin- osis and on STIs in WSW showed a positive association between a history of female sexual partners and risk of bacterial vaginosis [21, 26]. There was no evidence of a higher burden of STIs in WSW compared with the gen- eral population of adult women [21]. MSM and WSW In their global review, King et al. cal- culated an overall 2.47 times increased risk of lifetime suicide attempts in lesbian, gay and bisexual (LGB) people compared to heterosexuals; the risk ratio for life- time suicidal ideation was 2.04, and it was 2.05 for 12 months prevalence of depression, one of the most common mental illnesses [45]. The reviewers also calcu- lated a pooled risk ratio of 1.88 in gay and bisexual males for 12 months prevalence of anxiety disorders (specific disorders were not specified), but the results for lesbian and bisexual females were less convincing due to heterogeneity in the study methods (I2 = 49.2 %). The re- view also found that alcohol and substance dependence were at least 1.5 times more common in these popula- tions than in the heterosexual population. Marshal et al. calculated that the odds for substance use among LGB youth globally were 190 % higher than for heterosexual youth [46]. Transgender persons Zoni et al. found syphilis preva- lence rates ranging from 6.5 % in El Salvador to 43.3 % in Brazil, the latter being the highest rate among high- risk populations (MSM, sex workers and transgender persons) in Latin America and the Caribbean [27]. Pre- liminary results of an ongoing review on hepatitis B and C by PAHO in the region of the Americas show a higher burden for male-to-female transgender persons (per- sonal communication, Rafael Mazin, focal point for HIV/STIs and hepatitis in key populations, PAHO, 30 May 2014). Cancer Four reviews, two high and two low quality, included data on cancer in SGM; all were global in scope [32, 41– 43]. Three of these reviews were in MSM and 1 in WSW; no reviews were found on cancer burden in transgender persons. Transgender persons We found data on mental health in transgender persons in a systematic review on the prevalence of HIV and contextual factors potentially Page 6 of 9 Page 6 of 9 Blondeel et al. International Journal for Equity in Health (2016) 15:16 associated with HIV risk in the United States of America (USA). High rates of suicidal thoughts (weighted mean, 53.8 %) and lifetime suicide attempts (weighted mean, 31.4 %) were reported in male-to-female transgender persons [44]. Limited research on HIV in male-to-female trans- gender persons suggests a high burden. For WSW, a re- view generated no results but was low in quality [21]. For female-to-male transgender persons and intersex people we found no reviews. The feasibility of conduct- ing a systematic review on disease burden of HIV in these populations should be investigated. Violence Violence is one of the more visible health issues in SGM, and the subject of many advocacy efforts. We found four systematic reviews on the prevalence of vio- lence in SGM, including 1 global, 1 regional (North America and Europe) and 2 national-level reviews (USA) [37–40]. All four were on LGB people; there were no re- views on violence in transgender persons. Reviews on STIs reported a high burden of syphilis in MSM in Latin America, China and LMICs where preva- lence was measured. A report by the European Surveil- lance of Sexually Transmitted Infections (ESSTI) network confirms that MSM also bear a disproportion- ate burden of syphilis across Western Europe and that there is clear evidence that it has increased considerably [50]. Syphilis has been identified as a growing problem among MSM in a number of countries, based on the Global AIDS Response Progress Reports [51]. MSM and WSW A global review found high rates of physical assault (28 %) and sexual assault (27 %) in LGB individuals, and suggested that they experience more victimization than heterosexuals [37]. Peterson et al. concluded that rates of adult sexual assault among gay and bisexual males in North America and Europe far ex- ceed the rates in community samples of men [40]. LGB people in the USA seem to be at increased risk for sex- ual violence victimization compared with their hetero- sexual counterparts [38]. Focusing on the subset of intimate partner violence, Finnerman & Stephenson concluded that emergent evidence in the USA demon- strates that prevalence of intimate partner violence is high in male–male partnerships [39]. g HAV burden was not found to be higher in MSM compared to heterosexual men in high income countries [29], but a more recent report on viral hepatitis in Euro- pean MSM did show an elevated prevalence [52]. In- creasing attention is being paid to HBV as an STI in MSM. While a 2004, non-sysytematic, review on disease burden of HBV only mentioned homosexual activity as one of the risk factors, alongside heterosexual activity [53], a more recent epidemiological report estimated that HBV incidence among MSM is 20 times higher than in the general population [52]. The same report also looked at HCV, but did not clarify whether its high burden was only in HIV-positive MSM or in MSM in general [52]. Conclusions Our review primarily shows that there is a high burden of disease for certain subpopulations of SGM in HIV, STIs, STI-related cancers and mental health conditions, and that they also face high rates of violence. Secondly, our review revealed many knowledge gaps. Those gaps partly stem from a lack of original research, which needs to be addressed, but there is an equally urgent need to conduct high quality systematic and literature reviews to assess what we already know on the disease burden in SGM. Mental health is a poorly reviewed health issue in SGM. The most recent global systematic review on men- tal health in SGM, although high quality, dated from 2008 and suggested an elevated burden in a variety of mental health issues, but it did not include transgender persons [45]. Eating disorders and obesity were not dis- cussed, although they are mentioned in a review on the health of SGM by the United States Institute of Medi- cine [9]. Regarding substance use, we found that sexual orientation is an important mediating factor of adoles- cent substance use [46]. Adding to this, Bourne et al. conducted a global literature review on drug use in MSM and concluded that the prevalence of drug use is high [59]. Some party drugs used by MSM, such as crys- tal methamphetamine or gamma-butyrolactone, can have detrimental effects on mental and sexual health (an internet survey in Asia reported 4 % and 2.3 % use in MSM, respectively, in the last six months) [59]. We recommend that systematic reviews on HIV and HPV in MSM be regularly updated. Reviews on herpes in MSM, STIs in WSW, and on mental health, violence and substance use in MSM and WSW, urgently need to be updated. Special attention should be given to violence based on sexual orientation and gender identity. Global reviews on syphilis, hepatitis, C. trachomatis and N. gonorrhoeae in MSM, and on all of the most common STIs, mental health and violence in the transgender population need to be conducted. In particular, research on female-to-male transgender persons should be con- sidered, as there are virtually no epidemiologic data on the burden of disease in this population. Literature re- views should include publications on the burden of can- cers that are not related to infectious causes and other non-communicable diseases in all SGM. Discussion International Journal for Equity in Health (2016) 15:16 Page 7 of 9 Page 7 of 9 indicated that among all N. gonorrhoeae cases diagnosed in men in Europe in 2011, 53 % were in MSM [55]. Moreover, there are indications that MSM are one of the core groups that are key to the emergence, onward transmission and outbreaks of antimicrobial-resistant N. gonorrhoeae [56]. hotline calls, social service records and police reports [60]. All these sources indicated that violence against transgender persons starts early in life, that they are at risk for multiple types and repeated incidents of vio- lence, particularly sexual violence, and that this threat lasts throughout their lives. Except for the reviews that reported on cancer and mental health, there are no systematic reviews on non- communicable diseases in SGM. Nevertheless, there is a growing body of research on the health of SGM. We analysed data from systematic reviews only; therefore the results of research that have not yet been included in a systematic review are not reflected in this article. More extensive reporting, which includes the results of these studies and of studies on risk, contextual and contribut- ing factors of health disparities and specific health issues in SGM, is beyond the scope of this review. Methodo- logically, this review is limited by the databases we searched and the use of exclusively English search terms on Google Scholar. The burden of anal HPV is well documented in MSM; the review by Machalek at al. showed high prevalence in MSM in general and very high prevalence in HIV-positive MSM in particular [32]. We found no review on the prevalence of oral HPV, though studies show it is high in MSM, and is a risk factor for oropharyngeal cancer [57]. The systematic review on STI/HIV in WSW did not show a higher burden in this population [21]. Nonethe- less, the authors concluded that WSW should not be presumed to be at lower risk based on their sexual orientation, since they can acquire HIV and other STIs through other modes, including injection drug use and sexual contact with high-risk male partners. Available research on cancer burden in MSM focuses mainly on cancers that are causally linked to STIs; most other cancers have yet to be studied in this subpopula- tion [41]. Lee et al. Discussion Our review found that HIV and STIs are the most researched topics for those studying the disease burden in SGM, and that the subpopulation of MSM is the most intensively studied. A 2014 protocol for a global systematic review on the prevalence of HHV-8 described the investigators’ intention to examine the hypothesis that MSM have a high prevalence of the HHV-8 antibody – the infectious disease underlying Kaposi sarcoma – and to determine if the prevalence is increasing [54]. The results have not been published yet. The six included reviews on HIV in MSM (all pub- lished in 2007 or later) show a high burden in this popu- lation. UNAIDS reports that the median HIV prevalence among MSM exceeds 1 % in all regions of the world and is substantially higher than prevalence among men over- all, in every context studied [47]. Furthermore, there is no evidence of a decline in the HIV epidemic in MSM [18, 24, 47]. HIV prevalence among MSM in some low- income countries could be underreported because the data are too limited; male same-sex sexual behaviour takes multiple forms and HIV has huge potential to in- crease further in MSM in the next decade [48, 49]. Abu- raddad et al. indicated growing – in some cases rapidly growing – HIV epidemics in MSM in several countries, including Egypt, Morocco, Pakistan, Sudan, Tunisia and Yemen [49]. Systematic reviews of the existing research of HIV burden in MSM seem to be up to date and of reasonable quality, though original research and data are still lacking in many countries. Our results suggested a high burden of C. trachomatis in MSM, based on sparse data from medium quality re- views [34, 35]. Moreover, the most recent annual epi- demiological report of the European Centre for Disease Prevention and Control (ECDC), published in 2013, in- dicated that 99 % of cases of the L2b variant of C. trachomatis, which causes the majority of lymphogranu- loma venerum infections, are in MSM [55]. Among those cases with known HIV status, 88 % were HIV- positive. Data from systematic reviews on the burden of N. gonorrhoeae in SGM were too scarce to support any conclusions, but an ESTTI report suggested that MSM bear a disproportionate burden of gonococcal infection in many Western European and some Central and East- ern European countries [50]. The ECDC report also Blondeel et al. Discussion showed that there might be reason to believe there are also disparities in other cancers, as sexual minorities in the USA are 1.5 to 2.5 times more likely to be smokers than the heterosexual population [58]. Smoking is a major risk factor for lung cancer and a risk factor for a myriad of other cancers. Competing interests 15. Becker LA, Oxman AD. Chapter 22: Overviews of reviews. In: Higgins JPT, Green S (editors), Cochrane Handbook for Systematic Reviews of Interventions Version 5.1.0 (updated March 2011). The Cochrane Collaboration, 2011. Available from www.cochrane-handbook.org 15. Becker LA, Oxman AD. Chapter 22: Overviews of reviews. In: Higgins JPT, Green S (editors), Cochrane Handbook for Systematic Reviews of Interventions Version 5.1.0 (updated March 2011). The Cochrane Collaboration, 2011. Available from www.cochrane-handbook.org Authors’ contributions KB and ES performed the literature review. KB, DC, ES, MT, RK and LS conceived of the study, and participated in its design and coordination. KB wrote the manuscript, with the help of DC, LS, RK, IT, MT and ES. All authors read and approved the final manuscript. 16. Moher D, Liberati A, Tetzlaff J, Altman DG, The PRISMA Group. Preferred reporting items for systematic reviews and meta-analyses: The PRISMA Statement. PLoS Med. 2009;6(6):e1000097. 17. Shea BJ, Hamel C, Wells GA, Bouter LM, Kristjansson E, et al. AMSTAR is a reliable and valid measurement tool to assess the methodological quality of systematic reviews. J Clin Epidemiol. 2009;62(10):1013–20. Author details 1 1Ghent University, Ghent, Belgium. 2Department of Reproductive Health and Research, World Health Organization, Geneva, Switzerland. 3I.M. Sechenov First Moscow State Medical University, Moscow, Russian Federation. The majority of the currently available systematic reviews are on MSM and the burden of HIV and STIs. This sug- gests that a substantial portion of the burden of disease in SGM is related to their sexual behaviours, which means it is preventable. WHO and UNAIDS have been building on that knowledge, issuing guidelines, recommendations and tools, including tools for estimating the numbers of specific populations, and for monitoring and evaluating policies and interventions to remediate the burden of HIV and STI in these populations [2, 61–63]. Additional reviews should be conducted on the non-biological factors that contribute to higher disease burden. In order to provide universal access to health-care, more knowledge is needed on the barriers that SGM face in accessing health services, including the at- titudes of health-care providers, who are ethically bound to provide good quality services, regardless of the personal history or characteristics of the patient. Understanding these barriers and the additional health risks they impose is crucial to improving the health status of SGM. Received: 5 June 2015 Accepted: 13 January 2016 References 1. Preamble to the Constitution of the World Health Organization as adopted by the International Health Conference, New York, 19–22 June, 1946; signed on 22 July 1946 by the representatives of 61 States, entered into force on 7 April 1948. 2. Prevention and treatment of HIV and other sexually transmitted infections among men who have sex with men and transgender people: recommendations for a public health approach. Geneva: World Health Organization; 2011. 3. UNAIDS terminology guidelines (October 2011). Geneva: Joint United Nations Programme on HIV/AIDS (UNAIDS); 2011 4 Guidelines on estimating the size of populations most at risk to HIV 3. UNAIDS terminology guidelines (October 2011). Geneva: Joint United Nations Programme on HIV/AIDS (UNAIDS); 2011 4. Guidelines on estimating the size of populations most at risk to HIV. Geneva: World Health Organization; 2010. 5. Cáceres CF, Konda K, Pecheny M, Chatterjee A, Lyerla R. Estimating the number of men who have sex with men in low and middle income countries. Sex Transm Infect. 2006;82 Suppl 3:iii3–9. 6. Mumtaz G, Hilmi N, McFarland W, Kaplan RL, Akala FA, Semini I, et al. Are HIV epidemics among men who have sex with men emerging in the Middle East and North Africa?: a systematic review and data synthesis. PLoS Med. 2010;8(8):e1000444. 7. Winter S. Lost in transition: transgender people, rights and HIV vulnerability in the Asia-Pacific Region. New York: United Nations Development Programme; 2012. Acknowledgements h h ld l k The authors would like to thank Tomas Allan for contributing to the search strategy; Jane Patten of Green Ink (UK) for language, technical and copy-editing. 18. Dokubo EK, Kim A, Le L-V, Nadol PJ, Prybylski D, Wolfe MI. HIV incidence in Asia: a review of available data and assessment of the epidemic. AIDS Rev. 2013;15(2):67–76. Conclusions It would facili- tate this process if health research, surveys and statistical databases systematically included sexual orientation and gender identity as a demographic characteristic, where possible. There is also a geographical research gap since most of the systematic reviews included studies that were all or mostly from high-income countries. New Lastly our results show that MSM and WSW are con- fronted with more violence than their heterosexual counterparts. However, most of the studies were from the USA and other high-income countries; we might ex- pect to see even higher rates of violence in SGM in countries where homosexuality is criminalized. A study from the USA on violence in transgender persons assessed self-report surveys and needs assessments, Blondeel et al. International Journal for Equity in Health (2016) 15:16 Page 8 of 9 Page 8 of 9 Page 8 of 9 reviews could capture research from LMICs by broaden- ing and deepening search strategies. The quality of the systematic should also improve, as less than half were of high quality, Additional files 8. Mayer KH, Bradford JB, Makadon HJ, Stall R, Goldhammer H, Landers S. Sexual and gender minority health: what we know and what needs to be done. Am J Public Health. 2008;98(6):989–95. Additional file 1: Search strategy, PubMed, sexual and gender minorities. (DOCX 105 kb) Additional file 2: Summary table of review of systematic reviews. (XLSX 17 kb) Additional file 1: Search strategy, PubMed, sexual and gender minorities. (DOCX 105 kb) 9. Institute of Medicine, Committee on Lesbian, Gay, Bisexual, and Transgender Health Issues and Research Gaps and Opportunities. The health of lesbian, gay, bisexual, and transgender people: building a foundation for better understanding. Washington (DC): United States National Academy of Sciences; 2011. 9. Institute of Medicine, Committee on Lesbian, Gay, Bisexual, and Transgender Health Issues and Research Gaps and Opportunities. The health of lesbian, gay, bisexual, and transgender people: building a foundation for better understanding. Washington (DC): United States National Academy of Sciences; 2011. Additional file 2: Summary table of review of systematic reviews. (XLSX 17 kb) 10. Bränström R, van der Star A. All inclusive Public Health–what about LGBT populations? Eur J Public Health. 2013;23(3):353–4. 10. Bränström R, van der Star A. All inclusive Public Health–what about LGBT populations? Eur J Public Health. 2013;23(3):353–4. Abbreviations AIDS: acquired immunodeficiency syndrome; ECDC: European Centre for Disease Control and Prevention; ESSTI: The European Surveillance of Sexually Transmitted Infections; HAV: hepatitis A virus; HBV: hepatitis B virus; HCV: hepatitis C virus; HHV-8: human herpesvirus 8; HIV: human immunodeficiency virus; HPV: human papillomavirus; HSV-2: herpes simplex virus 2; LMIC: low- and middle-income country; MSM: men who have sex with men; PAHO: Pan American Health Organization; SGM: sexual and gender minorities; STI: sexually transmitted infection; UNAIDS: The Joint United Nations Programme on HIV and AIDS; WHO: World Health Organization; WSW: women who have sex with women. 11. Meeting the unique health-care needs of LGBTQ people. Editorial. Lancet. 2016; 387(10014): 95. 11. Meeting the unique health-care needs of LGBTQ people. Editorial. Lancet. 2016; 387(10014): 95. 12. Boehmer U. Twenty years of public health research: inclusion of lesbian, gay, bisexual, and transgender populations. Am J Public Health. 2002;92(7):1125–30. 12. Boehmer U. Twenty years of public health research: inclusion of lesbian, gay, bisexual, and transgender populations. Am J Public Health. 2002;92(7):1125–30. 13. Bogart LM, Revenson T, Whitfield KE, et al. Introduction to the special section on lesbian, gay, bisexual, and transgender (LGBT) health disparities Where we are and where we’re going. Ann Behav Med. 2014;47(1):1–4. 13. Bogart LM, Revenson T, Whitfield KE, et al. Introduction to the special section on lesbian, gay, bisexual, and transgender (LGBT) health disparities: Where we are and where we’re going. Ann Behav Med. 2014;47(1):1–4. 14. Smith V, Devane D, Begley CM, Clarke M. Methodology in conducting a systematic review of systematic reviews of healthcare interventions. BMC Med Res Methodol. 2011;11:15. 14. Smith V, Devane D, Begley CM, Clarke M. Methodology in conducting a systematic review of systematic reviews of healthcare interventions. BMC Med Res Methodol. 2011;11:15. Disclaimer Savage EJ, Hughes G, Ison C, Lowndes CM; The European Surveillance of Sexually Transmitted Infections (ESSTI) network. Syphilis and gonorrhoea in men who have sex with men: a European overview. Euro Surveill. 2009;14(47). 25. Sullivan PS, Jones JS, Baral SD. The global north: HIV epidemiology in high- income countries. Curr Opin HIV AIDS. 2014;9(2):199–205. 26. Fethers K, Fairley CK, Hocking JS, Gurrin LC, Bradshaw CS. Sexual risk factors and bacterial vaginosis: a systematic review and meta-analysis. Clin Infect Dis. 2008;47(11):1426–35. 51. Report on global sexually transmitted infection surveillance 2013. Geneva: World Health Organization; 2014 27. Zoni AC, González MA, Sjögren HW. Syphilis in the most at-risk populations in Latin America and the Caribbean: a systematic review. Int J Infect Dis. 2013;17(2):e84–92. 52. Urbanus AT, van Houdt R, van de Laar TJ, Coutinho RA. Viral hepatitis among men who have sex with men, epidemiology and public health consequences. Euro Surveill. 2009;14(47) 28. Lin CC, Gao X, Chen X-S, Chen Q, Cohen MS. China’s syphilis epidemic: a systematic review of seroprevalence studies. Sex Transm Dis. 2006;33(12):726–36. 53. Custer B, Sullivan SD, Hazlet TK, Iloeje U, Veenstra DL, Kowdley KV. Global epidemiology of hepatitis B virus. J Clin Gastroenterol. 2004;38 Suppl 3:S158–68. 29. Franco E, Giambi C, Ialacci R, Coppola RC, Zanetti AR. Risk groups for hepatitis A virus infection. Vaccine. 2003;21(19–20):2224–33. 54. Rohner E, Wyss N, Trelle S, Mbulaiteye SM, Egger M, Novak U, et al. HHV-8 seroprevalence: a global view. Syst Rev. 2014;3(1):11. 30. Hahné SJM, Veldhuijzen IK, Wiessing L, Lim T-A, Salminen M, Van De Laar M. Infection with hepatitis B and C virus in Europe: a systematic review of prevalence and cost-effectiveness of screening. BMC Infect Dis. 2013;13:181. 55. Annual Epidemiological Report 2013. Reporting on 2011 surveillance data and 2012 epidemic intelligence data. Stockholm: European Centre for Disease Prevention and Control; 2013 31. Hepatitis B and C in the EU neighbourhood: prevalence, burden of disease and screening policies. Stockholm: European Centre for Disease Prevention and Control; 2010. 56. Lewis DA. The role of core groups in the emergence and dissemination of antimicrobial-resistant N. gonorrhoeae. Sex Transm Infect. 2013;89 Suppl 4:iv47–51. 32. Machalek D, Poynten M, Jin F, Fairley CK, Farnsworth A, Garland SM, et al. Anal human papillomavirus infection and associated neoplastic lesions in men who have sex with men: a systematic review and meta-analysis. Lancet Oncol. 2012;13(5):487–500. 57. Disclaimer 19. Miller WM, Buckingham L, Sánchez-Domínguez MS, Morales-Miranda S, Paz- Bailey G. Systematic review of HIV prevalence studies among key populations in Latin America and the Caribbean. Salud Publica Mex. 2013;55 Suppl 1:S65–78. Lale Say, Doris Chou, Igor Toskin, Rajat Khosla, Elisa Scolaro and Marleen Temmerman are staff members of the World Health Organization. The authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the World Health Organization. 20. Operario D, Soma T, Underhill K. Sex work and HIV status among transgender women: systematic review and meta-analysis. J Acquir Immune Defic Syndr. 2008;48(1):97–103. 20. Operario D, Soma T, Underhill K. Sex work and HIV status among transgender women: systematic review and meta-analysis. J Acquir Immune Defic Syndr. 2008;48(1):97–103. Page 9 of 9 Page 9 of 9 Blondeel et al. International Journal for Equity in Health (2016) 15:16 21. Gorgos LM, Marrazzo JM. Sexually transmitted infections among women who have sex with women. Clin Infect Dis. 2011;53 Suppl 3:S84–91. 46. Marshal MP, Friedman MS, Stall R, King KM, Miles J, Gold M, et al. Sexual orientation and adolescent substance use: a meta-analysis and methodological review. Addiction. 2008;103(4):546–56. 22. Baral SD, Poteat T, Strömdahl S, Wirtz AL, Guadamuz TE, Beyrer C. Worldwide burden of HIV in transgender women: a systematic review an meta-analysis. Lancet Infect Dis. 2013;13(3):214–22. 47. Global report: UNAIDS report on the global AIDS epidemic 2013. Geneva: Joint United Nations Programme on HIV/AIDS; 2013 47. Global report: UNAIDS report on the global AIDS epide Joint United Nations Programme on HIV/AIDS; 2013 23. Baral S, Sifakis F, Cleghorn F, Beyrer C. Elevated risk for HIV infection among men who have sex with men in low- and middle-income countries 2000– 2006: a systematic review. PLoS Med. 2007;4(12):e339. 48. Van Griensven F, de Lind van Wijngaarden JW. A review of the epidemiology of HIV infection and prevention responses among MSM in Asia. AIDS. 2010;24 Suppl 3:S30–40. 49. 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On the Embryo of Welwitschia1
Annals of botany
1,910
public-domain
4,093
2 Pearson, 1909 A, pp. 364-368. [Annals of Botany, Vol. XXIV. No. XCVI. October, igio.] 1 Percy Sladen Memorial Expedition in South-west Africa, 1908-1909, Report No. 3. 2 P 1909 A 364 368 1 Percy Sladen Memorial Expedition in South-west Africa, 1908-1909, Report No. 3. 2 Pearson, 1909 A, pp. 364-368. 1 Percy Sladen Memorial Expedition in South-west Africa, 1908-1909, Report No. 3. 2 Pearson, 1909 A, pp. 364-368. [Annals of Botany, Vol. XXIV. No. XCVI. October, igio.] 3 F 2 . [Annals of Botany, Vol. XXIV. No. XCVI. October, igio.] 3 F 2 Percy Sladen Memorial Expedition in South west Africa, 1908 1909, Report No. 3. 2 Pearson, 1909 A, pp. 364-368. On the Embryo of Welwitschia.1 BY H. H. W. PEARSON, Sc.D., F.L.S. With Plate LXIV and two Figures in the Text. In the absence of any indications as to the later history of the terminal group of thirty-two cells it was provisionally compared with the corresponding region of the proembryo of Araucaria brasiliana, to which it bears a curious resemblance.1 And although it was known that the ' cap' cells of Wel- witschia are not thrown off in the stages immediately following,2 as is the case in Araucaria, it nevertheless seemed probable that the embryo was formed from similarly situated regions in the two cases, viz. from the so-called 'embryonic plate' (Text-fig. i,e.). It was further assumed that the cells of the lower ring in due course contributed additions to the suspensor.3 It was arranged that the Percy Sladen Memorial Expedition in South- west Africa should visit Welwitsch in Damaraland after the end of February in order to collect material of the later stages. The results now recorded have been obtained from ovules gathered there between March 2 and 9, 1909. An expedition to Welwitsch's own locality near Mossamedes in South Angola, in the following month, has yielded no additional information, as the older cones obtained there were diseased.4 This investigation has settled all the doubtful points referred to above. The development of the embryo, as far as the stage of Fig. 4, proceeds, apparently without any interruption, while the cone is still in position and intact; and since cones collected by Baines at Haikamchab on May 10, 1861, contained ripe seeds,5 it is probable that embryo-development is con- tinuous until the seed is mature. The period intervening between the occurrence of fertilization and the completion of the intraseminal growth of the embryo is thus less than four months. In this respect Welwitschia shows an agreement with Ephedra 6 rather than with Gnetunt; but in view of the extreme xerophytic conditions to which Welwitschia has become adapted this cannot be regarded as of phylogenetic significance. Stras- burger's statement that the ' cap ' cells are not thrown off is confirmed ; in the stage shown in Text-fig. 1 they are still the initial cells of the pro- embryo ; their descendants occupying a similar position retain this character until the superficial layer becomes dermatogen and a cell-mass underlying it at the apex is organized as a meristematic group ; the identification of the internal cell-plate (e.) as the 'embryonic plate' was therefore erroneous. With Plate LXIV and two Figures in the Text. With Plate LXIV and two Figures in the Text. With Plate LXIV and two Figures in the Text. With Plate LXIV and two Figures in the Text. AN l \ . f AN account of the development of the proembryo of Welwitschia up to l \ . the stage represented in the diagram (Text-fig, i) has been given in a former paper.2 In this condition the proembryo consists of a suspensor and a terminal cell-group. From the latter have been formed twenty-four of the twenty-five cells of which the suspensor consists ; it also gives rise to TEXT-FIG, I. Diagram of an almost median longitudinal section through the distal end of the pro-embryo of Welwitschia at ihe stage figured in Pearson, 1909 A, PI. 30, Fig. 85. p. s.\ ( primary ) «'. c. r.\ = I inner cortical ring > cells of the suspensor (cf. Pearson, 1. c , Fig. 87). 0. c. r. ) / outer cortical ring ) e. = 3 of the 8 cells of the ' presumed embryonic plate' (cf. Pearson, 1. c., Fig. 86 B). x. - 2 of the 16 cells of the ' lower ring' (cf. Pearson, 1. c, Fig. 86 B). c. = 4 of the ' cap' cells (cf. Pearson, 1. c, Fig. 86 A). the embryo itself. The terminal group at this stage contains (1) eight or more ' cap' cells (Text-fig. i,c); (2) a ring of sixteen peripheral cells just below the suspensor—the ' lower ring' [x.); this surrounds (3) an internal plate of eight cells, the ' presumed embryonic plate ' (e.). This was the latest stage found in material collected in Damaraland between January 21 and February 1, 1907. As it was seen many times it seemed possible that further development was preceded by a resting period. , 3 F 2 Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 Pearson.—On the Embryo of Welwitschia. 760 This suggested the further possibility that the completion of intraseminal growth might be deferred until after the fall of the seed ; in certain species of Gnetunt, as is well known, the embryo does not appear while the ovule is still in position, and this is probably characteristic for the genus. 1 Strasburger, 1879, Taf. sex. ' Cf. Hooker, 1863, PI. 10, Fig. 25. 5 Hooker, 1863, p. 3. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 Pearson.— On the Embryo of Welwitschia. 761 After the condition indicated in Text-fig. 1, the terminal initial (' cap' cells) undergo both periclinal and anticlinal divisions with the re that new cells are added beneath those of the plate e., and similar to and the number of cells in the superficial layer increases (PI. LXIV, Fig 6, 7). The cells of the' embryonic plate' (e.) may divide further ; they or descendants lie at the extreme tip of the primary root-cap of which form a part. Even as late as the stage of Fig. 3, all the superficial cells not ceased to divide by periclinal walls, though many of them have no d become constituents of a dermatogen, and in somewhat more adva stages they have all acquired this character. After the stage of F cell-division becomes localized in a more or less definite suba growing region. The activity of this meristematic group results in formation, on the side towards the suspensor, of a massive tissue whose cells are for the most part arranged in longitudinal rows. This is already indicated in Fig. 3, and becomes much more strongly marked in the axial core of later stages (' Periblem- saule')—see Figs. 4 and 5. For some time, therefore, the root-cap constitutes the greater part of the bulk of the embryo, in which character, as well as in the details of its formation, Welwitschia remains true to the Gymnosperm type. In the embryo shown in Fig. 4 the original meristematic group has become divided into two by permanent tissue; separate growing points for stem (St.) and root (R) are thus established. The stem apex quickly becomes externally dis- tinguishable from the rest of the embryo by reason of its smaller diameter and dome-like surface (Fig. 4). Its elongation is very slow compared with that of the r in the embryo of the mature seed (Fig. 5), in which the two regions are easily distinguished by the difference of breadth, the stem is hardly m than one-fifth of the length of the root. Strasburger showed that cotyledons arise early from the stem-dome (Text-fig. 2) ; they grow f rapidly and usually somewhat unequally (Fig. 5). In the embryo of mature seed, thin median sections disclose two small exogenous outgro from the stem apex, occupying axillary positions with respect to cotyledons. With Plate LXIV and two Figures in the Text. The suggestion that the cells of the lower ring (x.) produce further additions to the suspensor is confirmed. * 1. c , p. 155. * Pearson, 1909 B. « Land, 1907, p. 381. 1 Strasburger, 1879, Taf. sex. ' Cf. Hooker, 1863, PI. 10, Fig. 25. 5 Hooker, 1863, p. 3. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 Pearson.— On the Embryo of Welwitschia. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 TEXT-FIG. 2. Outline of longi- tudinal section through distal end of the embryo of Welwitschia (after Stras- burger, 1879, Taf. xxii, Fig. 91). s. = stem-apex ; c. = cotyledons ; r. = growing-point of root. Pearson.— On the Embryo of Welwitschia. Stages immediately following this are not available for c parison, but there can be no doubt that these are the ' lateral con Their appearance thus early in acropetal succession to the cotyledons 1 Cf. Bower, 1881, pp. 579, 580, Fig. vii. '•3. TEXT-FIG. 2. Outline of tudinal section through distal end embryo of Welwitschia (after burger, 1879, Taf. xxii, Fig. 91) s. = stem-apex ; c. = cotyle r. = growing-point of root. '•3. TEXT-FIG. 2. Outline of longi- tudinal section through distal end of the embryo of Welwitschia (after Stras- burger, 1879, Taf. xxii, Fig. 91). s. = stem-apex ; c. = cotyledons ; r. = growing-point of root. '•3. TEXT-FIG. 2. Outline of longi- tudinal section through distal end of the embryo of Welwitschia (after Stras- burger, 1879, Taf. xxii, Fig. 91). s. = stem-apex ; c. = cotyledons ; r. = growing-point of root. 1 Cf. Bower, 1881, pp. 579, 580, Fig. vii. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 Pearson.—On the Embryo of Welwitschia. 762 in their axils tends to confirm the view advanced by Bower x and more recently supported by Henriques, that they are axillary buds. Meantime the mass of the suspensor has greatly increased. The growth of the cells of the ' lower ring' (x) is seen in Fig. 1, while in Fig. 2 they already form part of the suspensor. The peripheral cells immediately beneath these (Fig. %,y) in their turn behave in the same way, and, as the embryonic mass elongates, acropetally developed additions to the suspensor are produced until this structure has attained its final form. These later formed suspensor cells frequently show a considerable degree of independ- ence of growth, as was observed by Hooker.2 Cases are seen in Fig. 1 and more markedly in Fig. 3. In both, suspensor-cells with free ends occur ; in the latter some are growing parallel with the main body of the suspensor (a), others appear to be spreading laterally (d), while two (b) have turned down- wards and are advancing into the endosperm in the same direction as the embryo. This may perhaps be of the nature of a structural adaptation to the growing demands of the embryo for food-supplies. 1 Bower, I.e.; Henriques, 1910. 3 Cf. Land, 1907, p. 280. 5 I.e..A,A- ' 2 Hooker, 1863, PI. x, Fig. 25. l Pearson, 1909, Text-figure,pltpa. 6 l-c,rf. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 Pearson.—On the Embryo of Welwitschia. 763 mass. While the mechanical force developed by the whole system is without doubt of second-rate importance compared with the results of enzyme-action in front of the flattened, bluntly-pointed tip of the embryo, the crushed cells which commonly lie in contact with it bear witness to the exertion of a definite pushing force. No ovule in which the endosperm was not obviously withered has been found to be without an embryo. This tends to confirm the observation previously recorded x that the second phase of the growth of the trophophyte is dependent upon the occurrence of fertilization—either directly or through the embryonic activity which follows it. One case only has been seen in which the one remaining embryo in an ovule was clearly breaking down. The proportion of fertile seeds in normal cones appears to be fairly high,2 and the efficiency of seed-production in Damaraland is in striking contrast to the rarity of the occurrence of successful germination in that region.3 y g g In early stages, as has been already recorded,4 the ovule usually con- tains a number of proembryos ; but sooner or later all but one disintegrate. It very rarely happens that an advanced ovule is polyembryonic owing to the persistent development of more than one proembryo. In one such case the larger of two embryos (about the stage of Fig. 3) lies deep in the axis of the endosperm, while a second (younger than Fig. 1), having pene- trated almost to the depth of the former, has turned abruptly through an angle of 1800 and now lies near the boundary of the disorganized region of the endosperm5 with its apex directed towards the nucellus. This appears to be another instance of the readiness with which the Welwitschia embryo changes its direction of growth in response to a nutritive stimulus.0 While no case of the branching of the suspensor has been observed, poly- embryony due to the branching of the embryo itself is fairly common. This frequently occurs in the manner indicated in Fig. 6, in which an approximate bifurcation has taken place. Examples of lateral branching, in which an embryo produces a second one smaller than itself, are by no means rare (Fig. 7). While the former may be compared with the fission of the embryonic group in Pinus and other Conifers, the latter recalls the remarkable proliferation of the suspensor in Gnetum Gnemon? 1 Pearson, 1909, pp. 352, 370. 2 Mr. Lynch informs me that of a considerable number of selected seeds sent to Cambridge from Damaraland in 1907, about 80 per cent, germinated. 3 Pearson, 1907, p. 536. 4 Pearson, 1909 A, p. 368. 5 Pearson, 1909 A, Text-fig, c. * 1. c, p. 364. 7 Bower, 1882, p. 284. A similar proliferation occurs in C. scandcm. Pearson.— On the Embryo of Welwitschia. In earlier stages, while the suspensor is still slender and compact and the embryonic cell-mass small, absorption by the cells of the peripheral layers of both regions is sufficient. But as they become more massive and the depletion of the endosperm advances, the difficulty of maintaining an increasing rate of absorption must become greater. The common behaviour of the younger suspensor-cells suggests that they have to some extent taken over the functions of rqot-hairs; morphologically, of course, they are outgrowths from the root-cap.3 At length the suspensor has assumed its maximum thickness, and henceforward the surface of the root-cap remains smooth (Fig. 4). An interesting and suggestive relation appears to exist between the life-conditions of the embryo in certain parts of its course and the structure of its suspensor. In early stages,4 when the young embryonic group is growing towards the endosperm, frequently by a route to some extent predetermined by the embryo-sac tube, the suspensor is simply the elongated hypobasal cell. As soon as it enters the endosperm where it meets competing embryos in a narrow area which quickly becomes depleted of food supplies, the suspensor thickens.6 There is very little doubt that the embryo which first reaches the starch-bearing region of the endosperm6 normally becomes the embryo of the seed, and, broadly speak- ing, the more quickly this occurs the greater is the chance that a fertile seed will result. A suspensor which has acquired some degree of rigidity by reason of the addition to its bulk of several series of peripheral cells, and whose more OF less spiral form gives to it a certain elasticity, will play an important part in assisting the embryo to penetrate the underlying cell-. 5 I.e..A,A- Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 Pearson.—On the Embryo of Welwitschia. 4 Pearson, 1909 A, p. 368. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 Pearson.—On the Embryo of Welwitschia. in which there is little doubt that the outer cells of the massive suspensor are epibasal in origin as they are in Welwitschia. More than two embryos in one ovule have not been certainly seen; in one doubtful case there are perhaps three. That the polyembryony of Welwitschia is very much more limited than in Gnetum is in keeping with the higher degree of specialization to which Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user Pearson.—On the Embryo of Welwitschia. 764 the former has attained. There appears to be no record of the presence of more than one embryo in the mature seed of Welwitschia, and no doubt here, as in Gnetum Gnemon, all but one sooner or later are crowded out of existence. The endosperm from which the stage shown in Fig. 3 was taken has almost exhausted the tissue in the remains of which it is enclosed. As Hooker1 observed, most of this tissue is not part of the original nucellus, but is mainly formed by intercalary growth below the insertion of the integument. The endosperm is quite free from the surrounding tissue, and has a smooth firm surface composed of a well-defined and regular cell-layer. Its shape is little changed from that outlined in Fig. 89 k of my former paper.2 The upper third is, however, broader in proportion, and the lower region slopes more gently to the broad tip. The cavity marked c in the figure last cited has extended with the further penetration of the embryo. Between the embryo and the lower end of the endosperm the cells of an axial cylinder are looser than those nearer the periphery; they contain for the most part very little visible starch and they are usually binucleate; occasionally they contain three or more nuclei. This condition is of common occurrence in the endosperm-cells of Gymnosperms in the neighs bourhood of growing embryos and archegonia.3 In Welwitschia the multinucleate state is the result of direct nuclear division. It is generally assumed that the seeds of Welwitschia retain their power of germinating for a long period. Some evidence bearing on this question is now forthcoming. A number of seeds collected in Damaraland in January, 1907, were stored in this laboratory. They were exposed to the atmosphere, but otherwise were kept as dry as possible. Four were sown in the last week of February, 1910. 1 Hooker, 1863, p. 33. See also Pearson, 1906, p. 287. 3 Pearson, 1. c, p. 356. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 SUMMARY. 1. The intraseminal development of the embryo is continuous, and is apparently completed before the seed falls. It occupies not more than four months from the time of fertilization. 1. The intraseminal development of the embryo is continuous, and is apparently completed before the seed falls. It occupies not more than four months from the time of fertilization. 2. A few terminal initial cells (Figs, i, 2, 6, 7) are replaced by a single massive meristematic group (Fig. 3) which in due course gives rise to distinct root and stem growing points (Fig. 4). g g p g 3. The ' lateral cones' are visible as small protuberances in the axils of the cotyledons in the embryo of the seed. 3. The ' lateral cones' are visible as small protuberances in the axils of the cotyledons in the embryo of the seed. y y 4. The suspensor becomes greatly increased in thickness by centrifugal additions formed, as in Ephedra, in acropetal succession from superficial cells of the root-cap. The later formed of these usually show a degree of independence of the rest of the suspensor in the direction of their growth, and it may be that they are specially adapted to the function of absorption. 5. In intermediate stages the ovules are frequently polyembryonic, owing to the branching of the embryonic mass. g g y 6. So far as is known the mature seed never contains more than one embryo. 7. Two seeds collected in Damaraland in January, 1907, germinated readily in April, 1910. BOTANICAL LABORATORY, SOUTH AFRICAN COLLEGE, CAPE TOWN. Pearson.—On the Embryo of Welwitschia. Of these, two have not germinated ; the cotyledons of one seedling, appeared above the ground on April 4 and those of a second followed after an interval of about fourteen days. The latter is living (May 21), but shows signs of damping off; the older of the two appears to be still thoroughly healthy and vigorous. These seeds were shed certainly not later than June or July, 1906. They have therefore retained their vitality for forty-three months, during which they have survived the almost continuously damp atmosphere of Cape Town and the low temperatures of three Cape winters—conditions which it might be expected would be particularly trying to the seeds of tropical desert plants. It is therefore probable that the most resistant seeds are capable of lying dormant for a much longer period under natural conditions. ' Pearson, 1909 A. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 Pearson.—On tJie Embryo of Welwitschia. Pearson.—On tJie Embryo of Welwitschia. 765 BOTANICAL LABORATORY, SOUTH AFRICAN COLLEGE, CAPE TOWN. Pearson.—On the Embryo of Welwitschia. 766 Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 LITERATURE CITED. BOWER, F. O., 1881: On the further development of Welwitschia mirabilis. QJ.M.S. xxl (N.S.), P- 571- P 571 , 1882: The Germination and Embryology of Gnetum. Gnemon. I.e. xxii (N.S.)( p. 278. p HENRIQUES, J., 1910 : Welwitschia mirabilis. Gardeners' Chronicle, April 2, 1910. HOOKER, J. D., 1863: On Welwitschia, a new genus of Gnetacese. Linn. Soc. Lond. Trans., xxiv, p. 1. p LAND, W. J. G., 1907 : Fertilization and Etnbryogeny in Ephedra trifurca. Botanical Gazette, xliv. 273. PEARSON, H. H. W., 1906 : Some Observations on Welwitschia mirabilis, Hook. fil. Phil. Tran3. Roy. Soc. B. 198, p. 265. y p 1907 : The Living Welwitschia. Nature, April 4, 1907. 1909 (A) : Further Observations on Welwitschia. Phil. Trans. Roy. Soc. B. 200, P- 331- , 1909 (B) : Percy Sladen Memorial Expedition in South-West Africa, 1908-9, ii. Nature, October 21, 1909. STRASBURGER, E., 1870 : Die Angiospermen und die Gymnospermen. Jena. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 EXPLANATION OF PLATE LXIV. Illustrating Prof. Pearson's paper on the Embryo of Welwitschia. All the figures are prepared from longitudinal and approximately median sections. Figs. 4 and 5 are microphotographs. g p g p Figs. 1-3, 6 and 7 are drawn under Zeiss D, ocular 2, with the aid of the camera lucida. x 305. Fig. 1. A stage somewhat more advanced than that of Text-fig. 1. x = cells of' lower ring'; c = apical initial cells. p Fig. 2. A slightly more advanced stage, x = additions to the suspensor derived from the cells of the ' lower ring ' ; y = the cells which will form the next additions to the Euspensor; c — apical initial cells. Fig. 2. A slightly more advanced stage, x = additions to the suspensor derived from the cells of the ' lower ring ' ; y = the cells which will form the next additions to the Euspensor; c — apical initial cells. Fig. 3. A more advanced stage, a, b, d = suspensor cells; end. = endosperm cells. Fig. 4. A more advanced stage in which the suspensor (S) has completed its growth in thi ness. St. = stem dome ; R = root meristem. This precedes the stage shown in Text-fig. 2. ness. St. = stem dome ; R = root meristem. This precedes the stage shown in Text-fig. 2. Fig. 5. Embryo of mature seed, c = cotyledons; I.e. = lateral cones; other lettering as in Fig 4 Fig. 5. Embryo of mature seed, c = cotyledons; I.e. = lateral cones; other lettering as Fig. 4. Fig. 6. Twin-embryos resulting from bifurcation. g Fig. 6. Twin-embryos resulting from bifurcation. g y g Fig. 1. A young embryo formed as a lateral branch from an older one. One of the initial cells of the latter is in course of division. Fig. 1. A young embryo formed as a lateral branch from an older one. One of the initial cells of the latter is in course of division. '•Aiuwdbs of Botany'. 0,-MS.J j I 1. c. b. PEARSON. WELWITSCHI A. from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 user h 2018 '•Aiuwdbs of Botany'. Vol. xxiv puxn '•Aiuwdbs of Botany'. St. b. PEARSON. WELWITSCHI A. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018 b. Downloaded from https://academic.oup.com/aob/article-abstract/os-24/4/759/183042 by Insead user on 08 March 2018
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Lipid Profiling and Stable Isotopic Data Analysis for Differentiation of Extra Virgin Olive Oils Based on Their Origin
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Lipid Profiling and Stable Isotopic Data Analysis for Differentiation of Extra Virgin Olive Oils Based on Their Origin Igor Luki´c 1,† , Alessio Da Ros 2,† , Graziano Guella 3 , Federica Camin 2, Domenico Masuero 2 , Nadia Mulinacci 4, Urska Vrhovsek 2,* and Fulvio Mattivi 2,3,* Igor Luki´c 1,† , Alessio Da Ros 2,† , Graziano Guella 3 , Federica Camin 2, Domenico Masuero 2 , Nadia Mulinacci 4, Urska Vrhovsek 2,* and Fulvio Mattivi 2,3,* 2 Fondazione Edmund Mach, Research and Innovation Centre, Via E. Mach 1, 38010 San Michele all’Adige, Italy; darosalessio92@gmail.com (A.D.R.); federica.camin@unitn.it (F.C.); domenico.masuero@fmach.it (D.M.) 3 Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo Trento, Italy; graziano.guella@unitn.it 4 NEUROFARBA, Pharmaceutical and Nutraceutical Division, University of Florence, Via Ugo Schiff6, 50019 Sesto Fiorentino, Italy; nadia.mulinacci@unifi.it Correspondence: urska.vrhovsek@fmach.it (U.V.); fu * Correspondence: urska.vrhovsek@fmach.it (U.V.); fulvio.mattivi@unitn.it (F.M.) Academic Editor: Roberto Fabiani Received: 14 November 2019; Accepted: 11 December 2019; Published: 18 December 2019 Abstract: To differentiate extra virgin olive oils (EVOO) according to the origin of purchase, such as monocultivar Italian EVOO with protected denomination of origin (PDO) and commercially-blended EVOO purchased in supermarkets, a number of samples was subjected to the analysis of various lipid species by liquid chromatography/mass spectrometry (LC-ESI-MS/MS, LC-ESI-IT-MS) and proton nuclear magnetic resonance analysis (1H-NMR). Many putative chemical markers were extracted as differentiators by uni- and multivariate statistical analysis. Commercially-blended EVOO contained higher concentrations of the majority of minor lipids, including free fatty acids, their alkyl (methyl and ethyl) esters, monoglycerides, and diglycerides, which may be indicative of a higher degree of triglyceride lipolysis in these than in monocultivar PDO EVOO. Triterpenoids and particular TAG species were also found in higher proportions in the samples from the commercially-blended EVOO class, suggesting a possible influence of factors such as the cultivar and geographical origin. The largest differences between the classes were determined for the concentrations of uvaol and oleanolic acid. The results of the analysis by isotopic ratio mass spectrometry (IRMS) were reasonably consistent with the information about the geographical origin declared on the labels of the investigated EVOOs, showing considerable variability, which possibly also contributed to the differences in lipid composition observed between the two investigated classes of EVOO. Keywords: extra virgin olive oil; lipids; LC-MS/MS; NMR; IRMS; PDO molecules molecules Molecules 2020, 25, 4; doi:10.3390/molecules25010004 1. Introduction Extra virgin olive oil (EVOO) is appreciated among consumers because of its specific flavor and nutritional properties. Due to its economic importance, EVOO is among the most common commodities subject to fraud and mislabeling, and for this reason it is protected by regulation. The international trade standard issued by the International Olive Council (IOC) [1] and the corresponding umbrella regulation in the European Union (EU) [2] include a set of analytical and sensory methods to test and confirm the quality grade and authenticity of olive oil. In EU, EVOO can be additionally protected Molecules 2020, 25, 4; doi:10.3390/molecules25010004 www.mdpi.com/journal/molecules Molecules 2020, 25, 4 Molecules 2020, 25, 4 2 of 20 by protected denomination of origin (PDO) [3]. PDO EVOOs are produced according to a set of specific rules set by the holder of a designation in a specification document, governing aspects such as olive cultivars used, cultivation, harvest and processing conditions, and oil physico-chemical and sensory characteristics. In our recent case study conducted on the Italian market it has been shown that oils labelled by the highest quality category grade (EVOO), despite meeting basic regulatory requirements, can differ significantly in qualitative terms [4]. Monocultivar PDO EVOOs purchased on family farms were found to be superior to those offered at the same time in supermarkets with respect to their volatile profiles and sensory quality. Such large heterogeneity within the EVOO category can certainly influence and distort consumers’ perception of EVOO quality and in a way discredit the reputation of EVOO in general. Having in mind that the heterogeneity of oils within the EVOO category with respect to origin of purchase is certainly among the less studied topics in the ever-growing scientific area of olive oil traceability and quality, more studies are needed to find reliable chemical markers able to discriminate EVOO based on this criterion. Such findings would significantly contribute in clarifying the interrelationship between EVOO origin, overall quality and price, and would as well provide a basis for designing additional measures of protection of the PDO EVOO class in general, which is most likely target of fraud by mislabeling due to its large economic importance [5]. y g y g g p Triglycerides (triacylglicerols—TAGs), which are basically esters of glycerol and fatty acids (FAs), are the main neutral lipid component of olive oil (ca. 98%) [6]. 1. Introduction Olive oil TAGs contain primarily oleic (C18:1), palmitic (C16:0), linoleic (C18:2n−6), stearic (C18:0), palmitoleic (C16:1), and linolenic (C18:3n−3) acids, while others occur in minor amounts. Monounsaturated FAs (MUFAs) and essential polyunsaturated FAs (PUFAs) are among the most important nutritional elements of EVOO. The consumption of MUFAs has been associated with decrease of several cardiovascular risk factors [7], while EVOO linoleic and linolenic acids are an important source of essential FAs in human nutrition [8]. The percentage of TAGs with equivalent carbon number 42 (ECN 42) in total TAGs, where ECN is the sum of the number of carbon atoms in three constituent FAs in TAG molecule subtracted by 2 × total of double bonds, can be used as a marker for the detection of the presence of seed oils in olive oil [2]. In combination with other olive oil constituents, TAGs have been successfully utilized as markers of varietal [9–11] and geographical origin of EVOO [11]. In virgin olive oils, diglycerides (DAGs) are present in a range of 1% to 3% in the form of 1,2- and 1,3-isomers, whose ratio has been used as a marker of olive oil “freshness” [12]. The percentage of total free FAs (FFAs or acidity) is one of the parameters which is evaluated for the purposes of olive oil quality categorization [1,2]. The composition of olive oil total FA (the sum of those bound with glycerol in TAGs and the FFA forms) is usually determined by gas chromatography with flame-ionization or mass spectral detection after TAG hydrolysis and methylation [2] and may provide important information about olive oil nutritional quality (level of FA unsaturation) and purity. In the last years, proton nuclear magnetic resonance (1H-NMR) spectral analysis of olive oil is often used to determine not only the % molar ratio of fatty acyl chains in TAG but also the relative amount of DAGs and, eventually, to detect the presence of peroxidized acyl chains in TAGs [13]. Several results have also proved the usefulness of FA composition and distribution on the glycerol moiety for the establishment of EVOO cultivar or geographical origin [14–16]. The concentration of alkyl esters of free FAs (FAAE), specifically ethyl esters, is included among the criteria for olive oil quality grade evaluation [1,2]. 1. Introduction These markers originate mostly from inappropriate handling of olive fruit and oil [17,18] so their concentrations may be used to detect fraudulent mixtures of EVOO with lower quality oils, including deodorized ones. It is general opinion that the standard profiling of TAGs, DAGs, and total FFAs has limited discriminative power to differentiate olive oils according to various criteria [19]. However, it was assumed that recent analytical developments and novel sensitive methods could be able to provide new, more specific data with more information on olive oil lipids that could be useful for EVOO differentiation. y p p more specific data with more information on olive oil lipids that could be useful for EVOO differentiation. In this work, we applied a multi-methodological approach based on several potent analytical techniques in order to find new reliable markers able to discriminate EVOO based on the origin p p In this work, we applied a multi-methodological approach based on several potent analytical techniques in order to find new reliable markers able to discriminate EVOO based on the origin Molecules 2020, 25, 4 3 of 20 of purchase. A method was developed based on liquid chromatography with triple quadrupole mass spectrometric detection (LC-ESI-MS/MS) for the simultaneous quantification of minor lipids, including the profiling of FFAs, which, to our knowledge, has been studied rather scarcely. As well, the method provided a more detailed composition of FA alkyl esters occurring in olive oil in relation to previous studies, supplemented by particular MAGs and triterpenoids. On the other hand, liquid chromatography with quadrupole ion-trap mass spectrometry (LC-ESI-IT-MS) was utilized for the profiling of major TAGs, but also aimed to the targeted detection of particular trace TAG species, such as C50:4, C50:3, and C56:3, as well as those containing FAs with odd number of carbon atoms, which, to our knowledge, have not been studied extensively until now. In order to provide more detailed and yet complementary data to those obtained by the other techniques mentioned above, all the samples were subjected to 1H-NMR quantitative analysis to obtain both the distribution among lipid species (TAG/DAG/FFA) and a reliable distribution of acyl chains unsaturation (saturated FA (SFA)/MUFA/PUFA). The latter parameter also allowed establishing the unsaturation index (UI) and the iodine value (IV), two useful chemical parameters in EVOO quality control. 1. Introduction p q y Besides quality in general, the most important aspect that defines a given PDO and drives the consumers’ preferences towards this class of EVOO is in fact the authenticity of its geographical origin. One of the most useful techniques to prove and authenticate the geographical origin of EVOO is stable isotope ratio analysis by isotope ratio mass spectrometry (IRMS) [20]. For example, the stable isotope ratio of C (13C/12C, expressed as δ13C) of palmitic, oleic, and linoleic FAs was successful in differentiating olive oils according to the country or region of provenience [20,21]. Both the δ13C and 18O/16O (δ18O) ratios determined for bulk olive oils from various countries were found to change according to the latitude, the distance from the sea and the environmental conditions during growing of the plants [22,23]. The δ13C and δ2H (2H/1H) of n-C29 alkanes were significantly more positive in olive oils from the southern compared with northern Mediterranean countries [24]. As for Italian EVOOs, works carried on δ13C and δ18O [25,26], also in combination with δ2H [27,28], proved that it wass possible to distinguish samples from different Italian macro areas, as well as Italian from other Mediterranean olive oils. The three isotopic ratios, in particular δ2H and δ18O, were found to be correlated to the climatic (mainly temperature) and geographical (mainly latitude and distance from the coast) characteristics and to the δ18O and δ2H of the surface waters as well to the year of production [25–28]. The δ2H values significantly distinguished olive oils produced on the Adriatic from those from the Tyrrhenian coast of Italy in each year [29]. The combination of isotopic analysis with 1H-NMR profiling achieved optimal discrimination between Greece, Spain, Italy, Turkey, Crete, France, and between Italy and Tunisia, the country from which the largest amount of olive oil is imported in Europe [30]. In this study, it was assumed that IRMS would be able to provide relevant information on the three isotopic ratios in the two investigated EVOO classes that could be useful for the confirmation of geographical origin declared on their labels, and possibly for their differentiation. The aim of this study was dual. In the first part, sensitive analytical methods based on complementary LC-MS and NMR techniques were applied to detect less known chemical markers among various lipid species able to differentiate Italian monocultivar PDO EVOOs obtained on family farms from those purchased in supermarkets. 1. Introduction The second goal was to verify the declared geographical origin of the EVOOs from the both classes by IRMS analysis. It was considered that such findings would significantly contribute to EVOO diversification on the market, and would help to clarify the interrelationship between EVOO origin, quality, and price, and in this way support the growth of the niche in the market segment of consumers informed and interested in healthy, quality products with remarkable diversity and clear identity. 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides and Triterpenoids 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides and Triterpenoids Validation parameters for the method of determination of minor lipid compounds in EVOO by LC-ESI-MS/MS are shown in Tables S3 and S4. All the calibration curves exhibited good linearity 4 of 20 Molecules 2020, 25, 4 (r2 values from 0.95 to 1.00). Limits of quantification ranged from 0.2 to 40 µg/L depending on the compound. The linearity data were used to assess the percentage of matrix effect (% ME), which was reported in Table S3. The matrix effect was found to be insignificant because the obtained variability was close to %RSD repeatability values [31]. Thus, curves prepared in solvent were selected for the quantification. The coefficients of variation (CV%) did not exceed 15% for intra-day assay and 20% for inter-day assay. The average recovery was in the range from 65% to 125% with %RSD less or equal 20%, which was considered satisfactory. The recovery values obtained surpassed 90% for 14 compounds, were between 80% and 90% for 4 compounds and between 70% and 80% for 3 compounds, with %RSD values between 1% and 11%. This indicated good accuracy, recovery, and precision of the method. It is worth mentioning that several lipids for which the method was also validated (Table S1), such as carnitines, glycerophospholipids, and sphingolipids, were not detected in the samples of this study, since their concentrations were below the determined limits of detection (LOD). In all the investigated EVOO samples 20 minor lipids were identified, including 10 free fatty acids (FFAs), six FFA methyl and ethyl esters, two monoglycerides (MAGs), and two triterpenoids (Table 1). The most abundant among FAAs was oleic (C18:1) followed by palmitic (C16:0), linoleic (C18:2), stearic (C18:0), and palmitoleic (C16:1) acids, which corresponded to the natural distribution of total FAs (esterified in TAGs + FFA) in EVOO in general [6]. The methyl and ethyl esters of the most abundant FFAs, that is oleates, palmitates, and linoleates, dominated the alkyl ester composition, while oleic and linoleic acids were a structural part of the only two identified MAGs (Table 1). Table 1. Concentrations (µg/g) of minor lipids in monocultivar protected designation of origin (PDO) and commercially-blended extra virgin olive oils obtained by LC-ESI-MS/MS analysis. An asterisk (*) in a row represents significant differences between mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides and Triterpenoids Table 1. Concentrations (µg/g) of minor lipids in monocultivar protected designation of origin (PDO) and commercially-blended extra virgin olive oils obtained by LC-ESI-MS/MS analysis. An asterisk (*) in a row represents significant differences between mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. Minor Lipids Origin/Class Monocultivar PDO Commercially-Blended Free fatty acids Palmitic acid (C16:0) 285.41 362.95 Palmitoleic acid (C16:1) 10.58 16.57 Stearic acid (C18:0) 27.41 43.39 Oleic acid (C18:1) 809.53 1045.52 Linoleic acid (C18:2) 70.52 93.10 Linolenic acid (C18:3) 5.67 9.76 * Arachidic acid (C20:0) 8.53 11.42 Behenic acid (C22:0) 8.52 9.45 Erucic acid (C22:1) 0.06 0.05 Lignoceric acid (C24:0) 21.85 27.04 Total free fatty acids 1248.09 1619.27 Free fatty acid esters Methyl oleate 4.02 7.09 * Methyl linoleate 0.05 0.24 * Ethyl palmitate 0.10 1.01 * Ethyl stearate 0.00 0.32 * Ethyl oleate 2.29 8.18 * Ethyl linoleate 0.38 1.04 * Total free fatty acid esters 6.83 17.87 * Monoglycerides 1-Oleoyl-rac-glycerol 30.11 53.29 * 1-Linoleoyl-rac-glycerol 8.77 12.84 * Total monoglycerides 38.88 66.13 * Triterpenoids Oleanolic acid 26.71 50.13 * Uvaol 4.58 14.04 * Total triterpenoids 31.28 64.17 * Minor Lipids Origin/Class Monocultivar PDO Commercially-Blended 5 of 20 Molecules 2020, 25, 4 FFAs in olive oil derive from the breakdown of TAGs by lipolysis. There are many factors which can affect the degree of TAG lipolysis, including anomalies during biosynthesis, microbial activity, and environmental factors. Infestation by the olive fly (Bactrocera oleae) is a major cause of high FFA content in olives. Damaged olive fruits, delayed fruit processing, and storage in inappropriate conditions result in increased lipolysis rates, while olive oil extraction which is not properly conducted (e.g., prolonged contact between oil and vegetation water) may also result in high FFA values [6,32]. Therefore, the content of FFA is directly related to the quality of olive oil and reflects the care taken from blossoming and fruit set to the eventual sale and consumption of the oil [33]. The FFA content, also known as acidity, is one of the main criteria used to establish different categories of olive oil: according to the European community, EVOO, as the highest quality category, must have FFA content below or equal to 0.8% (as oleic acid, w/w), as obtained by the standard titration method [2]. 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides and Triterpenoids In this work, the average total FFA concentration obtained by LC-ESI-MS/MS analysis did not exceed 0.2% in neither of the two investigated EVOO classes (Table 1). Although a tendency towards higher concentrations in commercially-blended than in PDO EVOO was noted for the majority of FFAs, statistically significant differences were found only for linolenic acid. Such a result was, to some extent, in accordance with a previous study in which low-priced EVOO samples were found to contain more FFAs than EVOOs of higher price [34]. FFA content was previously shown to increase during olive oil storage and aging [35,36]. In this work, in contrast to the monocultivar PDO EVOOs which were analyzed relatively fresh, the age of commercially-blended EVOOs was not declared by the producers/sellers and it was practically unknown. It was possible that the samples from the latter class were fully or partially composed from oils obtained in harvests prior to 2016, and that the increased concentrations of particular FFAs partially resulted from TAG chemical hydrolysis during aging. Despite the possible differences with respect to the EVOO age, it must be kept in mind that all the EVOOs included in this study were carefully selected and sampled at the same time, and were therefore valid and authentic representatives of the both classes of EVOOs offered on the market at that given moment. The content of fatty acid alkyl esters (FAAEs) was principally introduced among the chemical parameters controlled in olive oil quality evaluation [2] to detect blends including low quality olive oils with weak organoleptic defects [17,18]. FAAEs are formed by esterification of short-chain alcohols methanol and ethanol with FAAs yielding methyl and ethyl esters, respectively, although transesterification with triglycerides or partial glycerides may also be a source [37]. They are generally considered indicators of lower olive oil quality and their high concentration often indicate the use of olive fruits with fermentative alterations [17,38–40]. In fact, it was demonstrated that FAAE formation was not limited mainly by the content of FAA, but it appeared to be strongly related to the concentration of free alcohols in oil, among which ethanol can be produced exclusively by fermentation [37]. However, evidence exists that the content of FAAE can be relatively high even in high quality EVOO, and vice versa [41]. 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides and Triterpenoids In this study, the average total concentration of fatty acid ethyl esters (FAEEs) and the total FAAE concentration were below the maximum limit of 35 mg/kg prescribed by the European Commission regulation for EVOO [2]. Higher concentrations of all the identified FAAE/FAEEs were found in commercially-blended EVOOs (Table 1), which indicates the possibility that the olives used for the production of particular samples from this class were overripe or of lower quality suffering from fermentative alterations. Such results are in agreement with our previous report generated from a study with the same sample set, where commercially-blended olive oils were characterized by lower sensory quality on the average, with a number of samples having a sensory defect, including fusty/muddy sediment, vinegary/winey, or musty [4] which could have originated from undesirable fermentative processes, as reported earlier [38,42]. FAAE concentration was previously shown to increase during storage [41,43], which is another possible cause of the higher concentration found in commercially-blended EVOOs, which were possibly not fresh at the moment of sampling. y p y p g Similar to diglycerides (DAGs), the presence of MAGs in olive oil is a result of either incomplete biosynthesis of TAGs or their later hydrolysis during processing and storage [12,44]. In virgin olive oil, DAGs are present in the range of 1–2.8%, while MAGs are found in amounts lower than 0.25%, Molecules 2020, 25, 4 Molecules 2020, 25, 4 6 of 20 with a much higher proportion of those containing a single fatty acid on position 1 than on position 2 of glycerol moiety [45,46]. The identification of only two 1-MAG species in this work confirmed this phenomenon (Table 1). Both compounds, 1-oleoyl- and 1-linoleoyl-rac-glycerol were found in higher concentration in commercial–blended EVOO, confirming the possibility that a higher degree of TAG hydrolysis occurred in these than in PDO EVOOs. The largest portion of triterpenoids in olive fruit is located in its epicarp. Triterpenoid concentration in olive oil can be increased by longer malaxation durations and higher malaxation temperatures during olive processing, depending on the compound and olive cultivar [47]. High levels of particular triterpenoids may indicate the presence of olive pomace oil in EVOO, and the percentage of the sum of triterpene diols uvaol and erythrodiol with respect to total sterols is in fact included among the criteria which are evaluated in testing EVOO authenticity in EU [2]. 2.1. LC-ESI-MS/MS Analysis of Free Fatty Acids, Fatty Acid Methyl and Ethyl Esters, Monoglicerides and Triterpenoids Higher concentrations of the triterpenoids identified in this study, oleanolic acid and uvaol, were found in commercially-blended EVOO (Table 1). Although a possibility should not be neglected that the malaxation and processing parameters were the cause, it must be kept in mind that the content of triterpenoids strongly depends on cultivar origin [47,48], which is therefore another possible source of the observed difference. 2.2. LC-ESI-IT-MS Analysis of Triglycerides Relative proportions (%) of triglycerides (TAGs) obtained by LC-ESI-IT-MS analysis in monocultivar PDO and commercially-blended EVOO are reported in Table 2. As expected, TAGs consisting of the most abundant naturally occurring FAs in olive oil, the species 54:3, 52:2, 54:4, and 52:3, dominated the profiles in both classes of EVOO. The obtained profiles did not fully coincide with those obtainable by the official EU method [2], with some TAGs not reported and some additionally identified, which suggests the method applied in this study could be used as a complementary approach to the standard one for obtaining additional information. Table 2. Relative proportions (%) of triglycerides (TAGs) in monocultivar protected designation of origin (PDO) and commercially-blended extra virgin olive oils obtained by liquid chromatography with quadrupole ion-trap mass spectrometry (LC-ESI-IT-MS) analysis. An asterisk (*) in a row represents significant differences between mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. TAG Species † TAG Chains ‡ Origin/Class Monocultivar PDO Commercially-Blended TAG 50:1 18:1 16:0 16:0 5.83 5.44 TAG 50:2 18:1 16:1 16:0 3.06 2.84 TAG 50:3 - - - 0.63 0.70 TAG 50:4 - - - 0.07 0.08 TAG 52:1 18:1 18:0 16:0 2.32 2.47 TAG 52:2 18:1 18:1 16:0 19.10 19.06 TAG 52:3 18:2 18:1 16:0 10.36 * 9.64 TAG 52:4 18:3 18:1 16:0 3.38 3.13 TAG 52:5 - - - 0.46 0.42 TAG 52:6 - - - 0.05 * 0.03 TAG 53:2 18:1 18:1 17:0 0.42 0.44 TAG 53:3 18:1 18:1 17:1 0.68 0.70 TAG 53:4 - - - 0.12 0.14 TAG 54:1 - - - 0.68 0.80 * TAG 54:2 18:1 18:1 18:0 6.37 7.34 * TAG 54:3 18:1 18:1 18:1 25.40 26.59 TAG 54:4 18:2 18:1 18:1 11.86 11.56 TAG 54:5 18:3 18:1 18:1 4.55 4.47 TAG 54:6 - - - 0.74 0.70 TAG 56:1 - - - 0.16 0.18 TAG 56:2 20:0 18:1 18:1 1.47 1.51 TAG 56:3 20:1 18:1 18:1 1.63 1.53 7 of 20 Molecules 2020, 25, 4 Table 2. Cont. 2.2. LC-ESI-IT-MS Analysis of Triglycerides TAG Species † TAG Chains ‡ Origin/Class Monocultivar PDO Commercially-Blended TAG 56:4 - - - 0.43 0.38 TAG 58:1 - - - 0.06 0.06 TAG 58:2 22:0 18:1 18:1 0.38 0.39 TAG 58:3 - - - 0.11 0.10 TAG peroxides § - - - 0.77 0.72 † Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ number of carbon atoms: double bonds in each of the three fatty acids in the structure of the corresponding TAG; § proportion (%) of the sum of 52:2, 52:3, 54:3, 54:4, and 54:5 TAG peroxides in total TAGs. † Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ number of carbon atoms: double bonds in each of the three fatty acids in the structure of the corresponding TAG; § proportion (%) of the sum of 52:2, 52:3, 54:3, 54:4, and 54:5 TAG peroxides in total TAGs. The differences between the two EVOO classes with respect to average TAG composition were not large (Table 2). TAG composition is not evaluated among the parameters related to EVOO sensory quality, while a part of EVOO nutritional value linked to TAGs, related mainly to the FA unsaturation level, depends mostly on cultivar, geographical origin and fruit ripening degree [9–11,34]. The differences between the two classes of EVOO, observed for a relatively small number of TAG species, could be primarily ascribed to the abovementioned factors. TAGs 52:3 and 52:6 occurred in a higher average percentage in monocultivar PDO EVOO, while TAGs 54:1 and 54:2 stood out with higher values in commercially-blended EVOO (Table 2). The proportions of the TAG species that could possibly be associated with particular alterations in production with possible repercussions on olive oil quality, such as species that include FAs with odd number of carbon atoms (53:2 and 53:3) and TAG peroxides, did not differ between the two classes. The proportions of particular minor TAG isomers, not included in the official methods [2] and investigated rather scarcely in olive oil up to date, are reported in Table 3. Significant differences between the two EVOO classes were found only for the relative proportions of TAG 50:4 I and II species. † Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ Number of carbon atom double bonds in each of the three fatty acids in the structure of the corresponding TAG. Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ N double bonds in each of the three fatty acids in the structure of the corresponding TAG. † Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ Number of carbon atoms: double bonds in each of the three fatty acids in the structure of the corresponding TAG 2.3. H-NMR Analysis of Lipids The lipid (essentially TAG) composition of EVOO samples was established by measurement and analysis of the corresponding 1H-NMR spectra as described in Section 3.4. The main features of the spectra are outlined in Figure 1 reporting also one of the main TAG species present in olive oils (TAG 54:4, 18:1/18:1/18:2) as a model. The data reported in Table 4 were obtained by area peak integration and simple equations relating them to the number of protons at a given position. Figure 1. 400 MHz proton nuclear magnetic resonance (1H-NMR) spectrum of a monocultivar protected designation of origin (PDO) extra virgin olive oil sample in CDCl3 at 300 K. Figure 1. 400 MHz proton nuclear magnetic resonance (1H-NMR) spectrum of a monocultivar protected designation of origin (PDO) extra virgin olive oil sample in CDCl3 at 300 K. Table 4. Lipids in monocultivar protected designation of origin (PDO) and commercially-blended extra virgin olive oils obtained by NMR analysis. An asterisk (*) in a row represents significant differences between mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. Table 4. Lipids in monocultivar protected designation of origin (PDO) and commercially-blended extra virgin olive oils obtained by NMR analysis. An asterisk (*) in a row represents significant differences between mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. Table 4. Lipids in monocultivar protected designation of origin (PDO) and commercially-blended extra virgin olive oils obtained by NMR analysis. An asterisk (*) in a row represents significant differences between mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. Lipids Origin/Class Monocultivar PDO Commercially-Blended Total triglycerides (TAGs) 99.38 99.05 Total saturated fatty acids (SFA) 15.83 15.52 Total monounsaturated fatty acids (MUFA) 74.95 75.77 Linoleic acid in TAG (C18:2) 7.92 7.61 Linolenic acid in TAG (C18:3) 1.30 * 1.10 Unsaturation index (UI) 0.95 0.94 Iodine value (IV) 82.33 84.10 * Total 1,2-diacylglycerols (1,2-DAGs) 0.56 0.72 * Estimated free fatty acids and minor lipids 0.07 0.26 * In particular, the ratio of the peaks area F/H represents the best way to validate the approximations used in the approach for the analysis of edible oils relying on the large dominance of TAG species [49]. 2.2. LC-ESI-IT-MS Analysis of Triglycerides Although the source of the observed differences remained unexplained at this stage, and it could only be assumed that factors such as cultivar and geographical origin, respectively, could have had a significant effect, the results obtained are certainly intriguing and imply the need to further investigate the significance of the trace TAG species in olive oil. Table 3. Relative proportions (%) of minor triglycerides (TAGs) and particular TAG isomers in monocultivar protected designation of origin (PDO) and commercially-blended extra virgin olive oils obtained by HPLC-HRMS analysis. An asterisk (*) in a row represents significant differences between mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. TAG Species † TAG Chains ‡ Origin/Class Monocultivar PDO Commercially-Blended TAG 50:4 isomers TAG 50:4 I 18:2 16:1 16:1 24.54 31.20 * TAG 50:4 II 18:3 16:1 16:0 75.46 * 68.80 total - - - 100.00 100.00 TAG 50:3 isomers TAG 50:3 II 18:2 16:1 16:0 66.56 67.55 TAG 50:3 III 18:3 16:0 16:0 33.44 32.45 total 18:1 18:1 16:0 100.00 100.00 TAG 56:3 isomers TAG 56:3 I 20:1 18:1 18:1 71.63 71.96 TAG 56:3 II 20:0 18:2 18:1 28.37 28.04 total - - - 100.00 100.00 TAG 53 isomers TAG 53:4 - - - 10.12 10.41 TAG 53:3 18:1 18:1 17:1 56.17 54.79 TAG 53:2 18:1 18:1 17:0 33.71 34.80 total 18:1 18:1 18:0 100.00 100.00 † Number of carbon atoms: double bonds in the structure of the corresponding TAG; ‡ Number of carbon atoms: double bonds in each of the three fatty acids in the structure of the corresponding TAG. 8 of 20 Molecules 2020, 25, 4 2.3. H-NMR Analysis of Lipids Although the averaged UI (0.941 in the first set versus 0.950 in the second set) and iodine value (84.0 versus 84.5, respectively) of the two mentioned sets of commercially-blended EVOO were quite similar, the second set was characterized by significantly higher relative amounts of SFA and PUFA and lower amount of MUFA (oleic chain, essentially). The differences between the two classes of the investigated EVOO with respect to the 1H-NMR data can be seen in Table 4. Both classes were characterized by relatively similar major lipid parameters. Monocultivar EVOOs were distinguished by a higher level of linolenic acid and lower iodine value (IV), while a significant difference for unsaturation index (UI) was not found, meaning an unambiguous general conclusion about the difference between the two classes of EVOO with respect to the level of unsaturation could not be made at this point. Level of saturation of acyl chains in olive oil TAGs may depend on various factors, including geographical position and climate, as well as varietal origin [50]. It is possible that these were among the main sources of both intra- and inter-class variability of lipid composition observed in this study. Stereospecific distribution of FAs in DAG is known to be affected by several factors. 1,2-DAG isomers are commonly attributed to the incomplete biosynthesis of TAGs in olive fruit, whereas 1,3-DAGs are considered to derive mainly from enzymatic or chemical hydrolysis of TAGs before or during oil extraction [12]. It was shown that 1,2-, 1,3-, and total DAG concentrations in olive oil significantly increase as a result of alterations during processing, including, for example, prolonged storage of piled olives before processing [12,51]. During storage 1,2- species isomerize to more stable 1,3-DAGs, making the ratio of 1,3-/1,2-DAG a useful criterion indicative of olive oil age [12,44,51]. In this study, a higher proportion of 1,2-DAG fraction was found in commercially-blended than in PDO EVOO (Table 4), while 1,3-DAG isomers were not identified. Considering the contents of the other tentative indicators of olive oil age evaluated in this study, such as FFAs and FAAEs, it was tentatively assumed that commercially-blended EVOO were at least partially composed of olive oils obtained during harvests prior to 2016, meaning their age was older, on the average, than that of the PDO ones. 2.3. H-NMR Analysis of Lipids Its value should be exactly 1.500 in an oil containing only TAG species, since the signal F (δH ≈2.30 brt, -CH2 in α-position in the acyl chains) represents six protons and the signal H (δH ≈4.29 dd and δH ≈4.14 dd, -CH2 from sn-1,3 TAG) represents four protons. F/H values higher than 1.500 can be explained by the presence of DAG, MAG, and/or FFA which give their contribution to F but do not contribute to the H peak area. As much as the F/H ratio diverges from 1.500 the contribution of 9 of 20 Molecules 2020, 25, 4 DAG, MAG, and FFA becomes higher, but within the range 1.450 ≤F/H ≤1.550 the approach is still considered reliable. Thus, the F/H ratio indicates whether the approximations are correct and therefore produce trustworthy analytical data for the % molar fraction of SFA, MUFA, and PUFA fatty acyl chains in a targeted olive oil. In this work, the average F/H value of all the analyzed EVOO was 1.512 with a very small relative standard deviation of 0.5%, confirming the calculations were valid and reliable. y g A certain degree of intra-class heterogeneity was observed within both classes of investigated EVOO with respect to the relative proportions of total SFA, MUFA, and PUFA. Concerning the relative amount of the lipid acyl chains, a bimodal distribution of PDO EVOOs was noted, with a major set (14 of 20 PDO samples) showing a classical distribution of SFA/MUFA/PUFA = 15.1 ± 1.5/76.3 ± 1.4/8.6 ± 0.9, whilst the remaining lead to the averaged distribution values lower in MUFA, such as SFA/MUFA/PUFA = 16.1 ± 0.8/72.6 ± 0.8/10.4 ± 0.5. Worth of note, particularly unexpected distributions were observed in particular samples, such as in Ottobratico cultivar PDO EVOO from Reggio Calabria with SFA/MUFA/PUFA = 19.0 ± 0.3/70.8 ± 0.3/10.2 ± 0.2 (richer in SFA and PUFA), and in Taggiasca cultivar PDO EVOO from Imperia with SFA/MUFA/PUFA = 12.5 ± 0.1/80.0 ± 0.2/7.5 ± 0.1 (richer in MUFA). For commercially-blended EVOO a similar intra-class differentiation was observed, with the most populated set (19 of 25 samples) centered at average molar fractions SFA/MUFA/PUFA = 15.0 ± 0.9/76.9 ± 1.9/8.1 ± 15 and a minor set (6 of 25) centered at average molar fractions SFA/MUFA/PUFA = 17.1 ± 0.5/72.1 ± 1.2/10.8 ± 1.5. 2.4. Multivariate Statistical Analysis Principal component analysis (PCA) separated the samples belonging to the two classes of investigated EVOO according to the origin of purchase relatively successfully (Figure 2). Although monocultivar PDO EVOOs were produced from different olive cultivars grown in different geographical areas in Italy, they were grouped much closer to each other than the commercially-blended ones, suggesting a greater level of intra-class homogeneity with respect to the profile of lipids. It is possible that the presumed differences between the average age of the EVOOs from the two classes, and still a relatively homogenous geographical origin of Italian PDO in comparison to possibly heterogeneous provenience of the commercially-blended EVOOs (Italy and other EU countries), were among the causes. Several markers were found to be related to the commercially-blended EVOOs, including all the minor lipid species, such as FFAs, FAAEs, MAGs, and DAGs, and also particular TAG species and iodine value, which corresponded completely to the one-way ANOVA results. As mentioned above, the positions of the commercially-blended EVOO samples on Cartesian plane were rather dispersed, pointing to the very heterogeneous composition of minor lipids and potential quality of these samples. Molecules 2019, 10 of 20 Figure 2. (a) and (c) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the origin of purchase in two-dimensional space defined by the first three principal components, PC1, PC2, and PC3. Green cycles represent monocultivar protected designation of origin (PDO)EVOO purchased on family farms, while red cycles represent commercially-blended EVOO purchased in supermarkets (b) and (d) Factor loadings of selected variables, i.e., concentrations or proportions of various lipid species, obtained by LC-ESI-MS/MS, LC-ESI-IT-MS, and 1H-NMR, respectively, on PC1, PC2, and PC3. Relati ely ood e a atio obtai ed by hie a hi al lu te i a aly i o fi ed that the t o Figure 2. (a) and (c) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the origin of purchase in two-dimensional space defined by the first three principal components, PC1, PC2, and PC3. Green cycles represent monocultivar protected designation of origin (PDO)EVOO purchased on family farms, while red cycles represent commercially-blended EVOO purchased in supermarkets (b) and (d) Factor loadings of selected variables, i.e., concentrations or proportions of various lipid species, obtained by LC-ESI-MS/MS, LC-ESI-IT-MS, and 1H-NMR, respectively, on PC1, PC2, and PC3. Figure 2. 2.3. H-NMR Analysis of Lipids Knowing that the concentration of 1,2-DAGs decreases during storage, it was expected that the presumably older commercially-blended EVOO would be characterized by lower amounts in relation to PDO EVOO, but this was not the case. Nevertheless, the possibility cannot be rejected that the commercially-blended samples contained higher average concentration of 1,2-DAGs already at the moment of production and/or release on the market, which later decreased but were still higher than that found in monocultivar PDO EVOOs. The differences observed between the average estimated levels of FAA and other minor lipids found in the two classes of EVOO (Table 4) correspond well to those determined for particular FAAs, 10 of 20 Molecules 2020, 25, 4 FAAEs, and MAGs by the LC-ESI-MS/MS method (Table 1). Commercially-blended EVOOs were characterized by higher levels, which was possibly mainly a result of an increased degree of TAG lipolysis, although the contribution of other factors, such as different cultivars and geographical origin, as well as EVOO age and storage conditions, should not be completely excluded. 2.4. Multivariate Statistical Analysis (a) and (c) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the origin of purchase in two-dimensional space defined by the first three principal components, PC1, PC2, and PC3. Green cycles represent monocultivar protected designation of origin (PDO)EVOO purchased on family farms, while red cycles represent commercially-blended EVOO purchased in supermarkets (b) and (d) Factor loadings of selected variables, i.e., concentrations or proportions of various lipid species, obtained by LC-ESI-MS/MS, LC-ESI-IT-MS, and 1H-NMR, respectively, on PC1, PC2, and PC3. Figure 2. (a) and (c) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the origin of purchase in two-dimensional space defined by the first three principal components, PC1, PC2, and PC3. Green cycles represent monocultivar protected designation of origin (PDO)EVOO purchased on family farms, while red cycles represent commercially-blended EVOO purchased in supermarkets (b) and (d) Factor loadings of selected variables, i.e., concentrations or proportions of various lipid species, obtained by LC-ESI-MS/MS, LC-ESI-IT-MS, and 1H-NMR, respectively, on PC1, PC2, and PC3. 11 of 20 Molecules 2020, 25, 4 Molecules 2020, 25, 4 Relatively good separation obtained by hierarchical clustering analysis confirmed that the two investigated classes of EVOO differed notably with respect to the composition of lipids (Figure 3). Most of the conclusions were similar to those obtained by the PCA analysis: PDO EVOOs formed a more heterogeneous class, characterized by a smaller number of markers, while the commercially-blended EVOOs exhibited rather diverse lipid composition. Molecules 2019, 11 of 20 Figure 3. Hierarchical clustering analysis performed using lipid profiles found in Italian monocultivar protected designation of origin (PDO) extra virgin olive oils (EVOO) purchased on family farms and commercially-blended (CB) EVOO purchased in supermarkets in Italy. The heatmap was generated using 21 most significant compounds (the highest Fisher ratios). The rows in the heatmap represent lipids and the columns indicate samples. The colors of the heatmap cells indicate the abundance of lipids across different samples. The color gradient, ranging from dark blue through white to dark red, represents low middle and high abundance of lipid species Figure 3. Hierarchical clustering analysis performed using lipid profiles found in Italian monocultivar protected designation of origin (PDO) extra virgin olive oils (EVOO) purchased on family farms and commercially-blended (CB) EVOO purchased in supermarkets in Italy. The heatmap was generated using 21 most significant compounds (the highest Fisher ratios). 2.4. Multivariate Statistical Analysis The rows in the heatmap represent lipids and the columns indicate samples. The colors of the heatmap cells indicate the abundance of lipids across different samples. The color gradient, ranging from dark blue through white to dark red, represents low, middle, and high abundance of lipid species. Figure 3. Hierarchical clustering analysis performed using lipid profiles found in Italian monocultivar protected designation of origin (PDO) extra virgin olive oils (EVOO) purchased on family farms and commercially-blended (CB) EVOO purchased in supermarkets in Italy. The heatmap was generated using 21 most significant compounds (the highest Fisher ratios). The rows in the heatmap represent lipids and the columns indicate samples. The colors of the heatmap cells indicate the abundance of lipids across different samples. The color gradient, ranging from dark blue through white to dark red, e e e t lo iddle a d hi h abu da e of li id e ie Figure 3. Hierarchical clustering analysis performed using lipid profiles found in Italian monocultivar protected designation of origin (PDO) extra virgin olive oils (EVOO) purchased on family farms and commercially-blended (CB) EVOO purchased in supermarkets in Italy. The heatmap was generated using 21 most significant compounds (the highest Fisher ratios). The rows in the heatmap represent lipids and the columns indicate samples. The colors of the heatmap cells indicate the abundance of lipids across different samples. The color gradient, ranging from dark blue through white to dark red, represents low, middle, and high abundance of lipid species. PLSDA allowed a rather good differentiation of the two classes of investigated EVOO according to the origin of purchase (Figure 4). Interestingly, the highest variable importance in projection (VIP) scores were attributed to the triterpenoids, such as uvaol and oleanolic acid, which turned out to be the most important differentiators. Such a result confirmed once again the potential of the compounds from the olive oil unsaponifiable fraction to serve as markers according to various criteria. Besides triterpenoids, the 15 most important lipids according to PLSDA included particular FAAE and other minor lipid species abundant in commercially-blended EVOO, while certain TAGs fi d l d l i PDO EVOO PLSDA allowed a rather good differentiation of the two classes of investigated EVOO according to the origin of purchase (Figure 4). 2.4. Multivariate Statistical Analysis Interestingly, the highest variable importance in projection (VIP) scores were attributed to the triterpenoids, such as uvaol and oleanolic acid, which turned out to be the most important differentiators. Such a result confirmed once again the potential of the compounds from the olive oil unsaponifiable fraction to serve as markers according to various criteria. Besides triterpenoids, the 15 most important lipids according to PLSDA included particular FAAE and other minor lipid species abundant in commercially-blended EVOO, while certain TAGs were confirmed as related to monocultivar PDO EVOO. Molecules 2020, 25, 4 M l l 2019 12 of 20 f 12 of 20 12 f 20 Figure 4. (a) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the origin of purchase in two-dimensional space by partial least squares discriminant analysis. Green cycles represent monocultivar protected designation of origin (PDO) EVOO purchased on family farms, while red cycles represent commercially-blended (CB) EVOO purchased in supermarkets (b) variable importance in projection (VIP) scores of the variables (lipids) most useful for the differentiation of monocultivar PDO EVOO and commercially-blended EVOO. Figure 4. (a) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the origin of purchase in two-dimensional space by partial least squares discriminant analysis. Green cycles represent monocultivar protected designation of origin (PDO) EVOO purchased on family farms, while red cycles represent commercially-blended (CB) EVOO purchased in supermarkets (b) variable importance in projection (VIP) scores of the variables (lipids) most useful for the differentiation of monocultivar PDO EVOO and commercially-blended EVOO. fi f h l b ( ) Figure 4. (a) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the origin of purchase in two-dimensional space by partial least squares discriminant analysis. Green cycles represent monocultivar protected designation of origin (PDO) EVOO purchased on family farms, while red cycles represent commercially-blended (CB) EVOO purchased in supermarkets (b) variable importance in projection (VIP) scores of the variables (lipids) most useful for the differentiation of monocultivar PDO EVOO and commercially-blended EVOO. Figure 4. (a) Separation of olive oils sold as extra virgin olive oil (EVOO) in Italy according to the origin of purchase in two-dimensional space by partial least squares discriminant analysis. 2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS) 2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS) f f g p g y p p y The average values of δ13C, δ2H, and δ18O in monocultivar PDO and commercially-blended EVOO are reported in Table 5. Statistically significant differences were determined for δ2H and δ18O, with lower values found in monocultivar PDO EVOO. According to the literature [30], the isotopic values of olive oil increase with decreasing latitude. It is possible that the contribution of Italian monocultivar PDO EVOO originating from the orchards located further from the sea and at higher latitudes with colder climate (e.g., Brescia, Verona, and Garda PDOs) prevailed and significantly decreased the average δ2H and δ18O isotopic values in monocultivar PDO EVOO, the same as non- Italian commercial EVOO originating from lower latitudes in warmer EU Mediterranean countries possibly had a notable influence on increasing the average δ2H and δ18O values determined in The average values of δ13C, δ2H, and δ18O in monocultivar PDO and commercially-blended EVOO are reported in Table 5. Statistically significant differences were determined for δ2H and δ18O, with lower values found in monocultivar PDO EVOO. According to the literature [30], the isotopic values of olive oil increase with decreasing latitude. It is possible that the contribution of Italian monocultivar PDO EVOO originating from the orchards located further from the sea and at higher latitudes with colder climate (e.g., Brescia, Verona, and Garda PDOs) prevailed and significantly decreased the average δ2H and δ18O isotopic values in monocultivar PDO EVOO, the same as non-Italian commercial EVOO originating from lower latitudes in warmer EU Mediterranean countries possibly had a notable influence on increasing the average δ2H and δ18O values determined in commercially-blended EVOO. mmercially-blended EVOO. Table 5. Average values of stable isotopic ratios obtained for monocultivar protected designation of origin (PDO) and commercially-blended extra virgin olive oils obtained by isotope ratio mass Table 5. Average values of stable isotopic ratios obtained for monocultivar protected designation of origin (PDO) and commercially-blended extra virgin olive oils obtained by isotope ratio mass spectrometry (IRMS). An asterisk (*) in a row represents significant differences between mean values at p < 0.05 obtained by ANOVA and least significant difference (LSD) test. ometry (IRMS). An asterisk ( ) in a row represents significant differences between me .05 obtained by ANOVA and least significant difference (LSD) test. 2.4. Multivariate Statistical Analysis Green cycles represent monocultivar protected designation of origin (PDO) EVOO purchased on family farms, while red cycles represent commercially-blended (CB) EVOO purchased in supermarkets (b) variable importance in projection (VIP) scores of the variables (lipids) most useful for the differentiation of monocultivar PDO EVOO and commercially-blended EVOO. 2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS) 2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS) Stable Isotopic Ratios Origin/Class Monocultivar PDO Commercially-Blended δ13C −29.65 −29.44 δ2H −151.28 −144.96 * δ18O 23 89 26 10 * Stable Isotopic Ratios Origin/Class Monocultivar PDO Commercially-Blended δ13C −29.65 −29.44 δ2H −151.28 −144.96 * δ18O 23.89 26.10 * By correlating the two parameters more linked to geographical origin, i.e., δ2H and δ18O, it was possible to visualize different groupings (Figure 5). As already observed [27], Garda PDO EVOO (Casaliva cultivar) was characterized by the lowest δ2H and δ18O values, most probably due to the production area (far from the sea, higher latitude) and climate (colder than the Mediterranean one). The commercial non-Italian EU EVOO showed the highest δ2H and δ18O values, overlapping only with those of Ragusa PDO (Tonda Iblea cultivar), because the geographical and climatic characteristics of Sicily are similar to those of other European Mediterranean countries, as observed previously [30]. The commercially-blended EVOOs of Italian origin had δ2H and δ18O values By correlating the two parameters more linked to geographical origin, i.e., δ2H and δ18O, it was possible to visualize different groupings (Figure 5). As already observed [27], Garda PDO EVOO (Casaliva cultivar) was characterized by the lowest δ2H and δ18O values, most probably due to the production area (far from the sea, higher latitude) and climate (colder than the Mediterranean one). The commercial non-Italian EU EVOO showed the highest δ2H and δ18O values, overlapping only with those of Ragusa PDO (Tonda Iblea cultivar), because the geographical and climatic characteristics of Sicily are similar to those of other European Mediterranean countries, as observed previously [30]. The commercially-blended EVOOs of Italian origin had δ2H and δ18O values overlapping with those 13 of 20 13 of 20 Molecules 2020, 25, 4 Molecules 2019, of Italian monocultivar PDO with the exception of Garda PDO EVOO, which was as expected because the areas of production overlapped as well. overlapping with those of Italian monocultivar PDO with the exception of Garda PDO EVOO, which was as expected because the areas of production overlapped as well. Figure 5. Differentiation of Italian monocultivar protected designation of origin (PDO) extra virgin olive oils purchased on family farms and commercially-blended extra virgin olive oils (EU and Italian origin) purchased in supermarkets in Italy according to δ2H and δ18O stable isotopic ratios. Figure 5. 2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS) 2.5. Confirmation of Geographical Origin by Isotope Ratio Mass Spectrometry (IRMS) Differentiation of Italian monocultivar protected designation of origin (PDO) extra virgin olive oils purchased on family farms and commercially-blended extra virgin olive oils (EU and Italian origin) purchased in supermarkets in Italy according to δ2H and δ18O stable isotopic ratios. 3 Materials and Methods Figure 5. Differentiation of Italian monocultivar protected designation of origin (PDO) extra virgin olive oils purchased on family farms and commercially-blended extra virgin olive oils (EU and Italian origin) purchased in supermarkets in Italy according to δ2H and δ18O stable isotopic ratios. Figure 5. Differentiation of Italian monocultivar protected designation of origin (PDO) extra virgin olive oils purchased on family farms and commercially-blended extra virgin olive oils (EU and Italian origin) purchased in supermarkets in Italy according to δ2H and δ18O stable isotopic ratios. 3. Materials and Me 3.1. EVOO Samples 3.1. EVOO Samples After preliminary selection from a larger group of high quality monocultivar EVOOs with PDO, samples that were produced from olives of Italian cultivars harvested in 2016 were collected from different geographical areas in Italy (price range from 20 to 30 €/L), including Reggio Calabria (cultivar: Ottobratica; n = 3), Perugia (cultivar: Moraiolo; n = 3), Ragusa (cultivar: Tonda Iblea; n = 3), Grosseto (cultivar: Frantoio; n = 3), Imperia (cultivar: Taggiasca; n = 1), Brescia (Garda Bresciano PDO, cultivar: Moraiolo; n = 1), Verona (Garda Orientale PDO, cultivar: Leccino; n = 1), and Riva del Garda (Garda Trentino PDO, cultivar: Casaliva; n = 5). Furthermore, 25 commercially-blended EVOOs were selected according to Nielsen data (New York, NY, USA 2016) as among the most consumed during 2016 in Italy (price range from 3 to 12 €/L) and were purchased from Italian grocery stores (supermarkets), consisting of seven samples with Italian and 18 samples with EU origin declared on their labels. All the samples were stored in dark glass bottles at a controlled temperature of 15 °C After preliminary selection from a larger group of high quality monocultivar EVOOs with PDO, samples that were produced from olives of Italian cultivars harvested in 2016 were collected from different geographical areas in Italy (price range from 20 to 30 €/L), including Reggio Calabria (cultivar: Ottobratica; n = 3), Perugia (cultivar: Moraiolo; n = 3), Ragusa (cultivar: Tonda Iblea; n = 3), Grosseto (cultivar: Frantoio; n = 3), Imperia (cultivar: Taggiasca; n = 1), Brescia (Garda Bresciano PDO, cultivar: Moraiolo; n = 1), Verona (Garda Orientale PDO, cultivar: Leccino; n = 1), and Riva del Garda (Garda Trentino PDO, cultivar: Casaliva; n = 5). Furthermore, 25 commercially-blended EVOOs were selected according to Nielsen data (New York, NY, USA 2016) as among the most consumed during 2016 in Italy (price range from 3 to 12 €/L) and were purchased from Italian grocery stores (supermarkets), consisting of seven samples with Italian and 18 samples with EU origin declared on their labels. All the samples were stored in dark glass bottles at a controlled temperature of 15 ◦C before analysis, and gaseous N2 was added in the headspace to prevent oxidation each time the bottles were opened. 3.3. LC-ESI-MS/MS Analysis The samples were prepared by weighing 500 mg of oil in a 10 mL flask, brought to volume with a 2-propanol solution and internal standard (stearic acid d3 at 1 mg/L). The final solutions were filtered through 0.22 µm filters and transferred into 2 mL vials [52]. LC-ESI-MS/MS analysis of FFA and other lipids was carried out using a UHPLC Dionex 3000 (Thermo Fisher Scientific, Dreieich, Germany), coupled to an API 5500 triple-quadrupole mass spectrometer (Applied Biosystems/MDS Sciex, Toronto, ON, Canada) equipped with an electrospray source. Five microliters of sample were injected into the LC-ESI-MS/MS system using an autosampler (Dionex Thermo Fisher Scientific, Germany) kept at 10 ◦C. A reversed phase column Ascentis Express C18 (150 mm × 2.1 mm, 2.7 µm; Sigma, Milan, Italy) set at 55 ◦C was used for the compound separation. Flow-rate was 0.26 mL/min and the composition of mobile phases was: solvent A (CH3CN 40% in water, NH4COOH 10 mM and HCOOH 0.1%) and solvent B (CH3CH(OH)CH3 90%, CH3CN 10%, NH4COOH 10 mM and HCOOH 0.1%). Separation was carried out following a 30 min multistep linear gradient, according to the method reported by Della Corte et al. [53]. Selected chemical standards were used to construct calibration curves and data were expressed as mg/kg after normalization on the basis of the internal standard stearic acid d3. The targeted lipids were detected under multiple reaction monitoring (MRM) mode and the compounds were identified based on their reference standards, retention times, and qualifier and quantifier ions (Table S2). The chromatographic system and data acquisition were managed by Analyst™software version 1.6.1 (Applera Corporation, Norwalk, CT, USA). pp p For the method validation, the US Food and Drug Administration (FDA) recommendations for a bioanalytical method were followed [54]. The validation included the evaluation of linearity, sensitivity, variability, recovery, accuracy, and precision based on calibration standards and quality control (QC). Calibration curves were made in 2-propanol and lipid matrix [53,55] in order to evaluate the percentage of matrix effect (%ME) for each compound. The values were determined by comparing the equality in the slope ratio between the curves in solvent and matrix, using the following formula: %ME = 100% × (1 −slope solvent/slope matrix) [56]. The regression line was created with the least square fit, and the determination coefficient (r2) was also calculated. before analysis, and gaseo bottles were opened. 3.2. Standards and Solvents 3.2. Standards and Solvents The solvents used for the analysis of lipids in EVOO were LC-MS grade methanol, hexane, isopropanol and formic acid, purchased from Honeywell Riedel-de Haën (Seelze, Germany) and all aqueous solutions, including the HPLC mobile phase, were prepared with water purified using a The solvents used for the analysis of lipids in EVOO were LC-MS grade methanol, hexane, isopropanol and formic acid, purchased from Honeywell Riedel-de Haën (Seelze, Germany) and all aqueous solutions, including the HPLC mobile phase, were prepared with water purified using a Milli-Q system (Millipore, Vimodrone, Milan, Italy). All the analytical standards used for identification and calibration are listed in Table S1. 14 of 20 Molecules 2020, 25, 4 14 of 20 3.3. LC-ESI-MS/MS Analysis The linearity was evaluated by preparing different levels of independent calibration and adding increasing concentrations of each lipid in different concentration ranges. The sensitivity of the method was evaluated with limits of detection (LOD) and limits of quantification (LOQ) at the concentration in which the quantizer transitions showed a signal to noise ratio (S/N) of >3 and >10, respectively. To estimate the analytical variability, intra-day and inter-day parameters were calculated by injecting 10 times a middle concentration level QC sample on the same day and re-injecting it for six consecutive days. Intra-day and inter-day variability were evaluated by the coefficients of variation (CV%). The recovery test was carried out to verify the applicability of the LC-ESI-MS/MS technique, and it was determined as the average of the “measured value”/“the expected value” ratio (%). The precision values were calculated as relative standard deviation (%RSD) among the measures replicated in the QC sample. They were obtained by analyzing the same sample 10 times. Since the precision can vary with the concentration, it was appropriated to analyze at least three samples at different concentrations (low, medium, and high) with respect to the calibration range for each analyte. The accuracy was calculated as the difference between the calculated value and the theoretical value divided by the theoretical value, reported as the relative error percentage (%RE). 3.4. H-NMR Analysis of Lipids All the EVOO samples were prepared by addition and suitable mixing of 700 µL of deuterated solvent (CDCl3) to 200 µL of oil (solution about 200 mM) in a 5 mm NMR tube. All the 1H-NMR spectra were acquired at 300 K on a Bruker-Avance 400 MHz NMR spectrometer (Bruker, Bremen, Germany) by using a 5 mm BBI probe with 60◦hard pulse length of 6.6 µs at a transmission power of 0 db. For the acquisition, 32 K complex points were recorded, the spectral width was set to 10 ppm, the frequency offset was set to 4.8 ppm, the relaxation delay was set to 15 s, the acquisition time was 8.2 s, the number 15 of 20 Molecules 2020, 25, 4 of scans was set to 32, and the number of dummy scans was equal to 2. The total experimental time was 13 min. All spectra were acquired without spinning. The chemical shift scale was calibrated by using the residual proton signal of the deuterated solvent (CHCl3 signal at 7.260 ppm). The data were acquired using the software Topspin 2.1 (Bruker Biospin, Rheinstetten, Germany). The resulting spectra were processed manually and automatically with the software MestreNova 12.0.0 (Mestrelab Research SL, Santiago de Compostela, Spain) taking care to achieve good symmetry on all peaks. The baseline was corrected using a polynomial function. The integral data extracted from the spectra were analyzed using standard software (Microsoft Office Excel 2016). The ratio of the peaks area F/H (Figure 1) was tested to validate the approximations used in this study for calcuation of various lipid species, as suggested earlier [49]. The average F/H value of all the EVOO analyzed in this work was 1.512 with a very small relative standard deviation of 0.5%, confirming the approximations of the calculations were fulfilled. The data reported were obtained by the following procedures. The % molar fraction of α-linolenic acid (18:3) was obtained by the ratio of the peak area of ω-3 Me (δH = 0.97 t) with respect to the peak area of F (×2/3), the % molar fraction of linoleic acid (18:2) by the ratio of the peak area of bis-allylic protons (δH = 2.77 brt) with respect to the peak area of F minus the contribution of the previously evaluated % molar fraction of α-linolenic acid (i.e., %18:2 = %PUFA −%18:3). 3.5. LC-ESI-IT-MS Analysis of Triglycerides LC-ESI-IT-MS analysis of the olive oils was performed on a Hewlett-Packard Model 1100 Series liquid chromatograph coupled both to an Agilent 1100 Series DAD (Photo Diode-Array Detector) (Hewlett–Packard Development Company, L.P., Palo Alto, CA, USA), and to a Bruker Esquire-LC quadrupole ion-trap mass spectrometer equipped with atmospheric pressure ESI+ interface (ESI-IT-MS). Isocratic elution was applied with a flow of 0.3 mL/min by using a Kinetex C18 column (2.6 µm 100A 100 × 2.1 mm) (Phenomenex, Sydney, Australia) as stationary phase, and isopropanol:methanol 10/90 (v/v), 10 mM in ammonium acetate, as mobile phase. Samples were prepared by diluting 1:200 (5 mM) each EVOO with a solution of MeOH:CHCl3 8/2 (v/v), and 4 µL were injected. Relative quantitation of TAG species was established by peak area integration of the MS extracted ion currents of the corresponding major ions produced by ESI ionization by assuming the same response time for all the TAGs species. 3.4. H-NMR Analysis of Lipids Finally, MUFA (16:1 + 18:1, essentially) was evaluated by the peak area of allylic protons (δH = 2.01 brt) with respect to the peak area of F minus the contribution of the previously evaluated % molar fraction of PUFA, whilst SFA (16:0 + 18:0 essentially) was evaluated from total peak area of methyl protons (δH = 0.97 + δH = 0.89) with respect to the peak area of F (×2/3) minus the contribution of PUFA and MUFA. The relative contribution of 1,2-DAG was given by the integration of the peak at δH = 3.71 brd attributable to the -CH2 from sn-1,2-DAG, always present in minor amount in olive oils. From these data the average unsaturation index (UI) and the iodine value (IV) of the acyl chains in TAG were evaluated. Worth of note, the standard deviations of all the mentioned measurements, calculated from three technical replicates (ex novo acquisition and data analysis) of a given EVOO sample, were quite low (<1%) for SFA, MUFA, linoleic and linolenic fatty acyl chains, giving good reliability to the approach applied in this study. 3.6. IRMS Analysis The analysis of the stable isotope ratios of H, C and O was performed on the bulk olive oil. 13C/12C (δ13C) was measured (around 0.5 mg of oil) using an isotope ratio mass spectrometer IsoPrime (Isoprime Limited, Manchester, UK) following total combustion in an elemental analyzer (VARIO CUBE, Elementar, Hanau, Germany). 18O/16O (δ18O) and 2H/1H (δ2H) were measured (around 0.3 mg of oil) using an IRMS (Finnigan DELTA XP, Thermo Scientific, Bremen, Germany) coupled with a pyrolyzer (Finnigan TC/EA, high temperature conversion elemental analyzer, Thermo Scientific). For δ2H and δ18O analysis, the weighed samples were stored in a desiccator above P2O5 for at least four days before analysis, then put into an auto-sampler equipped with a suitable cover. During Molecules 2020, 25, 4 16 of 20 measurement, dryness was guaranteed by flushing nitrogen continuously over the samples. Before determining the δ2H values, the H3+ factor was verified to be lower than 8, as suggested in the instrumental manual. The values were denoted in delta in relation to the international V-PDB (Vienna-Pee Dee Belemnite) for δ13C and Vienna-standard mean ocean water (V-SMOW) for δ18O and δ2H, according to the following general equation: δi E = (i RSA −i RREF), where i is the mass number of the heavier isotope of element E, RSA is the respective isotope ratio of the sample and RREF is the relevant internationally recognized reference material [57]. The delta values were multiplied by 1000 and expressed in units “per mil” (%). The δ13C and δ2H values were calculated against two international reference materials (Icosanoic Acid Methyl Esters USGS70, δ13C value: −30.53% and δ2H value: −183.9% and USGS71, δ13C value: −10.5% and δ2H value: −4.9%), through the creation of a linear equation. δ18O was calculated against IAEA 601 (benzoic acid δ18O = +23.3%) and 602 (benzoic acid δ18O = +71.4%), through the creation of a linear equation. Data were therefore reported relative to V-PDB on a scale normalized to LSVEC-NBS19 for δ13C, and relative to the V-SMOW-SLAP scale for δ2H and δ18O. The uncertainty (2 s) of measurements, calculated following the Nordtest approach, which combines within-laboratory reproducibility standard deviation and laboratory bias using PT data [58], was < 0.3% for δ13C analysis, < 0.5% for δ18O and < 3% for δ2H. 3.7. Statistical Data Elaboration Data obtained by the LC-ESI-MS/MS analysis of minor lipids, LC-ESI-IT-MS profiling of TAGs, 1H-NMR analysis of major lipid parameters, and IRMS analysis in the investigated EVOO were subjected to one-way analysis of variance (ANOVA) and the average values were compared by least significant difference (LSD) test at the level of p < 0.05. The data were further processed by principal component analysis (PCA) in order to better visualize the differences between the two classes of EVOO and explain them on the basis of the content and composition of various lipid species. Prior to PCA, the original datasets were reduced to include only the lipids and parameters for which statistically significant difference between the two classes was determined by one-way ANOVA. Partial least squares discriminant analysis (PLSDA) was performed to extract the most useful variables among lipids for the differentiation of the two investigated classes of EVOO: variable importance in projection (VIP) scores for lipids were determined as the weighted sums of the squares of the weight in the PLSDA. Hierarchical clustering was conducted and a heatmap was generated by Ward algorithm and Euclidean distance analysis. Multivariate statistical elaboration was performed on mean-centered data. ANOVA and PCA data elaboration was performed using Statistica v. 13.2 software (StatSoft Inc., Tulsa, OK, USA), while PLSDA and cluster analysis was conducted using MetaboAnalyst v. 4.0 (http://www.metaboanalyst.ca) created at the University of Alberta, Canada [59]. 4. Conclusions LC-MS and NMR techniques were found to be potent tools to study the variability of various lipid species in EVOO. Their outputs were shown to be relatively complementary and their combined use successfully extracted several chemical markers useful for the differentiation of the two classes of EVOO with respect to the origin of purchase: monocultivar PDO EVOO from family farms vs. commercially-blended EVOO from supermarkets. Considering that the EVOO samples from both classes were characterized by known (for PDO) and declared/presumed (for commercially-blended) geographical and pedoclimatic heterogeneity and large variations in olive growing and oil producing parameters, the extracted markers could be considered relatively robust. Commercially-blended EVOO contained higher concentrations of the majority of minor lipids, including FAAs, FAAEs, MAGs, and DAGs, which may be indicative of a higher degree of TAG lipolysis in these than in monocultivar PDO EVOO. However, triterpenoids and particular TAG species were also found in higher concentrations/proportions in the samples from the commercially-blended EVOO class, suggesting a possible influence of other factors, including diverse cultivar and geographical origin, 17 of 20 Molecules 2020, 25, 4 17 of 20 respectively. The results of IRMS analysis were reasonably consistent with the information about the geographical origin declared on the labels of the investigated EVOOs, which showed considerable variability. The results of this study undoubtedly confirmed the heterogeneity of oils which are sold declared as EVOO in Italy in terms of their lipid composition and geographical origin. In that sense, the obtained findings could significantly contribute to EVOO diversification on the market, and could help to clarify the interrelationship between EVOO origin, quality, and price, and in this way support the growth of the niche in the market segment of consumers informed and interested in healthy, quality products with remarkable diversity and clear identity. Supplementary Materials: The following are available online, Table S1: standards of minor lipids used in the LC-ESI-MS/MS method development. Table S2: mass transitions (MRM) and instrumental parameters optimized for each metabolite for the analyses by LC-ESI-MS/MS. Table S3: method validation parameters for each metabolite for the analyses by LC-ESI-MS/MS - part I. Table S4: method validation parameters for each metabolite for the analyses by LC-ESI-MS/MS - part II. Author Contributions: Conceptualization, F.M., I.L., N.M., and U.V.; funding acquisition, F.M., U.V., and F.C., data curation, A.D.R., D.M., G.G., F.C., and I.L.; formal analysis, A.D.R., D.M., G.G., and F.C.; methodology, F.M. References 1. International Olive Council. COI/T.15/NC. Nº 3/Rev.13/2019. Trade Standard Applying to Olive Oils and Olive-Pomace Oils 2018. Available online: https://www.internationaloliveoil.org/wp-content/uploads/2019/ 11/COI-T.15-NC.-No-3-Rev.-13-2019-Eng.pdf (accessed on 12 December 2019). 2. European Economic Community. Commission Regulation (EEC) No 2568/91 of 11 July 1991 (and later modifications) on the characteristics of olive oil and olive-residue oil and the relevant methods of analysis. Off. J. Eur. Community 1991, L248, 1–83. 2. European Economic Community. Commission Regulation (EEC) No 2568/91 of 11 July 1991 (and later modifications) on the characteristics of olive oil and olive-residue oil and the relevant methods of analysis. Off. J. Eur. 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UK podiatrists’ experiences of podiatry services for people living with arthritis: a qualitative investigation
Journal of foot and ankle research
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McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 https://doi.org/10.1186/s13047-018-0262-5 McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 https://doi.org/10.1186/s13047-018-0262-5 Open Access UK podiatrists’ experiences of podiatry services for people living with arthritis: a qualitative investigation Louise McCulloch1* , Alan Borthwick1, Anthony Redmond2, Katherine Edwards3, Rafael Pinedo-Villanueva3, Daniel Prieto-Alhambra3, Andrew Judge3, Nigel K. Arden3 and Catherine J. Bowen1 Abstract Keywords: Arthritis, Podiatry, Footcare, Service provision * Correspondence: L.A.McCulloch@soton.ac.uk 1Faculty of Health Sciences, University of Southampton, Highfield Campus Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK Full list of author information is available at the end of the article * Correspondence: L.A.McCulloch@soton.ac.uk 1Faculty of Health Sciences, University of Southampton, Highfield Campus Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK Full list of author information is available at the end of the article * Correspondence: L.A.McCulloch@soton.ac.uk 1Faculty of Health Sciences, University of Southampton, Highfield Campus Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK Full list of author information is available at the end of the article © The Author(s). 2018 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: Provision of podiatry services, like other therapies in the UK, is an area that lacks guidance by the National Institute for Health and Care Excellence. Many individuals living with arthritis in the UK are not eligible to access NHS podiatry services. The primary aim of this investigation was to understand the views of podiatry clinicians on their experiences of referral, access, provision and treatment for foot problems for patients who have arthritis. Methods: Focus groups were undertaken to explore, in-depth, individual views of podiatrists working in the UK to gain feedback on experiences of barriers and facilitators to referral, access, provision and treatment for foot problems for individuals living with arthritis. A purposive sampling strategy was adopted and two, semi-structured, focus group interviews conducted, involving 12 podiatrists from both NHS and independent sectors. To account for geographical variations one focus group took place in each of 2 predetermined ‘zones’ of the UK; Yorkshire and Hampshire. Thematic analysis was employed to identify key meanings and report patterns within the data. Results: The key themes derived from the podiatry clinician focus groups suggest a variety of factors influencing demand for, and burden of, foot pain within the UK. Participants expressed frustration on having a service that accepts and treats patients according to their condition, rather than their complaint. Additionally, concern was conveyed over variations in the understanding of stakeholders’ views of what podiatry is and what podiatrists aim to achieve for patients. Conclusion: Podiatrists interviewed believed that many individuals living with arthritis in the UK are not eligible to access NHS podiatry services and that this may be, in part, due to confusion over what is known about podiatry and access criteria. Essentially, podiatrists interviewed called for a timely renaissance of current systems, to newer models of care that meet the foot care needs of individual patients’ circumstances and incorporate national multi-disciplinary guidance. Through this project, we have formulated key recommendations that are directed towards improving what other stakeholders (including GPs, commissioners and users of podiatry services) know about the effectiveness of podiatry and also to futureproof the profession of podiatry. Background emailed a brief overview of the study through the Colleges’ newswire. Those interested in joining the study were emailed an information sheet, along with the contact details of the primary investigator (LMc). Inter- ested podiatrists then contacted the primary investiga- tor (LMc) for additional information, to have any further questions answered and be screened against the project’s criteria. g Provision of podiatry services, like other health therapies in the UK, is an area that lacks guidance by the UK National Institute for Health and Care Excellence. There is a perceived lack of understanding of how to access treatment for foot problems, and limited understanding of what podiatry services can offer, by both patients and non-podiatric clinicians [1–6]. Many podiatry depart- ments have recently felt themselves unsettled by job cuts and recent changes in how services are commissioned has shifted focus towards management of acute wounds, specifically for the management and prevention of limb loss associated with diabetes [7, 8] The consequent im- pact of podiatry services reconfiguration of skill mix and services, away from management of foot pain associated with other chronic conditions such as rheumatoid arth- ritis and osteoarthritis, is not known. General Practi- tioners (GPs) are consulted by 15% of the reported 20 million people in the United Kingdom (UK) with symp- toms of rheumatic disease each year, forming up to 25% of a GPs workload [9]; with nearly 30% of the older population in chronic pain due to ‘arthritis’ [10] or a lessened quality of life [11], rheumatological disability is predicted to be a major public health concern in the coming years [12]. This loss of podiatry services from the UK NHS potentially puts the most frail and vulner- able people at risk of mobility loss [13, 14]. The primary aim of this investigation was to understand the views of podiatrists on their experiences of referral, access, provision and treatment for foot problems for patients who have arthritis. Arthritis was selected as the long-term condition to scrutinise due to feedback from our patient and public involvement (PPI) consultations as the one that caused the most confusion over access to foot-care. p j A purposive sampling strategy was undertaken, consistent with the qualitative study design adopted. Procedure Each focus group was conducted by the main researcher (LMc) supported by a second investigator (KE in Yorkshire; AB in Hampshire) as note-taker to aid with reflection, transcription and subsequent coding. General topics for discussion were identified with pre- determined ‘topic guide’ questions written prior to the focus groups. The topic guide was informed by, and con- structed from, the findings from analysis of a systematic review of the literature relative to evidence for podiatry and foot care conducted by the team [19]. Digital audio-recordings were transcribed, anonymised and imported into a data analysis package (N-Vivo 11). Using this and manual methods, codes were generated by noting recurring comments and used to categorise re- sponses by the researcher (LMc). The codes were re- fined, compared and grouped into similar features which served as potential themes. Thematic analysis was iden- tified as a suitable method to search for patterns related to podiatrists’ views on podiatry services for individual’s living with arthritis [16, 18]. Emerging themes were dis- cussed by the wider research team (LMc, AB, CB) for verification, identification of any additional areas of interest and consensus via discussion of patterns across the data. Potential themes were repeatedly discussed by the research team to identify any alternative interpreta- tions. The process of verifying themes as a team pro- vided a more rigorous approach, different perspectives and agreement on final themes. Background Participants were selected according to time since quali- fication, employer (NHS, independent or academia) and experience of managing foot health for individual’s living with arthritis, to ensure the study would capture insightful and meaningful data from a diversity of ex- perience, employments and perspectives. To enable a ‘snapshot’ of 2 representative areas of the UK, 2 zones were established; Yorkshire (North England) and Hamp- shire (South England) and a focus group interview was held in each of the zones. Methods A qualitative research study design was employed to en- able a deep exploration of podiatrists’ views, to gain feed- back on experiences of barriers and facilitators to referral, access, provision and treatment for foot problems for indi- viduals living with arthritis. Focus groups were chosen as the most appropriate approach to capture a large amount of information in a relatively short period of time [15] and allowed us to not only to identify the issues that the podia- trists’ raised, but also allowed for the observation of how podiatrists discussed the issues in a ‘natural’ social setting. The methods adopted reflected existing standards for ro- bustness in qualitative research, deploying triangulation of data, respondent validation and data saturation, which guided the final sample size [16–18]. © The Author(s). 2018 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. McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 Page 2 of 8 Page 2 of 8 Theme 2: ‘Condition vs Complaint’ This is confounded by an inherent frustration at a continuing dearth of understanding, of the scope, depth and value of podiatric practice, by non-podiatrists including patients: This theme presents podiatrists’ unease on how podiatry varies within current healthcare systems, with inconsist- ent approaches causing inequality, discrimination and discrepancy. An over reliance on tick boxes, and appar- ent detriment of clinical autonomy, means that people who are not currently ‘at risk’ (but could potentially be in the future) are able to access podiatry services, how- ever those who have high podiatric risk, but by tick box standards are not classified as such, are thus ‘ineligible’. Table 1 Key themes emergent from focus group interviews Themes with key quote Subthemes Theme 1: Evolving Professional Culture “Historically the commissioner’s never quite got around to finishing off writing the specification” AHPs understanding of Podiatry Commissioning Patients understanding of Podiatry Theme 2: ‘Condition vs Complaint’ “Is it about the patient who’s got diabetes or is it that they’ve got diabetic lower limb complications? Because the two are quite different.” Inequalities and eligibility Private sector versus NHS The current bandwagon Importance of Podiatry in Arthritis Theme 3: Transforming and Sustaining Podiatry “We really need to go to the top and make podiatry the same as dental care, the same as eye care, the same as hearing, audiology, you know, we’re just off the radar.” Equipping Podiatrists Building Podiatry Proposals for future shape of Podiatry Table 1 Key themes emergent from focus group interviews Themes with key quote Subthemes Theme 1: Evolving Professional Culture “Historically the commissioner’s never quite got around to finishing off writing the specification” AHPs understanding of Podiatry Commissioning Patients understanding of Podiatry Theme 2: ‘Condition vs Complaint’ “Is it about the patient who’s got diabetes or is it that they’ve got diabetic lower limb complications? Participants The study recruited 12 participants in total, six to each focus group. Of the clinical podiatrists interviewed, three Participants were recruited through their membership of the College of Podiatry UK. Potential participants were McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 Page 3 of 8 Page 3 of 8 “[HB1]: I think it’s still fairly common, from feedback from staff for …the start of the consultation with a new patient is actually getting them to understand why you want to know this.” You know, “what’s the medication got to do with you” et cetera. And that can actually take up some of the initial time that actually when explaining about why it’s important and actually you know “the feet are actually attached to the rest of your body”, that type of conversation. were solely NHS employed, three were solely in private practice, six worked in a variety of settings (including three working part-time in academia). NHS bandings (where applicable) ranged from 5 to 8. Fifteen codes were initially identified from the 2 focus group inter- views. Key themes were constructed via abductive ana- lysis, and are presented in Table 1 with the subthemes and one exemplar quote. An abridged summary, with excerpts of data drawn from the transcripts, is presented below. Quotes are allocated alphabetical codes where re- quired, for differentiation. [HG2]: That’s the “what’s that got to do with my feet?” [HB1]: “Yes… a big sum of that time is actually about just starting to drill down and set the scene with the patient about what we’re trying to achieve. And then on to what they want to achieve. With a bit more understanding why we’re taking medical history and how it’s relevant to what’s happening in their feet.” Theme 1: Evolving professional culture This theme presents clinical podiatrist’s perceptions on how podiatry has become shaped historically. Whilst current podiatry services are well received and valued, participants vocalised a perception that procurement of services can be based on sketchy knowledge and absent evidence: And recent changes and streamlining of NHS manage- ment structures was discussed: “I know with my locality, the proposal that was sent by the CCG, it was decided that actually they lacked the understanding about podiatry. And so it was, we would buy our local level and then send back to them, because otherwise they didn’t quite comprehend what we did. And so we were able to divide it into our separate areas, like nail surgery, routine care, diabetes and then send it back to them so that they had more of an understanding of what we actually did. So that is a problem.” [Podiatrist: LB1] “We’ve lost a lot of that middle-management podiatry managers, we haven’t got anybody really fighting for our service at the moment. And just replying to the comment about NHS practitioners, I’ve never, in the whole time that I’ve practiced podiatry, ever seen such disillusionment. I think that everybody’s burnt out at work, I think that they’re being managed by people that don’t actually understand what’s happening.” [LG1] Theme 2: ‘Condition vs Complaint’ Because the two are quite different.” Inequalities and eligibility Private sector versus NHS The current bandwagon Importance of Podiatry in Arthritis Theme 3: Transforming and Sustaining Podiatry “We really need to go to the top and make podiatry the same as dental care, the same as eye care, the same as hearing, audiology, you know, we’re just off the radar.” Equipping Podiatrists Building Podiatry Proposals for future shape of Podiatry Theme 1: Evolving Professional Culture “Historically the commissioner’s never quite got around to finishing off writing the specification” “I’m really reluctant to do that because a) you’ve got people with multi-pathologies and b) is it about the patient who’s got diabetes or is it that they’ve got diabetic lower limb complications? Because the two are quite different. And you know again it’s about back to ‘we shouldn’t just be providing services to people with diabetes, it’s about services for people with lower limb complications’… back to what I said earlier about some services that have got severe restrictions, you know you could be a 27 year old with diabetes playing rugby but you could technically get service because Theme 2: ‘Condition vs Complaint’ “Is it about the patient who’s got diabetes or is it that they’ve got diabetic lower limb complications? Because the two are quite different.” Theme 3: Transforming and Sustaining Podiatry Page 4 of 8 McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 you’ve got diabetes as opposed to actually having a need.” [HB1] people who see the patients when they present with those conditions…“and I’ve got sore feet” you know… “and actually got sore hands too”. But then it’s about getting the training of podiatrists as well, you know, they not just looking at the feet. If there are some red flags that come up like they do with diabetes…what do they do in class about diagnosing arthritis? We all should be...we shouldn’t just be doing the squeeze test to feet, we should be doing the squeeze test on the hands.” [HG1] The introduction of access criteria in practice is re- ported to have created a culture of exclusion to many vulnerable people, with podiatric clinicians alluding to cultures of ‘condition over complaint’ and ‘postcode lot- tery’. Podiatrists refer to an unmet need of foot-care and the consequential risk of foot-health deterioration. Theme 2: ‘Condition vs Complaint’ Con- fusion was felt to exist, around non-podiatrists’ under- standing what a status of high or low risk means. And with non-standardised criteria in use (‘pain’, ‘diabetes’ or specific long-term health conditions) eclectic podiatric services are being provided across the country. If eligibility systems are used, they should be set nationally, evidenced, agreed across professional groups and used consistently, whilst embracing expert clinical discretion. “We need care pathways … You know, I think we need to subdivide all the things that podiatry offers and have a tick box assessment sheet that we can actually offer to somebody that’s diagnosed with arthritis and make sure that there is an effective referral system…for that patient to know what care is available and what they can expect if they're presenting with certain conditions.” [LG1] “They tend to put the commissioned service versus service level agreements. So, a lot of diabetes services are commissioned. So they ‘have’ to provide that service, so even though we, in the acute trust run, you know, quite a full rheumatology foot service, as soon as we’re a man down in diabetes, people get pulled from arthritis clinics, from rheumatology, to cover diabetes. And that is just based on, purely commissioned services versus service level agreements. We have a service level agreement to provide treatment for Rheumatology patients…” [HG1] Clinicians suggested a preference for access to podiatry services being more person-centred, tailored to individuals: “I think there certainly needs to be evidence to show that there should be a pathway whereby all these patients get some sort of similar assessment to identify what their initial needs are. And maybe on an annual basis or even a three-yearly basis or something, just to ensure that then things can be identified early on to start actually taking place, whether it be footwear, whether it be on education or whether they need to change medication or whatever else... It has to be put up the agenda.” [LG1] Theme 3: Transforming and sustaining podiatry This theme captures practising clinicians’ views for the future shape of podiatry in modern healthcare: “It {resolving current constraints to podiatric access} is multifaceted; it is conversations with the commissioners about getting specification rights in the first place. Theme 2: ‘Condition vs Complaint’ It is discussions internally within health trusts around priorities and in some ways protecting what we’ve got … So the only way we can get around that {current constraints to podiatric access}, as I can see, is raising the profile of the profession. Raising the knowledge and raising the value of what we do and the cost efficiency of what we do.” [HB1] They propose a more multidisciplinary, coordinated approach to patient services, specifically requesting that arthritis and other long term health conditions have models of access and guidelines comparable to those for diabetes: Podiatrists want to see inequalities in service provision eliminated, offering a shift in the priorities of podiatric services to incorporate more long term conditions: “Pathways. Referral pathways, just like diabetes ...a bit more streamlined and a bit more easy to access.” [HG3] “Pathways. Referral pathways, just like diabetes ...a bit more streamlined and a bit more easy to access.” [HG3] Evolving professional culture Notably, podiatrists expressed key concerns of frustra- tion that, although podiatry has evolved as a profession, there remains a sense of misunderstanding, by non- podiatrists and patients, of the scope of practice and ability of podiatrists in what they do. The revelation that podiatrists believe their scope of practice is limited by the profile and image of the profession is not a new one. Earlier work has identified the hierarchical nature of the health professions [21] and the way in which podiatry has perceived itself as less visible and more misunder- stood than other comparable professions [22–24]. In our investigation, advances in scope of practice and a grow- ing presence in multi-disciplinary team (MDT) working were clearly considered important factors in raising the profile of the podiatry profession, however were per- ceived more evident in specific fields, such as diabetes foot care, and much less clear in primary care which is also evidenced widely in the literature [25]. They reported a need to work with other professionals to drive changes for more long term conditions: “And it's not just our profession that’ll link with them [public health], for the benefit of our patients because, you know, podiatry is one of them, you could have ENT in there, you could have physio in there, you’ve got other disciplines in there. They can all push this agenda forward and start saying, yes, here’s another one, it's a long-term condition that we need to be doing more for.” [LG1] Clinicians believed access to podiatry services should be transformed to fit modern healthcare needs, to meet the needs of patients within an evolving healthcare sys- tem, which incorporates building in onward referral to private sector podiatrists, into the NHS service: Key leaders in the profession, locally and nationally, were lauded for the development of services in the past and concern was voiced over the increasing trend for managers responsible for defending, promoting and commissioning podiatry services in today’s healthcare practices, to be non- podiatrists with limited knowledge of the scope of practice of the profession. The vital role of key, charismatic charac- ters in podiatry has been previously reported in the literature as being fundamental in developing and augment- ing the profession in specialisms such as diabetes [26], podiatric surgery [27] and rheumatology [28]. “Can I, can I bring something in there that’s quite important? “Pathways. Referral pathways, just like diabetes ...a bit more streamlined and a bit more easy to access.” [HG3] “Podiatry provides an opportunity to pick up long term conditions in the early stages, so we know that mechanically, arthritis in the foot is the second most common site for presentation so podiatrists can be a guard responsible for aiding, for new diagnosis for a patient and show them …you know some red flags for podiatry to go in, because they’re likely to be the “Make it more equal over the UK rather than just dependant on personality, and really that sums up what people said – going through more pathways, focussing on multidisciplinary teams.” [HG4] “If we had a more multidisciplinary coordinated approach it would be better for the patient. I know Page 5 of 8 McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 that we have access to all these other professions but sometimes those communications, are blocked, not blocked but they are strained because you’ve got to write a letter, and that’s got to go off, then someone’s got to sign it and… whereas if you had a better, multidisciplinary approach like we do in terms of diabetes then those patients would go through proper routes a lot quicker” [HG1] ‘foot care’ and embedding evidence within national and local guidelines [19–22]. The resultant key themes con- structed from our investigation are discussed below: ‘Condition vs Complaint’ Whilst the podiatrists interviewed in this study believe that their services are valued and appreciated by their patients, they express concern that only certain people can access NHS podiatry care in the UK. Interestingly, despite the evidencing of outcomes, cost effectiveness and quality of services being currently so important in the procurement and commissioning of NHS services, there continues to be a paucity of published evidence to show the ‘value’ that patients attribute to UK podiatry services and the interventions that podiatrists use, both in respect to its significant importance amongst health- care delivery and its impact upon patients’ quality of life. Patients who can afford it may choose to seek foot care expertise from the private sector, yet this excludes many. The implications are made clear. In the UK, the majority of NHS podiatry care is initiated from within the pri- mary care sector through referral from GPs [7]. Podiatric clinicians in this investigation suggested that Clinical Evolving professional culture We actually have a good NHS private practice working relationship in our area, the culture that we historically have had is that when a patient is deemed no longer eligible for treatment, that they’re discharged to the third sector. And you know, if you actually have a dentist, and the NHS can't meet your dental needs, you’re recommended that you can seek dentistry privately, the same with seeing an optician.” [LG1] Discussion Using focus group methodology and a thematic ap- proach to data analysis, this study has provided unique insights into UK podiatrists’ (based in 2 distinct regions of the UK, Yorkshire and Hampshire) perceptions of barriers and facilitators to referral, access, provision and treatment for foot problems for individuals living with arthritis. Our overarching findings indicate that podia- trists experience frustration about the role and status of podiatric services, the inequalities in service provision (between regions and between individuals) and the loss of clinical autonomy – fuelling an ethos of ‘condition over complaint’. The literature relating to foot healthcare supports the need to transform and shape podiatry by promoting the scope of practice, taking ownership of McCulloch et al. Journal of Foot and Ankle Research (2018) 11:27 Page 6 of 8 Page 6 of 8 Commissioning Groups (CCGs), comprising primary care GPs, were much less well informed about the po- tential health gains to be made through referral to podiatry than perhaps other services, or in diabetes care, where MDT working enhances professional profiles. As a result, podiatrists in this investigation noted that com- munity referral to podiatry is less well targeted than it might be, given the lack of understanding of the roles and skills of modern podiatrists [29] among GPs and other commissioners in primary care. This is reflective of recent analysis of GP referral patterns for foot pain, which found that the majority went to orthopaedics [30]. Interestingly this reflects the cultural and socio- historical context of the allied health professions, which occupied a lesser position within a complex health division of labour throughout most of the twentieth cen- tury [23, 31]. services to ‘cope’. Alternative foot health providers were broached, including charitable organisations and ‘nail bars’, where concerns were aired from both NHS and private sector practitioners, as were the incongruities of jointly managing patients between multiple providers. This echoes the views of other experts advocating podiatric intervention for those with foot health vulner- ability and pathology due to long term health conditions [36–39]. This, in turn, synchronises with NHS England’s (2014) 5 Year Forward View [40] for a healthcare system that demonstrates improvements in service outcomes, improves preventative care, enables the frail and elderly to stay healthy, independent and access individualised, person centred care. Discussion Frustration was reported over the prioritisation of UK NHS service provision according to the contract type, with commissioned services having priority over service level agreements, often prioritising one patient group, or clinic, over another. Furthermore confusion was expressed, by podiatrists in our investigations, on behalf of service users not eligible to access podiatry services when acquaintances were. Feedback from people who have chronic conditions is consistent with this, indicat- ing that patients are not accessing foot healthcare [1–3, 41] and that they are confused over referral pathways to podiatry services [2, 42, 43]. A sense of frustration was consistent through the dis- cussions on the disparity across the UK of accessibility to NHS podiatry services and the inequity between areas, patient groups and commissioning bodies. Eligibil- ity criteria, and the use of ‘tick box’ access, in combin- ation with a national public health drive, appears to have resulted in open eligibility to podiatry services for some patients, but limited or barred access for other patient groups who may have an equal or greater podiatric need. A sense of frustration was consistent through the dis- cussions on the disparity across the UK of accessibility to NHS podiatry services and the inequity between areas, patient groups and commissioning bodies. Eligibil- ity criteria, and the use of ‘tick box’ access, in combin- ation with a national public health drive, appears to have resulted in open eligibility to podiatry services for some patients, but limited or barred access for other patient groups who may have an equal or greater podiatric need. Whilst this is positive and inclusive for ‘eligible’ people, it excludes others. This allows access to podiatry services for people who may not need specialist podiatric intervention at the time, yet are able to access care be- cause they have a specific condition, albeit not affecting their feet. This, in turn appears to be causing inequities of condition over complaint. Barriers towards accessing podiatry care for individuals who have arthritis have been previously highlighted in other countries [32–34]. This is consistent with findings that the provision of foot care for people with rheumatoid arthritis is not driven by foot health characteristics such as foot pain or foot related disability [32, 35] and indicates that the role of podiatry in the prevention of deterioration of foot health is partially, but not fully, recognised. Transforming & sustaining podiatry Since the inception of podiatry in the early part of the twentieth century, podiatry models of care within the UK NHS have remained fairly static and the model of access and care within private practice has remained stable within the realms of financial accessibility [7]. Despite that, demand has shifted towards acute levels of care within the UK NHS. Changes to service access in the 1990s has led to resource allocation, guidance and prioritisation for patients with complex acute care needs, predominantly diabetes [19]. Provision of podiatry services for individuals with arth- ritis is an area that lacks guidance. Whilst participants of this study acknowledged the presence of some foot health guidelines for people with arthritic conditions, re- ferring specifically to the Arthritis and Musculoskeletal Alliance (ARMA) and NICE guidelines [44] for people with arthritis, they reported little recognition of, nor suf- ficient emphasis placed on, the use of these relevant guidelines by non-podiatry health professions or pa- tients. The deficiency in specific guidance for foot health for people arthritis conditions appears to be in contrast to the vast plethora of guidance available for foot care services and intervention for people with diabetes [19]. Indeed, current literature suggests existing foot health guidelines for people with arthritic conditions are not being utilised to their fullest advantage and there is a Alone, medical or podiatric pathology can place a per- son at mild, moderate or severe podiatric risk status. With comorbidities, this risk increases, in some cases significantly [36, 37]. Podiatrists are aware of the risk status and vulnerability of patients who do not have their podiatric needs met, including those who are ineli- gible for NHS care but cannot afford private sector care. From the concerns podiatrists expressed on behalf of their service users, came some consideration of alterna- tive foot care options that the public access. Private practice was represented positively in providing valuable services, from both private sector and NHS practi- tioners, including suggestion that it enables NHS McCulloch et al. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Conclusion The burden of foot pain for individuals living with arth- ritis in the UK is not insubstantial, yet many cannot ac- cess NHS podiatry services [7, 51]. The key themes derived from the podiatry clinician focus groups suggest that there are a variety of factors influencing demand for, and burden of, foot pain within the UK. Primarily, participants expressed frustration on having a service that accepts and treats patients according to their condi- tion, rather than their complaint. Secondly, concern was conveyed over variations in stakeholders’ understanding of what podiatry is and what podiatrists aim to achieve for patients. Essentially, podiatrists interviewed called for the reform of the current accessibility to services to one that matches the foot care needs of individual patients. Availability of data and materials h d h h f d f The data that support the findings of this study are available from the corresponding author upon reasonable request. Transforming & sustaining podiatry Journal of Foot and Ankle Research (2018) 11:27 Page 7 of 8 Page 7 of 8 Page 7 of 8 Clinicians are keen to explore alternative ways to pro- mote podiatry services for procurement and new models of service provision, to be more reflective of people’s in- dividual circumstances and believe that setting and implementing nationally set guidance is the optimal way to inform commissioning of podiatry services towards a more inclusive service provision. recognised need to improve the implementation of such guidance [45]. Whilst new models of foot care for indi- viduals who have inflammatory arthritis have been pro- posed [43, 46, 47] the recognition, development and implementation of guidance and pathways for other long term conditions that affect the feet (including osteoarth- ritis) is necessitated in a similar format to those for people with diabetes. Abbreviations h Podiatrists in this investigation considered that current UK health recommendations on recognition, transform- ation, sustainability and public health [40, 48] to be a timely opportunity for the profession to promote and re- establish podiatry’s full scope of practice to all stake- holders (patients, service managers, commissioners and other health professionals). They too encourage the de- velopment of new care models for podiatry, to meet the burden of foot pain in the UK and demands of modern healthcare. Podiatry has long been encouraged to become more versatile and involved in preventative healthcare [7, 49] and this now coordinates with recom- mendations for all AHPs [48]. Podiatrists interviewed believed change was needed, to sustain the provision of services and profession. Abbreviations ARMA: Arthritis and Musculoskeletal Alliance; GP: General Practitioner; NICE: National Institute for Health and Care Excellence Abbreviations ARMA: Arthritis and Musculoskeletal Alliance; GP: General Practitioner; NICE: National Institute for Health and Care Excellence Strengths and potential limitations This study examined the perceptions of podiatrists in two regions of the UK, as a potentially representative snapshot. By using the experiences of 2 diverse groups of podiatrists from two disparate regions, rich text and themes have been generated. Limitations are acknowl- edged as both are in England, therefore data may not be wholly representative of the four home UK nations (England, Scotland, Wales and Northern Ireland) mean- ing proposed themes may be more or less significant in other areas. This may, however, align with high degrees of variation in specialist rheumatology service provision across the UK, wherein podiatry remains a notably poorly represented profession [50]. Author details 1 1Faculty of Health Sciences, University of Southampton, Highfield Campus Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK. 2Faculty of Medicine & Health, Leeds Institute of Rheumatic & Musculoskeletal Medicine, Leeds, UK. 3Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK. 1Faculty of Health Sciences, University of Southampton, Highfield Campus Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK. 2Faculty of Medicine & Health, Leeds Institute of Rheumatic & Musculoskeletal Medicine, Leeds, UK. 3Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK. 1Faculty of Health Sciences, University of Southampton, Highfield Campus Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK. 2Faculty of Medicine & Health, Leeds Institute of Rheumatic & Musculoskeletal Medicine Leeds UK 3Nuffield Department of Orthopaedics 1Faculty of Health Sciences, University of Southampton, Highfield Campus Building 45, University Road, Southampton, Hampshire SO17 1BJ, UK. 2Faculty of Medicine & Health, Leeds Institute of Rheumatic & 3 Musculoskeletal Medicine, Leeds, UK. 3Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK. Received: 21 March 2018 Accepted: 6 May 2018 Competing interests Dr. Alan Borthwick is Editor UK and Prof Catherine Bowen is the Deputy Editor UK of the Journal of Foot and Ankle Research. It is journal policy that editors are removed from the peer review and editorial decision-making processes for papers they have co-authored. The remaining authors declare no conflicts of interest in relation to this work. Ethics approval and consent to participate Full ethical approval was gained (IRAS: 15/SW/0251). All participants provided written informed consent. Governance for the study was approved by the Faculty of Health Sciences, University of Southampton Ethics Committee via the ERGO (Ethics and Research Governance Online) online approval system. Acknowledgements g The authors would like to thank all the participants of the study and Andy Stow and Adam Thomas from the College of Podiatry who helped with study recruitment. Authors’ contributions CB, AB, AR, RP, DP, AJ and NA conceived the study. KE led on the systematic review of evidence for podiatry that underpins the topics for this study. LMc conducted the focus groups and extracted and produced the first draft. KE and AB collected notes and observed participants within the focus groups. LMc, AB, CB, analysed the data. LMc, AB, AR, KE, RP, DP, AJ, NA and CB critically reviewed the academic content and participated in producing the final draft. All authors read and approved the final manuscript. Funding This study was supported by a project grant from the College of Podiatry. CB is currently being supported to undertake Fellowship from The National Institute for Health Research. The views and opinions expressed herein are those of the authors and do not necessarily reflect those of National Institute for Health Research, NHS or the Department of Health. 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"They just scraped off the calluses": a mixed methods exploration of foot care access and provision for people with rheumatoid arthritis in south-western Sydney. Australia. J Foot Ankle Res. 2013a;6(1):34. 4. Formosa C, Gatt A. Chockalingam N (2016) a critical evaluation of existing diabetic foot screening guidelines. Rev Diabet Stud. 2016;13(2–3):158–86. g g 5. Menz HB, Jordan KP, Roddy E. Croft PR (2010) musculoskeletal foot problems in primary care: what influences older people to consult? Rheumatology (Oxford). 2010;49(11):2109–16. 33. Hendry GJ, Gibson KA, Pile K, Taylor L, du Toit V, Burns J, Rome K. Provision of foot health services for people with rheumatoid arthritis in new South Wales: a web-based survey of local podiatrists. J Foot Ankle Res. 2013b;6(1):35. 6. Lansdowne N, Brenton-Rule A, Carroll M. Rome K (2015) perceived barriers to the management of foot health in patients with rheumatic conditions. J Foot Ankle Res. 2015;8:14. 34. Lansdowne N, Brenton-Rule A, Carroll M, Rome K. Perceived barriers to the management of foot health in patients with rheumatic conditions. J Foot Ankle Res. 2015;8:14. 7. References d Boden, C (2007) Older People and ‘Person-Centred’ Podiatry: A Critical Evaluation of Two Models of Care, PhD thesis. 50. Ndosi M, Ferguson R, Backhouse MR, Bearne L, Ainsworth P, Ro 50. Ndosi M, Ferguson R, Backhouse MR, Bearne L, Ainsworth P, Roach A, Dennison E, Cherry L. National variation in the composition of rheumatology multidisciplinary teams: a cross-sectional study. Rheumatol Int. 2017;37(9):1453–9. 23. Larkin GV. Occupational monopoly and modern medicine. Cambridge: Cambridge University Press; 1983. 24. Vernon W, Borthwick A, Farndon L, Nancarrow S, Walker J. Issues of podiatry status in the UK. British Journal of Podiatry. 2005;8(1):6–10. 51. Hansard - Westminster Hall, Column 281WH, 4 Dec 2013 : Column 257WH. 25. Kerr M, Rayman G, Jeffcoate WJ. Cost of diabetic foot disease to the National Health Service in England. Diabet Med. 2014;31(12):1498–504. 26. Bacon D, Borthwick A. Charismatic authority in modern healthcare: the case of the ‘diabetes specialist podiatrist’. Sociology of Health & Illness. 2013; 35(7):1080–94. 27. Graham ML (2006) The Origins and Development of Podiatry in Britain 1969 to 1996, PhD thesis, University of Essex. 28. Graham A (2017) Foot health education for people with rheumatoid arthritis’ PhD thesis. 28. Graham A (2017) Foot health education for people with rheumatoid arthritis’ PhD thesis. 29. Health and Care Professions Council. Standards of Proficiency: Chiropodists/ Podiatrists. 2014 Available from: http://www.hcpc-uk.org/publications/ standards/index.asp?id=41 [cited 19th May 2017]; 29. Health and Care Professions Council. Standards of Proficiency: Chiropodists/ Podiatrists. 2014 Available from: http://www.hcpc-uk.org/publications/ standards/index.asp?id=41 [cited 19th May 2017];
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Diffraction separation and imaging based on curvelet domain cascade filter
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Diffraction separation and imaging based on curvelet domain cascade ¦lter Zongnan Chen  China University of Mining and Technology (Beijing) Jingtao Zhao Zongnan Chen  China University of Mining and Technology (Beijing) Jingtao Zhao Diffraction separation and imaging based on curvelet domain cascade filter Zongnan Chen1, Jingtao Zhao1,Suping Peng2 1 College of Geoscience and Survey Engineering, China University of Mining and Technology (Beijing), Beijing, China. E-mail: zlczn1995@163.com, diffzjt@163.com; 2 State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology (Beijing), Beijing, China. E-mail: psp@cumtb.edu.cn. Right Running Head: Curvelet-domain diffraction separation method di h i h il diff j 6 Corresponding author: Jingtao Zhao E-mail: diffzjt@163.com Research Article 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. Version of Record: A version of this preprint was published at Pure and Applied Geophysics on April 2nd, 2024. See the published version at https://doi.org/10.1007/s00024-024-03456-6. Curvelet-domain diffraction separation method ABSTRACT Diffraction separation plays an important role in high-resolution imaging of small-scale discontinuous geological bodies. These discontinuities or nonuniformities are related to the oil and gas migration path and reservoir space, and they are also common geological hazard factors in engineering. In the common offset domain, diffractions are hyperbolic, while reflections are mostly linear. The difficulty of diffraction separation technology is to suppress the reflected energy while retaining the diffraction energy. Curvelet is a sparse transformation with angle classification. Reflections are distributed in a few coefficient matrices after curvelet transformation, whereas diffractions are the opposite. Based on the significant difference between reflections and diffractions in the curvelet domain, a method of diffraction separation using cascaded filters in the curvelet domain is proposed. Cascade filters in the curvelet domain include high-pass filters and median filters. The adaptive high-pass filter can suppress the low-frequency part of reflections, and the median filter is used to suppress the high-frequency part of reflections. Numerical experiments show that the proposed method has good performance in eliminating tilt 1 1 Curvelet-domain diffraction separation method and horizontal reflections, as well as the ability to retain the polarity reversal characteristics of diffractions and more energy. Field application further verifies the potential value of this method in solving the identification of complex stratigraphic structures and small-scale discontinuities. and horizontal reflections, as well as the ability to retain the polarity reversal characteristics of diffractions and more energy. Field application further verifies the potential value of this method in solving the identification of complex stratigraphic structures and small-scale discontinuities. Keywords: diffraction separation, curvelet transform, median filter, high-pass filter 1. Introduction In resource and engineering geophysical exploration, it is a very meaningful task to locate the small-scale distributed geologic bodies such as micro-faults, pinches, fractures, and string beads (Lanbach et al 2000). During the propagation of seismic waves, distributed geologic bodies will become new sources and generate diffractions. Therefore, diffractions can indicate the position of faults in the seismic wavefield (Krey 1952) and contain valuable information regarding both the structure and composition of seismic media (Belfer et al 1998). However, the energy of diffraction is usually an order of magnitude lower than that of reflection, making it difficult to use diffraction in conventional seismic data processing flow (Landa and Keydar 1998). Independent diffraction imaging can avoid the shielding of specular reflection energy and improve the resolution of discontinuous geological bodies in seismic profiles (Khaidukov et al 2004). There are two types of diffraction imaging techniques. The first method uses the geometric difference between reflection and diffraction to separate the wavefield in various gathers, and then image the separated diffraction. Landa et al (1987) proposed that diffraction and reflection had obvious geometric differences in the common offset domain, and used travel-time correlation to extract diffraction. Fomel (2002) used the dominant local slope estimated by plane-wave destruction (PWD) filters to suppress linear signals. Since then, PWD has become the most widely used diffraction separation method in areas such as diffraction velocity analysis. 2 Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method (Gonzalez et al 2016; Yu et al 2017a; Lin et al 2018; Decker et al 2017). The Hilbert transform was used to locate the diffraction points, and the diffraction was extracted from both sides of the diffraction point using a double-branch Radon transform (Li et al 2018). Zhao et al (2019) used the spacing-varying median filter in the flattened shot domain to separate diffraction. Chen et al (2021) built a sparse inversion model based on Radon transform and Curvelet transform to separate diffractions in the common offset domain. Bakhtiari Rad et al (2018) used the width of the projected Fresnel zone to augment the filter, and then identify diffractions from reflections. With the extensive application of artificial intelligence in seismic exploration, the convolutional neural network is applied to diffraction separation (Sheng and Zhao 2022). Another method of diffraction imaging is to achieve diffraction separation and imaging by modifying the migration operator during the imaging process. Fomel et al (2007) performed diffraction velocity analysis in the post-stack domain to achieve high-resolution imaging. Berkovitch et al (2009) used a new local time correction formula to parameterize the diffraction travel time curve and achieve the flattening and focusing of diffraction events. Karimpouli et al (2015) proposed an apex-shifted Radon transform (ASRT) method to image diffractions in pre- stack data. The ASRT method used a diffraction hyperbolic trajectory similar to pre-stack time migration to locate the diffraction bodies and estimate their corresponding background velocity. To predict the reflection, Yu et al (2017b) focused on the pre-stack diffraction residual near the first Fresnel aperture and proposed a regularized L2-norm model with a smooth constraint on the local slope. Li et al (2020). used a Mahalanobis-based and phase-based attenuation function to modify the Kirchhoff migration formula in the full-azimuth dip-domain to realize diffraction separation. In this paper, we separate diffraction and reflection in the Curvelet domain, which is a sparse transform that is more suitable for curve characteristics (Shan et al 2009). In the common offset domain, reflections are mostly smooth linear events, whereas diffractions are still hyperbolic. We 3 Curvelet-domain diffraction separation method transform seismic data into the curvelet domain and then apply a cascade of median filter and frequency high-pass filter. 2. Method The basic theory of the proposed curvelet-domain diffraction separation method is to apply a cascade filter along the scale and angle parameters of the curvelet domain, which is effective in suppressing reflections and preserving weak diffractions. The proposed method is composed of the following elements. 2.1. Curvelet transform Curvelet-domain diffraction separation method The high pass filter is used to suppress the majority of the low- frequency energy of the reflection event, while the median filter is used to suppress the high- frequency linear energy of the reflection edge. Following the inverse curvelet transform, the diffraction retained by the cascade filter is restored to the data domain. This method utilizes the geometric differences between diffraction and reflection in the common offset domain, and belongs to the first type of diffraction separation method. Compared to current diffraction separation methods, it can better protect diffraction energy during the separation process. The diffraction separation and imaging effect of synthetic and field data confirm the method's feasibility and efficiency. This method of cascaded filter diffraction extraction based on Curvelet transform can obtain higher image quality for small-scale geological bodies and improve the resolution of seismic exploration. 2.1. Curvelet transform The Curvelet transform was proposed by Candes and Demanet (2003). It introduces a new compact curve frame sparse representation Fourier integral operator, and its fast discretization algorithm is realized by Candes et al (2006). Curvelet transform can accurately express seismic signals with the smallest coefficient and has a better-focusing effect on curve events (Ma and Plonka 2009). Therefore, it has many applications in denoising and wavefield separation (Demanet and Ying 2007; Cao et al 2015; Hu et al 2019; Zhang and Langston 2020). We use the curvelet theory introduced by Candes et al (2006) to describe the Curvelet transform. 4 4 Curvelet-domain diffraction separation method Let x be the spatial variable,  be the frequency variable, r and  be the polar coordinate parameters in the frequency domain. Two window functions W( )r and V( )r are established, which are called "radial window function" and "angle window function" respectively. They are smooth, non-negative, and real-valued. The window functions comply with the following conditions: ( ) ( ) 2 2 =1, 3 4,3 2 j j W r r  =−   (1) ( ) ( ) 2 1, 1 2,1 2 l V t l t  =− − = −  (2) (1) ( ) ( ) 2 1, 1 2,1 2 l V t l t  =− − = −  (2) (2) for all scales with 0 j j  , the frequency window function in the Fourier domain is defined as: for all scales with 0 j j  , the frequency window function in the Fourier domain is defined as: ( ) ( ) 2 3 4 2 , 2 2 2 j j j j U r W r V        − −   =       (3) (3) where 2 j     is the downward rounding of 2 j . The support of j U is a polar wedge. In order to obtain the real value curvelet, the symmetrical form ( ) ( ) , , j j U r U r    + + of equation (3) is used. where 2 j     is the downward rounding of 2 j . The support of j U is a polar wedge. 2.1. Curvelet transform In order to Define the “mother” curvelet ( ) j x  by Fourier transform. Define the “mother” curvelet ( ) j x  by Fourier transform. ( ) ( ) j j U     = (4) (4) In this way, all curvelets on the 2 j − scale can be obtained by rotating and translating from ( ) j x  : ( ) j x  : 1. Defines an isometric sequence of rotation angles 2 2 2 j l l   −    =  , where 0,1,2... l = , 0 2 l    ; 0 2 l    ; 2. and the sequence of translation parameters ( ) 2 1 2 , k k k = . with these notations, the curvelet at scale 2 j − , orientation l and position 2. and the sequence of translation parameters ( ) 2 1 2 , k k k = . with these notations, the curvelet at scale 2 j − , orientation l and position ( ) ( ) , 1 2 1 2 2 , 2 l j l j j kx R k k  − − − =   is defined by: ( ) ( ) , 1 2 1 2 2 , 2 l j l j j kx R k k  − − − =   is defined by: ( ) ( ) , 1 2 1 2 2 , 2 l j l j j kx R k k  − − − =   is defined by: Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method ( ) ( ) ( ) ( ) , , , l j l j l k j k x R x x    = − (5) (5) where R is the rotation by  radians. 2.1. Curvelet transform Thus, the curvelet coefficient of a function ( ) 2 2 f L R  is simply defined by itself and a curvelet , , j k l  with parameters: is simply defined by itself and a curvelet , , j k l  with parameters: ( ) ( ) ( ) 2 , , , , , , : , j l k j k l R c j l k f f x x dx   = =  (6) (6) according to equations (4) and (6), the curvelet domain represented by the curvelet coefficient is essentially a space-time domain. The curvelet tiling of space and frequency is completely displayed by Ma and Plonka (2010). Because our focus is on diffraction separation, we will not repeat the graph of the curvelet in this paper meticulously. However, to understand the application scenario of curvelet transformation, we designed a toy model and showed its wavefield and the corresponding curvelet domain expression (curvelet coefficient), as shown in Figure 1. 2.2. Cascade filter In the curvelet domain, the reflection events still behave linearly and only a few flat angles contain them. On the contrary, diffraction contains more angle information because of hyperbolic characteristics, so more curvelet coefficients are needed to describe diffraction. We only need to filter those angles containing reflection on each scale to suppress reflection. Only a few angles of diffraction and reflection coincide, in other words, only the curvelet coefficients in these angles need to be separated (such as Figure 1d). Curvelet transform, on the other hand, provides us with an angle classification filter to protect diffraction energy. In the curvelet domain, the interior of the reflection is low frequency, while the edge is high frequency. We use a high pass filter to suppress the low-frequency part and a median filter to suppress the high-frequency part of the reflection edge. The two filters are described below. The mathematical formulation of the high-pass filtering is as follows: Perform two-dimensional discrete Fourier transform on the curvelet domain coefficient matrix , 1 2 ( , ) j l c k k with scale = j and angle = l : 1 1 2 2 1 1 2 ( ) 1 2 , 1 2 0 0 ( , ) ( , ) K k K k M N i M N j l C K K c k k e  − − − + =  (7) (7) In order to suppress the reflection frequency as much as possible, we use ideal high-pass filtering 1 2 ( , ) H K K as follows: 1 2 0 1 2 1 2 0 0 ( , ) ( , ) 1 ( , ) D K K D H K K D K K D   =    (8) (8) 7 where D is the distance from the column sorting to the middle line in the C matrix, 0 D is set to one-sixth of the total number of columns in the C matrix. High-pass filtering effect by: 7 where D is the distance from the column sorting to the middle line in the C matrix, 0 D is set to one-sixth of the total number of columns in the C matrix. [Figure 1 is here] Fig 1 (a) 2D reflectance model containing a scatter and a horizontal reflector. (b) Synthetic data from the Kirchhoff forward modeling. (c) The curvelet coefficients of synthetic data. (d) Specific Curvelet domain coefficient matrix, when scale = 5 and angle = 8 Figure 1(a) presents a 2D geologic model in which a scatter is covered by a horizontal at a depth of 1km. The velocity of the background medium is 2 km/s. The synthetic data in Figure 1(b) is generated using Kirchhoff integral method and Ricker wavelet with the dominant frequency of 30Hz. There are 1000 receivers and shots with a space interval of 2m in the zero- offset data. The time length of synthetic data is 2 seconds. In Figure 1 (b), the hyperbolic event at 1km shows the response of scattering points respectively. The amplitude of horizontal events is about ten times that of hyperbolic diffraction. According to equation 6, we get the curvelet coefficient of Figure 1(b), as shown in Figure 1(c). In Figure 1(c), the coefficient close to the image center represents the low-frequency scale, and the coefficient far from the image center 6 6 Curvelet-domain diffraction separation method represents the high-frequency scale. It should be noted that there is no angle information in the curvelet coefficient of the smallest scale. We select a scale and angle parameter representing diffraction and reflection curvelet coefficients as a specific example, as shown in Figure 1(d). 2.2. Cascade filter represents the high-frequency scale. It should be noted that there is no angle information in the curvelet coefficient of the smallest scale. We select a scale and angle parameter representing diffraction and reflection curvelet coefficients as a specific example, as shown in Figure 1(d). 2.2. Cascade filter 2.2. Cascade filter High-pass filtering effect by: where D is the distance from the column sorting to the middle line in the C matrix, 0 D is set to one-sixth of the total number of columns in the C matrix. High-pass filtering effect by: where D is the distance from the column sorting to the middle line in the C matrix, 0 D is set to 7 one-sixth of the total number of columns in the C matrix. High-pass filtering effect by: xth of the total number of columns in the C matrix. High-pass filtering effect by: Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method 1 2 1 2 1 2 ( , ) ( , ) ( , ) H C K K C K K H K K =  (9) 1 2 1 2 1 2 ( , ) ( , ) ( , ) H C K K C K K H K K =  (9) 1 2 1 2 1 2 ( , ) ( , ) ( , ) H C K K C K K H K K =  1 2 1 2 1 2 ( , ) ( , ) ( , ) H C K K C K K H K K =  (9) the two-dimensional inverse Fourier transform is performed on 1 2 ( , ) H C K K to obtain the curvelet the two-dimensional inverse Fourier transform is performed on 1 2 ( , ) H C K K to obtain the curvelet coefficient matrix , 1 2 ( , ) H j l c k k after high pass filtering. [Figure 2 is here] Fig 2 (a) The spectrum in Figure 1 (d) is logarithmic, and the spectrum center is the lowest frequency; (b) The shape of the ideal high pass filter, we set it as a rectangular window; (c) Spectrum after ideal high pass filtering; (d) Curvelet coefficient matrix after high pass filtering Figure 2 shows an example of a high-pass filtering process using Figure 1d. Figure 2(a) shows the spectrum of Figure 1(d). As we can see, there are low-frequency reflections in the center of the spectrum, as well as relatively high-frequency diffraction on both sides of the image center line. Therefore, we improve the circular structure of the traditional high-pass filters. A rectangular high-pass filter (Figure 2(b)) can better suppress reflection and retain diffraction on the spectrum. The Curvelet coefficient matrix , 1 2 ( , ) H j l c k k obtained by high-pass filtering is shown in Figure 2(d). After removing the low frequency, the high frequency caused by reflection remains. Although they only appear in a small range of the spectrum, the linear high frequency caused by the reflection edge will bring the "ringing" phenomenon. We use a median filter to solve this trouble. The following is the mathematical principle of median filtering. , , , 1 arg min b p q A H M j l b a c C a c c c  = = −  (10) (10) where , , H M j l c denotes the output value of the median filter for the current location point , p q x ; , , 1 2 { , , , } p q p q A C c c c = , ,p q are the position index in a 2-D dimension, ,a b are indices in the filtering window. The symbol A means the fixed length of the filtering window. The curvelet coefficient matrix after median filtering is shown in Figure 3(a). where , , H M j l c denotes the output value of the median filter for the current location point , p q x ; , , 1 2 { , , , } p q p q A C c c c = , ,p q are the position index in a 2-D dimension, ,a b are indices in the filtering window. The symbol A means the fixed length of the filtering window. transform 2.3. Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method Inverse curvelet transform is carried out in the curvelet domain after cascade processing of the high pass filter and median filter. We have completed the separation of diffraction from the space-time domain(Figure 3(b))so far. [Figure 2 is here] The curvelet coefficient matrix after median filtering is shown in Figure 3(a). where , , H M j l c denotes the output value of the median filter for the current location point , p q x ; 8 Fig 3 (a) Figure 2 (d) after median filtering. (b) The diffraction obtained by inverse curve Fig 3 (a) Figure 2 (d) after median filtering. (b) The diffraction obtained by inverse curvelet [Figure 3 is here] [Figure 3 is here] [Figure 4 is here] Fig 4 The workflow of curvelet domain cascade filter diffraction separation method Fig 4 The workflow of curvelet domain cascade filter diffraction separation method One contribution of this method is to apply a cascade filter based on the curvelet transform, which makes it possible to separate diffraction in common offset gathers. Compared with other diffraction separation methods, it no doubt has inherent advantages as the diffractions in common offset gathers are distributed at multiple angles. Therefore, the curvelet domain has good performance in distinguishing geometric forms of reflection and diffraction. Selecting a specific curvelet domain for filtering can protect the amplitude of the two branches of diffraction. 2.3. Curvelet-domain diffraction separation method In the proposed curvelet-domain diffraction separation method, a combined operation of the high-pass filtering and median filtering is used to extract curvelet coefficient matrixes of diffractions. The forward transform and inverse transform of the curvelet is used to switch seismic data in the common offset domain and curvelet domain. The whole method framework (Figure 4) is outlined as follows: 1. Convert the common offset domain data to curvelet domain; 1. Convert the common offset domain data to curvelet domain; 2. Adaptively select the coefficient matrix according to the scale coefficient of the curvelet domain, which contains reflections and diffractions at the same dip angle; 3. Applying the two-dimensional discrete Fourier transform to the selected curvelet coefficient matrix; 4. Using the frequency domain ideal high-pass filter to suppress the low-frequency signal in the curvelet domain; 5. Applying the two-dimensional inverse discrete Fourier transform to obtain the curvelet coefficient matrix with diffraction coefficients; 6. Cascading the median filter to suppress the residual reflection edge and the "ringing" 9 Curvelet-domain diffraction separation method generated by the ideal high-pass filter; generated by the ideal high-pass filter; 7. Convert the curvelet domain to the common offset domain. 7. Convert the curvelet domain to the common offset domain. 3. Synthetic example The 2D fault model shown in Figure 5(a) is used to generate synthetic seismic data, which includes multiple faults and a horizontal reflector (reflection coefficient is 1). The media velocity is set to 1.5 km/s. The six faults with fault distances ranging from 80m to 180m are located in the transverse positions of 2.3km and 3.8km respectively. The specular reflection on both sides of the depression has different inclination, which can be used to test the proposed method's suppression effect on the inclined formation reflection events. The numerically synthetized Kirchhoff algorithm is used to generate 2D synthetic data with a dominant 30Hz Ricker wavelet. The surface observation system we designed is used to generate zero offset data, which includes 600 shots and receivers with a 10m space interval. The number of time samples is 1100, with a time interval of 2ms. The synthetic data in Figure 5(b) includes 20 edge diffractions and 10 reflections. The two branches of edge diffractions have opposite polarity. 10 [Figure 5 is here] 10 [Figure 5 is here] 10 10 Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method Fig 5 (a) Graben reflectance model including inclined strata and fault edges. (b) The synthetic seismic wave field forward simulated by Kirchhoff integral method Based on the curvelet transform, we can obtain curvelet coefficients of synthetic data. The angle quantity division of the curvelet coefficient is based on scale, and the number of scales is related to the size of input data. For the synthetic data we used, curvelet transform divides it into seven scales. In practical terms, the mesoscale parameters of the curvelet transform start from 0, but the computer can only start from 1 when calculating and saving. In this paper, we use the scale code displayed on the computer. We choose the "first" scale without angle parameters and the fifth scale divided into 64 angles as the presentation of cascade filtering in the curvelet domain (Figure 6). [Figure 6 is here] [Figure 6 is here] Fig 6 (a) Curvelet coefficient matrix of "first" scale; (b) The "first" scale curvelet coefficient matrix after cascade filtering; (c) 16 continuous angle windows on the fifth scale of curvelet domain; (d) The fifth scale after cascade filtering 11 Figure 6(a) shows the first scale curvelet coefficients obtained from the curvelet transformation of synthetic data. There is the same but fuzzy distribution pattern as the seismic data in the Spatio-temporal domain because the first scale of curvelet transform is the lowest frequency range representing the image contour. The proposed cascade filtering is applied to the first scale curvelet coefficient to obtain the diffraction curvelet coefficient as shown in Figure 6(b). Although the spatial shape of the wavefield is fuzzy in the curvelet domain, the hyperbolic shape of diffraction is better preserved than that of reflection. Figure 6(c) shows the coefficient matrix of 16 consecutive angular windows of the synthetic data on the fifth scale of the curvelet domain. As we can see, both reflections and diffractions are concentrated in different angle windows according to the inclination range. In curvelet transform, the number of angle windows will double for every two scales. So, we design an adaptive operator based on scale change to 11 Curvelet-domain diffraction separation method select part of the angle window for filtering. Figure 6(d) shows the results of cascade filtering. In the filtered coefficient matrix, the reflected curvelet coefficient is suppressed and the diffraction coefficient is retained. Moreover, in the coefficient matrixes, those are not selected for filtering, the curvelet coefficients representing the distal end of the diffraction two branches are all retained for the recovery of the diffraction wavefield. [Figure 7 is here] [Figure 7 is here] Fig 7 (a) Diffractions separated by cascade filtering method in curvelet domain; (b) Diffractions separated by traditional PWD method; (c) Curvelet domain cascade filtering method separates reflections; (d) Reflections separated by traditional PWD method; (e) Migration imaging of (a); (f) Migration imaging of (b) The separated diffraction wavefield is obtained by inverse curvelet transform using the curvelet coefficients after cascade filtering, as shown in Figure 7(a). Both horizontal and oblique reflections are well suppressed. The traditional PWD diffraction separation method is applied to synthetic data. The diffraction wavefield separated by the PWD method is shown in Figure 7(b). As we can see, the proposed method can better suppress the inclined reflection energy and retain the polarity reversal characteristic of edge diffraction. In order to illustrate the superior performance of the proposed method in protecting diffraction amplitude, we show the reflection separated by the curvelet domain cascade filtering method (Figure 7(c)) and PWD method (Figure 7(d)) respectively. The proposed method performs very well in the index of diffraction energy protection. In addition to the reflection wavefield of the PWD method, Chen et al (2021) also showed their reflection separation results, which contained significantly more diffraction than the proposed method. The migration imaging of the curvelet method and PWD method are shown in Figure 7(d) and (e), respectively. 12 The numerically synthetized example demonstrates the good performance of the proposed curvelet-domain diffraction separation method in eliminating strong reflections and separating 12 Curvelet-domain diffraction separation method diffractions. The diffraction image can accurately depict the fault edge, and therefore play a significant role in studying the Geological disaster causing factors and oil and gas migration pathway. diffractions. The diffraction image can accurately depict the fault edge, and therefore play a significant role in studying the Geological disaster causing factors and oil and gas migration pathway. Fig 8 Nankai DMO stacked data Fig 8 Nankai DMO stacked data Fig 9 (a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD Fig 9 (a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD method [Figure 9 is here] Fig 9 (a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD 4. Field data application It is necessary to carry out diffraction imaging in field seismic data because diffraction carries the information of underground small-scale scatterers and discontinuities. The Nankai deep-water field data with well-developed diffraction and variable reflection inclination is often used to test the performance of diffraction separation methods (Decker et al 2017, Chen et al 2021, Sheng et al 2022). The dip-moveout correction (DMO) stacked profile (Figure 8) is used to verify the availability of the proposed method. Due to the multi-stage geological structure, the wavefield is very complex. The migration imaging velocity is from Decker et al (2017). We can see that reflection and diffraction constitute shallow events. Due to the existence of a steep dip stratum, the energy of some diffraction is strong. Some weak diffraction will be masked by strong reflection in the 7.5-second part of the data. [Figure 8 is here] [Figure 11 is here] [Figure 11 is here] Fig 11 (a) The migration imaging comes from the diffractions separated by the proposed method; (b) Full wavefield migration imaging method We apply the proposed method to the field data, diffractions separated from the DMO stacked profile is shown in Figure 9(a). Figure 9(b) shows the same profile after applying the PWD method. We use red and yellow arrows respectively to indicate the difference between diffraction and reflection in the separated wavefield. It can be seen that the proposed method has more advantages than the traditional PWD method in suppressing steep angle reflection and 13 Curvelet-domain diffraction separation method protecting diffraction energy. In order to show the protection of diffraction amplitude by the two methods when separating the wavefield, the separated reflections are shown in Figure 10(a) and (b), respectively. There are fewer diffractions eliminated in the left figure. The reflection results demonstrate that the proposed method only filters part of curvelet domains, which protects the energy at the far end of the diffraction. The retention of diffraction amplitude highlights the location of small-scale discontinuous objects in seismic imaging, which is the basis for high- resolution imaging. [Figure 10 is here] [Figure 10 is here] Fig 10 (a) The reflections separated by the proposed method; (b) Reflections separated by the PWD method Figure 11(a) shows the time migration of the diffractions separated by the proposed method. Compared with the full wavefield migration imaging (b), the discontinuous geological bodies at 7.5 seconds are effectively revealed, and the special structures with strong reflection interference between 6.5 and 7 seconds are highlighted. The field stacked data application verifies the good performance of the proposed curvelet-domain cascade filtering diffraction separation method for eliminating strong reflections and separating weak diffractions. It opens a possibility for performing the separation of diffractions in the common-offset domain. The revealed micro faults and discontinuous geological bodies further show its potential value in high-resolution imaging research. 5. Discuss and conclusion Separating diffraction in the common offset domain is an important step to improve the 14 Curvelet-domain diffraction separation method spatial resolution of diffraction imaging. Diffraction and reflection show completely different geometric forms in the common offset domain, in which most of the reflection is linear and the diffraction is hyperbolic. The conventional common offset domain diffraction separation method not only suppresses the reflected energy but also weakens the originally weak diffraction energy. The proposed curvelet domain cascade filter diffraction separation method provides a new method for diffraction separation in the common offset domain, which can maintain the diffraction amplitude and the polarity reversal of edge diffraction. spatial resolution of diffraction imaging. Diffraction and reflection show completely different geometric forms in the common offset domain, in which most of the reflection is linear and the diffraction is hyperbolic. The conventional common offset domain diffraction separation method not only suppresses the reflected energy but also weakens the originally weak diffraction energy. The proposed curvelet domain cascade filter diffraction separation method provides a new method for diffraction separation in the common offset domain, which can maintain the diffraction amplitude and the polarity reversal of edge diffraction. The advantage of this method is that the curvelet transform can transform the energy of the space-time domain in different angle ranges to their own independent curvelet domain. Therefore, it can separate diffraction with more accurate reflection suppression. Through the cascade of the high pass filter and median filter, we suppress the low-frequency energy inside the reflection and the high-frequency energy at the edge of the reflection in the curvelet domain. The inverse curvelet transform can transform the filtered curvelet domain data into seismic diffraction wavefield, so as to realize diffraction separation imaging. We use a toy model to show the implementation process of the proposed method. The effectiveness and advantages of this method in diffraction separation are verified by examples of synthetic data and field data. This method can improve the resolution of discontinuous geological bodies in seismic data. We also conducted some interesting tests. For example, cascade filtering is directly applied to the data. It is found that cascade filtering cannot adapt to complex wavefields, and the diffraction energy loss is large in the separation process. We believe that the curvelet transform and its inverse transform provide a "working area" of cascade filtering, which is a key step to protect the diffraction vibration amplitude. Declarations Conflict of interest The authors declared that they have no conflicts of interest in this work. Conflict of interest The authors declared that they have no conflicts of interest in this work. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in Conflict of interest The authors declared that they have no conflicts of interest in this work. Conflict of interest The authors declared that they have no conflicts of interest in this work. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 5. Discuss and conclusion In addition, we apply the median filter and high pass filter respectively in the curvelet domain, rather than their cascade. When median filtering is used in the curvelet domain, the separation effect is the worst. A large number of reflections are 15 Curvelet-domain diffraction separation method retained in the data and cannot be separated. The reason is that even after curvelet transformation, the reflection is still a relatively low-frequency signal. The median filter is essentially a low-pass filter, so it cannot separate the wavefield. When high pass filtering is used in the curvelet domain, most of the reflected energy is suppressed. However, the edge part of the reflection cannot be removed. The reason is that the frequency of the reflection edge coincides with the diffraction and cannot be removed by frequency domain filtering. Acknowledgments This work is supported by the National Natural Science Foundation of China (Grant No. 42022031), National Key Research and Development Program of China(Grant No.2020YFE0201300), Fundamental Research Funds for the Central Universities (Grant No. grant no. 2021JCCXMT0, 2602020RC130). We thank Peng Research Group in CUMTB for support of this work. We express great appreciation to the anonymous reviewers and editors for promotion of this paper. References Bakhtiari Rad, P., Gajewski, D., & Macelloni, L. (2018). Diffraction separation based on the projected first Fresnel zone. Journal of Geophysics and Engineering, 15(6), 2507-2515. Belfer, I., Bruner, I., Keydar, S., Kravtsov, A., & Landa, E. (1998). Detection of shallow objects using refracted and diffracted seismic waves. Journal of Applied Geophysics, 38(3), 155-168. Berkovitch, A., Belfer, I., Hassin, Y., & Landa, E. (2009). Diffraction imaging by multifocusing. Geophysics, 74(6), WCA75-WCA81. Bakhtiari Rad, P., Gajewski, D., & Macelloni, L. (2018). Diffraction separation based on the projected first Fresnel zone. Journal of Geophysics and Engineering, 15(6), 2507-2515. Bakhtiari Rad, P., Gajewski, D., & Macelloni, L. (2018). Diffraction separation based on the projected first Fresnel zone. Journal of Geophysics and Engineering, 15(6), 2507-2515. Belfer, I., Bruner, I., Keydar, S., Kravtsov, A., & Landa, E. (1998). Detection of shallow objects using refracted and diffracted seismic waves. Journal of Applied Geophysics, 38(3), 155-168. Berkovitch, A., Belfer, I., Hassin, Y., & Landa, E. (2009). Diffraction imaging by multifocusing. Geophysics, 74(6), WCA75-WCA81. Berkovitch, A., Belfer, I., Hassin, Y., & Landa, E. (2009). Diffraction imaging by multifocusing. Geophysics, 74(6), WCA75-WCA81. 16 Curvelet-domain diffraction separation method Candes, E., & Demanet, L. (2003). Curvelets and Fourier integral operators. Comptes Rendus Mathematique, 336(5), 395-398. Candes, E., Demanet, L., Donoho, D., & Ying, L. (2006). Fast discrete curvelet transforms. multiscale modeling & simulation, 5(3), 861-899. Cao, J. J., Zhao, J. T., & Hu, Z. Y. (2015). 3D seismic denoising based on a low-redundancy curvelet transform. Journal of Geophysics and Engineering, 12(4), 566-576. Chen, X., Cao, J. J., Yang, H. L., Shi, S. J., & Guo, Y. S. (2022). Diffraction separation and imaging based on double sparse transforms. Petroleum Science, 19(2), 534-542. Decker, L., Merzlikin, D., & Fomel, S. (2017). Diffraction imaging and time-migration velocity analysis using oriented velocity continuation. Geophysics, 82(2), U25-U35. Demanet, L., & Ying, L. (2007, September). Curvelets and wave atoms for mirror-extended images. In Wavelets XII (Vol. 6701, pp. 202-215). SPIE. Fomel, S. (2002). Applications of plane-wave destruction filters. Geophysics, 67(6), 1946-1960. Fomel, S., Landa, E., & Taner, M. T. (2007). Poststack velocity analysis by separation and imaging of seismic diffractions. Geophysics, 72(6), U89-U94. Gonzalez, J. A., De Figueiredo, J. J., Coimbra, T. A., Schleicher, J., & Novais, A. (2016). Migration velocity analysis using residual diffraction moveout: A real-data example. Journal of Geophysics and Engineering, 13(4), 622-633. Hu, Z., Gao, J. H., & Liu, N. H. (2019). References Separation of blended seismic data using the synchrosqueezed curvelet transform. IEEE Geoscience and Remote Sensing Letters, 17(4), 711- 715. Karimpouli, S., Malehmir, A., Hassani, H., Khoshdel, H., & Nabi-Bidhendi, M. (2015). Automated diffraction delineation using an apex-shifted Radon transform. Journal of Geophysics and Engineering, 12(2), 199-209. Khaidukov, V., Landa, E., & Moser, T. J. (2004). Diffraction imaging by focusing-defocusing: An 17 17 Curvelet-domain diffraction separation method outlook on seismic superresolution. Geophysics, 69(6), 1478-1490. Krey, T. (1952). The significance of diffraction in the investigation of faults. Geophysics, 17(4), 843-858. Landa, E., Shtivelman, V., & Gelchinsky, B. (1987). A method for detection of diffracted waves on common‐offset sections. Geophysical prospecting, 35(4), 359-373. Landa, E., & Keydar, S. (1998). Seismic monitoring of diffraction images for detection of local heterogeneities. Geophysics, 63(3), 1093-1100. Laubach, S., Marrett, R., & Olson, J. (2000). New directions in fracture characterization. The Leading Edge, 19(7), 704-711. Li, C. J., Peng, S. P., Zhao, J. T., Cui, X. Q., Du, W. F., & Satibekova, S. (2018). Polarity- preserved diffraction extracting method using modified apex-shifted Radon transform and double-branch Radon transform. Journal of Geophysics and Engineering, 15(5), 1991-2000. Li, C. J., Zhao, J. T., Peng, S. P., Cui, X. Q., & Lin, P. (2020). Separating and imaging diffractions of seismic waves in the full-azimuth dip-angle domain. Journal of Geophysics and Engineering, 17(2), 339-356. Lin, P., Peng, S. P., Zhao, J. T., Cui, X. Q., & Du, W. F. (2018). A new scheme for velocity analysis and imaging of diffractions. Journal of Geophysics and Engineering, 15(3), 1084-1093. Ma, J. W., & Plonka, G. (2009). Computing with curvelets: from image processing to turbulent flows. Computing in Science & Engineering, 11(2), 72-80. Ma, J. W., & Plonka, G. (2009). Computing with curvelets: from image processing to turbulent flows. Computing in Science & Engineering, 11(2), 72-80. Ma, J. W., & Plonka, G. (2010). The curvelet transform. IEEE signal processing magazine, 27(2), 118-133. Shan, H., Ma, J. W., & Yang, H. Z. (2009). Comparisons of wavelets, contourlets and curvelets in seismic denoising. Journal of Applied Geophysics, 69(2), 103-115. Sheng, T. J., & Zhao, J. T. (2022). Separation and imaging of diffractions using a dilated convolutional neural network. Geophysics, 87(3), S117-S127. 18 Curvelet-domain diffraction separation method Curvelet-domain diffraction separation method Yu, C. X., Zhao, J. T., Wang, Y. F., & Qiu, Z. (2017). Sparse diffraction imaging method using an adaptive reweighting homotopy algorithm. Journal of Geophysics and Engineering, 14(1), 26-40. Yu, C. X., Zhao, J. T., & Wang, Y. F. (2017). Revealing small-scale diffracting discontinuities by an optimization inversion algorithm. Journal of Geophysics and Engineering, 14(1), 1-14. Zhang, J., & Langston, C. A. (2020). Separating the scattered wavefield from teleseismic P using curvelets on the long beach array data set. Geophysical Journal International, 220(2), 1112-1127. Zhao, J. T., Sun, X., Peng, S. P., Wei, W., & Liu, T. (2019). Separating prestack diffractions with SVMF in the flattened shot domain. Journal of Geophysics and Engineering, 16(2), 389-398. Yu, C. X., Zhao, J. T., Wang, Y. F., & Qiu, Z. (2017). Sparse diffraction imaging method using an adaptive reweighting homotopy algorithm. Journal of Geophysics and Engineering, 14(1), 26-40. Yu, C. X., Zhao, J. T., & Wang, Y. F. (2017). Revealing small-scale diffracting discontinuities by an optimization inversion algorithm. Journal of Geophysics and Engineering, 14(1), 1-14. Zhang, J., & Langston, C. A. (2020). Separating the scattered wavefield from teleseismic P using curvelets on the long beach array data set. Geophysical Journal International, 220(2), 1112-1127. Zhao, J. T., Sun, X., Peng, S. P., Wei, W., & Liu, T. (2019). Separating prestack diffractions with SVMF in the flattened shot domain. Journal of Geophysics and Engineering, 16(2), 389-398. 19 19 Figures g Figure 1 a) 2D re§ectance model containing a scatter and a horizontal re§ector. (b) Synthetic data from the Kirchhoff forward modeling. (c) The curvelet coe¨cients of synthetic data. (d) Speci¦c Curvelet domai coe¨cient matrix, when scale = 5 and angle = 8 Figure 1 (a) 2D re§ectance model containing a scatter and a horizontal re§ector. (b) Synthetic data from the Kirchhoff forward modeling. (c) The curvelet coe¨cients of synthetic data. (d) Speci¦c Curvelet domain coe¨cient matrix, when scale = 5 and angle = 8 Figure 2 (a) The spectrum in Figure 1 (d) is logarithmic, and the spectrum center is the lowest frequency; (b) The shape of the ideal high pass ¦lter, we set it as a rectangular window; (c) Spectrum after ideal high pass ¦ltering; (d) Curvelet coe¨cient matrix after high pass ¦ltering Figure 2 (a) The spectrum in Figure 1 (d) is logarithmic, and the spectrum center is the lowest frequency; (b) The shape of the ideal high pass ¦lter, we set it as a rectangular window; (c) Spectrum after ideal high pass ¦ltering; (d) Curvelet coe¨cient matrix after high pass ¦ltering Figure 3 (a) Figure 2 (d) after median ¦ltering. (b) The diffraction obtained by inverse curvelet transform Figure 3 (a) Figure 2 (d) after median ¦ltering. (b) The diffraction obtained by inverse curvelet transform (a) Figure 2 (d) after median ¦ltering. (b) The diffraction obtained by inverse curvelet transform (a) Figure 2 (d) after median ¦ltering. (b) The diffraction obtained by inverse curvelet transform (a) Figure 2 (d) after median ¦ltering. (b) The diffraction obtained by inverse curvelet transform Figure 4 The work§ow of curvelet domain cascade ¦lter diffraction separation method Figure 4 The work§ow of curvelet domain cascade ¦lter diffraction separation method Figure 5 (a) Graben re§ectance model including inclined strata and fault edges. (b) The synthetic seismic wave ¦eld forward simulated by Kirchhoff integral method Figure 5 (a) Graben re§ectance model including inclined strata and fault edges. (b) The synthetic seismic wave ¦eld forward simulated by Kirchhoff integral method (a) Graben re§ectance model including inclined strata and fault edges. (b) The synthetic seismic wave ¦eld forward simulated by Kirchhoff integral method Figure 6 (a) Curvelet coe¨cient matrix of "¦rst" scale; (b) The "¦rst" scale curvelet coe¨cient matrix after cascad ¦ltering; (c) 16 continuous angle windows on the ¦fth scale of curvelet domain; (d) The ¦fth scale after cascade ¦ltering Figure 6 (a) Curvelet coe¨cient matrix of "¦rst" scale; (b) The "¦rst" scale curvelet coe¨cient matrix after cascade ¦ltering; (c) 16 continuous angle windows on the ¦fth scale of curvelet domain; (d) The ¦fth scale after cascade ¦ltering (a) Curvelet coe¨cient matrix of "¦rst" scale; (b) The "¦rst" scale curvelet coe¨cient matrix after cascade ¦ltering; (c) 16 continuous angle windows on the ¦fth scale of curvelet domain; (d) The ¦fth scale after cascade ¦ltering (a) Curvelet coe¨cient matrix of "¦rst" scale; (b) The "¦rst" scale curvelet coe¨cient matrix after cascade ¦ltering; (c) 16 continuous angle windows on the ¦fth scale of curvelet domain; (d) The ¦fth scale after cascade ¦ltering Figure 7 (a) Diffractions separated by cascade ¦ltering method in curvelet domain; (b) Diffrac traditional PWD method; (c) Curvelet domain cascade ¦ltering method separates re§e Re§ections separated by traditional PWD method; (e) Migration imaging of (a); (f) Mi (b) Figure 7 (a) Diffractions separated by cascade ¦ltering method in curvelet domain; (b) Diffractions separated by traditional PWD method; (c) Curvelet domain cascade ¦ltering method separates re§ections; (d) Re§ections separated by traditional PWD method; (e) Migration imaging of (a); (f) Migration imaging of (b) Figure 7 (a) Diffractions separated by cascade ¦ltering method in curvelet domain; (b) Diffractions separated by traditional PWD method; (c) Curvelet domain cascade ¦ltering method separates re§ections; (d) Re§ections separated by traditional PWD method; (e) Migration imaging of (a); (f) Migration imaging of (b) (a) Diffractions separated by cascade ¦ltering method in curvelet domain; (b) Diffractions separated by traditional PWD method; (c) Curvelet domain cascade ¦ltering method separates re§ections; (d) Re§ections separated by traditional PWD method; (e) Migration imaging of (a); (f) Migration imaging of (b) (b) Figure 8 Nankai DMO stacked data Nankai DMO stacked data Figure 9 (a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD method Figure 9 (a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD method (a) Diffractions separated by the proposed method; (b) Diffractions separated by the PWD method Figure 10 Figure 10 Figure 10 (a) The re§ections separated by the proposed method; (b) Re§ections separated by the PWD method (a) The re§ections separated by the proposed method; (b) Re§ections separated by the PWD method (a) The re§ections separated by the proposed method; (b) Re§ections separated by the PWD method (a) The re§ections separated by the proposed method; (b) Re§ections separated by the PWD method Figure 11 (a) The migration imaging comes from the diffractions separated by the proposed method; (b) Full wave¦eld migration imaging Figure 11 (a) The migration imaging comes from the diffractions separated by the proposed method; (b) Full wave¦eld migration imaging (a) The migration imaging comes from the diffractions separated by the proposed method; (b) Full wave¦eld migration imaging (a) The migration imaging comes from the diffractions separated by the proposed method; (b) Full wave¦eld migration imaging
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The impact of ACE2 genetic polymorphisms (rs2106809 and rs2074192) on gender susceptibility to COVID-19 infection and recovery: A systematic review
Baghdad journal of biochemistry & applied biological sciences/Baghdad journal of biochemistry and applied biological sciences
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Keywords ACE2, COVID-19, gene polymorphism, gender, SARS-CoV-2 Keywords ACE2, COVID-19, gene polymorphism, gender, SARS-CoV-2 SYSTEMATIC REVIEW BAGHDAD JOURNAL OF BIOCHEMISTRY AND APPLIED BIOLOGICAL SCIENCES 2021, VOL. 2, NO. 03, 167-180, e-ISSN: 2706-9915 https://doi.org/10.47419/bjbabs.v2i03.53 The impact of ACE2 genetic polymorphisms (rs2106809 and rs2074192) on gender susceptibility to COVID-19 infection and recovery: A systematic review Ahmed A. Suleiman1, Tamadher A. Rafaa2, Ali M. Alrawi1 and Mustafa F. Dawood3 1Department of Biotechnology, College of Science, University of Anbar, Ramadi, Iraq 2The Presidency of the University of Anbar, Ramadi, Iraq 3College of Education for Pure Science, University of Anbar, Ramadi, Iraq SYSTEMATIC REVIEW BAGHDAD JOURNAL OF BIOCHEMISTRY AND APPLIED BIOLOGICAL SCIENCES 2021, VOL. 2, NO. 03, 167-180, e-ISSN: 2706-9915 https://doi.org/10.47419/bjbabs.v2i03.53 The impact of ACE2 genetic polymorphisms (rs2106809 and rs2074192) on gender susceptibility to COVID-19 infection and recovery: A systematic review Ahmed A. Suleiman1, Tamadher A. Rafaa2, Ali M. Alrawi1 and Mustafa F. Dawood3 1Department of Biotechnology, College of Science, University of Anbar, Ramadi, Iraq 2The Presidency of the University of Anbar, Ramadi, Iraq 3College of Education for Pure Science, University of Anbar, Ramadi, Iraq SYSTEMATIC REVIEW BAGHDAD JOURNAL OF BIOCHEMISTRY AND APPLIED BIOLOGICAL SCIENCES 2021, VOL. 2, NO. 03, 167-180, e-ISSN: 2706-9915 https://doi.org/10.47419/bjbabs.v2i03.53 The impact of ACE2 genetic polymorphisms (rs2106809 and rs2074192) on gender susceptibility to COVID-19 infection and recovery: A systematic review Ahmed A. Suleiman1, Tamadher A. Rafaa2, Ali M. Alrawi1 and Mustafa F. Dawood3 1Department of Biotechnology, College of Science, University of Anbar, Ramadi, Iraq 2The Presidency of the University of Anbar, Ramadi, Iraq 3College of Education for Pure Science, University of Anbar, Ramadi, Iraq 2021, VOL. 2, NO. 03, 167-180, e-ISSN: 2706-9915 https://doi.org/10.47419/bjbabs.v2i03.53 ABSTRACT Copyright: © 2021 Ahmed A. Suleiman, Tamadher A. Rafaa, Ali M. Al-Rawi, Mustafa F. Dawood Copyright: © 2021 Ahmed A. Suleiman, Tamadher A. Rafaa, Ali M. Al-Rawi, Mustafa F. Dawood ABSTRACT Background: Epidemiological studies revealed there is a difference in susceptibility to infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) because of differences in gender with age and males being more inflicted. There is a clear indication that deaths caused by coronavirus disease 2019 (COVID-19) in males appeared at a higher rate than females across 35 nations. The implication of associated disease-risk genes, involved in the susceptibility of COVID-19 such as the angiotensin-converting enzyme 2 (ACE2), has recently received considerable attention due to their role in severe injury of lung and mediated SARS-CoV-2 entry as a host receptor. Received 09-06-2021 Revised 04-09-2021 Accepted 07-09-2021 Published 23-09-2021 Corresponding Author Ahmed A. Suleiman ahmed.suleiman@uoanbar.edu.iq Objectives: Herein, we aimed to systematically review how two main genetic polymorphisms of ACE2 (rs2106809 and rs2074192) can affect the gender susceptibility to SARS-CoV-2 infection. Objectives: Herein, we aimed to systematically review how two main genetic polymorphisms of ACE2 (rs2106809 and rs2074192) can affect the gender susceptibility to SARS-CoV-2 infection. Department of Biotechnology, College of Science, University of Anbar, Ramadi, Iraq Methods: To conduct this systematic review, a literature search in PubMed, Google Scholar, ScienceDirect, and Nature was made for the period 2004 to 2020. We searched for the impact of ACE2 genetic polymorphisms (rs2106809 and rs2074192) on gender susceptibility.f DOI https://doi.org/10.47419/ bjbabs.v2i03.53 Pages: 167-180 Distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC-BY-NC 4.0), which permits use for any non-commercial purpose, distribution, and reproduction in any medium, provided that the original work is properly cited. DOI https://doi.org/10.47419/ bjbabs.v2i03.53 Pages: 167-180 Distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC-BY-NC 4.0), which permits use for any non-commercial purpose, distribution, and reproduction in any medium, provided that the original work is properly cited. Results: We noticed that there was a differential genotype distribution between males and females in various global populations whereas mutant variants were common in males compared to wild-type variants among females which may reflect differences in gender susceptibility to infection with SARS-CoV-2. Females are less susceptible to coronavirus as compare to males because of the expression of ACE2 receptor. It has a double role in favour of COVID-19 and against COVID-19. Conclusions: Male mortality is greater than female mortality, which might be attributed to the ACE2 deficiency in women. Epidemiological studies have shown that the differences in sex and age have different susceptibility to SARS-CoV-2 infection. INTRODUCTION Coronaviruses, a family of disease-causing viruses, responsible for diseases that threaten the humans on the earth such as severe acute respiratory syndrome (SARS),1 Middle East Respiratory Syndrome (MERS),1,2 and the recently declared coronavirus disease 2019 (COVID-19);3 and all are ranging from the mild to very severe pneumonia. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID- 19, is single strand RNA (ssRNA) virus comprmised of glycoprotein spikes, mediating the virus to enter in host cells.4 Recently, both epidemiological5 and experimental6 features of COVID-19 patients have been defined. In hypertensive patients, diabetics, obese, and the elderly, recent researches have shown a greater risk of infection.7 However, little evidence on the impact of ACE2 genetic polymorphisms on gender susceptibility to infection and the rate of COVID-19 are available. Phylogenetic research has led scientists to explore the host entry process of SARS-CoV-2 and found that it enters into the host cell by binding to ACE2 membrane receptors.8 Body parts including the respiratory tract, stomach, small intestine, skin, thymus, spleen, liver, bone marrow, and blood vessels are all vulnerable to COVID-19 infection due to an abun- dance of ACE2.9 In lung alveolar epithelial cells, ACE2 is expressed in larger amounts. Thus, it contributes in damaging the lungs in acute respiratory distress syndrome (ARDS) and pneumonia.10 SARS-CoV-2 has also been shown to form an association with the renin- angiotensin-aldosterone system (RAAS) via (ACE2) enzyme.11 Angiotensinogen is a key substrate for RAAS, which made in the liver, and split to pro- duce angiotensin 1 (also called pro-angiotensin), by the renin. The body has vasodilatory, anti-inflammatory and antioxidant properties attributed to the ACE2.12 The ACE2 catalytic domain is the extracellular portion of the cell, which can be destroyed, followed by the release of ADAM17 (metallopeptidase and disintegrin) into the blood Figure 1.13 The asso- ciation between ACE2 and SARS-CoV-2 has an important involvement and relationship to the severity of infection developing in the human body Figure 2.14 Furthermore, SARS-CoV-2-mediated infection has been shown to vary according to dif- ferences in age. For instance, elder patients are more vulnerable than children to COVID- 19. Knowing this relationship will pave a way for inventors and investigators to develop better options, assisting in the treatment of COVID-19. How to cite this article: Suleiman AA, Rafaa TA, Alrawi AM, Dawood MF. The impact of ACE2 genetic polymorphisms (rs2106809 and rs2074192) on gender susceptibility to COVID-19 infection and recovery: A systematic review. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2021;2(03):167-180. doi: bjbabs.v2i03.53 167 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 INTRODUCTION A study points out the possible sources of improved confrontation to COVID19 in youngsters compared to grownups due to ACE2 expression components, the double role of ACE2 in defending lesions (inflam- matory) along with detrimental effects of ACE2 which act as a molecular aim in promot- ing the virus entry. The objective of the authors is to provide evidence on the activities of the ACE2 enzyme in contradiction of or in service of the progression of COVID-19 to demonstrate the complexity of ACE2 enzyme behaviour during illness, this facilitates researchers’ chance to create safe vaccines and solutions for therapeutics. In turn, the study of the roles of ACE2 in different age groups, will also promote clarity, and study the receptor behavior in the present situation.15 The ACEs is one of the exopeptidases, which might be common to several peptides. It is predominantly found in the cell membrane, and firstly Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 168 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. Figure 1 The enzymaticflow of the renin-angiotensin system (RAS) depicts the main receptor systems, the biological activities of angiotensin 2 and Ang-(1-7), and the stability of ACE and ACE2. 7 A). RAS system showing the angiotensin peptide metabolic pathway as the initiator compound cleaved by renin (kidney) to form Ang 1 followed by ACE’s followed by Ang 2 to Ang (1 to 7) facilitated cleavage of ACE2. Ang 2 functions on the receptors of AT1 and AT2, while Ang (1 to 7) operates on the receptors of Mas and antagonizes the activities of the axis of Ang2/AT1R. B) Curbed ACE2 levels result in a balance change in the RAS to the Ang 2/AT1R (activator) axis, promoting the progression of the infection. Improved levels of ACE2 change the balance to the Ang (1 to 7)/MasR axis (inhibitor) via rhACE2, ACE2 activators, resulting in defence from viral infection. Figure 1 The enzymaticflow of the renin-angiotensin system (RAS) depicts the main receptor systems, the biological activities of angiotensin 2 and Ang-(1-7), and the stability of ACE and ACE2. 7 A). RAS system showing the angiotensin peptide metabolic pathway as the initiator compound cleaved by renin (kidney) to form Ang 1 followed by ACE’s followed by Ang 2 to Ang (1 to 7) facilitated cleavage of ACE2. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 INTRODUCTION Ang 2 functions on the receptors of AT1 and AT2, while Ang (1 to 7) operates on the receptors of Mas and antagonizes the activities of the axis of Ang2/AT1R. B) Curbed ACE2 levels result in a balance change in the RAS to the Ang 2/AT1R (activator) axis, promoting the progression of the infection. Improved levels of ACE2 change the balance to the Ang (1 to 7)/MasR axis (inhibitor) via rhACE2, ACE2 activators, resulting in defence from viral infection. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 169 Ahmed A., Suleiman; et al. The SNPs of ACE2 and COVID-19 Figure 2 Way of the entrance of the SARS-CoV-2 to host cell. 7 The protein S of the virus attaches to the human ACE2 receptor, when receptor-binding domain, human proteases triggered. It makes its way into the cell via the endosomal path. Then, viral RNA is translation and cytoplasm of ORF1a and considered to generate pp1a in additional pp1ab polyproteins. RTC proteases cleave these proteins, which promote the expansion of full length (−) RNA copies and RNA replicas and function as for full length (+) RNA genomes templates. A collection sub-genomic RNAs formed by fragmented transcription, with frequent open reading frames, Only the nearest (5′ end) is translated in this case. After the synthesis of viral structural proteins, the nucleocaspids are assembled in the cytoplasm. After that, there’s endoplasmic reticulum and Golgi apparatus budding through the lumen of the intermediate compartment. This is accompanied by releasing virions from the infested cell-mediated by exocytosis. Figure 2 Way of the entrance of the SARS-CoV-2 to host cell. 7 The protein S of the virus attaches to the human ACE2 receptor, when receptor-binding domain, human proteases triggered. It makes its way into the cell via the endosomal path. Then, viral RNA is translation and cytoplasm of ORF1a and considered to generate pp1a in additional pp1ab polyproteins. RTC proteases cleave these proteins, which promote the expansion of full length (−) RNA copies and RNA replicas and function as for full length (+) RNA genomes templates. A collection sub-genomic RNAs formed by fragmented transcription, with frequent open reading frames, Only the nearest (5′ end) is translated in this case. After the synthesis of viral structural proteins, the nucleocaspids are assembled in the cytoplasm. After that, there’s endoplasmic reticulum and Golgi apparatus budding through the lumen of the intermediate compartment. INTRODUCTION This is accompanied by releasing virions from the infested cell-mediated by exocytosis. reported in the year 2000.16 This discovery gave the angiotensin 2 attention, a dynamic peptide often referred to as angiotensin-(1-8). This is the basic cause of facilitating events including increased vasoconstriction, pro-inflammatory action, pro-fibrosis, and stimula- tion of aldosterone secretion by binding to angiotensin 1 (AT1) receptor. ACE2 works by deactivating angiotensin 2 and then converting it to angiotensin.17 Similarly, this active peptide inhibits angiotensin 2’s activity. Moreover, aminopeptidases enzyme is shown to deactivate angiotensin 2, it regulates the conversion of angiotensin 2 into angiotensin 3, resulting in activities like with angiotensin 2 receptors and an affinity of 30 times greater than that of AT1 receptors,17 resulting in effects such as increased natriuresis Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 170 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. and bradykinin, besides a vasodilation.18 and bradykinin, besides a vasodilation.18 and bradykinin, besides a vasodilation.18 y These components form an integral part of the process of renin-angiotensin aldosterone, consisting of pathways for initialization and prevention. Here the forthcoming consists of the receptor pathway for angiotensin 2 or angiotensin 1 or ACE1 or aldosterone, while the latter consists of the receptor pathway for angiotensin (1-7) or ACE2 or Mas, where the preventer pathway act as a blocker for the action of angiotensin 2 in the way for the initia- tor. Furthermore, ACE2 has been discovered to interact with AT1 receptors, angiotensin 2 receptor blockers have targeted these receptors, which are mediated by angiotensin 2, are opposed to the actions caused by this receptor, thus occupying the angiotensin 2 interac- tion site. This in turn, stimulates angiotensin 2 liberation, this is accompanied by enhanced ACE2 enzyme expression in the body. As indicated by sex-disaggregated information incor- porated by worldwide scientists, there is a clear indication that coronavirus-related deaths with males appeared at a higher rate than females across 35 nations (Worldwide Health 50/50). For example, the extent of deaths among people adds up to·13.3\7.4 in Italy, 4.7\2.8 in China, 8.4\4.7 in Spain, 10.6\6.6 in The Netherlands), and 4.0\1.7 in Ireland. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 INTRODUCTION It is hypothesized that, for example, Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 171 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. by encouraging coronavirus binding, the 2nd X chromosome may shield women from lethal polymorphisms that make COVID-19 more violent in men. Certainly, in a current report, weaker results in elder COVID-19 patients were due to the existence of lower ACE-2 levels and subsequent upregulation of proinflammatory pathways of angiotensin II (Ang II) in the body, which may render patients more vulnerable to systemic ’deleterious’ Ang II effects.14 In almost a yin/yang phase, ACE and ACE2 are produce, Ang II and Ang-1-7 are connected to one other after there is a vice versa relationship in their quantity one increases another decrease.25 Viruses enter into host cells due to ACE2, however, over expression can defend against harm (by decreasing Ang II and forming Ang-1-7). And, ACE2 exhibits metalloproteinase 17 (ADAM17) can ”shed” ACE2 from endothelial cells, This causes the release of bioactive and catalytic ectodomains into the circulation. Therefore, the ACE/ACE2 ratio is changed in different tissues, membrane-bound soluble, and the role of ACE2 is complicated. For exam- ple, it has been suggested that by restricting its attachment to cellular ACE2.26 Coronavirus could be reduced by soluble ACE2. However, Sama and colleague showed that in patients with heart failure (HF), males are associated with higher ACE2 plasma levels.27 Neverthe- less, the authors agree that there is no proof that there is a connection between membrane- bound ACE2 levels and shedding enzymes in the two genders. In fact, with preserved and reduced ejection, HF contains a higher amount of soluble ACE2 ejection fraction.28 Also, the expression of ACE2 tends to be decreased in postmenopausal women.29 Stimulatingly, transgender men subjected to treatments show substantially high (ACE2) levels expression and a high amount of Sertoli cells communicating ACE2 in the testis. Estrogens and andro- gens are declining by the passage of time,30 this weakening is likely to lead to a decrease in ACE2 expression with ageing in both genders. INTRODUCTION Gender equality index finding revealed also that women are at a greater risk of infection than males due to multiple factors: women commute via public transport, do grocery shopping, and sometimes dominate many professions Epidemiology studies revealed different gender and age have different susceptibility to contagion with SARS-CoV-2 with males and older age being the most inflicted.19 The implication of associated disease risk genes involved in the susceptibility of COVID-19 such as the ACE2 has recently received good attention due to its role in the acute injury of lungs.20 The genetic variants of ACE2 showed to be correlated with mixing angiotensin-(1-7) stages in females suffering from high blood pressure.21 ACE2 was made to work as a SARS-CoV-2 receptor. The gene ACE2 showed effective genetic polymorphisms among a different population around the globe which may influence the susceptibility to infection and/or disease progression to COVID-19.20 In this regard, this study sought to explore whether the genetic polymorphism in the ACE2 gene, particularly rs2106809 and rs2074192 would explain the genetic differences between males and females toward infection with SARS-CoV-2 in various parts of the world. The sex variations can be explained by multiple X-linked genes. fAmongst the main savouries of the lethality of the virus are cardiovascular comorbidities. The number of non-genetic, sex-independent fac- tors to alter vulnerability and mortality is enormous, with many others consisting on gender and cultural habits from various countries, should be considered. There are a few women dying, (young and elderly) than males (age-fellow). Actually, a series of possible methods can enlighten that why women are less susceptible toward serious COVID-19 infections. This is because the involvement of two factors including the transmembrane protease ser- ine 2 and ACE2, may be considered first of all.22 Although the receptor for the S protein of coronavirus is ACE2. The organs that are Although the receptor for the S protein of coronavirus is ACE2. The organs that are mainly targeted by SAR-CoV-2 contain ACE2. ACE2 has been suggested as a modulator of SARS-CoV-2 exposure in both sexes.23 The location of ACE2 is the X chromosome and in sites commonly escaping the inactivation of one X chromosome.24 It is also possible that this plays a significant role in women’s defence system. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 INTRODUCTION It is not so far clear whether the deadliness of SARS-CoV-2 is primarily due to the access and duplication of viruses or to an exaggerated inflammatory response.36 Numerous additional genes linked to X and Y can also explain gender differences.37 X and Y chromosome-encoded immune regulatory genes can clarify inferior virus-related loads and inflammation to decrease in women as compared to men.38 inferior virus related loads and inflammation to decrease in women as compared to men. The two X chromosomes control the immune system even though one of them is inactive. As well as moderating other proteins, including CD40L, CXCR3, and TLR8, the X chromo- some controls the immune system. These can be high-regulated in females and the response to both virus-related contagions and vaccines can be calculated. To recognize a precise gene name describing SARS-CoV-2 contagion differentially expressed genes (DEGs) net- work was developed.39 In addition, in modulating the intensity of COVID-19, gender dif- ferences in immune response, strong-minded by genetic factors, and hormones,37 can play a significant role. The number of CD4 + T cells also varies between genders, with women with a stronger immune response being higher.38 Lastly, non-genetic, gender-independent features can change vulnerability and death is huge, numerous additional factors, including gender and cultural behaviours, are likely to be considered in different countries. For exam- ple, there was a high in females because of social and religious activities (Report on the Epi- demiological Characteristics of Coronavirus Disease 2019. Additional gender-related cus- tom and an independent risk factor for worsening COVID-19 could be smoking. Smoking ratio and function ACE/ACE2 is not clear.ACE2 increase and enzyme activity decrease have been identified in numerous readings.40 We may risk that high levels of (ACE2) may enable entry of most viruses, while downregulation of ACE2 may clarify the severity of COVID-19 in smokers, at least in part.41 This study attempted to provide an answer for the variable infection and mortality rates of the SARS-CoV-2 between males and females worldwide INTRODUCTION It is not so far clear whether the deadliness of SARS-CoV-2 is primarily due to the access and duplication of viruses or to an exaggerated inflammatory response.36 Numerous additional genes linked to X and Y can also explain gender differences.37 X and Y chromosome-encoded immune regulatory genes can clarify inferior virus-related loads and inflammation to decrease in women as compared to men.38 The two X chromosomes control the immune system even though one of them is inactive. As well as moderating other proteins, including CD40L, CXCR3, and TLR8, the X chromo- some controls the immune system. These can be high-regulated in females and the response to both virus-related contagions and vaccines can be calculated. To recognize a precise gene name describing SARS-CoV-2 contagion differentially expressed genes (DEGs) net- work was developed.39 In addition, in modulating the intensity of COVID-19, gender dif- ferences in immune response, strong-minded by genetic factors, and hormones,37 can play a significant role. The number of CD4 + T cells also varies between genders, with women with a stronger immune response being higher.38 Lastly, non-genetic, gender-independent features can change vulnerability and death is huge, numerous additional factors, including gender and cultural behaviours, are likely to be considered in different countries. For exam- ple, there was a high in females because of social and religious activities (Report on the Epi- demiological Characteristics of Coronavirus Disease 2019. Additional gender-related cus- tom and an independent risk factor for worsening COVID-19 could be smoking. Smoking ratio and function ACE/ACE2 is not clear.ACE2 increase and enzyme activity decrease have been identified in numerous readings.40 We may risk that high levels of (ACE2) may enable entry of most viruses, while downregulation of ACE2 may clarify the severity of COVID-19 in smokers, at least in part.41 This study attempted to provide an answer for the variable infection and mortality rates of the SARS-CoV-2 between males and females worldwide by estrogens across the body, the ratio of ACE/ACE2 can transfer more in women than in men to the ACE2/Ang 1 to 7/MAS receptor axis. This may explain why women are shielded from the outcome of extreme COVID-19. We must understand, however, that there are variations in the ACE/ACE2 ratio that are tissue- and organ-specific, which can also be affected by exercise and medical conditions. INTRODUCTION It is not so far clear whether the deadliness of SARS-CoV-2 is primarily due to the access and duplication of viruses or to an exaggerated inflammatory response.36 Numerous additional genes linked to X and Y can also explain gender differences.37 X and Y chromosome-encoded immune regulatory genes can clarify inferior virus-related loads and inflammation to decrease in women as compared to men.38 The two X chromosomes control the immune system even though one of them is inactive. As well as moderating other proteins, including CD40L, CXCR3, and TLR8, the X chromo- some controls the immune system. These can be high-regulated in females and the response to both virus-related contagions and vaccines can be calculated. To recognize a precise gene name describing SARS-CoV-2 contagion differentially expressed genes (DEGs) net- work was developed.39 In addition, in modulating the intensity of COVID-19, gender dif- ferences in immune response, strong-minded by genetic factors, and hormones,37 can play a significant role. The number of CD4 + T cells also varies between genders, with women with a stronger immune response being higher.38 Lastly, non-genetic, gender-independent features can change vulnerability and death is huge, numerous additional factors, including gender and cultural behaviours, are likely to be considered in different countries. For exam- ple, there was a high in females because of social and religious activities (Report on the Epi- demiological Characteristics of Coronavirus Disease 2019. Additional gender-related cus- tom and an independent risk factor for worsening COVID-19 could be smoking. Smoking ratio and function ACE/ACE2 is not clear.ACE2 increase and enzyme activity decrease have been identified in numerous readings.40 We may risk that high levels of (ACE2) may enable entry of most viruses, while downregulation of ACE2 may clarify the severity of COVID-19 in smokers, at least in part.41 This study attempted to provide an answer for the variable infection and mortality rates of the SARS-CoV-2 between males and females worldwide by estrogens across the body, the ratio of ACE/ACE2 can transfer more in women than in men to the ACE2/Ang 1 to 7/MAS receptor axis. This may explain why women are shielded from the outcome of extreme COVID-19. We must understand, however, that there are variations in the ACE/ACE2 ratio that are tissue- and organ-specific, which can also be affected by exercise and medical conditions. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 INTRODUCTION The study of 2017 showed there are no differences in the two genders in the activity of serum of ACE and ACE2, although lower serum activity of ACE2 was observed in newer relative to older women.31 Overall, differ- ences in ACE and ACE2 expression can tend to specific to organs and age-dependent in both genders, in animals32 and humans with a less obvious function in soluble ACE226. It is a matter of investigation whether the level of ACE2 in the lungs are linked to the vulnerabil- ity and harshness of COVID-19.33 It was stated in a preprint red-top that monomers may have advanced ACE2 expression in the lungs compared to women,34 with potentially sig- nificant implications for COVID-19 infections, as the SARS-CoV-2 enter via respirational tract. However, enlarged permeability of capillary, clotting, fibrosis, and death of alveo- lar cells observed in both SARS and COVID-19.Explained by polymorphisms in ACE and ACE2 genes.35 Lung damage and respiratory failure can be explained by these effects. The role of ACE2 in COVID-19 is not completely clear but most evidence suggests that it may be advantageous to have a low membrane-bound ACE/ACE2 ratio. Certainly, ACE may be pro-inflammatory and pro-oxidant, whereas antioxidant and anti-inflammatory effects can be mediated by ACE2. In HF, soluble ACE2 is higher; it is not yet clear whether this is defensive or harmful or is just an epiphenomenon. Nevertheless, by controlling the activ- ity of the ADAM17 enzyme, inhibition of ACE2 shedding has been advised as a possible beneficial solution for heart failure.28 As the ACE2 expression on chromosome X affected Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 172 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. by estrogens across the body, the ratio of ACE/ACE2 can transfer more in women than in men to the ACE2/Ang 1 to 7/MAS receptor axis. This may explain why women are shielded from the outcome of extreme COVID-19. We must understand, however, that there are variations in the ACE/ACE2 ratio that are tissue- and organ-specific, which can also be affected by exercise and medical conditions. Quality assessment The quality of the included studies was checked independently by two authors (AAS and MFD) using a set of pre-defined criteria such as quality of research design, and completeness of extractable information. MATERIALS AND METHODS Literature search and strategy A systematic literature search was conducted on September 2020 in reputed literature databases and search engines (PubMed, Google Scholar, ScienceDirect, and Nature) by applying these keywords: (ACE), (ACE2), (COVID-19), (Polymorphism), (SNP), we con- ducted research and extracted the data that was relevant to research topic. A total of 150 research paper were retrieved from all the above-mentioned databases. From all these 150 publications, 30 research paper were closely related to our research topic after reading the paper’s title and abstract. It is not yet known whether this differential rate of susceptibility between genders to infection/mortality of SARS-CoV-2 is attributed to the genetic variants of the main host Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 173 Ahmed A., Suleiman; et al. The SNPs of ACE2 and COVID-19 receptor ACE2 in various ethnic populations. Therefore, two main genetic polymorphisms (rs2106809 and rs2074192) were screened and analyzed using previously published papers. All reviews, reports, opinions, commentaries, and non-full length research papers were excluded. Data extraction and quality evaluation The screening process was conducted independently by (title, abstract, full-text and data extraction) by three authors (AAS, TAR, and AMA), and in the event of a discrepancy between the three authors, the MFD is referred to as a co-creator of the consensus. The authors reviewed the full text of the article for further information and clarification when there is insufficient data. Data from eligible studies were extracted and summarized in an excel spreadsheet. The following information was extracted for each of the included studies: district name, study design, study area/city, study period, study design, sample types, study population, number of study participants. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 RESULTS AND DISCUSSION A total of 150 items were collected from all the databases mentioned previously. From these publications, 30 papers closely related to the topic of our study were selected. It was found that 6 researches2,5,6,39,42,43 match the objective of our study. The rest of the researches were only neglected for several reasons, including the small number of study participants, lack of focus on race, and non-full length articles. By analyzing public data, it was found that the two SNPs (rs2106809 and rs2074192) were expressed at variable proportions among different ethnic population around the world11. A summary of these findings as outlined in Table 1. The prevalent genotypes of rs2074192 among Caucasian males were almost dominated by TT mutant genotypes whereas CC or CT genotypes were common in females. On the other hand, the genotype trend was changed in the Asian female population as CC or CT (no mutant genotypes were observed) with no considerable difference among males than those observed with Caucasian. A similar pattern for the rs2106809 genotypes particularly among females in the Middle East and India. Taken together for both genetic polymorphisms, it appeared that males had a mutant genotype Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 174 Ahmed A., Suleiman; et al. The SNPs of ACE2 and COVID-19 compared to either wild or heterozygous mutant in females. Considering the limitation of sample size number, these data may suggest that the mutant genotype among males could contribute to the severity of infection in males compared to females around the world but the absence of such variants in females may explain the low infectivity/mortality rate seen among them. ABBREVIATIONS ACE2, angiotensin-converting enzyme; ARDS, acute respiratory distress syndrome; CDC, Disease Control and Prevention; HF, heart failure; NA, not available; RAAS, renin-angiotensin-aldosterone system; SARS, severe acute respiratory syndrome; ssRNA, single-stranded ribonucleic acid. CONCLUSIONS Many factors may affect COVID-19 infection and recovery such as immune response, smoking, and genetic alteration in many genes including ACE2. Females are less affected as compared to males because ACE2 gene is located on X chromosome and females have two copies of ACE2. This research is all about ACE2 and its impact on the gender suscep- tibility to infection and rate of recovery COVID-19. Patient body parts e.g. lungs, small intestine, stomach, liver blood vessels, bone marrow, skin, oral, nasal mucosa and kid- ney are most affected due to the presence of ACE2 which is the receptor of COVID-19. RAAS has been made in the liver and split into renin for angiotensin1 development which activated angiotensin 2 by ACE. ACE2 counters vasoconstrictions and pro-inflammatory activities which are opposed by ACE result. Elder patients are more vulnerable than chil- dren to COVID-19. Epidemiology studies showed different gender and age have dif- ferent susceptibility to contagion with SARS-CoV-2. ACE2 exhibited a high degree of genetic polymorphisms among a different population around the world. Both rs2106809 and rs2074192 would explain the genetic differences between males and females toward COVID-19. TMPRSS2 splits the S-protein preferring virus attachment to the cell mem- brane. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 Data availability Author is only responsible for the data in this script which may not reflect the opinion or policy of the journal. Ethical approvals Not applicable for systematic reviews. Funding resources This work didn’t receive any fund. Conflict of interest Not declared. Authors’ contributions All the author looks on the original idea and contributed to data collection, analysis, and interruptions. ACKNOWLEDGEMENTS The authors would like to express deep thanks to the University of Anbar, College of Science, Department of Biotechnology for their support in access for articles. The authors would like to express deep thanks to the University of Anba Department of Biotechnology for their support in access for articles. 175 Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 The SNPs of ACE2 and COVID-19 Ahmed A., Suleiman; et al. Table 1 Genotype distribution of ACE2 (rs2106809 and rs2074192) genetic polymorphisms among the different world population SNP Reference Genotype Most frequent genotype Country Race Wild type Hetero Homo mutant M F rs2106809 2 CC (M: 35.1%, F: 21.7%) CT (M: NA, F: 56.5%) TT (M: 64%, F: 50%) TT CT Egypt Middle Eastern 42 CC (M: NA, F: 85%) CT (M: NA, F: 10%) TT (M: NA, F: 5%) NA CC India Asia rs2074192 5 CC (M: 57.1%, F: 34%) CT (M: NA, F: 44.7%) TT (M: 42.9%, F: 21.4%) CC/TT CT Australia Caucasian 6 CC CT TT (M: 24.7%, F: 43.9%) NA TT Canada Caucasian 39 CC CT TT (M: 47%, F: 46.8%) TT TT Canada Caucasian 43 CC (M: NA, F: 38.7%) CT (M: NA, F: 41.1%) TT (M: NA, F: 19.8%) NA CC/CT China Asia Table 1 Genotype distribution of ACE2 (rs2106809 and rs2074192) genetic polymorphisms among the different world popu SNP Reference Genotype Most frequent genotype Wild type Hetero Homo mutant M F rs2106809 2 CC (M: 35.1%, F: 21.7%) CT (M: NA, F: 56.5%) TT (M: 64%, F: 50%) TT CT 42 CC (M: NA, F: 85%) CT (M: NA, F: 10%) TT (M: NA, F: 5%) NA CC rs2074192 5 CC (M: 57.1%, F: 34%) CT (M: NA, F: 44.7%) TT (M: 42.9%, F: 21.4%) CC/TT CT 6 CC CT TT (M: 24.7%, F: 43.9%) NA TT 39 CC CT TT (M: 47%, F: 46.8%) TT TT 43 CC (M: NA, F: 38.7%) CT (M: NA, F: 41.1%) TT (M: NA, F: 19.8%) NA CC/CT F, female; M, male. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 176 Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 176 Ahmed A., Suleiman; et al. The SNPs of ACE2 and COVID-19 DECLARATIONS DECLARATIONS Authors’ contributions All the author looks on the original idea and contributed to data collection, analysis, and interruptions. Baghdad Journal of Biochemistry and Applied Biological Sciences, 2(03) | 2021 | https://doi.org/10.47419/bjbabs.v2i03.53 REFERENCES 1. Jin JM, Bai P, He W. Gender Differences in Patients With COVID-19: Focus on Severity and Mortality. Front Public Heal. 2020;8:1–6. Available from: 10.3389/ fpubh.2020.00152. 1. Jin JM, Bai P, He W. Gender Differences in Patients With COVID-19: Focus on Severity and Mortality. Front Public Heal. 2020;8:1–6. Available from: 10.3389/ fpubh.2020.00152. 2. 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Utilization of RFID data to evaluate characteristics of private car commuters in Middle East Technical University campus
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Abstract Analyzing travel behavior of Middle East Technical University (METU) campus users via traditional survey approach requires great effort. However, using Radio Frequency IDentification (RFID) system installed at all the campus entry gates provided a cheaper and an effective approach to determine basic characteristics of the campus private car commuters. The RFID data combined with traveler details enabled the study of the arrival and departure car-based commute behavior of academic personnel, administrative personnel and students, separately. The results revealed that campus car-based travel demand is mainly active between 07:00 to 22:00. While the majority of the private car commuters arrive during 08:00-09:00, the evening peak is distributed over a much longer period from 15:00 to 19:00. Administrative personnel have sharper evening departures between 17:00-18:00, while academic ones show a more scattered pattern lasting longer. Car- traveler students mostly arrive later during 09:00-10:00 and start leaving the campus as early as 15:00 lasting until late evenings. Stay time of vehicles on campus revealed that 43% of all trips to campus lasted less than 15 minutes, especially during morning and evening peaks, suggesting that a high number of RFID card holders pass through the campus, possibly for pick-ups or drop-offs. A small reverse commute pattern occurred due to the trips generated by family members of those living in on-campus housing units. Orta Doğu Teknik Üniversitesi (ODTÜ) kampüs kullanıcılarının seyahat davranışını geleneksel anket yaklaşımı ile analiz etmek büyük çaba gerektirmektedir. Ancak, tüm kampüs giriş kapılarında kurulu radyo frekansı ile tanımlama sistemi (RFID) sistemi, yerleşkedeki düzenli özel araç kullanıcılarının temel özelliklerinin belirlemek için daha ucuz ve etkin bir yaklaşımın geliştirilmesine imkan sağlamaktadır. RFID verisinin kullanıcı bilgileriyle birlikte incelenmesi, akademik personel, idari personel ve öğrencilerin yolculuklardaki geliş ve gidiş davranışlarının ayrı ayrı çalışılmasına olanak sağlamıştır. Sonuçlar, özel araç tabanlı yolculuk talebinin 07.00-22.00 arasında aktif olduğu göstermektedir. Düzenli yolculuk yapanların çoğunluğu 08.00-09.00 arasında yerleşkeye giriş yaparken, akşam zirve saati 15.00’dan 19.00’a kadar daha uzun periyoda dağılmıştır. İdari personel akşamları belirgin bir şekilde 17.00-18.00 arasında çıkarken akademik personel araç çıkışı daha dağınık ve uzun süren bir profil göstermektedir. Özel araç kullanan öğrenciler çoğunlukla 09.00-10.00 saatleri arasında gelmekte ve çıkışları 15.00’dan itibaren gece geç saatlere kadar sürmektedir. Araçların yerleşke içinde kalma süreleri, özellikle sabah ve akşam zirve saatler boyunca, %43’ünün 15 dakikadan daha az kaldığını göstermektedir; bu da birçok taşıt pulu sahibinin büyük olasılıkla eş/çocuk alma/bırakma için yerleşkeden geçtiğini düşündürmektedir. Abstract Zirve saatlerde tespit edilen ters yönlü düzenli bir yolculuk akımı, kampüs içinde yaşayanların aile bireyleri tarafından gerçekleştirilen yolculuklardan kaynaklanmaktadır. Keywords: Commute travel, Travel demand, Travel behavior Anahtar kelimeler: Düzenli yolculuklar, Yolculuk talebi, Yolculuk davranışı Yolculuk davranışı (a nursery, an elementary and a high school) for the children of campus workers, which contribute to the commute travel behavior, as well. (a nursery, an elementary and a high school) for the children of campus workers, which contribute to the commute travel behavior, as well. doi: 10.5505/pajes.2015.68725 Research Article/Araştırma Makalesi doi: 10.5505/pajes.2015.68725 Research Article/Araştırma Makalesi Received/Geliş Tarihi: 16.10.2014, Accepted/Kabul Tarihi: 28.01.2015 * Corresponding author/Yazışılan Yazar Öz Orta Doğu Teknik Üniversitesi yerleşkesindeki düzenli özel araç kullananların karakteristiklerinin değerlendirilmesinde RFID verisi kullanımı Oruç ALTINTAŞI1*, Hediye TÜYDEŞ YAMAN1 1Department of Civil Engineering, Faculty of Engineering, Middle East Technical University, Ankara, Turkey. aoruc@metu.edu.tr, htuydes@metu.edu.tr 1 Introduction Big university campuses may generate a travel demand like a small city, where a strong commute behavior is inevitable. In the case of Middle East Technical University (METU) campus in Ankara, Turkey, we see a total population over 30000 people, and 21000 of them are students: omitting the approximately 6000 students living in dormitories, 15000 students regularly commute; while only 2000 of them hold stickers for private car usage, the remaining mainly use public transit and paratransit services in accessing to the campus. Out of 4300 people who work as faculty and administrative personnel at METU, only 350 of them live in on-campus housing units; among the non- campus dwellers, a significant portion of the administrative personnel use commute buses provided by the university, and most of the academics use private car. The research and development park on campus, called Technopolis, has a population of 3000, and is another region triggering commute travel. Besides, the campus also has K-12 educational units METU campus originally developed outside the city limits at a distance of approximately 13 km to the city center. Currently, it is surrounded by the city and access is controlled at 3 main gates (Gate A1, A4 and A7) as shown in Figure 1. The campus is accessible by bus and minibus services operated by the municipality or privately, departing from the city center. However, private car is an ever-increasing commute mode. In order to monitor and control the campus road network usage, Radio Frequency IDentification (RFID) system is installed at the main entry gates; RFID stickers are granted to faculty and administrative personnel directly, and to students in limited number. Additionally, RFID gate is in use to control the traffic from Technopolis to campus (see Figure 1). The determination of the travel behavior of METU campus users requires traditional survey approaches, which would 171 Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016 O. Altıntaşı, H. Tüydeş Yaman Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016 O. Altıntaşı, H. Tüydeş Yaman Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016 O. Altıntaşı, H. Tüydeş Yaman riding with a friend or on a bus. Another study conducted by Gilhooly and Low [5] investigated the primary school travel behavior in Midlothian, Scotland, via survey of 1008 primary school children and 776 parents. They stated that travel behavior was significantly influenced by age and the distance from school. 1 Introduction As an evaluation of parking management on Beijing University of Aeronautics and Astronautics, China, Huayan et al. [6] obtained inflow and outflow of vehicles during the day and calculated the average parking stay time of vehicles and drew conclusions about the travel behavior of university travelers. need a big amount of resources. However, the integration of a series of data from different campus data sources (RFID and video recordings) provided a cheaper and an effective approach to determine the basic characteristics of the campus commute behavior, which is the main focus of this study. The layout of this paper is as follows: After a brief review of literature on commute travel studies in university campuses in Section 2, the RFID data analysis approach is summarized in Section 3, followed by the major commute behavior findings summarized in Section 4 and followed by the discussion and conclusions in the last section. There has been no campus travel study that took advantage of data from new technologies, such as RFID, mostly because, such data does not include traditional travel demand data; but, it is mainly being used to develop parking management policies for university campuses. It enables identification of the vehicle movements, records the vehicle data, analyzes the traffic pattern different time of a day, manages staffing peak hour traffic and relieves congestion [7]. Arizona State University, in USA, installed RFID system to all parking lots to implement parking management strategies, such as more parking charges for students [8]. Wayne State University, in USA, installed RFID system to the campus parking lot locations to implement parking charges for different commute travelers [9]. University of Wisconsin, in Madison, in USA, RFID system was installed to the gate activation in parking ramps to investigate the environmental impact the RFID gate project has on starting/stopping at the gate entrance. The results showed a significant savings in fuel due to reduction in start, stop and idle time [10]. Furthermore, Portland State University, in USA, RFID system was used to track their employees who sign up for a bike commute incentives program [11]. 4 METU commute traveler characteristics To study the commute characteristics, a whole week RFID data from Nov 21-25, 2011 was processed. To give an idea of the scale, the statistics from Wednesday of the control week is summarized in Table 2. The analysis result showed that 91% of the vehicles tracked by RFID systems were private cars (the remaining was the bus, taxi and minibuses serving the campus). It shows that the majority of the motorized vehicle demand in the METU campus was due to the private car access. To validate the results from RFID data, video recordings of the security cameras at the entry gates were processed for another Wednesday, which showed that there were almost 3000 additional vehicle entries, some of which can be due to daily fluctuations but the majority is due to the vehicles visiting the campus. In the video recordings, the difference between the total entries (15280) and exits (14828) was very small, suggesting that the majority of the vehicles did not stay overnight. However, this difference in the RFID data was 5074 movements due to significantly lower number of recorded exits. Further calculation of the entry-to-exit ratios for each gate from RFID and video data showed that the majority of this difference was caused by a reading error in the exit lanes of the gate A1 (see Table 2). Exit behavior in this study is underestimated; however, this systematic error happened throughout the whole observation day and affects all the cardholder types similarly. Thus, it does not create any bias on the time of the day or the cardholder type analysis. In the current study, the existence of RFID control system for private car users at all campus access gates made it possible to capture the mobility of all the car-based commuters. As the RIFD sticker includes the license plate number, sticker type, and the entry and exit location (see Table 1), it was possible to obtain campus entry and exit information for all the movements of different commuter types (academic and administrative personnel, students, Technopolis workers, and parents of elementary-high school children). Tabulation of the entry and exit movements hourly (or in 15-minute intervals, if desired) easily provides the daily campus profiles. Further processing the RFID data for every unique license plate enabled the detection of all the recorded movements of the vehicles, leading to matching of entry-exit pattern that would define a “trip” (see Table 1). 2 Literature review The analysis of the travel behavior of campus users has been the focus of many studies so far. Zhou [1] studied the commute behaviors of university students in Los Angeles. He stated that improvement of multimodal transportation system and discounts in public transit may greatly change the travel behavior of students. Miralles-Guasch and Domene [2] determined the travel pattern and transportation challenges of university travelers in Barcelona through an online survey, where the lack of adequate infrastructure, the marginal role of walking and cycling and longer time involved in using public transport were detected as the main barriers to shift from private car to non-motorized modes. Akar et al. [3] also examined the travel patterns of the campus community at Ohio State University. The results demonstrated that students were more likely to travel by alternative modes compared to faculty members. Limanond et al. [4] studied the travel behavior of 130 students who live on campus in a rural university, and found that males and females had similar travel pattern; students owning a car preferred driving and non-car owners preferred Figure 1: The location and the layout of METU Campus. Figure 1: The location and the layout of METU Campus. 172 Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016 O. Altıntaşı, H. Tüydeş Yaman Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016 O. Altıntaşı, H. Tüydeş Yaman 3 Utilization of RFID data to evaluate commute behavior endanger the study of basic characteristics of the campus commute behaviors. 3 RFID data would have some reliability issues, as well. Due to some reading errors, it is possible to miss an entry or an exit of a vehicle, which would leave unmatched recording. However, an unmatched trip can be due to an over-night or late stay in the campus, or leaving the car in the campus and having a return trip with another mode for some reason. Similarly, an exit with a missing entry could indicate a car trip from a previous day. The RFID data can be further analyzed to reveal travel pattern behavior, if supported with additional counts and/or data processing. Nevertheless, the location of the RFID readers in a region would inherently shape the capability and limits of such evaluations; if a region has limited entry points which are fully RFID controlled creating a closed network like METU campus, it would provide a very rich data that could portray campus access behaviors of the commuters, but it would not reveal much about their destinations or route choice within the campus. If not, RFID data would reveal information about the behavior of users enrolled in the system only, which means it would be a sample of the whole commuter; in such cases, it is important to consider the enrollment conditions, to get an idea about the randomness of the sampling. While evaluating the benefits of RFID data usage, it should be kept in mind that traditional commute behavior studies rely on sampling in their surveys, which may include some sources of bias, themselves. But, RFID data-based evaluations would present “revealed” behaviors as opposed to “stated” ones in the survey-based approaches. Thus, it is impossible to capture everything about commute trips via either survey-based or RFID-based approaches, and it is important to understand the limitations and sources of bias in the natures of the different approaches. 4 METU commute traveler characteristics Even though it was not needed in the campus daily profile calculation, the minor gate controlling the access to/from Technopolis is also considered as a gate in the trip detections so that the trips destined to and originating from Technopolis region could be identified separately. Moreover, calculation of a “stay time” for a trip, which is simply the difference of the exit and entry times, sheds more light on the commuter behavior of the campus user. As the trips and their stay times can be time-stamped, it is possible to see the change in the stay times in a day. 4.3 Stay times of private car commuters The stay time analysis results in Table 3 of the METU campus users showed that in the overall evaluations, 42.8% of the trips by the RFID cardholders were “short stay”, that is less than 15 minutes. A second major traveler group stayed between 1-5 hours (22.9% in a day), which is more like a half workday time. Only 16.1% had long stays of 5-10 hours suggesting that they may be academic or administrative personnel. The low percentage of the long stays in spite of the large number of personnel may be due to the fact that some of the personnel had multiple trips in and out of the campus. • Administrative personnel showed a sharper morning arrival (see Figure 3) and evening departure times (see Figure 4), parallel to definitions of their work hours between 08:30-17:30, which is expected as their work schedules are more definite. • Academic personnel had also a sharp morning arrival peak. A major exit demand was observed during the evening hours, which started from 15:00 and continued until 21:00. The small peak in the exit profile during 08:00-09:00, may very well be the private car users of families of academic personnel residing on campus creating the reverse commute. During the early morning hours (07:00 to 10:00), more than 40 % of the entering vehicles stayed for a short time, 20-30% stayed almost the whole work day (5-10 hours), while another major group stayed half a day (1-5hours). The further investigation of the RFID cardholders among these drivers revealed that the major short stays were performed by Technopolis workers (46.0%). While academic and students had almost same ratio (17.5%), the parents of the children at the elementary and high school constituted 11.7%. • The entry profile of student travelers showed that travel to the campus started to increase after 08:00; a delayed morning peak was seen around 09:00- 10:00 (see Figure 3). After, entries gradually decrease during the day. The exits of students started from 08:00 and gradually increased throughout the day (see Figure 4). After that, they had again scattered evening peak that start from as early as 15:00 and continue until 20:00. The short stay ratios were predominant in the evening hours (between 17:00-20:00), exceeding 60%. The traveler distributions in these short stays were: 35.7% for Technopolis workers, 28.1% for academics, 24.0% for students and 8.2% for administrative personnel. 4.1 Campus daily travel profile The RFID gate data can simply be used to derive the daily demand profile of METU campus and to detect the peak hours. Daily analyses revealed very small variations between the weekdays in METU campus [12], thus, the average entry and exit profiles is used to illustrate the travel demand profile as shown in Figure 2. Both entry and exit profiles support the existence of the urban commute behavior among the METU campus travelers, where majority lived in the city and arrived METU as their workplace. Only a small reverse commute pattern was observed due to the on-campus housing population. The characteristics of the daily commute profile were as follows: Normally, trips detected from an RFID data processing should be regarded as “commute trips” directly; the purpose of the trips must be checked. However, in the case of METU campus RFID data study, it should be noted that METU grants RFID data only to campus commuters, which dismisses any concern on the matter. Secondly, although the majority of the commute trips are “work” trips, which are expected to happen in the morning and in the evening, it is not possible to generalize it for every campus user, as some would be working the late evening and night shifts in different units. Thirdly, it is not possible to know the true origin or destination of these trips from RFID data, yet, the lack of such information does not necessarily  A major entry demand was observed between 07:00- 09:00; during which hourly arrivals reach up to 3000. Then, the campus entry demand gradually decreased until 11:00; after a small peak around 12:00, entry demand was almost constant at a rate of 1000 vehicles/hour until 18:00, after which it diminished significantly till midnight.  The exit profile of METU campus showed little activity until 07:00, after which the number of exiting vehicles increased creating the first peak between 08:00-09:00 with 1500 exits. This may be due to i) 173 Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016 O. Altıntaşı, H. Tüydeş Yaman commuting from the family members of personnel residing in the on-campus housing units, and ii) car users doing quick drop-off for a campus user. The second peak was seen at noon (12:00-13:00) with 1200 exits. The majority of the exit demand was scattered over time, starting from 15:00 to 19:00, which revealed the highest volume (over 2300) during 17:00-18:00. 4.2 Commute behavior of different campus travelers Availability of the cardholder information in the RFID data revealed more about the commute behaviors of the different campus users. The extensive analysis of the commute behaviors of the academic and administrative personnel and students was provided in [12], which can be summarized as follows, for the sake of continuity: 4.1 Campus daily travel profile After 19:00, the number of exiting vehicles gradually decreased. • Private car usage among Technopolis workers was a major component of the campus car usage. Their movements suggested a much clearer “work” trip purpose with sharper arrival and departure time windows. Their entries started as early as 06:00 and continue until 09:00, after which it dropped significantly (see Figure 3). The second peak during lunch time definitely indicated a strong “lunch trip” demand which showed a typical urban travel demand profile. Lastly, parents of children were active only at 08:00-09:00 and 15:00-16:00. • Private car usage among Technopolis workers was a major component of the campus car usage. Their movements suggested a much clearer “work” trip purpose with sharper arrival and departure time windows. Their entries started as early as 06:00 and continue until 09:00, after which it dropped significantly (see Figure 3). The second peak during lunch time definitely indicated a strong “lunch trip” demand which showed a typical urban travel demand profile. Lastly, parents of children were active only at 08:00-09:00 and 15:00-16:00. 4.3 Stay times of private car commuters Only 4.2% of the total short trips were performed by the parents of the children, which is proportional to the number of stickers provided. p p p Table 1: Vehicle movements as a result of RFID gate data processing. License Plate Sticker Type Time 1 Gate Entry/Exit Time 2 Gate Entry/Exit 01HJ361 Academic 07:54 A1 Entry 12:00 A4 Exit 06AC651 Student 15:05 A4 Entry 19:49 A4 Exit Table 2: METU campus vehicle activity statistics. RFID data Nov 23, 2011 (Wed) Video data Oct 19, 2011 (Wed) All Vehicles Private Cars All Vehicles Private Cars Total Entry 12194 11471 15280 14363 Exit 7120 6694 14828 13938 Entry-Exit 5074 4777 452 425 All Vehicles Gate # Ratio # Ratio A1 Entry 5354 3.61 5746 0.94 Exit 1482 6066 A4 Entry 4116 1.16 5839 1.01 Exit 3562 5777 A7 Entry 2724 1.31 3695 1.24 Exit 2076 2985 Table 1: Vehicle movements as a result of RFID gate data processing. 174 Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016 O. Altıntaşı, H. Tüydeş Yaman Figure 2: Average daily travel profile of METU campus on 21-25 November 2011. Figure 2: Average daily travel profile of METU campus on 21-25 November 2011. Figure 2: Average daily travel profile of METU campus on 21-25 November 2011. Figure 2: Average daily travel profile of METU campus on 21-25 November 2011. Figure 3: Entry profiles of major traveler groups in a day. Figure 4: Exit profiles of major traveler groups in a day. Figure 3: Entry profiles of major traveler groups in a day. Figure 3: Entry profiles of major traveler groups in a day. Figure 4: Exit profiles of major traveler groups in a day. 175 Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016 O. Altıntaşı, H. Tüydeş Yaman Table 3: Campus stay time of vehicles by entry time. 4.3 Stay times of private car commuters Entry Time # of Trips Stay Time (Nov 23, 2011) (% vehicles) 0-15 min 15-30 min 30 min-1h 1h-5h 5h-10h 10h > 7-8 177 44.1 0.6 5.6 14.7 21.5 13.6 8-9 1210 47.4 6.2 2.5 11.7 26.6 5.7 9-10 821 39.0 3.3 3.7 16.3 31.8 6.0 10-11 414 21.7 5.6 6.5 30.2 32.1 3.9 11-12 319 26.6 8.2 9.4 27.3 27.6 0.9 12-13 394 27.2 5.3 7.6 41.4 18.0 0.5 13-14 465 37.4 5.6 6.5 39.8 10.8 --- 14-15 378 28.8 10.1 16.9 37.6 6.6 --- 15-16 415 38.3 18.6 13.0 26.7 3.4 --- 16-17 393 46.1 16.5 12.5 23.2 1.8 --- 17-18 494 62.3 12.8 5.3 18.6 1.0 --- 18-19 393 63.9 9.2 5.9 19.8 1.3 --- 19-20 212 54.7 11.8 12.7 20.8 --- --- 20-21 167 65.3 10.8 8.4 15.6 --- --- 21-22 92 60.9 12.0 19.6 7.6 --- --- Total 6344 42.8 8.4 7.3 22.9 16.1 2.6 *: Out of 12194 entries, there were a total 6344 trips with matched entry and exit times. Table 3: Campus stay time of vehicles by entry time. a good thing in terms of smaller demand for on-campus parking, if it is because of a pick-up/drop-off a campus user. But, smaller rates of longer stays (up to 4 or 8 hours) show that the current congestion on campus parking lots is due to the almost must private car usage to access to/within the campus, which can be improved by addressing campus commute needs of both students and personnel in a broader perspective. 5 Conclusions Despite the need for traditional survey studies in commute behavior studies, even for campuses, data collected from other systems can be beneficial to understand basics of mobility within the study area, and even in a very cost-effective way. For example, availability of RFID control for all the private car commuters at all the campus entry gates in the METU campus provided the daily travel profile of the campus. Furthermore, detection of a relatively small reverse peak hour brought up the issue of commuting of family members of academic personnel living on campus. The license plate and time stamp in the RFID data made it possible to detect over 6300 trips from approximately 12200 RFID entry records in a day, which makes almost a 50% sampling rate; this is higher than any sampling ratio aimed in a traditional survey. However, the lack of purpose for the trips identified from RFID data does not enable the identification of all components of commute behaviors clearly and creates some room for speculation. In the longer run, RFID data can be collected over a long period of time, such as an academic semester, using which differences across weekdays, or the effects of weather condition on commute behavior can be evaluated which may be the focus of future studies. Furthermore, the travel behavior of each individual commute traveler can be followed over a long time which provides to build more comprehensive campus transportation model for different commute travelers. Finally, installing the RFID system to all parking lots in METU campus enables to analyze the time dependent parking lot capacity analysis, to analyze campus travel time analysis and to develop parking management policies for METU campus, which can be also considered in future studies. Furthermore, RFID cardholder type information made it possible to study commuter arrival and departure times of the different campus users, which showed that administrative personnel travel demand is more likely to be served with morning and evening commuter buses, as they have more definite work hours, whereas academic personnel needs more flexible services, if any kind of shared-ride models would be promoted for more sustainable campus transportation. Students on the other hand show a definite delayed arrival and a much longer exit profile, which should be better supported with municipal public transit services to discourage private car usage in this group. 6 References [1] Zhou J. “Sustainable commute in a car-dominant city: factors affecting alternative mode choices among university students”. Transportation Research Part A, 46(7), 1013-1029, 2012. [2] Miralles-Guasch C, Domene E. “Sustainable transport challenges in a Suburban University: The case of the autonomous university of Barcelona”. Transport Policy, 17(6), 454-463, 2010. [3] Akar G, Flynn C, Namgung M. “Travel choices and links to transportation demand management: Case study at Ohio State University”. Journal of the Transportation Research Board, 2319, 77-85, 2012. Campus stay time analysis showed that there had been a great number of vehicles stayed on campus less than 15 minutes, which means a transit usage of the campus is high. This may be 176 Pamukkale Univ Muh Bilim Derg, 22(3), 171-177, 2016 O. Altıntaşı, H. Tüydeş Yaman [9] Wayne State University. “Parking and Transportation Services”. http://parking.wayne.edu/students/assigned.php (20.01.2015). [4] Limanond T, Butsingkorn T, Chermkhunthod C. “Travel behavior of university students who live on campus: A case study of a Rural University in Asia”. Transport Policy, 18(1), 163-171, 2011. [5] Gilhooly P, Low DJ. “Primary school travel behavior in Midlothian, UK”. Institution of Civil Engineers-Municipal Engineer, 158(2), 129-136, 2005. [10] University of Wisconsin. “Campus Transportation Committee Annual Report 2008-2009”. Madison, USA, 2213, 2010. [11] Oregon Department of Transportation. “Multimodal Transportation Program Project Application”. www.ocwcog.org/Files/Harrisburg%20Application.pdf (20.01.2015). [6] Huayan S, Wenji L, Haijun H. “Empirical study of parking problem on university campus”. Journal of Transportation Systems Engineering and Information Technology, 7(2), 135-140, 2007. [12] Altintasi O. Assessment of Scenarios for Sustainable Transportation at METU Campus. MSc Thesis, Middle East Technical University, Ankara, Turkey, 2013. [7] Knowledge Arabia. “RFID Car Parking Solutions”. http://kateck.com/node/49 (20.01.2015). [8] The University of Arizona. “Parking and Transportation Services”. https://parking.arizona.edu/permits/rfid.php (20.01.2015). 177
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Design of a multi-center immunophenotyping analysis of peripheral blood, sputum and bronchoalveolar lavage fluid in the Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS)
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* Correspondence: jlcurtis@umich.edu 2Pulmonary & Critical Care Medicine Section, Medicine Service, VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA 3Pulmonary & Critical Care Medicine Division, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI 48109, USA Full list of author information is available at the end of the article Freeman et al. Journal of Translational Medicine (2015) 13:19 DOI 10.1186/s12967-014-0374-z Design of a multi-center immunophenotyping analysis of peripheral blood, sputum and bronchoalveolar lavage fluid in the Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) Design of a multi-center immunophenotyping analysis of peripheral blood, sputum and bronchoalveolar lavage fluid in the Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) Christine M Freeman1,3, Sean Crudgington3, Valerie R Stolberg1, Jeanette P Brown3, Joanne Sonstein3, Neil E Alexis4, Claire M Doerschuk5, Patricia V Basta6, Elizabeth E Carretta6, David J Couper6, Annette T Hastie7, Robert J Kaner8, Wanda K O’Neal6, Robert Paine III9, Stephen I Rennard10, Daichi Shimbo11, Prescott G Woodruff12, Michelle Zeidler13 and Jeffrey L Curtis2,3,14* RESEARCH Open Access Background four flow cytometry laboratories analyzed identical per- ipheral blood specimens, identified the importance of standardizing the model of flow cytometer, the antibody reagents and fluorochromes, the procedure for sample preparation and the procedure for sample analysis [7]. Many multicenter trials continue to stain the sample lo- cally and use the flow cytometry instruments that are available at each participating institution [8-10]. Other studies have employed fixatives to stabilize receptor ex- pression before staining, particularly in peripheral blood samples, with subsequent centralized core staining and flow cytometric analysis has also been explored; however preservation of individual surface markers by this ap- proach was variable [11,12]. Chronic obstructive pulmonary disease (COPD) is a chronic disease that is defined by the presence of airflow limitation that is not fully reversible. COPD is the third- leading cause of death in the United States [1] and is projected to become the fifth-leading cause of disease burden worldwide by the year 2020 [2]. COPD is associ- ated with a persistent inflammatory immune response in the lungs in response to inhaled oxidants, including in- door air pollution from biomass fuels and cigarette smoke [3]. However, COPD is a complex disease involv- ing more than just airflow obstruction. In many patients, COPD is associated with systemic manifestations or co- morbidities that can result in reduced quality of life and increased mortality [4]. There is significant heterogeneity between COPD patients with regard to symptoms, clin- ical characteristics and co-morbidities, physiology, im- aging, response to therapy, decline in lung function and survival [5]. Identifying subtypes of patients may lead to more targeted and personalized therapeutic treatment. The goal of this sub-study is to provide state-of-the- art immunophenotyping of sputum, blood and BAL to be correlated with the abundance of other clinical, radio- graphic, physiological, genetic and biomarker data being collected on this cohort. We took the approach of “just-in- time” provision of reagents from a centralized Immunophe- notyping Core, which prepares the 12-color antibody panels and ships them to the institutions as needed. On the day when samples are collected at each clinical site, they are stained without pre-fixation, then fixed and shipped over- night express on cold packs to the Immunophenotyping Core for data acquisition and analysis on a single flow cyt- ometer. The choice of leukocyte cell types and their recep- tors was based on a series of pre-specified hypotheses plus research interests of the coauthors. Background This interim report demonstrates the feasibility of our approach, which may be of value in the design of multicenter trials in COPD or other disease states. The Subpopulations and Intermediate Outcomes in COPD Study (SPIROMICS) is an ongoing multicenter observational study funded by the National Heart, Lung and Blood Institute, NIH, with a primary goal of identi- fying homogenous subgroups of patients with COPD [6]. SPIROMICS is currently assembling a prospective co- hort of 3200 participants for the collection and analysis of extensive phenotypic, biomarker, genetic, genomic and clinical data. In a subset of 300 subjects, peripheral blood, sputum and bronchoalveolar lavage (BAL) is be- ing collected to immunophenotype multiple cell popula- tions using flow cytometry. Cell populations of interest, including neutrophils, monocytes, macrophages, eosino- phils, dendritic cells, T cells and B cells, as well as their activation states, are being identified using a 12-color antibody panel. (Continued from previous page) (Continued from previous page) Conclusions: Our study design, which relies on bi-directional communication between clinical centers and the Core according to a pre-specified protocol, appears to reduce several sources of variability often seen in flow cytometric studies involving multiple clinical sites. Because leukocytes contribute to lung pathology in COPD, these analyses will help achieve SPIROMICS aims of identifying subgroups of patients with specific COPD phenotypes. Future analyses will correlate cell-surface markers on a given cell type with smoking history, spirometry, airway measurements, and other parameters. Trial registration: This study was registered with ClinicalTrials.gov as NCT01969344. Keywords: Human, COPD, Flow cytometry, Sputum, Bronchoalveolar lavage, Immunophenotyping Abstract Background: Subpopulations and Intermediate Outcomes in COPD Study (SPIROMICS) is a multi-center longitudinal, observational study to identify novel phenotypes and biomarkers of chronic obstructive pulmonary disease (COPD). In a subset of 300 subjects enrolled at six clinical centers, we are performing flow cytometric analyses of leukocytes from induced sputum, bronchoalveolar lavage (BAL) and peripheral blood. To minimize several sources of variability, we use a “just-in-time” design that permits immediate staining without pre-fixation of samples, followed by centralized analysis on a single instrument. Methods: The Immunophenotyping Core prepares 12-color antibody panels, which are shipped to the six Clinical Centers shortly before study visits. Sputum induction occurs at least two weeks before a bronchoscopy visit, at which time peripheral blood and bronchoalveolar lavage are collected. Immunostaining is performed at each clinical site on the day that the samples are collected. Samples are fixed and express shipped to the Immunophenotyping Core for data acquisition on a single modified LSR II flow cytometer. Results are analyzed using FACS Diva and FloJo software and cross-checked by Core scientists who are blinded to subject data. Results: Thus far, a total of 152 sputum samples and 117 samples of blood and BAL have been returned to the Immunophenotyping Core. Initial quality checks indicate useable data from 126 sputum samples (83%), 106 blood samples (91%) and 91 BAL samples (78%). In all three sample types, we are able to identify and characterize the activation state or subset of multiple leukocyte cell populations (including CD4+ and CD8+ T cells, B cells, monocytes, macrophages, neutrophils and eosinophils), thereby demonstrating the validity of the antibody panel. (Continued on next page) © 2015 Freeman et al.; licensee BioMed Central. 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. Page 2 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Materials and methods Ethics statement All clinical investigations are conducted according to the principles of the Declaration of Helsinki. The study protocol was approved by the individual institutional review boards (Columbia University; Weill Cornell Medical College; University of California Los Angeles; University of California San Francisco; University of Michigan, University of Utah; Wake Forest University). All participants Immunofluorescence analysis by flow cytometry is the gold-standard for defining leukocyte populations. How- ever, due to the complexity and sensitivity of flow cy- tometry, there are significant methodological hurdles when applied to a multicenter trial. Early studies from the Multicenter AIDS Cohort Study (MACS), in which Page 3 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 understand the purpose of the study and provide writ- ten informed consent before they undergo any research activities or procedures. about the subjects at the time of the flow cytometry ana- lysis, as the only link between sample labels and subject IDs is held by the GIC. Once antibodies are aliquoted, tubes are capped and centrifuged at 300 × g for 5 minutes, the tubes are placed in wire tacks, which are wrapped in aluminum foil to shield them from light, and are stored at 4°C until ship- ment. Tubes are affixed with a sample-specific label (which can later be matched by the GIC to specific subject information) and then are shipped from the Immunophe- notyping Core to the Clinical Centers between 3–7 days before the scheduled appointment. The Immunopheno- typing Core notifies the Clinical Center by email that the assay tubes have been shipped and provides the tracking information. When assays are shipped, the Immunophe- notyping Core records the assay ID number from the la- bels, plus the date and Clinical Center to which that particular assay was shipped. This information is trans- mitted to the GIC. Study design and logistics A subgroup of 50 subjects from each of six clinical sites (total n = 300) is being enrolled from the parent SPIRO- MICS study. The enrollment strata for the bronchoscopy sub-study are described in Table 1. Subjects participate in this sub-study during two separate visits. At the first visit, a sputum sample is collected by induction. In the second visit, which takes place two to four weeks later, peripheral blood and bronchoalveolar lavage samples are collected. The SPIROMICS clinical sites are broadly distributed geographically, being located in Ann Arbor (University of Michigan); Los Angeles (University of California); New York City (Columbia & Cornell Universities); Salt Lake City (University of Utah); San Francisco (University of California); and Winston-Salem (Wake Forest University). To assure efficient communication, we follow a stan- dardized notification process. Study coordinators at the Clinical Centers are required to notify both the Immu- nophenotyping Core and their local collaborating la- boratory as soon as the first bronchoscopy sub-study visit is scheduled, so that antibody panels can be pre- pared and shipped overnight to that site. Notification occurs by email to multiple individuals at both the clinical sites and the Immunophenotyping Core, to minimize the chance that an absence of one individual will interfere with the tight shipping schedule. The individuals primarily responsible for this protocol at both the Clinical Centers and the Immunophenotyping Core follow a strict pol- icy of immediately “replying to all” at both sites, con- firming receipt of each email and repeating back the received information, to affirm that the message has been received correctly. An identical process of email communication between the Clinical Centers, the Immunophenotyping Core and the GIC is followed once the sample has been collected, stained and fixed. Thus, the GIC records the date on which an assay was shipped; the Immunophenotyping Core records the date on which it was received, facilitating prompt location of any assays that become delayed or lost in transit. To reduce the chance that assays will not be properly chilled during transit, shipping in either dir- ection is permitted only Monday through Thursdays. Additionally, care is taken to assure that the timing of holidays (especially Federal, given that the Immunophe- notyping Core is a VA facility) is considered before ship- ments are released. Biospecimen collection d Sputum induction was performed according to the methods of Alexis et al. [13]. Personnel at the clinical sites involved in sputum induction and sample process- ing received onsite, in-person training from Dr. Alexis. Briefly, subjects undergo seven-minute exposures to in- creasing concentrations of aerosolized hypertonic saline by inhaling via a mouthpiece. To minimize oral contam- ination of induced sputum specimens, subjects are asked to rinse their mouths with water, to blow their noses and to clear their throat at the end of each inhalation period, then to “cough from their chest” and immediately Next, assay tubes, each containing all the antibodies (or isotype controls) for a given cell type or groups of re- lated cell types, are prepared by the Immunophenotyp- ing Core. Each tube is identified using labels supplied by the SPIROMICS Genomics and Informatics Core (GIC) at the University of North Carolina. These labels are spe- cific to sample type and subject, but do not include the SPIROMICS-wide subject identifier. Thus, the Immuno- phenotyping Core is blinded to any clinical information Table 1 Planned subject enrollment distribution by strata Never-smokers Smokers without airflow obstruction Smokers with mild to moderate COPD Smokers with severe COPD Smoking status <1 pack year >20 pack years >20 pack years >20 pack years Lung function FEV1/FVC >0.7 FEV1/FVC >0.7 FEV1 > 50% predicted 50% > FEV1 > 30% predicted Sample size N = 60 (20%) N = 60 (20%) N = 140 (47%) N = 40 (13%) Table 1 Planned subject enrollment distribution by strata Freeman et al. Journal of Translational Medicine (2015) 13:19 Page 4 of 17 phycoerythrin Texas red (PE-TR), phycoerythrin-cyanine 7 (PE-Cy7), allophycocyanin (APC), allophycocyanin- cyanine 7 (APC-Cy7), BD Horizon™V500 (V500), Pacific Blue, Alexa Fluor 700 (AF 700), and QDot® 655. Vendors from which antibodies were purchased include Biolegend (San Diego, CA), eBioscience (San Diego, CA), BD Biosciences (San Jose, CA), R&D Systems (Minneapolis, MN), Miltenyi Biotec (Auburn CA), and Invitrogen (Carlsbad, CA). Antibodies against CX3CR1, CD133, and their respective isotypes, were purchased unconju- gated, and we used Lightning-Link antibody labeling kit (Novus Biologicals, Littleton, CO) to conjugate these anti- bodies to APC-Cy7 and Atto 700, respectively. expectorate into a cup without holding the specimen in their mouths. To assure subject safety, spirometry is per- formed during the inhalation period and again at the end of each seven minute exposure. Biospecimen collection d The saline concentrations used and frequency of spirometric testing vary according to the subject’s baseline forced expiratory volume in 1 sec- ond (FEV1). Subjects with baseline FEV1 ≥50% predicted inhale 3%, 4% and 5% saline, and undergo spirometry two minutes into each exposure and at the end of the expos- ure. By contrast, subjects with baseline FEV1 < 50% pre- dicted inhale 0.9% and 3% saline, and undergo spirometry at 1, 2, 5 and 7 minutes of exposure. If at any point the FEV1 decreases by >20% from baseline, the induction is stopped; otherwise, subjects either continue the current exposure period or proceed to the next saline concentra- tion. Sputum samples were kept on ice throughout the in- duction procedure and processed for immunophenotyping immediately following collection. Antibodies are centrally prepared for each clinical site at the Immunophenotyping Core at the VA Ann Arbor Healthcare System. Antibodies are aliquoted into flow tubes (BD #352008 and #35203; Becton Dickinson) which are capped, placed in a rack (Fisher #14-793-14), and covered with aluminum foil. Antibodies are shipped overnight in a Styrofoam box with multiple cold packs, frozen to −20°C, and typically arrive at the clinical site 1–3 days before the study visit. At the second visit, during which blood and BAL are collected, post-bronchodilator FEV1 is measured before any procedures. Only subjects with an FEV1 > 30% pre- dicted that day are allowed to participate in the bron- choscopy visit. At the time of IV placement, blood is drawn into a 10 ml heparin plasma tube, and immedi- ately to the laboratory for immunophenotyping staining. A complete blood count (CBC) is also collected, and processed by the medical center clinical laboratory. Staining of samples At each clinical site, mucus plugs from the sputum sam- ple are selected, weighed, and then incubated with 1× Sputolysin® Reagent (EMD Millipore, Billerica, MA) in a 37°C water bath for 20 minutes. Samples are washed and filtered before resuspending the cell pellet in Staining Buffer with FBS (BD #340345; BD Biosciences). The spu- tum assay antibody tubes from the Immunophenotyping Core are briefly centrifuged and then the entire sputum sample is divided among seven antibody tubes (100 μL per tube). Tubes are covered with aluminum foil and incubated at room temperature for 25 minutes with con- tinuous shaking or rocking (depending on the equip- ment available at the clinical site laboratory). After the incubation, samples are washed with 2 mL Staining Buffer, centrifuged, and resuspended for storage in 2% freshly-prepared formaldehyde in PBS. Tubes are then stored at 4°C in a rack wrapped in aluminum foil before being shipped back to the Immunophenotyping Core. The BAL sample for Immunophenotyping is only one portion of collection of multiple samples that comprise the entire Bronchoscopy sub-study. BAL is performed in the right middle lobe and lingula by instilling two aliquots of 40 mL and one aliquot of 50 mL of sterile saline per lobe (i.e., 130 mL per lobe, total volume = 260 mL per subject), which is withdrawn by gentle manual suction. The BAL return is collected into specifically designated specimen traps, kept on ice. The BAL from both lung sites was pooled and used for immunophenotyping. Antibody panels d d We designed 12-color monoclonal antibody panels with isotype controls to analyze multiple leukocyte popula- tions. The antibody panel, with clones listed in paren- theses, is shown in Table 2. The panels for BAL and sputum differ from the panel for peripheral blood in that they do not contain antibodies for basophils or endothelial cells. Additionally, the sputum panel does not contain antibodies for dendritic cells or B cells. These choices were made based on pilot data from our laboratory indi- cating that these cell types were present in such low fre- quency as to be impractical to identify. Antibodies and isotype-matched controls were directly conjugated to either fluorescein isothiocyanate (FITC), eFluor 450, phycoerythrin (PE), phycoerythrin-cyanine 5 (PE-Cy5), peridinin chlorophyll protein-cyanin 5.5 (PerCP-Cy5.5), BAL samples are centrifuged and resuspended in Staining Buffer, then 100 μL of the BAL sample is added to each of the BAL assay antibody tubes. Staining then proceeds as described above for sputum samples. Blood tubes are inverted eight times and then 100 μL of the undiluted blood sample is added to each of the blood assay antibody tubes. Similar to the staining pro- cedure for sputum and BAL, samples are incubated with the antibodies for 25 minutes. Next, to remove red blood cells, 2 mL of 1× BD Pharm Lyse (BD Biosciences) are added to each tube and incubated at room temperature for another 25 minutes. *not included in BAL samples; #not included in sputum samples. Statistical analysis Statistical analysis Analyses were performed using GraphPad Prism 6.0 (GraphPad Software, Inc., La Jolla, CA) on a Macintosh Quad-Core Intel Xeon computer running OS 10.10 (Apple; Cupertino, CA). A two-tailed p value of < 0.05 was considered to indicate significance. Sample acquisition success rate p q As of September 17, 2014, a total of 152 sputum samples and 117 blood/BAL samples had been returned to the Immunophenotyping Core. Disparity between collection of sputum samples and of blood plus BAL samples from what was planned appears to have resulted primarily from missed or yet to be completed return visits, and not from any adverse events related to the study proce- dures. For each specimen, we performed an initial ana- lysis of the number of CD45+ cells in sputum, blood, and BAL, stratified by clinical site. Samples averaged 7.7×104 ± 8.2×104 (mean ± SD), 8.9×104 ± 10.7×104, and 20.3×104 ± 36.6x104 CD45+ events (leukocytes) per tube for sputum, BAL and blood, respectively. Samples con- taining fewer than 1×104 leukocytes are deemed un- usable and are not analyzed. Low cell yield was most typically seen in the sputum and BAL samples. We have deliberately not yet broken the codes linking samples to subjects, so that initial analyses are not biased by know- ledge of clinical data. Data are collected using FACSDiva software (BD Biosciences) with automatic compensation. CS&T Research beads (BD Biosciences) are used during instrument setup to maintain baseline performance values, thereby ensuring that the cytometer performed the same every time. Because cell yields varied, we collect all possible events to maximize our ability to detect rare populations. Within 1–2 days after the sample has been run on the flow cytometer, we perform an initial quality check. We record the absolute number of CD45+ leukocytes in the sample and also look at the percentage of low side scat- ter cells, indicative of lymphocytes, and high side scatter cells, such as macrophages, neutrophils, and monocytes. Our preliminary analyses indicate that a total of 126 of 152 sputum samples (83%), 106 of 117 blood samples (91%) and 91 of 117 BAL samples (78%) provided usable data (Table 3). It seems likely that there may have been a Antibody panels d d All analyses undergo a secondary evaluation by a third individual (CMF) to help maintain consistency in the gating and analysis between samples. Data, including analysis files, are immediately backed up to DVD-R disks. Antibody panels d d Samples are centrifuged and Table 2 Standardized antibody panel Leukocyte population Fluorochrome (directly conjugated to monoclonal antibody) FITC PE PE-Cy5 PerCP-Cy5.5 PE-TR PE-Cy7 APC APC-Cy7 V500 Pacific blue AF 700 QDot 655 Surface antigen detected with monoclonal antibody clone used (italicized) Dendritic cells# BDCA-2 AC144 BDCA-1 AD5-8E7 CD123 6H6 CCR2 TG5 CD45 HI30 CD103 B-Ly7 BDCA-3 AD5- 14H12 CX3CR1 2A9-1 HLA-DR L243 CD11c 3.9 CD11b CBRM1/5 CD3 7D6 & CD19 SJ25-C1 Mø & monocytes CD14 HCD14 CCR6 R6H1 CD16 3G8 CCR2 TG5 CD45 HI30 TLR2 T2.5 CD206 15-2 CX3CR1 2A9-1 HLA-DR L243 CD11c 3.9 CD11b CBRM1/5 Mø & monocytes CD14 HCD14 Axl 108737 CD16 3G8 DC-Sign 9E9A8 CD45 HI30 TLR4 HTA125 Mertk 125518 HLA-DR L243 CD11c 3.9 CD11b CBRM1/5 Basophils*# CD33 HIM3-4 CD9C3-3A2 CD13 TuK1 CD203c NP4D6 CD45 HI30 CD63 H5C6 CD22 HIB22 CD34 581 HLA-DR L243 CD69 FN50 CD11b CBRM1/5 CD19 SJ25-C1 Eosinophils CD49d 9 F10 CDw125 A14 CD16 3G8 CD69 FN50 CD45 HI30 CCR3 5E8 CD34 581 CD11b CBRM1/5 Neutrophils CD177 MEM-166 CD16b CLB-gran 11.5 CXCR1 8 F1 CD66b G10F5 CD45 HI30 TLR4 HTA125 CXCR2 5E8 CD10 HI10a TLR2 T2.5 CD11b CBRM1/5 Endothelial cells*# CD33 HIM3-4 CD146 SHM-57 VCAM-1 STA VEGFR2 HKDR-1 CD45 HI30 PECAM WM59 CD144 16B1 CD34 581 ICAM-1 HCD54 CD133 293C3 CD37D6 & CD19 SJ25-C1 B cells# IgD IA6-2 CD80 2D10.4 CD86 B7-2 CD27 O323 CD45 HI30 CXCR4 12G5 CD23 EBVCS-5 CD20 2H7 CD38 HIT2 CD19 SJ25-C1 T cells γδ -TCR B1.1 CTLA-4 14D3 CD28 CD28.2 CD27 O323 CD45 HI30 ICOS ISA-3 CD56 CMSSB CD62L DREG-56 CD3 UCHT1 CD8 OKT-8 CD4 OKT-4 T cells CCR7 150503 CCR5 T21/8 CXCR3 1C6 CD27 O323 CD45 HI30 CD56 CMSSB CD62L DREG-56 CD3 UCHT1 CD8 OKT-8 CD4 OKT-4 # Page 6 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 washed with Staining Buffer before being stored in 2% formaldehyde in a refrigerator wrapped in aluminum foil. on Macintosh Quad-Core Intel Xeon computers running OS X 10.10.1 (Apple; Cupertino, CA). We use pre-printed sample report forms and a flow analysis worksheet to standardize the process. All analyses undergo a secondary evaluation by a third individual (CMF) to help maintain consistency in the gating and analysis between samples. Data, including analysis files, are immediately backed up to DVD-R disks. on Macintosh Quad-Core Intel Xeon computers running OS X 10.10.1 (Apple; Cupertino, CA). We use pre-printed sample report forms and a flow analysis worksheet to standardize the process. Flow cytometry instrument setup and data acquisition Flow cytometry instrument setup and data acquisition Samples are wrapped in aluminum foil and are shipped overnight in a Styrofoam box with cold packs to the Immunophenotyping Core. Upon arrival, samples are physically inspected and any issues (e.g. cracked tubes, inconsistent volumes, missing tubes) are recorded along with the sample ID. Samples are transferred to a 96-well U-bottom plate and data are acquired on an LSR II flow cytometer (BD Bioscience, San Jose, CA) with a High Throughput Sampler, equipped with the following four lasers, listed with their associated fluorochromes and fil- ter sets: 488 nm blue laser (APC-Cy7: 735 nm long-pass (LP), 780/60 nm short band-pass (SBP); AF700: 690 nm LP, 730/45 nm SBP; APC: 660/20 nm SBP); 405 nm vio- let laser (Qdot655: 630 nm LP, 660/20 nm SBP; Horizon V500: 505 LP, 530/30 SBP; Pacific Blue: 450/50 SBP); 633 nm red HeNe laser (PerCP-Cy5.5: 685 nm LP, 695/ 40 SBP; FITC: 505 LP, 530/30 SBP); and a 561 nm yellow-green laser (PE-Cy7: 735 nm LP, 780/60 nm SBP; PE-Cy5: 635 nm LP, 670/30 nm SBP; PE-TR: 600 nm LP, 610/20 nm SBP; PE: 582/15 nm SBP). Flow cytometry data analysis Data are analyzed by two trained individuals (SC, VRS) using FlowJo software v.9.6.2 (Tree Star, Ashland, OR) Table 3 Number and percentage of usable specimens by clinical site Site 1 Site 2 Site 3 Site 4 Site 5 Site 6 Total Sputum visits, n: 16 26 38 30 23 19 152 Usable specimens, n 13 21 34 27 17 14 126 Usable specimens,% 81% 81% 89% 90% 74% 74% 83% Blood & BAL visits, n: 7 26 28 19 19 18 117 Usable blood specimens, n 6 22 25 19 17 17 106 Usable blood specimens, % 86% 85% 89% 100% 89% 94% 91% Usable BAL specimens, n 6 21 22 12 15 15 91 Usable BAL specimens, % 86% 81% 76% 63% 79% 83% 78% Table 3 Number and percentage of usable specimens by clinical site Freeman et al. Journal of Translational Medicine (2015) 13:19 Page 7 of 17 the vast majority of antigens were unaffected by duration of storage in PFA. learning curve in obtaining or processing the samples, particularly sputum. The percentage of usable sputum data has increased from 69% in 2012, to 88% in 2013, and 92% in 2014. BAL samples also showed a modest in- crease: 71% usable samples in 2012, 78% in 2013 and 80% in 2014 (data not shown). Identification of T cell populations in blood, sputum and BAL Lung T cells have been linked to progression of COPD, especially of emphysema, in multiple studies [14-19]. We used a combination of anti-CD45 (leukocyte common antigen), forward and side light scatter properties, and dif- ferential expression of lineage-specific surface markers to identify leukocyte populations, as has been previously shown to be effective for sputum leukocytes [13,20]. To identify CD4+ and CD8+ T cells, we first gated on CD45+ CD3+ cells with a low side scatter. Representative staining demonstrates the ability of this strategy plus comparison to isotype controls to distinguish CD4+ and CD8+ T cells in blood, BAL and sputum (Figure 2). The numbers in each quadrant indicate the percentage of that subset among all CD45+ cells. These numbers are consistent with what other studies have found in sputum [21], blood and BAL [22]. Processing errors may also account for some of the unusable data. Identification of macrophage populations in sputum and BAL Alveolar macrophage (AMø) numbers are increased and their function is altered in COPD [23]. There is consider- able interest in whether polarization of their gene prod- ucts drives inflammation in COPD [24,25]. To identify AMø, we gated on CD45+, auto-fluorescent cells and then selected HLA-DR+ CD11c + cells (Figure 3). This ap- proach was chosen after a preliminary analysis of a var- iety of alternative gating approaches, including use of Mertk (a putative pan-Mø marker in mice) [26], as the one giving the most unambiguous distinction of mature AMø. Although CD11b is included in the panel for ana- lysis, we did not use it to gate on macrophages, as AMø have been shown to be negative for CD11b, unless acti- vated, therefore their expression is not uniformly positive [27]. As expected, BAL samples contained the largest percentage of macrophages. As the numbers of subjects increase, this dataset will be analyzed further for correl- ation of macrophage surface receptor expression with spirometrically-defined disease severity and other clin- ical data. Flow cytometry data analysis The most commonly detected processing error was resuspension of the samples in an incorrect fixative volume, such that the concentration of parafor- maldehyde, which must be held constant to stabilize the light scatter and antibody labeling, was likely much lower than the 2% specified in the protocol. Other less common errors result from shipping delays, which re- sulted in samples no longer protected by the ice packs; cracked tubes with low or missing sample; and improp- erly capped tubes, resulting in loss of entire samples. Al- though there was variation between clinical sites in the percentage of usable samples of different types, no site was routinely underperforming compared to the other sites (Table 3), supporting our impression that random errors, rather that systematic problems, were responsible for lost data. Duration between fixation and data acquisition has only minor effect on fluorescence intensity One variable in this study is the duration between fixa- tive addition and data acquisition on the flow cytometer. This duration typically varies between two and seven days, because sites that have study visits on Thursday or Friday are unable to ship specimens until the following Monday. To determine whether time of storage in PFA affected fluorescent intensity, in locally-performed pilot experiments, we analyzed blood and BAL samples at days 2, 5, and 7 post-PFA. Results indicated no differ- ence in forward scatter, side scatter or CD45+ staining (not shown). Among 68 surface molecules, fluorescence intensity for 61 was either unaffected by storage in PFA, as shown for CD16 (Figure 1A), or had modest increases in specific staining and in the corresponding isotype control, such that there was no difference in overall positive staining. In blood specimens, antibodies against TLR4 (PE-Cy7), gamma-delta T cell receptor (FITC), and CCR7 (FITC) had increased specific fluorescence (relative to isotype control) from day 2 to day 5, but no further increase at day 7 (data not shown). In BAL specimens, antibodies against BDCA-1 (PE), CX3CR1 (APC-Cy7), and TLR2 (eFluor 450) also showed mod- est increases in specific fluorescence at days 5 and 7 (Figure 1B). Only CD103 (PE-Cy7) in the BAL samples exhibited decreased fluorescent intensity, which was seen at both days 5 and 7 (Figure 2C). Although small in absolute terms, these changes will need to be accounted for in future analyses. Importantly, however, staining for Identification of monocyte populations in blood, sputum and BAL Monocytes constitute 5 to 10% of peripheral blood leu- kocytes where they circulate for several days before mi- grating into tissues. The degree to which recruitment of blood monocytes contributes to the expansion of the mononuclear phagocyte population in COPD is con- tested. Monocytes were originally divided into “classical” CD14++ CD16- cells and “nonclassical” CD14+ CD16+ cells. The classical monocytes were considered to be Page 8 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Figure 1 Storage in PFA affects fluorescent intensity of specific surface receptor-monoclonal antibody combinations. After addition of PFA, BAL samples were divided into three samples and data was acquired after storage at 4°C for either 2, 5, or 7 days. A) CD16 (and the majority of the surface antigens) showed no change in fluorescent intensity between days 2, 5, and 7. B) TLR2 showed an increase in fluorescent intensity at day 5 and at day 7. C) CD103 was the only receptor to show a decrease in fluorescent intensity at days 5 and 7. Figure 1 Storage in PFA affects fluorescent intensity of specific surface receptor-monoclonal antibody combinations. After addition of PFA, BAL samples were divided into three samples and data was acquired after storage at 4°C for either 2, 5, or 7 days. A) CD16 (and the majority of the surface antigens) showed no change in fluorescent intensity between days 2, 5, and 7. B) TLR2 showed an increase in fluorescent intensity at day 5 and at day 7. C) CD103 was the only receptor to show a decrease in fluorescent intensity at days 5 and 7. after gating on CD45+, non-autofluorescent cells with a medium side-scatter that were HLA-DR+, relative to iso- type controls (Figure 4A-4C). We chose to define mono- cytes by HLA-DR+ staining, rather than expression of CD11b (typically positive on monocytes in peripheral blood) or CD11c (negative on blood monocytes, but po- tentially upregulated in GM-CSF-rich environments such as the lungs), so that we could independently analyze ex- pression of the latter two markers in samples other than blood. As shown in the representative staining (Figure 4D), we can easily see distinct populations for the classical, non-classical, and intermediate monocytes in peripheral blood. better at secreting proinflammatory cytokines and con- stitute the majority of all monocytes in healthy persons, whereas the nonclassical monocytes more closely resem- ble resident tissue macrophages [28-30]. Identification of monocyte populations in blood, sputum and BAL A third subset of peripheral blood monocytes, termed “intermediate” monocytes are CD14++ CD16+ [31]. It is not clear whether these intermediate monocytes have a biologic- ally meaningful role or are an intermediate step in the differentiation of monocytes but they have been shown to be increased in certain conditions including rheuma- toid arthritis and severe asthma [32]. In our study, monocytes were readily identified in all three compartments using CD14 and CD16 antibodies, Page 9 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Figure 2 Representative staining of CD4+ and CD8+ T lymphocytes in blood, BAL, and sputum. Samples of peripheral blood (A, D), BAL (B, E) and sputum (C, F) were gated on cells that were CD45+, CD3+, and had a low side-scatter. Next, using the isotype control (A-C), quadrants denoting specific staining for CD4 (horizontal axis) and CD8 (vertical axis) were determined (D-F). Numbers in the CD4+ and CD8+ quadrants represent the percent of each subset among all CD45+ cells. Figure 2 Representative staining of CD4+ and CD8+ T lymphocytes in blood, BAL, and sputum. Samples of peripheral blood (A, D), BAL (B, E) and sputum (C, F) were gated on cells that were CD45+, CD3+, and had a low side-scatter. Next, using the isotype control (A-C), quadrants denoting specific staining for CD4 (horizontal axis) and CD8 (vertical axis) were determined (D-F). Numbers in the CD4+ and CD8+ quadrants represent the percent of each subset among all CD45+ cells. In the BAL and sputum, monocytes were distinct from alveolar macrophages due to their reduced size and granularity, evident by forward scatter and side scatter (data not shown). Monocytes were again divided into the three populations: classical, intermediate, and non- classical (Figure 4E, 4F). The populations appear to be more limited to the classical and intermediate pheno- types, reminiscent of a gating strategy developed by Brittan et al. [33] which uses the terms “inducible” and “resident”, respectively, due to the observation that LPS inhalation resulted in an increase in the CD14++ CD16- population, in comparison to a saline-treated group, but the CD14++ CD16+ population was unchanged between groups [33]. We also found that the monocytes from BAL and sputum were predominantly CD14++ CD16+, the so-called “resident” monocytes (Figures 4E, 4F). Identification of monocyte populations in blood, sputum and BAL Numbers represent the percent of AMø among all CD45+ cells. were identified as being double positive for HLA-DR and BDCA-3 (CD141). To identify pDC, we selected cells that were CD123+ and BDCA-2 (CD303) +. although it is now recognized that this acute phase react- ant has important actions independent of elastase inhib- ition [36]. Hence, clarifying the exact role of neutrophils in COPD phenotypes is an important goal. We identified neutrophils by gating on CD45+, high side scatter cells and then, based on appropriate isotype control (Figures 6A-6C), selected cells that were positive for two neutrophil-specific surface markers [37], CD16b and CD66b (Figure 6D-6 F). From the representative staining we saw that neutrophils were most abundant in blood and sputum samples, as expected, and were very infrequent in BAL. Using this method we were able to identify mDC1 subsets in blood and BAL (Figure 5). Similar results were found for mDC2 and pDCs (data not shown). CD11c, CD11b, and CD103, which are also routinely used to identify DCs, were also included in the panel for DCs. Future analyses could utilize these markers to perform more in-depth analysis of DC subsets and to compare al- ternative methods of DC identification. Identification of monocyte populations in blood, sputum and BAL Identification of myeloid dendritic cell (mDC) populations in blood, sputum and BAL In the present study, we examined markers of three human pulmonary DC subsets: myeloid DC type 1 (mDC1), myeloid DC type 2 (mDC2), and plasmacytoid DCs (pDCs). DCs were only analyzed in BAL and blood due to concerns that they would be too small of a popu- lation to identify in sputum. To identify the DC subsets, we used blood dendritic cell antigen (BDCA) markers, which we and others have previously shown accurately identifies these cell types in lung parenchyma [34,35]. First, CD45+ cells were selected followed by exclusion of cells that were positive for either CD3 or CD19+ cells, and of cells with a high forward scatter or high side-scatter. Next, mDC1 cells were identified as being double-positive for HLA-DR and BDCA-1 (CD1c), whereas mDC2 cells Identification of myeloid dendritic cell (mDC) populations in blood, sputum and BAL In the present study, we examined markers of three human pulmonary DC subsets: myeloid DC type 1 (mDC1), myeloid DC type 2 (mDC2), and plasmacytoid DCs (pDCs). DCs were only analyzed in BAL and blood due to concerns that they would be too small of a popu- lation to identify in sputum. To identify the DC subsets, we used blood dendritic cell antigen (BDCA) markers, which we and others have previously shown accurately identifies these cell types in lung parenchyma [34,35]. First, CD45+ cells were selected followed by exclusion of cells that were positive for either CD3 or CD19+ cells, and of cells with a high forward scatter or high side-scatter. Next, mDC1 cells were identified as being double-positive for HLA-DR and BDCA-1 (CD1c), whereas mDC2 cells Freeman et al. Journal of Translational Medicine (2015) 13:19 Page 10 of 17 Figure 3 Representative staining of macrophages in BAL and sputum. To identify macrophages in samples of BAL (A, C) and sputum (B, D), we gated on CD45+ auto-fluorescent cells and used isotype controls (A,B) to gate on cells specifically staining for HLA-DR+ CD11c + (C, D). Numbers represent the percent of AMø among all CD45+ cells. Figure 3 Representative staining of macrophages in BAL and sputum. To identify macrophages in samples of BAL (A, C) and sputum (B, D), we gated on CD45+ auto-fluorescent cells and used isotype controls (A,B) to gate on cells specifically staining for HLA-DR+ CD11c + (C, D). Identification of neutrophil populations in blood, sputum and BAL In peripheral blood samples, we also observed a CD66b + CD16b- population (R1 in Figure 6D), which was not present in the BAL or sputum samples. In design- ing this study, we had hypothesized that in COPD subjects we might see a population of circulating neutrophils The concept that neutrophils contribute centrally to emphysema stems primarily from genetic deficiency of alpha-1 antiprotease, which inhibits neutrophil elastase, Page 11 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Figure 4 CD14 and CD16 identify populations of monocytes in blood, BAL, and sputum. To identify monocyte in samples of peripheral blood (A, D), BAL (B, E) and sputum (C, F), we first gated on non-autofluorescent, CD45+ cells with a medium side-scatter, then using isotype controls (A-C), chose HLA-DR+ cells (D-E). In all analyses, we then separated the monocytes into “classical” CD14++ CD16- cells (R1), “intermediate” CD14++ CD16+ (R2), and “nonclassical” CD14+ CD16+ (R3) cells. Numbers represent the percent of each monocyte subset among all CD45+ cells. Figure 4 CD14 and CD16 identify populations of monocytes in blood, BAL, and sputum. To identify monocyte in samples of peripheral blood (A, D), BAL (B, E) and sputum (C, F), we first gated on non-autofluorescent, CD45+ cells with a medium side-scatter, then using isotype controls (A-C), chose HLA-DR+ cells (D-E). In all analyses, we then separated the monocytes into “classical” CD14++ CD16- cells (R1), “intermediate” CD14++ CD16+ (R2), and “nonclassical” CD14+ CD16+ (R3) cells. Numbers represent the percent of each monocyte subset among all CD45+ cells. recently released from the bone marrow, identifiable as CD16b- (low) and CD10- cells [38]. We gated on both CD16b low and high populations and analyzed expres- sion of CD10 (Figure 6B). The CD66b + CD16b- cells had reduced expression of CD10, especially in com- parison to the CD66b + CD16b + cells, suggesting that we are able to identify a population of circulating im- mature neutrophils. to be positive for CD16. Eosinophils do contain intra- cellular CD16 and it has been shown that blood eosino- phils express surface CD16 when stimulated in vitro with platelet-activating factor or IFN-γ [43]. Hence, these pre- liminary data are compatible with activation of eosinophils in the airways of some subjects with COPD. In future studies once we have data on all subjects, we will look for correlations between eosinophil CD16 expression and clinical characteristics. Discussion This interim analysis, describing the design and early data collection of a clinical trial involving six clinical centers throughout the United States, demonstrates the feasibility of our approach of “just-in-time” provision of antibodies, distributed staining and fixation, and cen- tralized analysis to perform 12-color immunophenotyping of samples from three different tissue origins. We have demonstrated successful identification of multiple leukocyte cell populations, including CD4+ and CD8+ T cells, Eosinophilic lung inflammation appears to identify a sub- set of COPD patients who are more responsive to cortico- steroids or leukotriene inhibition [39-41]. We identified eosinophils in blood and BAL by first gating on CD45+ high side scatter cells and then identifying cells that, compared to isotype controls (Figure 7A-7C) were CCR3+ and CD16- [42] (Figure 7D-7F). In sputum samples, we also identified a cell population that was CCR3+ but based on the isotype control, they appeared Page 12 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Figure 5 BDCA-1 and HLA-DR identify mDC1 cells in blood and BAL. To identify dendritic cells in samples of peripheral blood (A, C) and BAL (B, D), we first gated on CD45+ cells, then excluded CD3+, CD19+, and cells with a high forward and side-scatter, and finally using isotype controls (A,B), chose HLA-DR and BDCA-1 double-positive cells (C,D). Numbers represent the percent of mDC1 cells among all CD45+ cells. Figure 5 BDCA-1 and HLA-DR identify mDC1 cells in blood and BAL. To identify dendritic cells in samples of peripheral blood (A, C) and BAL (B, D), we first gated on CD45+ cells, then excluded CD3+, CD19+, and cells with a high forward and side-scatter, and finally using isotype controls (A,B), chose HLA-DR and BDCA-1 double-positive cells (C,D). Numbers represent the percent of mDC1 cells among all CD45+ cells. allows us to standardize three out of those four variables. In our study, all samples are run on the same instrument, a modified LSR II flow cytometer containing a high- throughput sampler to improve efficiency of analysis and a yellow-green laser that permits use of multiple PE- conjugated fluorochromes. Data are collected and ana- lyzed by a small team of highly trained scientists with adherence to a standardized gating strategy and fre- quent evaluation of the raw data and instrument con- trols. Discussion We have even minimized variability in the antibody reagents and fluorochromes by preparing the antibodies at the centralized core before shipping them to the Clinical Centers. In comparison, other multicen- ter trials have opted to combine local sample staining with the flow cytometry instruments that are available at each participating institution, although often the monocytes, macrophages, neutrophils, and eosinophils, in blood, BAL and sputum, thereby demonstrating the validity of our antibody panel and the fixation method. We have also shown that the vast majority of samples provide usable data, supporting the feasibility of this logistic approach. This design should be considered for immunophenotyping in comparable clinical studies in other disease states. Our approach differs from that of several other multicen- ter trials. The Multicenter AIDS Cohort Study (MACS) used four flow cytometry laboratories to analyze identical peripheral blood specimens. MACS identified the import- ance of standardizing the following variables: (1) the model of flow cytometer; (2) the antibody reagents and fluorochromes; (3) the procedure for sample preparation; and (4) the procedure for sample analysis [7]. Our approach Freeman et al. Journal of Translational Medicine (2015) 13:19 Page 13 of 17 Figure 6 Representative staining of neutrophils in blood, BAL, and sputum. To identify neutrophils in samples of peripheral blood (A, D), BAL (B, E) and sputum (C, F), we gated on CD45+, high side-scatter cells that were positive for both CD16b (horizontal axis) and CD66b (vertical axis), relative to isotype controls (A-C). Numbers in the quadrants (D-F) represent the percent of the major neutrophil population among all CD45+ cells. In the blood analysis (panel D), a CD16b- (low) CD66b + population was also identified (R1). G) Histograms depicting expression of CD10 in the R1 (blue line) and R2 (green line) populations, relative to isotype control (red line). Figure 6 Representative staining of neutrophils in blood, BAL, and sputum. To identify neutrophils in samples of peripheral blood (A, D), BAL (B, E) and sputum (C, F), we gated on CD45+, high side-scatter cells that were positive for both CD16b (horizontal axis) and CD66b (vertical axis), relative to isotype controls (A-C). Numbers in the quadrants (D-F) represent the percent of the major neutrophil population among all CD45+ cells. In the blood analysis (panel D), a CD16b- (low) CD66b + population was also identified (R1). Discussion G) Histograms depicting expression of CD10 in the R1 (blue line) and R2 (green line) populations, relative to isotype control (red line). Figure 6 Representative staining of neutrophils in blood, BAL, and sputum. To identify neutrophils in samples of peripheral blood (A, D), BAL (B, E) and sputum (C, F), we gated on CD45+, high side-scatter cells that were positive for both CD16b (horizontal axis) and CD66b (vertical axis), relative to isotype controls (A-C). Numbers in the quadrants (D-F) represent the percent of the major neutrophil population among all CD45+ cells. In the blood analysis (panel D), a CD16b- (low) CD66b + population was also identified (R1). G) Histograms depicting expression of CD10 in the R1 (blue line) and R2 (green line) populations, relative to isotype control (red line). instruments vary in type of instrument and number of lasers [8-10]. Della Porta et al. attempted to control for this variability by including daily instrument quality controls, including fluorescence standardization, to en- sure consistent operation. However, the analysis was not centrally reviewed and was performed using multiple platforms [10]. In the study by Benevolo et al., laboratories had either a 3- or 4-color instruments, which resulted in the use of different antibody panels between centers. To minimize that variable, all data in that study were reviewed by a single person [9]. instruments vary in type of instrument and number of lasers [8-10]. Della Porta et al. attempted to control for this variability by including daily instrument quality controls, including fluorescence standardization, to en- sure consistent operation. However, the analysis was not centrally reviewed and was performed using multiple platforms [10]. In the study by Benevolo et al., laboratories had either a 3- or 4-color instruments, which resulted in the use of different antibody panels between centers. To Although in our study there is a single procedure for sample preparation, given that six different sites are re- sponsible for staining the samples, there is likely some variability being introduced at this stage. We considered the idea of cryopreserving or stabilizing samples and then shipping them to a centralized flow cytometry core for staining and analysis, but ultimately decided against Page 14 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Figure 7 Eosinophils in blood, BAL, and sputum express CCR3 but have variable expression of CD16. Discussion To identify eosinophils in samples of peripheral blood (A, D), BAL (B, E) and sputum (C, F), we gated on cells that were CD45+ with a high side scatter that were also CCR3+ (vertical axis), relative to isotype controls (A-C). In blood (panel D) and BAL samples (panel E), eosinophils were also CD16- (horizontal axis). In sputum samples (panel F), eosinophils were positive for CD16. Numbers represent the percent of each subset among all CD45+ cells. Figure 7 Eosinophils in blood, BAL, and sputum express CCR3 but have variable expression of CD16. To identify eosinophils in samples of peripheral blood (A, D), BAL (B, E) and sputum (C, F), we gated on cells that were CD45+ with a high side scatter that were also CCR3+ (vertical axis), relative to isotype controls (A-C). In blood (panel D) and BAL samples (panel E), eosinophils were also CD16- (horizontal axis). In sputum samples (panel F), eosinophils were positive for CD16. Numbers represent the percent of each subset among all CD45+ cells. this approach, as the preservation of individual surface antigens is quite variable [11,12] (and our own unpub- lished data from pilot experiments). For the most part, our preliminary analyses have not demonstrated system- atic differences between clinical centers for staining efficiency. been shown to result in a slight decrease in fluorescent in- tensity [44] and a decrease in forward scatter and side scatter [45]. Our analysis of changes in fluorescence inten- sity for 68 leukocyte surface receptors for up to seven days generally agrees with a previous analysis showing that staining generally remained consistent and highly repro- ducible at days 1, 3 and 5 post-staining [44]. However, we found better preservation of staining intensity at day 7 than in that previous study, although two of the four re- ceptors they studied were also stable at 7 days, suggesting that these changes are receptor-specific. Furthermore, we did not observe a change in forward scatter and side scat- ter. Of the molecules that were affected by storage in PFA in our study, only CD103 had decreased fluorescent inten- sity. The other markers that were affected, TLR4, gamma- delta T cell receptor, CCR7, BDCA-1, CX3CR1 and TLR2 actually had a slight increase in fluorescent intensity. Discussion In more detailed analyses, we will need to take this change in Another variable that we are unable to control entirely using this approach is the amount of time that the sam- ples remain in PFA before data collection on the flow cytometer. Although we stipulate that sites send samples back as soon as possible, samples that are collected on a Thursday or Friday are not shipped until the next Monday. Excluding those days from sample collection was not compatible with the overall logistics of the Bronchoscopy sub-study. An essential feature of our study design was sample fixation using 2% paraformaldehyde post-staining to permit delayed analysis. However, paraformaldehyde it- self affects flow cytometry readings. Staining with PFA has Page 15 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 fluorescence into account for samples that were unable to be analyzed within 2 days. Acknowledgments We are grateful to SPIROMICS participants for their willingness to participate in this study and to the Study Coordinators and staff who though their hard work make this study possible. SPIROMICS is funded by the National Heart, Lung, and Blood Institute NHLBI (NHLBI-HR-08-08) with support from a variety of industry partners whose representatives serve on the SPIROMICS External Scientific Board. Specifically, SPIROMICS is funded by contract from the NHLBI: HHSN268200900013C, HHSN268200900014C, HHSN268200900015C, HHSN268200900016C, HHSN268200900017C, HHSN268200900018C, HHSN2682009000019C, HHSN268200900020C. Private sector contributions to SPIROMICS are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). CMF and JLC are supported in part by funding from the Clinical Research & Development Service, Department of Veterans Affairs. We are grateful to SPIROMICS participants for their willingness to participate in this study and to the Study Coordinators and staff who though their hard work make this study possible. SPIROMICS is funded by the National Heart, Lung, and Blood Institute NHLBI (NHLBI-HR-08-08) with support from a variety of industry partners whose representatives serve on the SPIROMICS External Scientific Board. Specifically, SPIROMICS is funded by contract from the NHLBI: HHSN268200900013C, HHSN268200900014C, HHSN268200900015C, HHSN268200900016C, HHSN268200900017C, HHSN268200900018C, HHSN2682009000019C, HHSN268200900020C. Private sector contributions to SPIROMICS are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). CMF and JLC are supported in part by funding from the Clinical Research & Development Service, Department of Veterans Affairs. Conclusion l In conclusion, we have demonstrated the feasibility of providing state-of-the-art immunophenotyping of spu- tum, peripheral blood and BAL in a multicenter obser- vational study of COPD biomarkers. Key features of our approach that minimize potential sources of experimen- tal variation include “just-in-time” provision of reagents from a centralized Immunophenotyping Core, local im- munostaining and fixation, and return of samples for analysis on a single flow cytometer. The choice of leukocyte cell types and their receptors was based on a series of pre-specified hypotheses plus research interests of the coauthors. This interim report demonstrates the success of our approach, which may be of value in the design of multicenter trials in other disease states. Enroll- ment to this sub-study is anticipated to be completed in the summer of 2015, so results should be analyzed and published over the next two years. Competing interests Competing interests SC, VRS, JPB, JS, NEA, CMD, PVB, EEC, DJC, ATH, WKO, RJK, RP, DS, MZ: These authors declare that they have no competing interests. CMF and JLC have grant support from MedImmune, Ltd. to analyze lung NK cells in human lungs resected for clinical indications. SIR has received money for service on advisory boards of the following companies: A2B Bio, Almirall, CSL Behring, Dailchi Sanyko, Novartis, Nycomed and Pfizer; and as a consultant to: Almirall, APT Pharma/Brtinall, AstraZeneca, Boehringer Ingelheim, Chiesi, Decision Resource, Dunn Group, Easton Associates, Gerson, GlaxoSmithKline, MedImmune, Novartis, Pearl, Roche, Takeda, Theravance. PGW has a research grant from Pfizer and is a consultant for Genentech, Roche, BI, J&J, NeoStem, Novartis, Astra Zeneca and Merck. He is co-inventor on a patent for asthma biomarkers. g Roche, BI, J&J, NeoStem, Novartis, Astra Zeneca and Merck. He is co-inventor on a patent for asthma biomarkers. Authors’ contributions CMF d i d h CMF co-designed the antibody panel and the experimental design, wrote the original manuscript draft and oversaw all aspects of flow cytometric data analysis. SC, VRS, JPB and JS participated in assay preparation, coordination with clinical sites, data acquisition, and data analysis. NEA, CMD, SIR and PGW participated in study design. PVB, EEC, DJC, and WKO provided data coordinating support. ATH, JRH, RJK, RP, DS, PGW and MZ oversaw sample collection and preparation at the clinical sites. JLC conceived of the study, participated in its design and helped prepare the manuscript. All authors read and approved the final manuscript. Part of our future analysis strategy will be to correlate the relative proportions of a given cell type in BAL ver- sus sputum versus blood in the same subject. Other ana- lyses will correlate cell-surface markers on a given cell type with smoking history, spirometry, airway measure- ments, and other parameters. As part of the parent SPIROMICS project, individuals will also be character- ized via physiological, imaging, biochemical, and genetic parameters. These data will also be available for correlat- ing with immunophenotyping analyses. Abbreviations BAL B h l Abbreviations BAL: Bronchoalveolar lavage; COPD: Chronic obstructive pulmonary disease; MACS: Multicenter AIDS Cohort Study; PFA: Paraformaldehyde; SPIROMICS: Subpopulations and Intermediate Outcomes in COPD Study. BAL: Bronchoalveolar lavage; COPD: Chronic obstructive pulmonary disease; MACS: Multicenter AIDS Cohort Study; PFA: Paraformaldehyde; SPIROMICS: Subpopulations and Intermediate Outcomes in COPD Study. Consent Written informed consent was obtained from each participant for the publication of this report and any accompanying images. An additional limitation of this study is the lack of a live/dead exclusion gate. FSC and SSC gating was used to eliminate cell debris, but cannot guarantee that all dead cells were excluded. A final limitation is that the protocol of the current SPIROMICS Immunophenotyp- ing project does not include staining of intracellular antigens, isolation of specific cell types or in vitro stimu- lation to induce production of gene products such as cy- tokines or inflammatory mediators. We considered those undertakings premature until we had both demonstrated the ability of this multi-center experimental design to produce usable surface staining data, and had advanced the characterization of specific cell types in our popula- tion. However, given the technical success illustrated by these results, we believe that such extension are entirely feasible and should be an important goal of future stud- ies in this cohort. 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Author details 1R h S 1Research Service, VA Ann Arbor Healthcare System, Ann Arbor, MI, 48105, USA. 2Pulmonary & Critical Care Medicine Section, Medicine Service, VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA. 3Pulmonary & Critical Care Medicine Division, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI 48109, USA. 4Center for Environmental Medicine, Asthma, and Lung Biology, Chapel Hill, NC 27599, USA. 5Center for Airways Disease, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. 6Marsico Lung Institute/University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. 7Center for Genomics and Personalized Medicine, Wake Forest University, Winston-Salem, NC 27157, USA. 8Division of Pulmonary and Critical Care Medicine, Departments of Medicine and Genetic Medicine, Weill Cornell Medical College, New York, NY 10021, USA. 9Division of Pulmonary, Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA. 10Pulmonary, Critical Care, Sleep and Allergy Division, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA. 11Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA. 12Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of California at San Page 16 of 17 Freeman et al. Journal of Translational Medicine (2015) 13:19 Page 16 of 17 Francisco, San Francisco, CA 94143, USA. 13Division of Pulmonary, Critical Care, and Sleep Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA. 14Pulmonary and Critical Care Medicine Section (506/111G), Department of Veterans Affairs Healthsystem, 2215 Fuller Road, Ann Arbor, MI 48105-2303, USA. 21. Leckie MJ, Jenkins GR, Khan J, Smith SJ, Walker C, Barnes PJ, et al. Sputum T lymphocytes in asthma, COPD and healthy subjects have the phenotype of activated intraepithelial T cells (CD69+ CD103+). Thorax. 2003;58:23–9. 22. Heron M, Grutters JC, ten Dam-Molenkamp KM, Hijdra D, van Heugten- Roeling A, Claessen AM, et al. Bronchoalveolar lavage cell pattern from healthy human lung. Clin Exp Immunol. 2012;167:523–31. References J Leukoc Biol. 2009;86:479–89. 14. Majori M, Corradi M, Caminati A, Cacciani G, Bertacco S, Pesci A. 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Anti-IL-5 (mepolizumab) therapy reduces eosinophil activation ex vivo and increases IL-5 and IL-5 receptor levels. J Allergy Clin Immunol. 2008;121:1473–83. 1483 e1471-1474. 19. Freeman CM, Martinez FJ, Han MK, Washko Jr GR, McCubbrey AL, Chensue SW, et al. Lung CD8+ T cells in COPD have increased expression of bacterial TLRs. Respir Res. 2013;14:13. 43. Davoine F, Labonte I, Ferland C, Mazer B, Chakir J, Laviolette M. Role and modulation of CD16 expression on eosinophils by cytokines and immune complexes. Int Arch Allergy Immunol. 2004;134:165–72. 20. Lay JC, Peden DB, Alexis NE. Received: 27 November 2014 Accepted: 26 December 2014 Received: 27 November 2014 Accepted: 26 December 2014 23. Hiemstra PS. Altered macrophage function in chronic obstructive pulmonary disease. Ann Am Thorac Soc. 2013;10(Suppl):S180–5. 24. Woodruff PG, Koth LL, Yang YH, Rodriguez MW, Favoreto S, Dolganov GM, et al. A distinctive alveolar macrophage activation state induced by cigarette smoking. Am J Respir Crit Care Med. 2005;172:1383–92. 44. Atar OD, Eisert C, Pokov I, Serebruany VL. Stability validation of paraformaldehyde-fixed samples for the assessment of the platelet PECAM-1, P-selectin, and PAR-1 thrombin receptor by flow cytometry. J Thromb Thrombolysis. 2010;30:79–83. 45. Stewart JC, Villasmil ML, Frampton MW. Changes in fluorescence intensity of selected leukocyte surface markers following fixation. Cytometry A. 2007;71:379–85. 46. Hodge S, Hodge G, Nairn J, Holmes M, Reynolds PN. Increased airway granzyme B and perforin in current and ex-smoking COPD subjects. COPD. 2006;3:179–87. 47. Kim WD, Chi HS, Choe KH, Oh YM, Lee SD, Kim KR, et al. A possible role for CD8+ and non-CD8+ cell granzyme B in early small airway wall remodelling in centrilobular emphysema. Respirology. 2013;18:688–96. 45. Stewart JC, Villasmil ML, Frampton MW. Changes in fluorescence intensity of selected leukocyte surface markers following fixation. Cytometry A. 2007;71:379–85. Freeman et al. Journal of Translational Medicine (2015) 13:19 46. Hodge S, Hodge G, Nairn J, Holmes M, Reynolds PN. Increased airway granzyme B and perforin in current and ex-smoking COPD subjects. COPD. 2006;3:179–87. 44. Atar OD, Eisert C, Pokov I, Serebruany VL. Stability validation of paraformaldehyde-fixed samples for the assessment of the platelet PECAM-1, P-selectin, and PAR-1 thrombin receptor by flow cytometry. J Thromb Thrombolysis. 2010;30:79–83. 47. Kim WD, Chi HS, Choe KH, Oh YM, Lee SD, Kim KR, et al. A possible role for CD8+ and non-CD8+ cell granzyme B in early small airway wall remodelling in centrilobular emphysema. Respirology. 2013;18:688–96. References Flow cytometry of sputum: assessing inflammation and immune response elements in the bronchial airways. Inhal Toxicol. 2011;23:392–406. Page 17 of 17 Freeman et al. 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The long non-coding RNA LINC01013 enhances invasion of human anaplastic large-cell lymphoma
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The long non-coding RNA LINC01013 enhances invasion of human anaplastic large-cell lymphoma Received: 31 May 2016 Accepted: 22 February 2017 Published: xx xx xxxx I-Hsiao Chung1, Pei-Hsuan Lu1,2, Yang-Hsiang Lin1, Ming-Ming Tsai3,4, Yun-Wen Lin1, Chau- Ting Yeh5 & Kwang-Huei Lin1,5,6 Anaplastic large-cell lymphoma (ALCL) is a rare type of highly malignant, non-Hodgkin lymphoma (NHL). Currently, only studies on the chimeric oncogene NPM-ALK have reported a link to ALCL progression. However, the specific molecular mechanisms underlying the invasion of ALCL are still unclear. Here, we sought to investigate differentially expressed, long non-coding RNAs (lncRNAs) in ALCL and their potential biological function. Our microarray analyses revealed that LINC01013, a novel non-coding RNA gene, was highly expressed in clinical specimens of ALCL and was significantly upregulated in invasive ALCL cell lines. Knockdown of LINC01013 suppressed tumor cell invasion; conversely, its overexpression enhanced tumor cell invasion. LINC01013-induced invasion was mediated by activation of the epithelial-to-mesenchymal transition (EMT)-associated proteins, snail and fibronectin. Specifically, LINC01013 induced snail, resulting in activation of fibronectin and enhanced ALCL cell invasion. Collectively, these findings support a potential role for LINC01013 in cancer cell invasion through the snail-fibronectin activation cascade and suggest that LINC01013 could potentially be utilized as a metastasis marker in ALCL. ALCL is a distinct subset of non-Hodgkin T-cell lymphoma associated with the presence of large pleomor- phic and aberrant cells that express CD30 and T-cell markers1. The well known t(2;5)(p23;q35) translocation is the most frequent genetic background in ALCL. This translocation was identified from the resulting fusion of the receptor tyrosine kinase (RTK), anaplastic lymphoma kinase (ALK), with nucleophosmin (NPM)2. This NPM-ALK fusion protein, which is highly tyrosine phosphorylated and recruits more than 40 proteins, has been reported to promote ALCL progression by triggering activation of transduction pathways primarily involved in proliferative and antiapoptotic responses3, 4. Nevertheless, neither ALK nor other recurrent translocations are expressed in approximately 15–40% of ALCL cases5. Although the current World Health Organization classifi- cation of lymphomas places ALK(+) and ALK(−) ALCL in the same category, more recent studies suggest that these two types of lymphomas, as well as cutaneous ALCL, might correspond to different entities.h y y gf The majority of ALK(+) ALCL cases are diagnosed at advanced stages (III and IV) that display systemic dis- ease with generalized lymphadenopathy and extranodal metastasis, especially in the skin and in soft tissues, such as the liver, lung, and spleen6. Similar observations were made in NPM-ALK transgenic mice, confirming that ALK(+) malignancies are very invasive7. www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 Results E i Expression of lncRNA in ALCL. To identify aberrantly expressed lncRNAs, we characterized lncRNA expression patterns in ALCL specimens using oligonucleotide arrays. Overall, 51 altered lncRNAs were identi- fied in ALCL; 20 were up-regulated and 31 were down-regulated (Fig. 1a). We investigated these overexpressed lncRNAs for their potential function in ALCL progression, focusing on the top five non-coding genes (fold change > 3.5), BMS1P20, LINC01013, MIR503HG, RNF144A-AS1 and CACNA1G-AS1 (Table 1). We validated the increased expression of these genes in clinical specimens of ALCL, showing that expression levels were increased ~10-fold for BMS1P20, ~17-fold for LINC01013, ~19-fold for MIR503HG, ~5-fold for CACNA1G-AS1 and ~15-fold for RNF144A-AS1 (Fig. 1b). Collectively, these results confirm that these five lncRNAs are highly expressed in ALCL. LINC01013 is associated with ALCL cell invasion. To verify the specific functions of lncRNAs in ALCL, we selected three ALK(+) ALCL cell lines: SR-786 (low-invasive), KARPAS-299 (moderately invasive) and Matrigel-selected KARPAS-invasive cells (high-invasive) (Fig. 2a). The expression levels of the lncRNAs, BMS1P20, LINC01013, MIR503HG, CACNA1G-AS1 and RNF144A-AS1 were determined in these cell lines (Fig. 2b). Notably, LINC01013 was highly expressed in the more invasive KARPAS-invasive cell line (Fig. 2b, left panel), suggesting that LINC01013 may be played a pivotal role in ALCL cell invasion. LINC01013 depletion suppresses ALCL cell invasion. To determine the effects of LINC01013 on cell invasion, we established LINC01013-knockdown KASPAS-299 and KASPAS-invasive cell lines. Notably, KASPAS-299 and KASPAS-invasive cell lines depleted of LINC01013 displayed significantly decreased invasion (~2-fold) compared with control cells (Fig. 3a). The epithelial-to-mesenchymal transition (EMT)-associated markers, snail and fibronectin, were also significantly decreased in LINC01013-depleted cells compared with con- trol cells (Fig. 3b,c). Snail, a transcription factor associated with cancer metastasis, regulates fibronectin to pro- mote lymphoma cell invasion. Similarly, depletion of snail in KASPAS-299 and KASPAS-invasive cells decreased invasion ability compared with control cells (Fig. 4a), and markedly down-regulated fibronectin (Fig. 4b,c). The expression levels of other Snail targets or EMT regulators have no effect between control and snail-depleted cells (Fig. S1) or control and LINC01013-depleted cells (Fig. S2). Taken together, these data confirm the requirement of LINC01013 to accelerate tumor cell invasion and implicate the snail-fibronectin cascade in this process. LINC01013 promotes ALCL cell invasion by activating the snail pathway. To further confirm the involvement of snail activation in LINC01013-induced phenotypic changes, we performed invasion assays using LINC01013-overexpressing cells. Results E i Notably, LINC01013-overexpressing SR-786 cells (SR-786-LINC01013) displayed significantly increased invasion (~2–3-fold) compared with parental SR-786 cell controls (Fig. 5a,b, left panel), and this phenotype was attenuated by snail depletion (Fig. 5a, right panel). SR-786-LINC01013 cells also exhibited marked upregulation of snail and fibronectin, an increase that was specifically blocked by depletion of snail (Fig. 5b, right panel, and c). Collectively, these results support a potential role of LINC01013 in promoting cancer cell invasion through activation of the snail-fibronectin cascade in ALCL (Fig. 5d). The long non-coding RNA LINC01013 enhances invasion of human anaplastic large-cell lymphoma However, the specific regulatory mechanisms underlying the invasion of ALK(+) ALCL are still unclear. Recent reports have demonstrated the important role of non-protein–coding RNA (ncRNA) components of the human genome, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), in cancer forma- tion or development8, 9. Many types of ncRNA play pivotal roles in cancer biology10, 11. LncRNAs are aberrantly 1Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.). 2Department of Dermatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan (R.O.C.). 3Department of Nursing, Chang Gung University of Science and Technology, Taoyuan, Taiwan (R.O.C.). 4Department of General Surgery, Chang Gung Memorial Hospital, Chiayi, Taiwan (R.O.C.). 5Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan (R.O.C.). 6Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan (R.O.C.). I-Hsiao Chung and Pei-Hsuan Lu contributed equally to this work. Correspondence and requests for materials should be addressed to K.-H.L. (email: khlin@mail.cgu.edu.tw) Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 1 www.nature.com/scientificreports/ expressed in various kinds of cancer, and the expression levels of certain lncRNAs are associated with disease pro- gression or diagnosis, or might serve as potential therapeutic targets12–14. Further, the clinical significance of the contribution of lncRNAs to ALCL development and the key roles of lncRNA functional networks are currently unknown. In this study, we investigated the invasion activity involving ALK and the molecular mechanisms underlying the pathogenesis of ALK(+) ALCL. We found that several lncRNA genes were highly expressed in ALCL clin- ical specimens and hypothesized that their functions were associated with cancer progression. Specifically, our microarray analysis revealed that LINC01013 (long intergenic non-protein–coding RNA 1013), a novel lncRNA that has not been linked to human cancer in the literature, is overexpressed in clinical specimens of ALCL and is significantly up-regulated in invasive ALK(+) ALCL cell lines. We further investigated and characterized this aberrantly expressed lncRNA in ALCL to determine whether it can be used as a novel biomarker and/or thera- peutic target for ALCL. Discussion No recent studies have reported an association between lncRNAs and ALCL progression or, by extension, the involvement of an lncRNA-mediated mechanism in the invasion of ALCL. To identify specific pathways under- lying ALCL carcinogenesis, we used an oligonucleotide microarray analysis of ncRNA genes to identify lncRNAs that were differentially expressed in ALCL. We further evaluated clinical specimens for aberrantly expressed lncR- NAs to identify potential biomarkers of ALCL invasion. Notably, we found that the novel lncRNA, LINC01013, is highly expressed in ALCL specimens and showed that its expression is positively correlated with the invasiv- ity of ALK(+) cells. Gain- and loss-of-function experimental strategies clearly demonstrated that LINC01013 enhanced ALK(+) ALCL cell invasion. Thus, LINC01013 may be a novel oncogene that could serve as an invasion marker for ALK(+) ALCL metastases. LncRNAs are important regulators of gene expression and are thought to have a wide range of functions in cellular and developmental processes16–18. The functions of a few lncRNAs have been experimentally defined19, 20. These studies have demonstrated the involvement of lncRNAs in fundamental processes of gene regulation, including chromatin modification, direct transcriptional regulation, RNA processing, post-translational regu- lation of protein activity or localization, and miRNA modulation. In the current study, we demonstrated that LINC01013 promotes an increase in mRNA and protein expression levels of snail and fibronectin, indicating the involvement of lncRNA in the transcriptional regulation of downstream genes. Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 2 www.nature.com/scientificreports/ Figure 1. Analysis and validation of lncRNAs in ALCL specimens. (a) Schematic diagram showing application of gene expression microarrays (~7419 lncRNAs) to the analysis of lncRNAs. These lncRNAs were selected based on the cut-off value. The 20 up-regulated (fold change > 2.0) and 31 down-regulated (fold change < 0.5) lncRNA were filtered and narrowed down form data base. (b) Expression levels of LncRNAs in ALCL specimens (3 paired specimens of patients) were measured by q-RT-PCR. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Figure 1. Analysis and validation of lncRNAs in ALCL of gene expression microarrays ( 7419 lncRNAs) to th Figure 1. Analysis and validation of lncRNAs in ALCL specimens. (a) Schematic diagram showing application of gene expression microarrays (~7419 lncRNAs) to the analysis of lncRNAs. These lncRNAs were selected based on the cut-off value. The 20 up-regulated (fold change > 2.0) and 31 down-regulated (fold change < 0.5) lncRNA were filtered and narrowed down form data base. www.nature.com/scientificreports/ www.nature.com/scientificreports/ Gene Symbol Fold change BMS1P20 6.707 LINC01013 5.025 MIR503HG 4.419 CACNA1G-AS1 3.712 RNF144A-AS1 3.631 LOC100506027 3.300 MIAT 3.119 FLJ42709 2.767 LOC100506013 2.734 SNORD113-2 2.605 FLJ42709 2.503 MIAT 2.444 LOC339240 2.255 KIAA0125 2.226 MIAT 2.215 MIAT 2.209 MIAT 2.150 SNORD114-11 2.006 SNORD111B 2.004 MIAT 2.001 Table 1. Up-regulated lncRNAs of anaplastic large T cell lymphoma (ALK+). T/N > 2.0. Table 1. Up-regulated lncRNAs of anaplastic large T cell lymphoma (ALK+). T/N > 2.0. activator of transcription) pathways24, 25. Activation of STAT3 is associated with a specific signature that includes several transcription factors (e.g., CEBP/β), cell cycle (e.g., cyclin D, c-myc) and survival/apoptosis molecules (e.g., Bcl-A2, Bcl-XL, survivin, MCL-1), and cell-adhesion proteins26. These studies have demonstrated the regu- lation of coding genes and their cross-talk in ALCL tumor formation. Several reports have shown that miRNAs, a type of short non-coding RNA, regulate ALCL malignancies. For example, miR-29a expression was found to modulate apoptosis through inhibition of MCL-1 expression in ALCL27; ectopic expression of miR-150 inhib- its proliferation and blocks S-phase entry of ALK(+) cells28; and downregulation of miR-16 induces vascular endothelial growth factor (VEGF) expression in ALK(+) ALCL29. However, the detailed role of long non-coding genes in the pathogenesis of ALCL is still unclear and may represent an important avenue for future research.i g p g y p p In conclusion, this study is the first to demonstrate the involvement of an lncRNA in ALCL tumor progres- sion. The results provide new insights into the mechanism by which the lncRNA, LINC01013, contributes to the promotion of ALCL cell invasion, showing that it acts through activation of the snail-fibronectin cascade. Our findings collectively support a potential role of LINC01013 in ALCL progression and suggest that LINC01013 expression could be effectively utilized as a metastatic marker in ALCL. Discussion (b) Expression levels of LncRNAs in ALCL specimens (3 paired specimens of patients) were measured by q-RT-PCR. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). The mesenchymal marker snail is a core transcription factor in the EMT process that stimulates expression of the downstream target gene encoding fibronectin to enhance cancer invasion21. To date, few studies have linked the regulation of lncRNA and snail/fibronectin in lymphoma. LINC01013 enhances invasion abilities in ALK(+) ALCL cell lines and may stimulate metastasis through activation of snail-fibronectin components. Our findings are consistent with the conclusion that activation of these mesenchymal markers leads to ALCL cell metastasis. Previous studies of ALCL progression have focused on NPM1-ALK translocation and its relative contribu- tion to pathogenesis22. Fusions of ALK have oncogenic potential because their aberrant tyrosine kinase activ- ity enhances cell proliferation and survival and promotes cytoskeletal earrangement23. NPM1-ALK–interacting molecules ultimately lead to the activation of key pathways, including RAS/ERK (extracellular signal-regulated kinase), phospholipase C (PLC-γ), phosphoinositide 3-kinase (PI3K), and JAK/STAT (signal transducer and The mesenchymal marker snail is a core transcription factor in the EMT process that stimulates expression of the downstream target gene encoding fibronectin to enhance cancer invasion21. To date, few studies have linked the regulation of lncRNA and snail/fibronectin in lymphoma. LINC01013 enhances invasion abilities in ALK(+) ALCL cell lines and may stimulate metastasis through activation of snail-fibronectin components. Our findings are consistent with the conclusion that activation of these mesenchymal markers leads to ALCL cell metastasis. y Previous studies of ALCL progression have focused on NPM1-ALK translocation and its relative contribu- tion to pathogenesis22. Fusions of ALK have oncogenic potential because their aberrant tyrosine kinase activ- ity enhances cell proliferation and survival and promotes cytoskeletal earrangement23. NPM1-ALK–interacting molecules ultimately lead to the activation of key pathways, including RAS/ERK (extracellular signal-regulated kinase), phospholipase C (PLC-γ), phosphoinositide 3-kinase (PI3K), and JAK/STAT (signal transducer and Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 3 Materials and Methods Ethics statement. All the experiments were performed in accordance with the approved guidelines of the Chang Gung Memorial Hospital Institutions Review Board (IRB: 103-3205B). Informed consent was obtained from all patients involved in this study. Tissue specimens. A total of ALCL tumor tissue and adjacent noncancerous mucosa were obtained from Department of Dermatology, Chang Gung Memorial Hospital. RNA extraction and gene expression microarrays. Total RNA from paired ALCL tumor tissue and adjacent noncancerous mucosa samples (N = 3) were extracted using the TRIzol reagent (Life Technologies, Rockville, MD, USA), as described previously15. Total RNA (20 μg) was used for labeling and hybridization with the SurePrint G3 Human Gene Expression array (Agilent, Welgene Biotech, Taiwan) containing 7419 lncRNAs and 27958 human genes. Slides were scanned and intensities were acquired using GenePix Pro 4.1 software (Axon Instruments Inc. Foster City, CA, USA). Cell culture. SR-786, KARPAS-299, and Matrigel-selected KARPAS-invasive human ALK(+) ALCL cell lines were routinely cultured at 37 °C in a humidified atmosphere of 95% air and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% or 15% fetal bovine serum (FBS). The references for SR-786 and KARPAS-299 cell lines are Human Cell Culture Vol. III, 355–370 (J.R.W. Masters and B.O. Palsson). These are human ALK(+) large T cell lymphoma cell lines. KASPAS-invasive cells were harvested form three rounds of Matrigel-selected (invasion assay) KASPAS-299. Cloning of LINC01013. cDNA was synthesized from total RNA (1 μg) using Superscript II reverse tran- scriptase (Invitrogen, Carlsbad, CA, USA) and random hexamer primers (Invitrogen). LINC01013 was amplified by polymerase chain reaction (PCR) using the primer pair 5′-CAG GAA GCC AGC ATT TTT AAT-3′ (forward) and 5′-CAA ATA ATA TCT TGC TTT TAT-3′ (reverse), and the following thermocycling conditions: 30 cycles Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 4 www.nature.com/scientificreports/ ntificreports/ Figure 2. LINC01013 is associated with tumor-invasive functions. (a) Left panel: Invasion ability was analyzed in SR-786, KARPAS-299, and KARPAS-invasive cell lines using Transwell assays. Invasion activity was determined by counting the number of cells traversing the Matrigel to the lower chamber. Transwell filters were stained with crystal violet. Right panel: Quantification of invasion ability. (b) BMS1P20, LINC01013, MIR503HG, RNF144A-AS1 and CACNA1G-AS1 expression levels in three cell lines were measured by q-RT- PCR. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Figure 2. LINC01013 is associated with tumor-invasive functions. Materials and Methods (a) Left panel: Invasion ability was analyzed in SR-786, KARPAS-299, and KARPAS-invasive cell lines using Transwell assays. Invasion activity was determined by counting the number of cells traversing the Matrigel to the lower chamber. Transwell filters were stained with crystal violet. Right panel: Quantification of invasion ability. (b) BMS1P20, LINC01013, MIR503HG, RNF144A-AS1 and CACNA1G-AS1 expression levels in three cell lines were measured by q-RT- PCR. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Figure 2. LINC01013 is associated with tumor-invasive functions. (a) Left panel: Invasion ability was analyzed in SR-786, KARPAS-299, and KARPAS-invasive cell lines using Transwell assays. Invasion activity was determined by counting the number of cells traversing the Matrigel to the lower chamber. Transwell filters were stained with crystal violet. Right panel: Quantification of invasion ability. (b) BMS1P20, LINC01013, MIR503HG, RNF144A-AS1 and CACNA1G-AS1 expression levels in three cell lines were measured by q-RT- PCR. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). at 95 °C for 1 min, 58 °C for 1 min, and 72 °C for 2 min. The LINC01013 open reading frame was ligated into the pcDNA 3.0 expression vector, and the resulting construct was sequenced to confirm the presence of the gene. t 95 °C for 1 min, 58 °C for 1 min, and 72 °C for 2 min. The LINC01013 open reading frame was ligated into the cDNA 3.0 expression vector, and the resulting construct was sequenced to confirm the presence of the gene. Immunoblot analysis. Total cell lysates and conditioned media were prepared, and protein concentrations were determined using a Bradford assay kit (Pierce Biotechnology, Rockford, IL, USA). Equivalent amounts of protein were fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) on a 10% gel. Separated proteins were transferred to a nitrocellulose membrane (pH 7.9; Amersham Biosciences Inc., Piscataway, NJ, USA), blocked with 5% non-fat powdered milk, and incubated with specific anti-snail (Cell Signaling Technology, Cell Signaling, Danvers, USA; #6615) and anti-fibronectin (Santa Cruz Biotechnology, Santa Cruz, CA, USA; sc-9068) primary antibodies at 4 °C overnight. After washing, membranes were incubated with horseradish peroxidase (HRP)-conjugated anti-mouse, anti-rabbit or anti-goat IgG secondary antibody, as appropriate, for 1 h at room temperature. Immune complexes were visualized using an enhanced chemilumines- cence (ECL) detection kit (Amersham) and Fuji X-ray film. Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 5 entificreports/ Figure 3. LINC01013 depletion suppresses ALCL cell invasion. Materials and Methods (a) Left panel: The invasion ability of KARPAS-299 and KARPAS-invasive cell lines was analyzed using Transwell assays under LINC01013-depleted (LINC01013 KD) and control (Luc.) conditions. Right panel: Quantification of invasive ability and LINC01013 expression levels. (b) Snail and fibronectin expression levels in these cell lines were determined by q-RT-PCR (c) and Western blot analysis. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 3. LINC01013 depletion suppresses ALCL cell invasion. (a) Left panel: The invasion ability of KARPAS-299 and KARPAS-invasive cell lines was analyzed using Transwell assays under LINC01013-depleted (LINC01013 KD) and control (Luc.) conditions. Right panel: Quantification of invasive ability and LINC01013 expression levels. (b) Snail and fibronectin expression levels in these cell lines were determined by q-RT-PCR (c) and Western blot analysis. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Establishing SR-786 cell lines stably overexpressing LINC01013. The SR-786 cell line, grown in 10-cm cell culture dishes, was transfected with the LINC01013 expression plasmid using the Lipofectamine rea- gent (Invitrogen). After 24 h, transformants were selected from transfected cells by growing in medium con- taining the antibiotic neomycin G418 (400–800 μg/ml) for 2–3 weeks. Survival clones were pooled and used to western blot or functional assay. Expression levels of LINC01013 RNA in the selected clones were determined using quantitative reverse transcription-PCR (q-RT-PCR). shRNA-mediated LINC01013 knockdown. Short hairpin RNA (shRNA) sequences targeting LINC01013 were purchased from the National RNAi Core Facility (Institute of Molecular Biology, Academia Sinica, Taiwan). The KARPAS-299 and KARPAS-invasive cell lines were transiently transfected with shRNA tar- geting the endogenous LINC01013 gene using the TurboFect reagent (Invitrogen). LINC01013 repression was confirmed by q-RT-PCR. Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 6 www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 5. LINC01013 acts through the snail-fibronectin cascade to enhance cell invasion. (a) The invasion ability of SR-786 and SR-786-LINC01013 cells was analyzed using Transwell assays under snail-depleted (Snail KD) and control (Luc.) conditions. (b) Left panel: Quantification of invasive ability and LINC01013 expression levels. Right panel: Snail and fibronectin expression levels in these cell lines were determined by q-RT-PCR (c) and Western blot analysis. (d) Schematic depiction of LINC01013 promotion of ALCL invasion through activation of the snail-fibronectin cascade. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Figure 5. LINC01013 acts through the snail-fibronectin cascade to enhance cell invasion. (a) The invasion ability of SR-786 and SR-786-LINC01013 cells was analyzed using Transwell assays under snail-depleted (Snail KD) and control (Luc.) conditions. (b) Left panel: Quantification of invasive ability and LINC01013 expression levels. Right panel: Snail and fibronectin expression levels in these cell lines were determined by q-RT-PCR (c) and Western blot analysis. (d) Schematic depiction of LINC01013 promotion of ALCL invasion through activation of the snail-fibronectin cascade. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Matrigel (Becton-Dickinson). For both assays, the pore size of the upper chamber was 8 mm. The medium in the upper chamber was serum-free DMEM, and the lower chamber contained DMEM supplemented with 20% FBS, included as a chemoattractant. After incubation for 24 h at 37 °C, cells traversing the filter from the upper to lower chamber were stained with crystal violet and counted. Experiments were repeated at least three times. Matrigel (Becton-Dickinson). For both assays, the pore size of the upper chamber was 8 mm. The medium in the upper chamber was serum-free DMEM, and the lower chamber contained DMEM supplemented with 20% FBS, included as a chemoattractant. After incubation for 24 h at 37 °C, cells traversing the filter from the upper to lower chamber were stained with crystal violet and counted. Experiments were repeated at least three times. Statistical analysis. Data are expressed as mean values ± SEM of at least three experiments. Statistical anal- yses were performed using Student’s t test and one-way analysis of variance (ANOVA). Where appropriate, the Mann–Whitney U test or Fisher’s exact test was used to compare two groups; a Kruskal–Wallis test or Pearson’s χ2 test was used if more than two groups were compared. The relationship between the results of two different exam- inations was analyzed with Spearman’s correlation test. www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 4. Snail depletion suppresses ALCL cell invasion. (a) Left panel: Invasion ability of KARPAS-299 and KARPAS-invasive cell lines was analyzed using Transwell assays under snail-depleted (Snail KD) and control (Luc.) conditions. Right panel: Quantification of invasion assay results. (b) Snail and fibronectin expression levels in these cell lines were determined by q-RT-PC (c) and Western blot analysis. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). Figure 4. Snail depletion suppresses ALCL cell invasion. (a) Left panel: Invasion ability of KARPAS-299 and KARPAS-invasive cell lines was analyzed using Transwell assays under snail-depleted (Snail KD) and control (Luc.) conditions. Right panel: Quantification of invasion assay results. (b) Snail and fibronectin expression levels in these cell lines were determined by q-RT-PC (c) and Western blot analysis. Differences were analyzed using a Kruskal-Wallis test (*P < 0.05). shRNA-mediated snail knockdown. Short hairpin RNA (shRNA) sequences targeting snail were pur- chased from the National RNAi Core Facility (Institute of Molecular Biology, Academia Sinica, Taiwan). The SR-786, SR-786-LINC01013, KARPAS-299 and KARPAS-invasive cell lines were transiently transfected with shRNA targeting endogenous snail mRNA using the TurboFect reagent (Invitrogen). Snail repression was con- firmed by Western blot analysis. shRNA-mediated snail knockdown. Short hairpin RNA (shRNA) sequences targeting snail were pur- chased from the National RNAi Core Facility (Institute of Molecular Biology, Academia Sinica, Taiwan). The SR-786, SR-786-LINC01013, KARPAS-299 and KARPAS-invasive cell lines were transiently transfected with shRNA targeting endogenous snail mRNA using the TurboFect reagent (Invitrogen). Snail repression was con- firmed by Western blot analysis. Invasion assays. The influence of LINC01013 on invasion ability in vitro was determined by Transwell assay (Falcon BD, Franklin Lakes, NJ) using LINC01013-depleted KARPAS-299 or LINC01013-overexpressed SR-786 cells, as described previously15. Briefly, cell density was adjusted to 105 cells/ml, and 100 μl of the suspension was seeded into upper chambers of the Transwell plate, either coated (invasion) or not coated (migration) with Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 7 Acknowledgementsh g This work is supported by grants from the Chang Gung Memorial Hospital (CMRPG3D1841 to P.H.L. and MRP130, CMRPD1D0381, 0382, 0383 to K.H.L.). g This work is supported by grants from the Chang Gung Memorial Hospital (CMRPG3D1841 to P.H.L. BMRP130, CMRPD1D0381, 0382, 0383 to K.H.L.). References Constitutive control of AKT1 gene expression by JUNB/CJUN in ALK+ anaplastic large-cell lymphoma: a novel crosstalk mechanism Leukemia 29 2162 2172 doi 10 1038/le 2015127 (2015) chemosensitivity in ALK-positive anaplastic large cell lymphoma. Leuk Lymphoma 1–9, doi:10.3109/10428194.2015.1068306 (2015) 5. Atsaves, V. et al. Constitutive control of AKT1 gene expression by JUNB/CJUN in ALK+ anaplastic large-cell lymphoma: a nove crosstalk mechanism. Leukemia 29, 2162–2172, doi:10.1038/leu2015127 (2015). 6. Crescenzo, R. et al. Convergent mutations and kinase fusions lead to oncogenic STAT3 activation in anaplastic large cell lymphoma Cancer Cell 27, 516–532, doi:10.1016/j.ccell.2015.03.006 (2015). g Cancer Cell 27, 516–532, doi:10.1016/j.ccell.2015.03.006 (2015) j 7. Desjobert, C. et al. MiR-29a down-regulation in ALK-positive anaplastic large cell lymphomas contributes to apoptosis blockade through MCL-1 overexpression. Blood 117, 6627–6637, doi:10.1182/blood-2010-09-301994 (2011). g 8. Hoareau-Aveilla, C. et al. Reversal of microRNA-150 silencing disadvantages crizotinib-resistant NPM-ALK(+) cell growth. J Clin Invest 125, 3505–3518, doi:10.1172/JCI78488 (2015). 29. Dejean, E. et al. 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Atsaves, V. et al. www.nature.com/scientificreports/ P-values < 0.05 were considered statistically significant. 8 Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 www.nature.com/scientificreports/ Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 Additional Information Supplementary information accompanies this paper at doi:10.1038/s41598-017-00382-7 Supplementary information accompanies this paper at doi:10.1038/s41598-017-00382-7 Competing Interests: The authors declare that they have no competing interests. Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Scientific Reports | 7: 295 | DOI:10.1038/s41598-017-00382-7 9 www.nature.com/scientificreports/ This work is licensed under a Creative Commons Attribution 4.0 International License. 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Klinische und histopathologische Beobachtungen an einem intra vitam diagnostizierten Fall von bronchialem Adenocarcinom mit Hautmetastasen
Journal of cancer research and clinical oncology
1,910
public-domain
9,257
I. ( A u s d e m I n s t i t u t ffir spez. P a t h o l . i n n e r e r K r a n k h e i t e n d e r K g l . U n i v e r s i t ~ t P a v i a [Prof. M:. A s c o l i ] . - - A u s d e m L a b o r a t o r i u m ffir a l l g e m . P a t h o l o g i e u n d H i s t o l o g i e [Prof. C. G o l g i ] . ) Klinische und histopathologische Beobachtungen an einem intra vitam diagnostizierten Fall yon bronchialem •denocarcinom mit Itautmetastasen. ~ron Laigi Stropeni. (Hierzu Tafel I.) Wenn auch die F'~lle yon Carcinom der Bronchien heutzutage nicht mehr jene grosse Seltenheit bilden, wie sie L a n g e r h a n s mit. Rticksicht auf seine Zeit wohl mit Recht hinstellte, so halte ich es doch fiir angezeigt, nachstehenden Fall aazuffihren, nicht nut, weii demselben eine vollst~indige kliniscbe Beobachtung zuteil geworden - - die einschl'~gige K.~uistik wurde ja gr6sstenteils yon Fachm~nnern der pathologischon Anatomie zusammengestellt - - soadern vor allem deshalb, well er mir ein gewisses Interesse darzubieten schien und schIiesslich auch wegea der Eigentfimlichkei~ mancher klinischea bzw. pathologisch-anatomischen Erscheinungen sowie der intra vitam mit Sicherheit und Genauigkeit gestellten Diagnose. Z u s a m m e n f a s s u n g der K r a n k e n g e s c h i c h t e . M. V[, 35 Jahre alt, Haush~ilterin, verheiratet, aus Zinasco (Provinz Pavia) tritt am 10. Dezember 1908 in die Klinik ein. Anamnese: Keine Erinnerung beztiglich der Voreltern. Der Vater starb 75 Jahre alt; an wolcher Krankheit ist unbekannt, die Mutter in ihrem 42. Jahre infolge einer Zwillingsgeburt. Von 5 Kindern ist Pat. das j/ingste, eine Schwester ist an Lunge~schwindsucht gestorben, 3 Brfider sind noch am Leben und gesund. In ihrer Kindheit erkraukte Pat. an Masern, im ftinften Lebensjahre an Diphtheritis; mit I2 Jahren stellten sich die ersten Menses ein. Mit 20 Jahren heiratete sie einen gesunden Mann: sechsmaligo Konzeption, jedoch nut viormal ausgetragene Schwangerschaft; die geborenen Kinder sind noch am Leben und gesund. Mit Zeitschriff fiir ,Krebsforschung. 9. Bd. i. Heft. 1 L. S t r o p e n i~ Fall yon bronchialem Adenoearcinom. 25 Jahron wurde sie yon einem Schlundabszess befallen; derselbe 5ffnete sieh spontan und heilte in etwa vierzehn Tagen. In ihrem 31. Jahre litt sio im Laufo einor Stillung an Mastitis. Im Oktober 1907 stelite sich links heftiges, bei tiefem Inspirium sich steigerndes, mit Fieber und troekenem Husten einhergehendes Seitenstechen ein; die als Pleuritis diagnostizierte Erkrankung hatte einen akuten Verlauf und heilte in etwa vierzehn Tagen dureh Pinselungen mit Jodtinktur. Veto Monat November 1907 bis zum Monat M~irz 1908 vollkommenes Wohlbefinden. Von dieser Zeit an begann Pat. h~iufig leiehte, nut selten heftige stechende Schmerzen am Thorax zu verspfiren, dieselben traten in der Regel links auf und mit vieltiigigen Zwisehenpausen; ihr Sitz war ein variabler: bald wurden sic auf die Seite, bald auf die Sehulter, bald w~eder auf den R@ken verlegt; sic wurden beim Atmen stErker, 5fret stellte sich gleiehzeitig und naehher Husten ein, mitunter trocken 7 zuweilen hingegen mit zEhem, klebrigem, nur ausnahmsweise Blutstreifen enthaltendemAuswurf. Gleichzeitig Unlust zur Arbeit, Appetitlosigkeit, m~ssiges Fieber, Kopfschmerzen, so dass w~hrend der seltenen schwereren Anfiille sich Patientin zu Bert legen musste. Durch eine nicht n~iher zu bestimmende Behandlung per os und dureh wiederholtes Finseln mit Jodtinktur versehwanden die krankhaften Erseheinungen 7 um aber nach einer bzw. zwei Woohen wieder aufzutreten. In den Intervallen ffihlte sieh Patientin vollkommen wohl. Unter diesem Abweohseln yon Wohl- und Unwohlsein verlief das Frfihjahr und der Sommer; anfangs Oktober aber gestaltete sich das Krankheitsbild zu einem bedenklicheren: links am Thorax stellte sieh heftiges, intermittierendes~ h/iufig auftretendes Seitenstechen ein, ferner Mattigkeit, Kopfweh, leiehtes Fieber, leiehte Atemnot, jedoch ohno Husten oder Auswurf. Naeh ein paar Woehen trat eine geringe Besserung ein und Pat. verliess das Bett. Aber recht bald musste si~ dasselbe wegen eines ganz gleiehen: yon hohem Fieber, sp~irliehem schleimigen Auswurf, Kopfschmerzen, Atemnot begleiteten rechts aufgetretenen Schmerzes wieder aufsuehen. Derselbe war liings der zehnten gippe Iokalisiert, stellte sieh anfallsweise ein - - wobei jeder Anfall ungef~hr zohn Minuten anhielt - - ; hierauf wurde er allm~hlieh schw~icher aber kontinuierlieh, mit Exazerbationen boim Tiefatmen und Nachlassen beim Liegen auf tier schmerzhaften Seite. Da Pat. keine Besserung zu erzielen vermoehte, suchte sie am 10. Dezember die Klinik auf. S t a t u s p r a e s e n s : Die Kranke klagt fiber allgemeine Sohw~iche, Appetitlosigkeit, Atemnot~ Sehmerz hinten reehts an der Thoraxbasis, l~ings der zehnten Rippe lokalisiert, kontinuierlich~ zu gewissen Tagesstunden sich steigernd. Pat. ist bei vollem Bewasstsein. Gesichtsausdruck leidend; obligate aktive Riiekenlage. Skelett kr~iftig, Muskelmassen entwickelt~ Fettpolster erhalten~ Haut braunfarbig~ feucht, elastiseh; keine 0edeme wahrnehmbar, keine Lymphganglien palpierbar. Temperatur 38, Atmung 44, Puls 98. An Hals und Kopf nichts Bemerkenswertes. T h o r a x : Stark asymmetrisch wegen st~irkerer huswSlbung der rechten H~ilf~e; die in tote retrahiert erscheinende linke H~ilfte weist - - jedoch nur vorn zwei erheblichere Einsenkungen auf, deren eine die zwei ersten ttippen, die anderr die fiinfte und sechste betrifft. Supra- und lnh'aklavikulargruben beider- - L. S t r o p e n i , Fall yon bronchialem Adenocaroinom. 3 seits eingesunken~ Interkostalriiume fiach, epigastrischer Winkel stumpf. Hinten Abfiachung der linken Thoraxh~ilfte an der Basis~ die rechte dagegen hervorragend. Vorwiegend kostal% wegen mangelhafter Ausdehnung der ~usserst schwach bewegliohen linken H~lfte asymmetrische Atmung; ebenso ist hinten an der Basis die Ausdehnung der reehten eine geringe. Kechter Thorax elastisch~ weniger links. Die rechtsseitige zehnte Rippe yon der Angularis scapulae bis zur mittleren Axiltaris druckempfindlich. Ffihlharer Stimmfremitus links-vorn-unten abgeschw~icht~ hinted Yon der Schulterblattgr~ite naeh unten aufgehoben; rechts erhalten. Die rechte Lungenspitze ragt um etwa 4 cm fiber das Schlfisselbein hinauf; die unteren K~nder haben normale Lage. Die linke Lungenspitze ist retrahiert und fiberragt nur um 2 cm das Schliisselbein. Die aktive Bewegliehkeit ist links nahezu aufgehoben; reehts auf der mittleren hxillaris betr~igt dieselbe 1 em. Perkussionssohall hell rechts vorn~ etwas ged~impft hinten an der Basis. Links hinten oben his zur Spina scapulae allmiihlich deutlicher werdende Hypophonese; yon dieser Stell~ ab vollst~ndige Diimpfung mit starkem Widerstand. Vorn oben hoher tympanitischer Sehall; derselbe zeigt weder Wintriehschen noch Gerhardtschen Schallwechsel; unten ged~mpfter Schall; die D~mpfungsgrenze vorl~uft veto unteren Rand der sechsten Rippe zwischen der Hemiklavikularis und der vorderen Axillaris~ auf dieser letzteren zum fiinften Interkostalraum~ erreieht auf der mittleren Axillaris die fiinfte Rippe und geht in die hintere D~mpfung fiber. Das Groeeosche paravertebrale Dreieck ist hinten reehts unten nicht vorhanden. Reehts vesikul~res Atmen~ hinted gross-~ mittel- und ldeinblasiges nieht klingendes Rasseln. Links iiberall abgeschw~chtes Atmen~ gross- und mittelblasige sehwach konsonierendo Rasselgeriiusche auf der Spitze und in der Axillargegend~ in welcher amphorisehes Atmen bestoht; vorn zerstreutes feinblasiges und subkrepierendes Rasseln; hinten ~iusserst schwache Atmung bis zur Schultcrblattgr~t% Stille an der Basis. Dutch die Probepunktion am unteren Winkel des linken Schulterblattes wcrden 2 ccm einer trfiben zitronengelben~ spoutan gerinnenden Fliissigkeit herausbefSrdert; Rivaltasche Reaktion negativ; Sediment aus vorwiegend einkernigen Leukozyten bcstehend; Agarausstriche steril. Frobepunktion ira achten Interkostalraum rechts negativ. Die Herzgegend nicht hervorgewSlbt; Spitzenstoss nicht sichtbar~ im fiinften Interkostalraum links, 1/2 cm innerhalb der Papillarlinie schwaeh fiihlbar. Die relative D~impfung ist durch eine yon der dritten Rippe auf der Parasternalis abgehendo, schr~ig naeh unten und aussen verlaufende~ schliesslich mit der Spitze zusammenfallende Linie begrenzt; die rechtsseitige Grenze reicht bis .9 ern welt rechts veto Sternalrand im vierten Interl~ostalraum. Die HerztSne siad schwach, dumpf, tier vernehmbar. Puls leicht arhythmisch. Nichts Nennenswertes beider Palpation und Perkussion der A b d o m i n a l organe. G e w i c h t : 44~500 kg. H a m : Strohgelb, sauer~ Durchschnittsmenge 500 ecru. Spez. Gew. 1021, Eiweiss~ Zucker, Blut fehlend; im Sediment wenige Epithelzellen der Harnblasr und unteren tlarnweg% sp~irliche Leukozyten.. 1" L. S t r o p e n i , Fall yon bronchialem Adenocarcinom. F ~ize s: breiartig~ gelbbraun ; niehts Bemerkenswertes bei der mikroskopischen Untersuchung. B l u t : Rote BlutkSrperehen 4000000; weisse 7000. Die mikroskopische Untersuchung (F~rbung nach R o m a n o w ski) ergibt keinen pathologischen Befund, ausser leichter Polyohromatophilie. S p u t u m : Schleimig-eitrig, nummul~r~ sp~rlioh~ Untersuehung auf K o c h sche Bazillen negativ~ ebenso jene auf elastische Fasern, sowie auf neoplastisch verd~ehtige Elemente; biologische Probe darch Einffihrung des Auswurfs in die PeritonealhShle zweier Meerschweinohen negativ. W~ihrend ihres Aufenthaltes in der l(linik zeigt Patientin eine langsame aber doeh fortschreitende Verschlimmerung~ ohne jedoch hierbei ein kachektisches Aussehen zu gewinnen. KSrpertemperatur morgens normal bzw. subfebril mit Steigerungen bis 38750--39 0 am Abend ; profuse Na~htsehweisse. Mitunter Schfittelfrost~ wobei das Fieber 2--3 Tage unausgesetzt anh~lt, um sodann seinen gewShnlichen Verlauf wieder zu nehmen. Appetit stets gering~ die Funktionen des Verdauungsapparats trage, die fast t~iglich vorgenommene Untersuehung des Harns hat niemals etwas Bemerkenswertes ergeben ; B en ee- J o n e s scher E[weisskSrper nicht vorhanden. Das SputurTl wird zu einem ziemlieh reichliehen ohne oder mit nur ~iusserst wenigen Blatstreifen~ yon. sehleimig-eitriger Beschaffenheit~ ohne bemerkenswerte mikroskopisohe Merkmale. Die Konfiguration des Thorax bleibt w~hrend des ganzen Aufenthaltes in der Klinik nahezu unver~,ndert, ebenso die Perkussions- und Auskultationsbefunde; nur in tier zweiten H~.lfte des November treten Anzeichen eines m~issigen perikardialen Ergusses auf, der dann in etwa zehn Tagen raseh wieder zur Resorption kam. Gegen Ende Januar beginnt der Stimmfremitus auoh auf der linken hinteren D~mpfungszone - - wenn auch etwas abgesehw~eht - - ffihlbar zu werden; eine ausgepr~gte Hyp(~phonese breitet sich allm~ihlich fiber den ganzen vorderen Lungenbezirk aus~ die subklavikul~re Grube ausgenommen, we der Perkussionssehall 7 stets hoch tympanitisch bleibt, die bestandig sehwache Atmung aber einen amphoriscben Charakter angenommen hat und die HerztSne mit einem ausgesprochen metallischen Klang fortgeleitet werden. Es werden zu versehiedenen Zeiten am ]inken Thorax ffinf Probepunktionen vorgenommen mit negativem Erfolge oder nur wenige Tr0pfen hellroter~ blutiger Flfissigkeit entleert; zweimal bekommt man mit Miihe ein pear Kubikzentimeter einer zitronengelben durehsiehtigen Flfissigkeit heraus, bei welcher die R i v a l t a sche Probe positiv ausfiillt und die mikroskopische Untersuehung sp~irliehe Leukozyten und wenige rote BlutkSrperehen zeigt; Kulturen bleiben steril. Die Kutanreaktion mit 25 proz. Tuberknlin ergibt wiederholt und stets negativen Erfolg. Die Kranke klagt h/~ufig fiber Sohmerzen neuralgischen Charakters, bald am linken Thorax~ bald am rechten, bald an den Extremit~ten, we dieselben insbesondere gegen Mitre Januar heftiger auftreten, um niemals mehr g~nzlir zu verschwinden. Bei einer allgemeinen Untersuchung, der die Kranke am 31. J a n u a r unterzogen- wird~ bemerkt man am unteren Drittel des linken Armes~ dicht unter der Epitrochlea eine kleine Geschwulst. Dieselbe ist haselnussgross~ hart~ fibrSs~ auf dan darunter- und umliegenden Geweben verschieblich, innig abet auf eine nur sehr kurze Strecke mit der vollkommen intakten Haut zusammenhangend~ an und L. S t r o p e n i , Fall yon bronchialem Adenocarcinom. f~ir sich schmerzlos und nieht druokempfindlich. Es wird keineLymphdrfise palpiert~ weder in der Axillar-~ noch in der Supra- bzw. Infraklavikular-~ noch in der Zervikalgegend. Mit Zustimmung der Krankeo wird der soeben besehriebene kleine Tumor am 1. Februar abgetragen. Am 2. Februar 7 w~hrend Patien~in nach dem Weehsel der W~isehe wieder in ihr Bert gelegt wird~ klagt sie fiber einen am linken Oberschenkel p15tzlieh aufgetretenen Sehmerz; bei der Untersuehung zeigt sich ein 0bersehenkelbruch an der Vereinigungsstelle des oberen mit dem mittleren Drittel. An den Leisten sind keine Ganglien zu fiihlen. Mit Rficksieht auf dieses unerwartete Vorkommnis werden nun regelm~ssig und mit grSsserer Frequenz Blutuntersuchungen angestellt (Deckglastrockenpr~iparat% F~rbung nach R o m a n o w s k i oder J e n n e r ) . Einzig wichtiger Befund hierbei: das Vorhandensein yon Myelozyten in sehr sp~irlieher Menge (1 pCt. der weissen BlutkSrperehen). Die mit der Tralaionsmethode behandelte Fraktur heilte niemals wieder: an der verletzten Stelle war zuletzt eine harte fihrSse Masse durehfiihlbar; dieselbe war mit dem Knoehen verwachsen und nur bei Druek oder bei aktiven bzw.passiven Bewegungsversuchen schmerzhaft. Am 26. Februar maeht sieh entspreehend dem unteren Rande des grossen Pektoralis, etwas unterhalb der M o h r e n h e i m s e h e n Grube ein zweiter kleiner Tumor bemerkbar, mit denselben Merkmalen wio der am hrme abgetragene; eine wallnussgrosse Gesehwulst wir~t aueh an der Nabelnarbe angetroffen, ganz gleieh beschaffen wie die beiden oben besehriebenen. Nirgends sind ver~'Ssserte Lymph. drfisen zu palpieren. Klein% harte, verschiebliehe Ganglien beginnen anfangs M~irz in der reehten und linken Axillargegend und an den Leiston fiihlbar zu werden; keines jedoeh am Halse oder in der Sapraklavikulargrube. Allm~ihlicher Kr~ifteverfall; am 15. M~rz 8 Uhr frfih Exitus. I. P a t h o l o g i s c h - a n a t o m i s c h e r Teil. Die mikroskopische Untersuchung der wiihrend des Lebens am Arme abgetragenen kleinen Geschwulst ergab~ d a s s e s sich um eine aus tells kubischen, tells zylindrischen Epithelzellen bestehende Neubildung handelte. Diese Zellen begrenzten mehrere den Alveolen einer Driise sehr Ahnlich sehende HohlrS.ume yon verschiedener Gestalt und GrSsse und waren reich an Protoplasma; letzteres war hell und schien an mancher Stelle des Sehnittes einen sich intensiver f~rbenden, dem Driisenlumen zugekehrten schmalen Saum zu besitzen, ohne dass selbst feinere F i i r b u n g s m e t h o d e n wie z. B. die yon S a u e r fiir den Bfirstenbesatz e m p f o h l e n e - es gestattet h~ttten, eine Differenzierung in F~iden und Wimpern wahrzunehmen. Der dem Basalteile der Zelle niiher gelegene Kern war gross, eif0rmig gestaltet~ nahezu bl~ischenartig mit sp~rlichem Chromatinnetz, zuweilen in Karyokinese begriffen. Hie und da war der Zellenbelag unterbrochen; die Zellkgirper waren L. Stropeni, Fall yon bronchialem Adenocarcinom. zerfallen, ja zerstSrt, und ihre Triimmer waren in den Lumina der Alveolen bemerkbar. Diese Epithelien lagen nicht auf einer elastischen Membran, vielmehr befand sich zwische,~ den ZellstrRngen ein aus sehr feinen, selten zu st~rkeren auff~lligeren Biindeln vereinigten Bindegewebsfasern bestehendes Stroma. An vielen Stellen war die sonst so gleichm~issige Struktur der Geschwulst durch ein wirres, stfirmisches Durcheinander yon Strangen atypischer, poly~drischer oder kubischer Zellen ver~indert, die ordnungslos und ohne eine bestimmte Richtung und hie und da eine mehr oder weniger weite H6hle begrenzend in die Tiefe des umliegenden Bindegewebes drangen. Diese Hohlrliume sowie die derjenigen Pattie des Tumors, die man als die typisch adenomat0se bezeichnen k6nnte, hatten tells das Aussehen vou AIveolen, tells yon R6hrchen und waren mit einer bald homogenen, bald granulSsen, im allgemeinen jedoch fibrilliiren Substanz angefiillt, worin Zelldetritus und Kerntrfimmer zu sehen waren. Der Tumor sass im Unterhautgewebe ohne irgend welchen Zusammenhang mit den Hautepithelien, doch waren die Sch'weissdrfisen so welt 'r gerfickt, dass ihre Kn~uel mit den Grenzen der Neubildung in Berfihrung getreten waren; an einigen Stellen bekam man den Eindruck, als ob diese Hautgebilde in Kontinuit~tsbeziehtulgen zu ddr Geschwulst stiinden. Es wird daher wohl kaum befremden, wenn mit Rficksicht auf die Aehnlichkeit dieser Befunde mit den von P e t e r s e n , Unna, C a m p a n i n i u. a. mitgeteilten ich anfangs der Ansicht war, man h~,tte es mit einem Adenocarcinom der Schweissdrfisen zu tun. Allein derartige Ne(lbildungen kommeu so selten vor~ dass es gerechtfertigt erscheinen musst% wenn fiber die Herkunft des untersuchten Tumors Zweifel aufstiegen und ich reich daher be-. m[ihte, yon der im ersten Augenblick gestellten Diagnose reich besser ztl fiberzeugen. Icb. suchte daher die Beschaffenheit des Inhaltes der Drfisenriiume zu bestimmen: mit Hilfe d e r - wegea des dabei sich rot fiirbenden Kolloids so vorzfiglich spezifischen - - Trainaschen Methode bekam ich eine lila-blaue F~i.rbung, wobei das Thionin eine metachromatische Rotfiirbung lieferte und das Meyersehe Muzikarmin durch elektive Farbung dieser Substanz gleichfalls den Beweis lieferte, dass es sich um Schleim handelte. Es zeigte sich somit deutlich, dass hier nicht eine primate Geschwulst vorliegen musste, sondern eine Metastas% fiir welche Annahme das u der anderen Hautgeschwfilstchen sowie die bereits oben erw~.hnte spontane Fraktur sprach. Diese Metastase musste notwendigerweise yon einem Adenocarcinom herstammeu, das in einem Schleimdriisen enthaltenden Gewebe zustaude gekommen. Auf Grund der welter unten angeffihrten Eriirterung fiber die Symptomatologie und mit Rficksicht auf das oben erwlihnte Ergebnis der mikro- L. Stropeni, Fall yon bronchialem Adenocarcinom. skopischen Untersuchung wurde nachstehende Diagnose gestellt und dem Obduzenten fibergeben : C a r c i n o m des l i n k e n H a u p t b r o n c h u s , i i b e r g r e i f e n d auf die g a u z e d a z u g e h S r i g e Lunge; E r w e i c h u n g , K a v e r n e n b i l d u n g und r e a k t i v e P l e u r i t i s ; M e t a s t a s e n an der H a u t , an den L y m p h driisen, am K n o c h e n m a r k mit k o n s e k u t i v e r F r a k t u r des l i n k e n Femurs. Bei der yon Prof. T r a i n a ausgeffihrten Obduktion land sich die klinische Diagnose in allen Punkten besti~tigt, wobei noch andere unauffMlig verlaufene Metastasen zutage kamen. Ich iibergehe hier alles im Sektionsprotokoll nicht streng Interessierende und beschriinke reich lediglich auf die Mitteilung der bemerkenswertesten bei der Leichemmtersuchung erhobenen Befnnde. Bei ErSffnung des Thorax stellen sich rechts alte Verwachsungen heraus; ebensolche auch links, sehr z~ihe und ganz besonders in tier diaphragmatischen Pleura dick. Verwachsungen bestehen auch zwischen der Thoraxwand und dem Perikardium, welches letztere Entziindungsvorg~inge mit serofibrinOsem h'~imorrhagischem Exsudat erkennen liisst. Entsprechend der linken V o r k a m m e r hiingt das Perikardium durch eine die oberste Partie des Mediastinum, den Lungenhilus, die peribronchialen Lymphganglien, den Bogen der Aorta und den absteigenden Anteil derselben zu einem einzigen Klumpen involvierende grauliche Masse mit der Pleura innig zusammen. Die ]inke Lunge ist kleiner, an der Spitze retrahiert, nicht erschlafft, hart, stellenweise mit weisslichen, verschieden grossen Kn6tchen von fibriiser Konsistenz besetzt. Die rechte Lunge zeigt neben Emphysemherden auch noch spiirliche neoplastische Knoten. Dureh einen in der Richtung des Hilus gefiihrten Schnitt wird die linke Lunge ihrer Liingsachse nacb und dabei auch die darunter liegende Milz geteilt. Auf der Schnittfli~che wird, entsprechend der Bifurkation der grossen Bronchien eine harte, graue, druckwiderstehende, yon erhabenen Strangen durchzogene Masse angetroffen, welche in die beiden Lappen des Organs in ihrer dem Hilus zugekehrten Seite eindringt und hierbei die Bronchien und die als schwarze Knoten auf der schmutzig-weissen Neoplasie hervortretenden peribronchialen Lymphdrfisen einhiillt. Durch diese Masse ziehen die Bronchien hindurch; infolgedessen sieht dieselbe wie ein BadesChwamm durchlOchert aus; das Bronchiallumen ist hierbei durch Granulationen und Unebenheiten der Schleimhaut - - die mitunter auch vollst~ndigen Versehluss bedingen kiinnen - - etwas verengert. Solche Unebenheiten der Bronchialschleimhaut nehmen im Hauptbronchus ihren Anfang, ungefahr 4 cm entfernt yon der Luftr(ihrenbifurkation und in Form yon knotenartigen Erhabenheiten und harten, derben L. Stropeni, Fall yon bronchialem Adenocarcinom. Streifen~ die das Bronchiallumen bis auf ein Drittel reduzieren und sich dann in die Bronchien des oberen bzw. unteren Lappens welter fortsetzen. Es finden sich keine Spuren eines in diese neoplastische Zentralmasse eingehiillten Parenchyms; yon der soeben genannten Masse gehen jedoch vereinzelte weisslich gefiirbte Strange ab, welche in die beiden Lappen eindringen, ohne aber jene eigentiimliche Tendenz, den Verzweigungen der Bronchien zu folgen, die Wolf als so charakteristisch ffir Bronchialcarcinome bezeichnet hat, dasses auch schon makroskopisch eine sichere Diagnose in diesem Sinne gestatte. Hie und da in der Lunge weissliche Knoten, anseheinend yon der Hauptmasse getrennt; ebenso unter der Pleura. Das schw[irzlich gefarbte, an mehreren Stellen atelektatisehe, hepatisierte Lungenparenehym weist -au.~serst kieine Ka~,ernen und Bronehiektasien auf, aus denen bei Druck Sehleimeiterkltimpehen mit Gewebsfetzen heraustreten. Die Spitze wird yon einer dieht unter der Pleura befindliehen taubeneigrossen, glatte, harte Wiinde besitzenden leeren Kaverne eingenommen; andere haselnussgrosse, im allgemeinen an der Peripherie unter der Pleura gelegene Kavernen nehmen den unteren Lappen ein; einige haben glatte, polierte, andere rauhe, zerfressene Wiinde, wo das Gewebe mit der grSssten Leiehtigkeit in Form yon sehwarzbraunen, zerreissliehen, reichlieh Detritus und eitrigen Sehleim enthaltenden Massen sieh abl6st; der Tumor dringt hliufig in diese Wlinde ein, wobei er denselben eine grSssere Harte und Festigkeit verleiht. Rechts Lungenstauung mit emphysematisehen Horden und nnter der Pleura vereinzelte neoplastische Knoten. Das I-terz zeigt sieh - - yon den bereits beschriebeneu das Perikardium betreffenden Erseheinungen abgesehen - - schlaff; die Vorkammern mit Fibringerinnseln erfiillt; die linke yore Tumor direkt e r g r i f f e n - wobei letzterer nieht bis zam Endokardium vorgerfiekt ist --- an der Spitze ein auf das Myokardium und Epikardium sieh besehrfi.nkender haselnussgrosser metastatischer Knoten. Oas Myokard fettig entartet. Kein Hineitiwuehern des Tumors in die grossen MediastinalgeNsse, deren Wandungen slimtlieh yon der neoplastisehen Masse dnrchsetzt und eingehiillt sind; !etztere hatte jedoeh keine VergrSsserung des Mediastinums veranlasst. L e b e r mit zahlreiehen versehieden grossen, teilweise benabelten Metastasen. L i n k e Niere: Zahlreiche Metastasen; in d'er r e c h t e n nur spiirliehe. Milz: Ausgedehnte Verwachsungen mit dem Zwerehfell; zaMreiche Metastasen; ein grosser Infarkt am oberen Pol. K n o c h e n : Im oberen Drittel des reehten Femur Fraktur mit einer mannsfaustgrossen, aueh das Knochenmark einnehmenden neoplastischen L. Stropeni, Fall yon bronchialem Adenocaroinom. Wucherung; aeoplastische Erweichungsherde in den KSrpern zweier Brustund eines Lendenwirbels. Sch~tdel: Drei Metastasen im Schi~deldach von der GrSsse eiaes Fiinfcentimesstiickes, auf die Dura iibergreifend. Gross- und K l e i n h i r n : Interstitielles Oedem~ keine Metastase. t I i s t o l o g i s c h e U n t e r s u c h u n g des T u m o r s . - Auf Schnitten, die parallel zur Langsachse des linken Hauptbronchus hergestellt wurden~ ist der Uebergang yore gesunden Gewebe ins neoplastische deutlich wahrnehmbar. Im vom Carcinom erfassten Teile zeigt sich der Bronchus yon einem schweren~ mit Riicksicht auf die Natur und die Dauer der Lungenerkrankung wohl begreifiichen Entztindungsprozess ergriffen; das submukSse Gewebe ist stark infiltriert~ das zylindrische Flimmerepithel stellenweise abgelSst oder zerstSrt~ doch zeigen die in den tieferen Schichten sitzenden Drfisenacini keine VerRnderungen und die anatomische Strukmr der Bronchialwand ist nicht deformiert. In dem Masse aber~ als die kleinzellige Infiltration dem neoplastischen Herde naher kommt, wird dieselbe auch ansehnlicher; die Tubuli der Schleimdrfisen zeigen sich erweitert~ das Epithel ist grSsstenteils abgeschuppt und seine Reste liegen im Lumen des Kanals angehiiuft; keine Wacherung~ weder typisch noch atypisch und keine Karyokinese. Weniger tief und zwar dicht unter dem Bronchialepithel liegen grosse Zellen mit den iiblichen protoplasmatischen Farbstoffen intensiv tingierbar~ zu isoliert im Bindegewebe stehenden Haufen vereinigt; nliher der Stelle der starksten careinomatiisen Wucherung verwandeln sich diese kleinen Schollen in dickere Striinge7 die sich his zum Knorpel herabsenken~ anscheinend ohne irgend welchen Zusammenhang mit d e n Schleimdriisen oder mit der Hauptmasse des Tumors. Der Kern dieser Zellen ist gross, bl~schenfSrmig, selten in Karyokinese begriffen, das Protoplasma reichlich, gut tingierbar~ mitunter einen dicken Muzinklumpen enthaltend; hier liegen die Zellen fast tiberall um ungleichmiissige, den Drfisenalveolen Rhnlich sehende Hohlr~tume angeordnet, und zeigen dann einen~ der Hohlfl~che des Alveolus zugekehrten, mit den das Muzin farbenden Stoffen intensiv tingierbaren schmaleu Saum. In diesem letzteren Anteil sind die in den frtiheren wahrnehmbar gewesenen DriisenkSrper nicht mehr sichtbar. Obe~J zeigt das Flimmerepithel keine Veranderungen, die yon den bereits beschriebenen abweichen. Weiterhin aber schmelzen alle diese krebsigen Anh~tufungen zu einer einzigen mit atypischen Zellen wirr durchsetzten Masse zusammen~ welche die ganze Wand des Bronchus ersetzt, in das Lumen desselben in ungleichm!issiger Weise hineinwuchert und letzteres verengert; nur in den zwischen den Erhabenheiten des Tumors liegenden Furchen sieht man zuweilen Reihen yon Flimmerepithelien auf der diese von der darunter liegenden Neubildung scheidenden Basalmembran gelagert. Die neoplastische Masse besteht nahezu 10 L. Stropeni, Fall yon bronchialem Adenocarcinom. ganz aus Zellen mit sehr spiirlichen Trabekeln und aus mit filamentiisem Schleim gefiillten ovalen Hohlraumen; Schleimklumpen finden sich auch im Protoplasma maneher im Inneren yon massiven earcinomatSsen Strangen gedr~ngt sitzenden Zellen. Der Charakter dieser Zellen ist in allem der bereits angegebene. In dem dem Bronchiallumen anliegenden Tell zeigt der Tumor deutliche Erosion and Nekrose sowie starke leukozytare Infiltration; in der Tiefe reicht er his an die Knorpelringe heran, ohne jedoch dieselben anzugreifen: er umgeht dieselbert und dringt dureh zwei benachbarte Ringe hindurch in das darunter liegende Bindegewebe ein. Hier tritt der Tumor nicht mehr als eine dicht gedrangte Masse und ansehnliche Wucherung auf, sondern in der Form yon spiirlichen Zapfen, welche mit Schleim angefiillte Alveolen begrenzen und durch weite Bindegewebsbfindel mit wenigen darin eingelagerten Kernen voneinander getrennt sind; lctztere zeigen welt um sich greifende Vorg/i.nge yon hyaliner Entartung und Nekrose, yon denen haufig auch die neoplastischen Epithelialelemente betroffen sind. Oefters nimmt dieses Bindegewebe die typische Muzinfarbung schwach an, als ob es selber die schleimige Entartung erfahren h~,tte oder mit Schleim durchtrankt ware. Die gleichen pathologisch-anatomischen Veranderungen sind in den anderen Nebenbronchien anzutreffen. Auf Querschnitten der sekundaren und tertiaren Abzweigungen, dio eine Untersuchung des ganzen Bronchus gestatten, sieht man, dass deE" Tumor nicht die ganze Bronchialwand ergriffen 7 sondern sich auf einen Teil derselben beschrankt hat und hierbei etwas ins Lumen hineingewuchert ist, welch' letzteres dadurch verengert, aber doch immer noch durchgangig geblieben ist; dagegen ist er in d i e Tiefe gewachsen, fiber die Knorpel hinaus, ohne jedoch in dieselben einzudringen. Makroskopisch untersucht~ hatte sich die Lunge als eine an vielen Stellen atelektatische, zahlreiche HShlen enthaltende erwiesen; bei Untersuchung des in deE" Nahe dieser H6111en getegenen L u n g e n g e w e b e s mochten nun die Schnitte was immer fiir einer Partie der Lunge entnommen sein - - zeigte sich das Lungenparenchym stets in unkenntlicher Weise verandert, so dass die Vermutung gerechtfertigt erschien, es sei funk.tionsunfahig geworden. Ueberall bestand eine auffallige kleinzellige Infiltration, fibrSse Bindegewebsstr[~nge, sehr zahlreiche Anhaufungen von Plasmazellen, insbesondere um die Gefasse herum, difl[use Blutungen und Verdickung des viszeralen Pleurablattes, welches nicht mehr mit Epithel bekleidet, sondern in eine yon Krebsstrangen dnrchsetzte, mit neoplastischen Schollen und Haufen yon Plasmazellen besate fibrSse Schwarte umgewandelt war. Bei einer so reiehlichen Bindegewebswucherung waren die elastischen Fasern in sparlicher Anzahl und nur um die 6efasse herum vorhanden; L. Stropeni, Fall yon bronchialem Adenocarcinom. 11 viele dieser letzteren~ namentlich die grSsseren, waren dutch deutlich erkennbare in Organisation begriffene Thromben verschlossen, in denen es mir aber niemals gelungen ist~ Krebszellen ausfindig zu machen. In der Wand einer an der Lungenspitze befindlichen Kaverne habe ich zahlreiehe Riesenzellen angetroffen yon dem gleichen Typus wie die L a n g e r h a n s schen der Tuberkeln; dieselben lagen neben einander gereiht am Rande des Hohlraums 7 einige davon teilweise schon losgelSst~ als ob sie nahe daran w'~ren ill letzteren hineinzufallen; es fehlten jedoch Epitheloidzellen und Kaseifikationsvorg~nge. In dem eine andere H~ihle umgebenden Gewebe liessen sich zwei Partien deutiich yon einander unterscheiden: die eine der Pleura entsprechend aus Bindegewebsbalken zusammengesetzt, yon Strii.ngen und Schli~uchen durchzogen~ die den bereits beschriebenen ganz Rhnlich waren; die andere war dem Lumen der HShle zugekehrt und bestand aus mehrkernigen Massen, Plasmazellen, zahllosen nekrotischen und nekrobiotischen Zellen mit nicht tingierbarem Kern, aus kurzen Abschnitten yon Stiitzbindegeweb% ferner aus einer diffusen Infiltration yon ahgeplatteten grossen Zellen mit scharf begrenztem, polymorphem Protoplasma und blaschenf~hnlichem~ h~ufig in Karyokinese begriffenem Kern; 5fter fanden sieh zwei oder mehrere Kerne in der gleichen Zelle. Offenbar handelt es sich um Krebszellen~ allein ihre Gestalt und vor allem infiltratartige Verteilung war grundverschieden yon jener der fibrigen Lungenpartien; bei fieissigem Nachsuchen war es jedoch mSglich, eine deutlich ausgepragte Kontinuit~t und einen Uebergang yon einer Form in die andere wahrzunehmen. In den M e t a s t a s e n zeigte die Struktur der Neoplasie eine welt adenomatSsere Beschaffenheit als in der Lunge und entsprach im a|lgemeinen den ersten Anffaben fiber die wiihrend des Lebens abgetragene kleine Gesehwulst. Ebenso in den fibrigen Hautknoten des Thorax und des Abdomens 7 in der Niere und in der Milz, wo aber auch zahlreieh% wohl auf Embolie durch vom Blutkreislauf mitgerissene Tumormassen zurfickzufiihrende Infarkte vorhanden waren. lm H e r z e n war der Knoten an der Spitze gut umschrieben und offenbar ein metastatischer; an der linken Kammer gingen die Zellhaufen in jene des Lungenhilus fiber. Die Fasern des Myokards erschienen infolge dieses Eindringens yon heterogenen Zel[en in Begleitung yon reichlichem Bindegewebe auseinander-bzw, zusammengedr~ngt oder zerstSrt; das Endokardium war intakt~ das Epikardium hingegen gleiehfalls befallen und stark verdickt, in gleicher Weise wie dies bezfiglich der Pleura beobaehtet worden. In den Knochen~ namentlich am Femur~ befanden sich die Krebszapfen mitten in einem nekrotischen Gewebe mit ordnungs- und richtungslos 12 L. Stropeni, Fall yon bronchialem Adenocarcinom. zerstreut liegenden Trabekeln an einem fibrtisen, zum grossen Teil in schleimiger Entartung begriffenen Gewebe. Im Femur, an der Frakturstelle, war keine Spur yon Knoehenmark mehr erkennbar, aber die gleiche heterogene, tumultuarische Struktur war sowohl an tier Peripherie als auch in der Mitte der den Fraktnrherd verdeckenden fibrSsen Masse anzutreffen. Das Mark der vom Tumor nicht ergriffenen Pattie zeigte den Typus des gelben Marks, aber sonst nichts Bemerkenswertes. Will man nun eine Diagnose stellen~ so glaube ich, man sei zur Annahme berechtigt, dass hier ein von den Schleimdrfisen der Bronchialwand ausgegangenes A d e n o c a r c i n o m vorlag. Diese an und ffir sich sehr seltene Art yon Tumoren wird yon einigen Autoren eifrig erSrtert und angezweifelt, namentlich yon Pass] er~ der nicht nut bei zwei seiner von ihm mitgeteilten FaIle - - der histologischen Beschreibung nach, dem meinen ahnlich - - einen glandularen Ursprung in Abrede stetlt~ sondern auch alle frfiheren yon L a n g h a n s , T i l l m a n n , Beck, S t i l l i n g , H o y l e u. a. geschilderten entschieden in Frage stellt, obwohl die zwei ersten der genannten Autoren innige, unmittelbare Beziehungen der Schleimdriisen zu den Krebsstrangen beschrieben hatten. Allerdings liefern viele der selbst nach Erseheinen yon P a s s l e r s Arbeit als Carcinome der Schleiaidriisen beschriebenen Falle so sparliche Anhaltspunkte ftir eine Diagnose, dass einige Autoren, wie L. B. Meunier und L6vy redlich erkl'~rt haben, dass ,,cette origine admise par Chiari', Z i e g l e r , B i r s c h - H i r s c h f e l d , ne peut 6tre aftirm6e d'une far formelle." Auch kann die Neigung der Epithelzellen zur Bildung schleimhaltiger Acini wohl kaum dazu geniigen - - wenn auch Davis und Le C o u n t noch gelegentlich eines neueren Falles dies angenommen - - uns yon dem glandularen Ursprung des Tumors zu iiberzeugen. Denn, wie P $ s s l e r scharfsinnig bemerkt und F r i e d l a n d e r experimentell nachgewiesen hat, ist es einer Wucherung des Deckepithels der Bronchien wohl m6gli~h, eine adenomatSse Struktur anzunehmen; andererseits ist es aber allgemein bekannt, dass auch im normalen Bronchialepithel kelchfSrmige Zellen zu finden sind, we]che Schleim erzeugen. Uebrigens ist das Bronchialepithel nicht gerade das einzige, welches derartige adenomatSse Wucherungen darzubieten vermag, vielmehr kommt diese Fahigkeit auch noch anderen Deekepithelien zu, wie z. B. jenem der Gehirnventrikel und Plexus choroidei ( K a u f m a n n ) . Auch hier zeigen sich Neoplasmen, die man mit Rficksieht auf ih,'e Struktur (Alveolen und Infuudibuli mit darin enthaltenem Schleim, s o dass man - - wie im Falle K a u f m a n n s - - an einen Darmpolyp erinnert wird) als Adenocarcinome bezeichnet hat. In diesen Fallen ruft die Wucherung des Bindegewebsstromas die Anordnu~g ill Papillen und Alveolen hervor; dieselben k0nne,l L. Stropeni~ Fall yon bronchialem Adenocaroinom. 13 dann infolge der schleimigen Degeneration des Bindegewebes selbst das Aussehen yon Schleim enthaltenden R0hren und Schl'~uchen gewinnen, und dies in einem Epithel 7 das~ normalerweise weder Driisen enth~lt, noch iiberhaupt eine Schleimabsonderung aufweist. Es kiinnte daher die Diagnose Adenocarcinom leichtfertig erscheinen. Im vortiegenden Fall aber hat die genaue Untersuchung der Neubildung und ihrer Metastasen jeden Zweifel an der Entstehung des Tumors aus den Schleimdrfisen beseitigt. Denn nicht nur in den neugebildeten Schlliuchen, sondern auch in durchaus atypischen Zellen sowohl in der Lung% als auch in den Knoten anderweitiger Organe - - ist Schleim enth'dten~ ein Befund~ der dem yon T r a i n a neuerdings beschriebenen (Kolloidtropfen in atypischen Zellen eines Carcinoms der Schilddriise) vollkommen entspricht. Hier kann somit ffir die Gegenwart yon Schleim nicht eine Entartung des Stiitzbindegewebes~ sondern nur die T~tigkeit der Zellen selbst verantwortlich gemacht werden. Es kiinnte jedoeh die Vermutung aufsteigen, dass diese Zellen yon den kelchfSrmigen des •ronchialepithels herstammten~ welche letzteren~ wie im Falle H e l l y s , sich gleichfalls in den neugebildeten Strangen finden kSnnen. Allein in den oben beschriebenen adenomatSsen Alveolen findet sich Schleim in allen den Sehlauch umlagernden Elementen~ sowie in jenem Tell derselben, der dem Lumen des Kanals zugekehrt ist, was darauf hindeutet, dass die schleimbildende Tiitigkeit nieht einzig nnd allein auf einige Zellen der Neoplasie beschriinkt~ sondern eine samtlichen Zellen zukommende ist. In Anbetracht nun dieser Befunde, in Anbetracht des Umstandes, dass hier Flimmerzellen~ wie solche doch in F~tllen yon Neubildung des bronchialert Deckepithels beschrieben wurden, fehlten~ in Anbetracht vor allem des fast in jeder Gegend so ausgesprochen glandulliren Baues de," Geschwulst~ trage ich kein Bedenken~ obige Diagnose auf: Adenocarcinom~ yon den Driisen der B r o n c h i a l w a n d h e r s t a m m e n d , ffir die einzig zul~ssige zu halten. An einigen Stellen hat dieses Adenocarcinom, ein bei Drfisenkrebsen nicht seltenes Vorkommnis~ seine adenomat6se Struktur eingebfisst und dessert Bestandteile zeigen sich dann, wie ich bereits angegeben~ in Form einer diffnsen Krebsinfiltration mit polymorphen haufig mosaikartg angeo,'dneten Zelle% g-~nziich verschieden yon jenen~ die Strange bzw. Alveolen bilden. So erkliirt sich de,m auch~ wie eine Neoplasie bronchialen Ursprungs, wenn sie den obeu angegebenen Typus aufweist~ noch mehr aber~ wenn sich die Zellen i,1 den Lungenalveolen anhiiufen~ oder auch nur eif6rmige Klumpen in der veriinderten Lunge bilden, als eine yon den Epithelien der Lungenalveolen herstammende angesprochen werden kaun, falls es nicht 14 L. S t r o p o n i, Fall yon bronohialom Adenocarr gelingt -- wie i m Falle H e l l y s und in dem aIlerj.'fingsten yon R a v e n n a die sonst so wenig nachweisbaren urspriinglichen Verttnderungen der Bronchien zu Gesicht zu bekommen. Denn, ist auch Wolfs Angabe, - - es sei die Diagnose auf Bronchialcarcinom an makroskopisehen Schnitten leieht zu stellen, wegen der daran sichtbaren entlang der Bronchienverzweigungen fortschreitenden Neoplasie eine zutreffende, so ist sie es doch nieht in absoluter Weise und wtirde die praktisehe An.wendung der yon D a l L a g o zitierten Angabe L a r d i l l o n s - - es sei bei der Differentialdiagnose zwischen Bronchialund Langencarcinom das erste und grSssere Gewicht auf die makroskopischen Befunde zu legen - - unfehlbar za lrrttimern fiihren. Nur eine genaue mikroskopische Uatersuchung vermag den Ursprung dieser Neubildungen zu ermitteln und hli.uiig ist auch auf diese Weise nur eine Wahrscheinlichkeitsdiagnose mSglich, oder es l~sst sich eine Diagnose tiberhaupt nieht formulieren, wie im Falle P e p e r e s , wo die anscheinend in Hepatisierung begriffene Lunge in Wirkliehkeit in eine Zylinderzellen enthaltende Krebsmasse umgewandelt war, sowie in dem yon L 5 h l e i n mitgeteilten, einen cysto-papillaren Lungentumor betreffend. Die grosse N e i g u n g zu Metastasen und die Ausbreitung dersr in die verschiedenartigsten Organe, sogar bis in das Gehirn~ ist, wie dies auch neuerdings B u d a y und K a r r e n s t e i n dargetan haben~ ein Priirogativ des Bronchialcarcinoms; vielleicht ist dieselbe~ wie W o l f annimmt~ bedingt durch die rasche Invasion der peribronchialen Driisen, sowie durctl das leicht mOgliche Eindringen in die Blutgefiisse. Gleiehfalls sehr hi~ufig ist auch noch die schleimige Entartung des Stfitzbindegewebes des Tumors und der Metastasen von Carcinomen anderweitiger Schleimhi~ute, namentlich des, Magens ( L a d e n ) . Es bewahrt sich hier nur einfach das Gesetz~ dass den Krebsmetastasen die Fi~higkeit zukommt~ das ursprfingliche Gewebe nicht ntir in bezug auf Struktur~ sondern aueh in bezug auf die Faaktion der einzelnen Zellen zu reprocluzieren; ebenso sehr haufig ist auch das Vorkommen yon Kolloid in den metastatischen Zellen von Schilddrfisenkrebsen ( F l a t a u und K o e l i c h e n , T r a i n a n. a.). Es kann somit in manchen Fallen ziemlich leicht gelingen~ mit Riicksicht auf die Untersnchung einer Metastase zur Diagnose der prim~ren Gcschwulst zu gelangen, wenn auch nicht genau bezfiglich der Stelle ihres Sitzes -- wie dies eben in] vorliegenden Falle mSglich gewesen - - doch wenigstens beziiglich des Organs~ wo sic ihren Ul~prung gehabt hat. Recht selten mfissen aber jene Fii.lle sein - - und mir ist es aucl~ tats~chlich bisher nicht gegliickt~ einen derselben kennen zu lernen - - , in denen~ wie im vorliegenden 7 es gehmgen w,tre, auf Grund der histologisehen Untersuchung einer Hautmetastase den Ausgangspunkt der Geschwulst genau - - L. Stropeni, Fall yon bronchialem Adenocarcinom. 15 festzustellen; bei unserer Kranken ist niimlich die Provenienz der Neoplasie yon der Bronchialwand eben im Hinblick auf die Ergebnisse der mikroskopischen Untersuchung der Metastase diagnostiziert worden 7 Ergebnisse, die auf eine Entstehung aus einem Schleimdrfisen enthaltenden Organ hinwiesen. Die Sache ware an und ffir sich kein gar so seltenes Vorkommnis, wenn nicht - - wie Daus und P e t r i dargetan haben - - die Hautmetastasen yon Carcinomen der Innenorgane eine ausserordentlich grosse Seltenheit waren. Speziell bei Lungencarcinomen aber hat sich besagtes Vorkommnis als ein h6chst seltenes erwiesen, und auch in den neusten Zusammenstellungen yon selbst zahlreichen F~illen (Watsuji 6 F~ll% B u d a y 11, K a r r e n s t e i n 32) findet sich davon kein einziger. II. Klinischer Teil. S'~mtliche Autoren 7 die sich mit der Symptomatologie des Bronchialund des Lungencarcinoms befasst haben~ haben sich fibereinstimmend dahin ausgesprochen, dass die Zeichen dieser Erkrankung i~usserst unbestimmt und bei einer ganzen Reihe anderer Krankheiten anzutreffen sind und dass kein Syndptom ein pathognomonisches ist - - ausgenommen vielleicht die Gegenwart yon Tumorfetzen im Sputum --, was jedoch auch bei einem Car~inom des Mediastinums vorkommen kiinnte, wenn dasselbe nach Perforation des Bronchus Ausli~ufer in diesen letzteren hineintreibt. So ~tussert sich in diesem Sinne schon E b s t e i n in seinem grundlegenden diesbezfiglichen Aufsatz, und dieser Ansicht huldigen noeh andere neuere, nicht minder hervorragende Autoren ( A u f r e c h t , H o f f m a n n , B e n d a , Q u e i r o l o ) . Wenn nun also Verlauf uud Anamnese kein Licht in die Sache bringen, so kann begreiflicherweise eine Diagnose iiberhaupt nicht oder nur mit grosser Unsicherheit gestellt werden. In diesem meinen Falle eben sind weder die anamnestischen Angaben, noch - - eine lange Zeit hindurch - der Verlauf dazu geeignet gewesen, eine genaue Diagnose zu erm6gtieheo. Denn der Beginn der Krankheit, die friiher bestandene Pleuritis, das Vorkommen eines Falles yon Tuberkulose bei Kollateralverwandten, die Lokalisierung der Erkrankung links, w:,'~hrend, wie dies auch durch die neusten Statistiken ( H a b e r f e l d ) erwiesen ist, das Carcinom viel haufiger rechts zustande kommt als links, die Retraktion der Spitze, dos Vorhandensein yon Zerst6rungsherden, das Fehlen yon Drfisenanschweltungen an der Achsel u n d d e r Supraklavikulargrube, das eitrig-schleimige, sp-~rliche Blutstreifen enthaltende Sputum, vor allem aber dos verhRltnism~tssig jugendliche Alter der Kranken, sowie das Verhalten des Fiebers, alles dies bildete einen symptomatischen Komplex, der die Diagnose auf Tuberkulose lenkte. 16 L. Str op e ni 7 Fall yon bronchialem Adenocarcinom. Freilieh erschien die M6glichkeit eines Carcinoms durch diese Gesamtheit yon Symptomen keineswegs in formeller~ absoIuter Weise ausgeschlossen~ denn die Kasuistik dieser Form weist woh] Typen auf, bei denen derartige Erscheinungen in grSsserer oder geringerer Zahl nebeneinander vorkommen kSnnen, so dass die F~lle yon Lungenneoplasie grSsstenteils mit der Diagnose: Tuberkulose oder mit der mehr allgemeinen yon Lungenschwindsucht zur Obduktion gelangten. Was das Alter. angeht~ so findet sich je ein Fall yon Lungenearcinose bei einem 7jlihrigen M~t~tchen ( N u s c h e l e r ) und einem 51/2 Jahre alten Knaben (Mac Aldowie) verzeichnet. Mit Rficksicht auf die unendlich gr~ssere Frequenz der Tuberkulose im Vergleich zu den Lungenneoplasien und auf dte ziemlich genaue Uebereinstimmung der Befunde hatte die Tuberkulose die grSssere Wahrscheinlichkeit fiir sich. Allein eine Reihe anderweitiger Momente stand mit diesem Urteil in Widerspruch, so der negative Ausfall der Tuberkulinreaktion~ die Abwesenheit yon Bazil]en und elastischen Fasern im Sputum: die negativ ausgefaliene Probe bei dem mit dem Auswurf inokulierten Meerschweinchen. Beziiglich der Kutanreaktion gibt es bekanntlich Fiille yon fortgeschrittener Tuberkulose, wo diese Reaktion ausbleibt; aber das "trotz der wiederholt angestellten mikroskopischen Untersuchung konstante Fehlen yon Tuberkelbazillen hatte gegen das Bestehen eines tuberkulSsen Prozesses kein geringes Gewicht, um so mehr aber als das Sputum einer oftmaligen Prfifung unterzogen worden war, unter anderem auch in der Hoffnang~ Tumorfragmente darin zu finden, ja, gelegentlich habe ich sogar die dichteren Klumpen des Auswurfs in Paraffin eingebettet; das Sputum wurde zuerst in eine Eprouvette gebracht~ darin absetzen gelassen, hierauf der Boden der Eprouvette eingeschlagen; die dabei heraustretenden Klumpen wurden mit der Schere durchschnitten und in die Fixierflfissigkeit (Alkohol oder Sublimat) fallen gelassen. Auf diese Weise bekam ich Massen, die hinreichend derb waren~ um weitere Manipulationen zu vertragen; die Schnitte wurden nach W e i g e r t s Verfahren ffir elastische Fasern behandelt und nach G r a m , L S f f l e r und Koch ffir die Mikroorganismen neugefarbt. Neben diesen Argumeaten gese]lte sich zur Unsicherheit noch ein drittes~ welches innerhalb gewisser Grenzen den Gedanken an eine Lungenneoplasie reehtfertigen machte: ich meine namlich die Thoraxd~tmpfung bei normal grossem Weilschen Raume, die Retraktion des Thorax und die normale Lage des Mediastinums. Allein alle diese Erscheinungen sind auch teilweise bei Brustfellentzfindungen in dem Adh~isionen und Retraktionen aufweisenden Stadium anzutreffen. Al[erdings brachte eine so schwere und insbesondere so ungleichmiissige Retraktion des Thorax~ wie sie sich eben in unserem Falle L. Stroponi, Fall yon bronchialem Aclenocarcinom. 17 darstellte, jenes Symptom der Krebsinflltration in Erinnerung, das yon W a l s h e beschrieben, yon Z a g a r i bekltmpft und in seiner theoretischen Grundlage erschiittert, yon Q u e i r o l o wieder best'9.tigt und unter dem 3~amen ,,Walshesches Symptom" zu neuer Geltung gebracht und schliesslich in einer Reihe von Fallen yon Neoplasie der Pleura bzw. der Lunge (Dean, D. Lewis~ B e z z o l a , C a l a b r e s e u. a.) nachgewiesen worden ist. Dabei daft jedoch nicht vergessen werden, dass in den meisten dieser FMle gleichzeitig mit der Retraktion auch noch ein 5fter reichliches hamorrhagisches Exsudat bestand, w~hrend in uaserem Falle es nur mit Mfihe gelungen war, 2--3 ccm einer meistens vollstlindig serSsen Fliissigkeit herauszubekommen. Es fehlte somit in diesem Falle jener scharfe, sofort auffallende, ffir die Carcinomdiagnose einen vortrefflichen Anhaltspunkt bietende Gegensatz zwischen der Retraktion des Thorax und dem Vorhandensein eines Ergusses. Wenn fiberhaupt, hiitte hier also ein ,,Cancer en cuirasse" angenommen werden mfissen. Etwas aufgehellt wurden diese ziemlich dunklen Verh'~ltnisse dutch zwei neu hinzugetretene wichtige Vorkommnisse: das Auftreten des Hautkn6tchens und die Fraktur des Femurs. Freilich hatte man, bevor das Ergebnis der mikroskopisehen Untersuchung des Hautknotens bekannt geworden~ die Fraktur dutch die - - wenn auch etwas kfinstliehe - - Annahme einer direkten traumatischen Einwirkung erkIi~ren kSnnen, letztere etwa bedingt durch eine pliitzlich ausgefiihrte Bewegung, die schon an und fiir sich hingereicht hii.tte~ bei einem bereits seit lange bettliigerigen, wenig genlihrten, durch zahlreiche Sehwangersehaften geschwiichten Frauenzimmer einen Knochenbruch zu veranlassen. Und dies umsomehr, als al|e Versuche dureh tief eindringende Probepanktionen an der Frakturstelle eineu Krebsherd festzustellen, fehlsehlugen und andere Zeichen einer Markneoplasie, wie Albumosurie, speziel] aber die eharakteristisehen Blutmerkmale vermisst wurden, und ein so geringer als eine Folge der Frakmr leichter zu deutender Prozentsatz an Myelozyten doch nieht zu diagnostisehen Schltissen berechtigen konnte. Bekanntlich sind in einem Teile der F'~lle von Knoehenmarkca,'einose die Verli.nderungen des Blutbildes derart ausgesprochen und h~ufig so imponierend, dass sie sogar - - wie im Falle R o t k y s -- die Erseheimmgen der perniziSsen Ani~mie darbieten kSnnen. Die mit hi~matologischem Befunde ausgestatteten F~ille yon Krebsmetastase des Kn0chenmarks sind allerdings selten, doch kSnnen gewisse eigentfimliche Verlinderungen der Blutkrasis auch schon an und ffir sich eine Diagnose gestatte n. Entscheidender war das Ergebnis der Untersuchung der kleinen Hautgeschwulst, so dass es nunmehr nieht sehwer gelang, auch die fibrigen Symptome zn einem harmonischen, eine sichere Diagnose gewlthrleistendea Zeitschrift f f r Krebsforsehung. 9. Bd. 1. Heir. .o 18 L. Stroponi, Fall yon bronchialem Adenocarcinom. Ganzen zu vere!nigen. Selbst jene Vorkommnisse, die den Zweifel am Vorhandensein einer Neoplasie zu rechtfertigen s c h i e n e n - wie der Fieberverlauf und das ganzliche Fehlen yon Krebmassen im Sputum - - erschienen nun aufgekl~rt. Es stimmte n~mlich der Fieberverlauf mit der Zerst6,'ung der Lunge und der Sekretstauung in den Bronehiektasien und Kavernen mit konsekutiver, durch die dabei eingetretenen autolytisehen Vorg'~nge (F. MUller) und die T~tigkeit der Bakterien bedingter Resorption pyrogener Produkte. Das Fehlen yon Krebszellen im Sputum kann mit Rficksicht auf die geringe Zahl der F'~lle, ill denen sic angetroffen wurden wohl kaum befremden. Denn, wahrend manche Autoren, wie E o k e r s d o r f f , behaupten, dass, wenn man nach denselben mit der gleiehen Beharrlichkeit suchen wfird% wie dies bezf@ich der Kochsehen Bazillen zu geschehen pflegt, sic gewiss sehr h~ufig anzutreffen waren, behaupten ander% wie Wolf, sogar, dass ,,der nach oftmaliger Untersuchung des Sputums erlangte negative Befund gerade ffir Carcinom pathognomonisch ist." Wie Wolf ausfahrt, wird die Permeabilitfit der Bronchien durch die Druckwirkung cter vergr6sserten Lymphdr~isen sehon fraher beeintr'~ehtigt als das Carcinom an und far sich so welt gewaehsen ist, dass es die Durchgangigkeit der Bronehien in Frage stellt. Es tritt infolgedessen eine zylindrische Erweiterung der feineren Bronchien mit Sekretstauung ein; im Sekret sammeln sieh hierauf die Entziindungskeime an, wodurch pu~ride Bronchitis und bronchiektatische Kavernen zur Entstehung kommen, indem sich nun dieselben in einen Bronchus ~ffnen, erzeugen sic ausgedehnte ZerstSrungen des Lungengewebes und aueh des neoplastischen Gewebes selbst. Daher kommt es, dass man zwar zuweilen Tumorfetzen im Sputum vorfindet; h'~ufiger aber dieselben so tiefgreifende Veranderungcn erfahren haben, dass es nicht mehr gelingt~ sic zu identifizieren. So halle in dem Falle E c k e r s d o r f f s wo sich im Schleimsekret des Hauptbronchus einer Leiche, Krebsnetze~ Zapfen und grosse polymorphe Zellen vorfanden - - der Tumor keinerlei Ver~.nderungen im Lumen der Bronchien hervorgerufen, so dass die unmittelbar vorher abgel~sten Tumorpartikel mit dem Auswurf herausbefSrdert werden konnten; in den F~llen H e r r m a n n s handelte es sich entweder um weiehe, medull~re Tumoren, die, am Hilus in die Bronchien eingedrungen, ausserst leicht zerfallen konnten (Fall I und IV), oder um Oarcinome der peripheren Teile (tier Spitze, Fail I): in den FMlen, wo die Konsistenz eine harte und der Tumor am Hilus lokalisiert war (Fall II und III und in einem Fall yon W e i n b e r g e r ) , so dass er zur Bronchostenose und Sekretstauung Anlass gab, wurde im Sputum nicht vorgefanden. Was das Fehlen yon ausgepr~igten, dureh die Knoeheametastasen bedingten h~matologisehen Merkmalen angeht, so glaube ich wohl kaum, es - - L. Stropeni~ Fall yon bronchialem Adenocarcinom. 19 lasse sich hier die fiir den so oft zitierten Fall yon N o t h n a g e l gegebene Erkl~rung heranziehen - - dass nitmlich das Knochengewebe veto neoplastischen ggnzlich eingenommen und dutch dasselbe ersetzt worden; im vorliegenden Falle waren die Knoehenmetastasen auf das Femur und auf eine geringe AnzahI Wirbel beschr~tnkt, und die mikroskopische Untersuchung des Marks verschiedener Knochen sowie der in der N~he des Tumors gelegenen Teile hat es erm6glicht, festzustellen, dass die Neubildung nicht jene Ausbreitung erlangt hatte, die man im Hinblick auf das Fehlen yon charakteristischen Kundgebungen im Blute h'~tte erwarten k6mmn. Zu]~ssiger erscheiut bier wohl eher die Annahme einer schwachen Reaktion seiteus des Knochenmarks, gesteigert unter anderem auch dutch die im Laufe befindliche Krankheit. Literaturverzeielmis. h s c o l i , M.~ Sulla diagnosi differenziale dei tumori del midollo csseo in base al reperto ematolcgico. 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Lewis~ Endothelioma of the pleura with report of case. Transact. Chicago Path. see. 1905. April. Vol. Vl. p. 256. Daus, Ueber sekundSxe Hautkrebse. Virchows Archly. Bd. 190. H. 2. DSmeny~ Zur Kenntnis des Lungencareinoms. Zeitschr. f. Heilkund% Abt. f. path. Anat. 190~. S. 407. E b s t e i n , Zur Lehro rum I~[rebs der Bronchieu u. der Lungen. Deutsche reed. Wochenschr. 1890. S. 921. E c k e r s d o r f f , Zwei F~ille yon primiirem Sarkom tier Lunge. Zentralbl. fl allg. Path. u. path. Anat. 1906. Bd. XVII. S. 355. 2* 20 L. S t r o p e n i , Fall yon bronchialem Adonocarcinom. F l a t a u u. K o e l i c h e n , Carcinoma ossis frontalis, parietalis etc. als Metastase eines Adenoma colloides glandutae thyreoideae. Deutsche Zeitschr. f. Nervenheilk. 1906. Bd. 31 (3/4). F r i e d l i i n d er, Ueber Epithelwucherung u. Krebs. Strassburg 1877. G o e t s c h , Ueber den Einfluss yon Carcinommetastasen auf das Knochengewebe. Zieglers Beitriige. Bd. 39. 1906. S. 218. 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S. 470. L4vy~ D'un cas de cancer broncho-pulmonaire. Arch. g4n. de m4d. 1895. p. 346. L i i h l e i n , Zystisch-papill~irer Lungentumor. Verhandl. d. Deutschen path. Ges. 1908. S. 111. Mac A l d o w i e , The Lancet. Oct. 1876. p. 570; zit. nach Ebstein. Meunier~ Un cas de cancer bronchique. Arch. g4n. de m4d. 1895. Vol. 1. p. 343. M o r e l l i , Ein Fall yon prim~irem Lungenkrebs. Deutsche reed. Wochenschr. 1907. S. 805. M o r e s e h i , Carcinoma al polmone con diffus, alla pleura. Boll soc. reed. chit. Pavia 1907. N u s c h e l e r , Schweiz. Korr.-Blatt. 1875. Nr. 24; zit. nach Ebstein. P iissle!', Ueber das primiire Carcinom der Lunge. u Arch. Bd. 145. 1896. S. 191--278. Pbp or e, Ueber eine seltene m akr. Form yon Lungenkrebs. Zentralbl, f. allg. Path. Bd. XV. 1904. S. 948. P e r l s , Zur Kasuistik des Lungencarcinoms. Virchows Arch. 1872. Bd. 56. S. 437. P r e t i , Metastasi caneerigne sottocutanee. Gazzetta reed. italiana. 1909. Q u e i r o l o , Lezioni di clinica medica e lavori sperimentali. Pisa 1905. p. 73. R a v e n n a , Contribution '~ l'4tude du cancer primitif du poumon. Arch. de m4d. exp. 1909. T. XX[. p. 87. K e i n h a r d , Der primate Lungenkrebs. Arch. d. Heilk. XIX. S. 369. R o t k y , Knochencarcinose, die unter Erscheinungen der perniziSsen Aniimie verlief. Prag. reed. Wochenschr. 1906. Nr. 3. L. S t r o p e n i , Fall yon bronchialem Adenocarcinom. 21 S i e g e r t , Zur Histogenese der primiiren Lungenkrebse. Virchows Arch. Bd. 134. S. 387. S t i l l i n g , Ueber primiixen Krebs der Bronchien usw. Virchows Arch. Bd. 83. 1881. S. 77. T i l l m a n n , 3 F~ille yon primgrem Lungencarcinom. Diss. Halle 1889. T r a i n a , Atti della societ~ italiana dl patologia. V. giunione. Palermo 1908. W a t s u j i , Zeitschr. f. Krebsforsch. 1904. Bd. 1. W e i n b e r g e r , Beitrag zur I(iinik tier malignen Lungengesehwiitste. Zeitschr. L Heilk. 1901. Abt. fi interne Meal. Bd. 22. S. 78--103. Woif, Der prim~ire Lungenkrebs. Fortschr. d. Med. 1895. Bd. 13. S. 725. Zad e7 Ein primgres Magencarcinom mit Skelettmetastasen usw. Zieglers Beitfiige. Bd. 37. 1904. Z a g a r i , Della diagnosi de[ tumori maligni prim. della pleura e del polmone. E r k l i t r u n g tier F i g u r e n a u f Tafel I. Figur I. Durchschnitt oines Bronchus. Uebergangspunkt vender hypertrophische Driisen enthaltenden Schleimhaut ins neoplastische Gewehe. Das Bronchialepithel ist wohl yon der unterstehenden Tumormasse abgrenzbar. SchleimfErbung mit Meyers Muzikarmin. Obj. 35 mm apochr. Zeiss, Ok. 3. Figur 2. Metastatischer Knoten der Leher: Atypische Alveolen yon Schleim erfiillt; neoplastische Zellen Schleimklumpen einschliessend. Obj. 4 mm Zeiss, Ok. 4 kemp. FJgur 3. Lungenschnitt mit neopIastischen Elementen infiltriert. Obj. 4 mm Zeiss, Ok. 4 kemp.
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Interlocuções esportivas: uma dobradinha entre Brasil e Argentina
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Interlocuções esportivas: uma dobradinha entre Brasil e Argentina Mariane da Silva Pisani Doutora em Antropologia - Universidade Federal do Piauí. Monica da Silva Araujo Doutora em Antropologia - Universidade Federal do Piauí. Mariane Pisani: Primeiramente agradecemos a disponibilidade de vocês em nos conceder essa entrevista. Em segundo lugar, gostaríamos de pedir que vocês falem sobre as suas trajetórias acadêmicas, abordando um pouco dos principais trabalhos escritos, conceitos desenvolvidos e utilizados. Estamos pensando, de maneira mais específica, em uma aproximação das Ciências Sociais com as práticas esportivas e de lazer. Verônica Moreira: Bom, no meu caso eu gostaria de destacar o primeiro trabalho desenvolvido a partir da minha tese de Licenciatura em Antropologia, pela Faculdade de Filosofia e Letras da Universidade de Buenos Aires que eu defendi no ano de 2001. A minha pesquisa foi sobre e com os torcedores do Clube Atlético Independente. Eu comecei essa pesquisa em 1998/99, e como estava realizando o meu primeiro trabalho de campo, me custou bastante começar e saber o que eu queria fazer. Finalmente fiz esse trabalho com as pessoas que integram o que, popularmente, se conhece como "Barra Brava", o grupo de torcidas vinculadas principalmente à expressão da violência. Na Argentina, o movimento dos Barra Brava é considerado um problema gravíssimo sem que se consiga chegar a uma solução. Revista Entrerios, Vol. 5, n. 2, p. 99-116 (2023) 99 Então, naquele momento, a pesquisa em campo foi me levando a esse grupo em particular e eu fui me interessando muito em saber como se organizavam. Eles tinham uma estrutura muito complexa, uma estrutura hierárquica e também territorial dividida por bairros, e eu procurava entender como se organizavam, como as lideranças eram construídas e como legitimavam essa posição de autoridade. Logicamente também apareceu uma categoria que é típica na Argentina denominada “aguanter”, que é uma categoria por meio da qual os torcedores constroem sua identidade e que possui múltiplos significados associados à "barra" de futebol. O seu significado se refere às práticas de combate, de pôr o corpo nos enfrentamentos físicos. Também era muito típico nesse momento a prática do roubo de certos objetos entre as torcidas, sendo o mais significativo o roubo das bandeiras. Então, para recuperarem a bandeira deviam mostrar que tinham “aguanter”. Não era só recuperar a bandeira, mas também roubar a bandeira alheia. Eu interpretei tudo isso utilizando a teoria da honra e da vergonha, também muito discutível e típica da antropologia mediterrânea. Interlocuções esportivas: uma dobradinha entre Brasil e Argentina Ou seja, eu estava pensando em como esses "jogos de recuperação dos bens" tinham a ver com a ideia de construir uma honra e também a vergonha, ou deixar em estado de humilhação o grupo rival. Então, essas práticas levavam as torcidas, de maneira constante, a um círculo de violência. As políticas públicas ao serem feitas e para que sejam efetivas precisam compreender essas lógicas dos “aguanters”. Essa foi a minha primeira investigação e depois continuei com uma pesquisa independente, pensando mais na questão de como era a política no interior da instituição. Os clubes na Argentina são associações civis sem fins lucrativos e isso faz com que a cada dois, três ou quatro anos, realizem eleições no clube para eleger autoridades. E aí se armam campanhas políticas, os sócios e as sócias se organizam para apresentar um candidato para liderar alguma lista em particular. Então, me interessava pensar na política no ponto de vista dos sócios e das sócias, e também, no que destaca a literatura do Brasil, pensando no tempo da política, em como se armava o tempo de campanha eleitoral no clube, o momento em que acontecia a política, das conversações entre os torcedores, os sócios e as sócias, além dos dirigentes. O interesse por esse tema também foi esculpido no momento de defesa da minha tese, quando um antropólogo que trabalhava com a temática, Fernando Alvim, me questionou sobre o rigor em que se construíam os momentos políticos nas “barras”. Ele me perguntou se parecia um recorte de tempo onde a política aparecia ou se haviam movimentações políticas de maneira cotidiana. Ou seja, como se houvesse uma construção momentânea ou se a política estava sempre presente. Depois, na tese de doutorado trabalhei pontualmente com os dirigentes de futebol pensando, por exemplo, 100 Pisani; Araujo na relevância que tinha o conceito de território para a construção do perfil dos dirigentes. O Club Atlético Independiente3 esteve sempre em uma cidade muito ao sul de Buenos Aires e a relação entre o clube e o território é muito forte. Os dirigentes historicamente eram pessoas conhecidas na cidade. Pessoas, por exemplo, que atuavam em profissões liberais: advogado, médico ou comerciantes. E no momento em que eu fiz esse trabalho de campo, aproximadamente entre 2007 e 2008, isso já estava se modificando. 3 Clube de futebol da Argentina, fundado em 1905 que tem sua sede social e seu estádio na cidade de Avellaneda, Província de Buenos Aires. Interlocuções esportivas: uma dobradinha entre Brasil e Argentina Haviam pessoas com esse perfil tradicional, por exemplo, Julian Brandon que foi presidente do ALFA durante 33 anos e também dirigente do Independiente. Era uma pessoa empresária ou comerciante que entrou como dirigente e depois se converteu em presidente da ALFA. No momento em que eu comecei a fazer o trabalho de campo isso começou a se modificar, e o que eu compreendi era que estávamos em um ponto em que havia dirigentes com o perfil mais tradicional e outras pessoas que poderiam ser classificadas como “outsiders”. Há um capítulo na tese em que discorro sobre como nas “barras” algumas pessoas estabeleciam relações de clientela com os dirigentes, ou seja, que essas relações de clientela não eram unicamente um “toma lá, dá cá" de dinheiro por apoio político, mas como estavam também atravessadas pelos afetos e pelas realidades destes torcedores. Luiz Rojo: Diferente da Verônica, o início da minha trajetória na Antropologia não passa pela Antropologia dos Esportes, do estudo dos esportes. Eu fiz a minha dissertação de mestrado, e depois a tese de doutorado, discutindo fundamentalmente a questão das amizades, esse era o meu tema central de pesquisa. No mestrado eu estudei as relações de amizade entre estudantes de Medicina, e ali eu desenvolvi um conceito de “amizade grupal”, porque até então a teoria sobre relações de amizade privilegiava os estudos, praticamente todos, lidando com sociedades ocidentais, com muito pouca discussão de amizade fora desse registro, e acabava se desenvolvendo uma noção de amizade a partir de uma relação pessoa-pessoa. Então, não se pensava a ideia da amizade para além dessas escolhas individuais, mesmo quando isso envolvia um leque de outras relações. E o que eu percebi dentro dessa pesquisa é que a ideia do grupo de amigos, a amizade que se desenvolvia dentro do grupo, era muito mais relevante para aquelas pessoas do que as relações de amizade um-a-um. Muitas vezes, fora daqueles espaços grupais praticamente não havia interação individual, dois-a-dois. Em todos os momentos, não só na universidade, - até para pensar nos caminhos e escolhas comuns - mas também nos aniversários, nos eventos sociais da vida do centro acadêmico, as relações eram 101 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Interlocuções exportivas: uma dobradinha entre Brasil e Argentina sempre do grupo como um todo. Interlocuções esportivas: uma dobradinha entre Brasil e Argentina Chegando ao ponto em que para alguém chegar ao grupo não bastava ser apresentado por uma das pessoas do grupo, mas tinha que ser incorporada ao grupo como um todo. Essas ações tornavam esse grupo com fronteiras muito bem definidas. Quando eu terminei o mestrado, tendo desenvolvido um pouco esse conceito, a minha ideia era buscar continuar esse estudo sobre amizade, mas agora em um lugar em que a ideia de grupo tivesse mais consolidada, tivesse mais afirmada. Acabei conhecendo por acaso em uma revista uma comunidade naturista no Rio Grande do Sul e que apontava muito para essa ideia dos naturistas como um grupo muito coeso, muito fechado. Fiz minha tese de doutorado lá, trabalhando novamente o conceito de amizade, mas também acabei me dando conta de que por ser uma comunidade naturista eu tinha que trabalhar com o conceito de comunidade e corporalidade. Foi a partir desses dois momentos que conheci e me aproximei da professora Simone Guedes4. Isso aconteceu no finalzinho do meu doutorado, por acaso em uma Reunião de Antropologia do Mercosul, na cidade de Florianópolis. Começamos a conversar sobre essa questão do esporte e ela me convidou para fazer parte de uma rede mais ampla de pesquisas. Assim, logo que terminei meu doutorado, em 2005, eu participei da minha primeira Reunião Brasileira de Antropologia, na cidade de Olinda. Ali fui trazendo, pouco a pouco, as discussões que tinha realizado sobre amizade no mestrado e no doutorado. Para além da questão das relações sociais, trabalhei com a ideia da amizade como emoção. Eu trabalho com um referencial teórico para pensar como que as narrações, os comentários, as colunas jornalísticas, em época dos jogos olímpicos, construiu o discurso sobre a identidade nacional, sobre gênero, sobre questões étnico-raciais… Então, é o meu primeiro trabalho discutindo a questão do esporte pensando, principalmente, a partir da Catherine Lutz e da Lila Abu-Lughod, duas teóricas na Antropologia das Emoções e que pensam a emoção como sendo construída no contexto em que ela está sendo vivenciada, não como uma coisa meramente interna, quase que biológica . Então, eu utilizei essa literatura para pensar o contexto dos eventos esportivos. 4 Simoni Lahud Guedes (1950 - 2019), antropóloga brasileira, professora da Universidade Federal Fluminense e pesquisadora da área de Antropologia do Esporte. Interlocuções esportivas: uma dobradinha entre Brasil e Argentina A partir daí a relação com a Simone se aprofunda, ela vai me supervisionar no pós-doutorado e, seguindo esta minha preocupação, minha busca por esses esportes olímpicos, por não pesquisar futebol, eu acabo fazendo um projeto comparativo entre o Rio de Janeiro e Montevidéu para estudar a questão do gênero no hipismo. Principalmente motivado pelo fato de que o hipismo é o único esporte olímpico, talvez o único esporte de todos, do qual não há nenhum tipo de separação de categorias entre homens e mulheres. Todas Pisani; Araujo 4 Simoni Lahud Guedes (1950 - 2019), antropóloga brasileira, professora da Universidade Federal Fluminense e pesquisadora da área de Antropologia do Esporte. 102 102 Pisani; Araujo as provas são necessariamente mistas. Então eu fui estudar essa relação do gênero dentro do hipismo, isso acabou me motivando depois para a pesquisa posterior na vela, na qual eu vou aprofundando a questão dos debates entre sexo e gênero, a partir da noção de performance da Judith Butler, mas com uma leitura do conceito que eu sei que é muito particular. Então, eu vou pensar o quanto que essas performances, quando repetidas em determinados contextos,- dialogando com a “Catherine Lutz” e com a “Abu-Lughod” - acabam por produzir gênero. E isso eu já tinha discutido na pesquisa do hipismo quando transformo categorias nativas, como as modalidades de salto e adestramento, em categorias analíticas de gênero. Eu discuto que o salto e o adestramento seriam dois gêneros dentro do hipismo porque eles produziriam performances próprias e, naquele contexto específico, independeria se era o caso de um cavaleiro ou uma amazona. Ou seja, cavaleiros e amazonas performariam uma identidade de gênero específica quando no momento do convívio ali, não apenas da prova em si, mas em todo o convívio dentro do ambiente. Na pesquisa da vela que está para ser publicada agora como livro, e que eu espero que saia já no início de 2023, eu vou trabalhar a partir do conceito que é bastante utilizado de sociabilidade, homossociabilidade e heterossociabilidade, mas eu vou transpor isso para um conceito de sociabilidade “homo gênero” e sociabilidade “hétero gênero”, ou seja, pensando e discutindo como que esses conceitos de homossociabilidade acabava reifincando o sexo: homem e mulher. Um grupo de homens juntos seria uma homossociabilidade? E eu coloco: “mas se essas pessoas forem de gêneros diferentes?”. Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Interlocuções esportivas: uma dobradinha entre Brasil e Argentina Ou seja, já havia trabalhado com aficionados, sócios, dirigentes, então acreditei que era o momento de trabalhar com atletas. E em um esporte que para mim era muito desconhecido. Pelo menos para mim, quanto mais estranho, melhor. Então, o fato de eu ter escolhido o boxe como um esporte para investigar tem a ver com isso, com não entender nada do que estava acontecendo no ringue.. E falando agora em dimensões, creio também que o que acontece, pelo menos junto à Universidade de Buenos Aires, no Instituto de Investigação Gino Germani da Faculdade de Ciências Sociais, é que o grupo segue sendo pequeno. Não é um grupo como eu vejo que funciona no Brasil, com grupos ou núcleos de pesquisa de diferentes universidades. Eu penso que o Brasil está muito adiantado com o tema. Por exemplo, fazem apenas cinco anos que explodiu toda a discussão sobre gênero e sexualidades aqui na Argentina. Vocês já estavam discutindo isso faz tempo. E há outra pergunta que você havia feito, Mônica… Mônica: Vocês dois acabaram falando sobre algo que já estava previsto na entrevista, que é como vocês foram construindo as suas trajetórias rumo à Antropologia dos Esportes. Gostaríamos que vocês falassem sobre pertencimento acadêmico, sobre os grupos de pesquisa aos quais estão associados, de qual lugar estão produzindo ciência. Além disso, o que vocês pretendem pesquisar e desenvolver em um horizonte próximo? Verônica Moreira: No meu caso, faz tempo que eu quero realizar um trabalho sobre o boxe. Idealizo isso já faz um tempo. Na RAM de Curitiba, em 2011, apresentei um trabalho sobre isso. Por diferentes motivos, não realizei esse trabalho de campo com regularidade naquele momento, mas agora estou realizando essa pesquisa com profundidade. O que acontece na Argentina é que muitas produções são sobre futebol. Daí a importância que tem em se trabalhar com outros esportes. E essas outras pesquisas estão se multiplicando para temas como corrida, golfe, dentre outros. Em uma coletânea que fizemos em 2013, há trabalhos sobre diferentes objetos de estudo, mas o futebol segue sendo o tema que mais atrai nas investigações. Então, no meu caso, quando eu terminei a minha formação, pensei “eu gostaria de trabalhar com atletas”. Ou seja, já havia trabalhado com aficionados, sócios, dirigentes, então acreditei que era o momento de trabalhar com atletas. E em um esporte que para mim era muito desconhecido. Interlocuções esportivas: uma dobradinha entre Brasil e Argentina Pelo menos para mim, quanto mais estranho, melhor. Então, o fato de eu ter escolhido o boxe como um esporte para investigar tem a ver com isso, com não entender nada do que estava acontecendo no ringue.. E falando agora em dimensões, creio também que o que acontece, pelo menos junto à Universidade de Buenos Aires, no Instituto de Investigação Gino Germani da Faculdade de Ciências Sociais, é que o grupo segue sendo pequeno. Não é um grupo como eu vejo que funciona no Brasil, com grupos ou núcleos de pesquisa de diferentes universidades. Eu penso que o Brasil está muito adiantado com o tema. Por exemplo, fazem apenas cinco anos que explodiu toda a discussão sobre gênero e sexualidades aqui na Argentina. Vocês já estavam discutindo isso faz tempo. E há outra pergunta que você havia feito, Mônica… Interlocuções esportivas: uma dobradinha entre Brasil e Argentina E, então, pensando novamente com a “Butler” não apenas a ideia de sexo, gênero e sexualidade, mas dois tipo de gêneros diferentes, continuaramos a falar de uma homossociabilidade? E aí eu desenvolvo o conceito de sociabilidade “homo gênero” e sociabilidade “hétero gênero” para pensar sociabilidades nos quais, por exemplo, fossem só homens, mas de gênero diferentes ou só mulheres de gêneros diferentes. Então, isso é um pouco dessa trajetória que depois fui aprofundando e comecei a desenvolver mais na vela junto com a questão da corporalidade. Para pensar a questão da identidade e corporalidade nos esportes adaptados, tive uma influência enorme ao ter sido membro da banca de doutorado da Mônica Araujo; a leitura da tese da Mônica me inspirou muito. Eu me lembro que eu saí da defesa falando “algum dia eu vou pesquisar essa questão do esporte para pessoas com deficiência”, e fiz um trabalho acompanhando a ANDEF, que é a Associação Niteroiense dos Deficientes Físicos, pensando a questão do esporte de alto rendimento. Em relação a isso, agora estou no momento inicial de uma outra pesquisa sobre políticas públicas esportivas para pessoas com deficiência e na semana que vem estarei 103 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Mônica: Vocês dois acabaram falando sobre algo que já estava previsto na entrevista, que é como vocês foram construindo as suas trajetórias rumo à Antropologia dos Esportes. Gostaríamos que vocês falassem sobre pertencimento acadêmico, sobre os grupos de pesquisa aos quais estão associados, de qual lugar estão produzindo ciência. Além disso, o que vocês pretendem pesquisar e desenvolver em um horizonte próximo? Verônica Moreira: No meu caso, faz tempo que eu quero realizar um trabalho sobre o boxe. Idealizo isso já faz um tempo. Na RAM de Curitiba, em 2011, apresentei um trabalho sobre isso. Por diferentes motivos, não realizei esse trabalho de campo com regularidade naquele momento, mas agora estou realizando essa pesquisa com profundidade. O que acontece na Argentina é que muitas produções são sobre futebol. Daí a importância que tem em se trabalhar com outros esportes. E essas outras pesquisas estão se multiplicando para temas como corrida, golfe, dentre outros. Em uma coletânea que fizemos em 2013, há trabalhos sobre diferentes objetos de estudo, mas o futebol segue sendo o tema que mais atrai nas investigações. Então, no meu caso, quando eu terminei a minha formação, pensei “eu gostaria de trabalhar com atletas”. Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Mônica: Sim. E quais são os seus horizontes de pesquisa daqui pra frente? Mônica: Sim. E quais são os seus horizontes de pesquisa daqui pra frente? Veronica Moreira: No meu caso, e também como diretora de um projeto de investigação no Instituto, a ideia é trabalhar sobre diferentes objetos de estudo como o boxe, a corrida (running), o futebol também, e crossfit. Nesses casos, pensando no cruzamento entre corpo e gênero, que está como um tema muito presente na agenda de discussão, também em outras universidades; insisto em dizer que não tanto como 104 Pisani; Araujo no Brasil. Há interesse em se trabalhar outras questões que não tem a ver unicamente com a violência no futebol, ainda que isso sempre esteja aí como estudo. Trabalhar com torcidas e violências ainda é uma linha de investigação muito interessante, mas, no meu caso, a ideia é diversificar o olhar para outros esportes, incluindo a discussão sobre o capacitismo e o corpo com deficiência. Para mim é um tema rico, um super tema para investigar. Isso seria como uma aspiração, como um objetivo no futuro. Mônica: E você, Luiz? Mônica: E você, Luiz? Luiz Rojo: Primeiro, assim, eu vou só completar um pouquinho a pergunta anterior. Mônica: Sim. Luiz Rojo: Olhando retrospectivamente, chama a minha atenção algo que fala um pouco desse processo da implantação da Antropologia dos Esportes no Brasil. Tanto na minha dissertação de mestrado quanto na tese de doutorado, haviam partes dedicadas à questão esportiva. E esse foi o ponto de encontro para conversar com a Simone Guedes. Eu acompanhei uma semana a realização das olimpíadas regionais dos estudantes de medicina, e então fiz um capítulo sobre isso na dissertação do mestrado. Lá tem um item chamado Mens Pulchra in Corpore Pulchro que acabou sendo meu primeiro artigo na área de esportes, que é um item do capítulo da tese de doutorado falando sobre as práticas esportivas entre naturistas. Mas eu escrevi isso sem nenhum referencial teórico sobre esporte porque simplesmente não chegava até então aos meus ouvidos. Estava se constituindo, estava avançando. A primeira reunião da RBA com o grupo de esportes, mostra um pouco como esse processo foi ganhando corpo. E eu peguei justamente essa transição na hora que a Antropologia do Esportes está começando a se constituir de forma institucional. Respondendo mais especificamente à última pergunta, o que eu estou buscando cada vez mais agora é juntar duas paixões. Eu vivi uma paixão muito intensamente antes de mergulhar na antropologia, que foi a vida política. Em certo momento, houve uma parada quase total quando eu fui me dedicar a terminar a graduação, mestrado, doutorado, entrar na universidade, realizar as primeiras pesquisas… E recentemente, já há seis, sete anos, eu fui retomando a minha vivência política, mas até então como duas coisas muito separadas, a vida política e a vida acadêmica. E agora, escrevi um artigo, que foi publicado na revista da ALA, sobre o impacto do giro à direita na América Latina sobre a discussão dos esportes no Brasil, e também tenho discutido essa questão das políticas públicas esportivas em relação ao esporte de pessoas com deficiência. Mônica: E você, Luiz? Pensando sobre isso, que foi uma das coisas que eu estava falando no Chile na outra semana, quando a gente olha hoje para 105 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina o Brasil, o reconhecemos como uma potência do esporte paralímpico, em termos de quadro de medalhas, em termos de ter medalhas em diversas modalidades, de ter uma equipe como a de futebol de pessoas com deficiência visual que rivaliza com a Argentina. É um bom tema de pesquisa, a questão do futebol né, mas o futebol de pessoas com deficiência visual é uma equipe quase que imbatível historicamente. Mas ao mesmo tempo, se você olha para as ruas, para os parques, para as praias, para os espaços públicos, é muito, muito raro você encontrar uma pessoa com deficiência praticando algum esporte. Você olha corridas de rua no Rio de Janeiro ou em outros locais, às vezes mil, duas mil, cinco mil pessoas correndo e você raramente encontra, quando encontra são duas, três pessoas, na maioria atletas que estão aproveitando aquele espaço para um treinamento específico, para alguma coisa, e não pessoas que correm como a maioria dos demais e estão ali praticando um esporte. Então, o que eu tenho me dedicado cada vez mais é pensar isso: quais são as motivações, quais são as questões políticas, sociais, culturais, corporais que envolvem essa inexistência da prática esportiva - e não diria só de lazer - de pessoas com deficiência e da inexistência de políticas públicas específicas para esse setor da população. Por exemplo, hoje, é cada vez mais impossível, felizmente, você ter projetos e atuações que excluem completamente as mulheres. É cada vez mais difícil, felizmente também, ter políticas públicas que excluam a população afro-brasileira. Agora, é completamente aceitável que você tenha políticas públicas que excluam completamente as pessoas com deficiência. Então, estamos em que momento dessas lutas sociais, dessas questões do próprio movimento nacional de pessoas com deficiência, da questão da incorporação do esporte e dessas temáticas dentro das políticas públicas brasileiras? Agora esse é o meu eixo principal de desenvolvimento de pesquisa. Mariane: O campo dos estudos dos esportes, especialmente na área de Antropologia, tem se expandido e se consolidado nos últimos anos, tendo em vista a publicação de um livro no Brasil dos vinte anos dos estudos da área de Antropologia dos Esportes, Lazer e outras práticas. Mônica: E você, Luiz? A gente pode destacar sobretudo nesse movimento de expansão o trabalho do Conselho Latinoamericano de Ciências Sociais e a União Internacional de Antropologia e Etnologia, por exemplo. Vocês poderiam comentar como esses espaços foram sendo construídos e constituídos, e também um pouco da participação de vocês nesses lugares? Verônica Moreira: Antes de responder a esta pergunta, eu quero destacar o Movimento Nenhuma a Menos, na Argentina, que é um movimento que denuncia o número de feminicídios no país, a partir da morte de uma jovem. Isto começou em 2015 106 Pisani; Araujo e a temática sobre a violência de gênero explodiu logo em seguida, assim como toda uma movimentação nas ruas. Isso impactou muito como eu me entendo na academia e nas investigações. As perguntas sobre os gêneros e as sexualidades surgiram das mãos de jovens que estavam começando as suas investigações de doutorado. Isso para mim é um ato bastante revelador e muito interessante. Agora essas pessoas já estão formadas e usam as suas teses e outras produções dentro de uma agenda social e política a nível nacional. Sobre a rede CLACSO… A CLACSO é uma rede de estudo comparativo latinoamericana e a ideia é que investigadores, investigadoras e pessoas em formação estejam em contato para discutir diversos temas e assuntos que podem ser as questões de gênero, mas também discussão sobre políticas públicas. Aliás, este canal especificamente está bastante obstruído, pois nos custa muito chegar para contribuir e realizar políticas públicas concretas sobre determinados temas. E ainda sobre esse tema da política pública, que também está presente na CLACSO, sentimos na nossa própria pele os desafios quando se trata da questão da violência no futebol. Temos muito material elaborado sobre o tema, mas tudo muito fragmentado, entende? A rede tem isto: estão presentes discussões sobre gêneros, sexualidades e políticas públicas como carro chefe e ao longo do tempo foi-se somando pessoas de diferentes países. Acredito que em 1999 foi a primeira formação do grupo de trabalho dedicado às Ciências Sociais e esportes. E eu me lembro que nesse momento eram umas quinze pessoas mais ou menos, com países como Brasil, Argentina, Equador… Bom, eram muitos poucos países. Atualmente a rede tem setenta pessoas e os seguintes países: Argentina, Brasil, Chile, Bolívia, Colômbia, Porto Rico, Cuba, Equador, México, Paraguai, Peru e Uruguai. Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Mônica: E você, Luiz? O que eu quero dizer com isso é que podemos observar que há uma ampliação da incorporação de novos países que antigamente não participavam desses congressos que assistimos, onde se trabalha sobretudo o tema dos esportes. Ou seja, cresceu a produção a nível de outros países. E de toda maneira, eu chamo a atenção para as dificuldades, para o fato do quanto é complexo sustentar uma rede que funcione da forma como idealmente pensamos que deve funcionar. É muito complexo porque todas essas setenta pessoas estão trabalhando em pares. Algumas pessoas produziram algumas coisas como, por exemplo, o boletim dedicado à Copa América Feminina. Fizemos uma reunião na pandemia e, naquele momento, foi bom poder conectar pessoas de diferentes países e ter diálogos muito enriquecedores. Fizemos dois bate-papos muito interessantes: um sobre a formação de futebolistas e outro em que discutimos raça. Eu acho que a CLACSO, sendo um conselho latino americano, possui uma abertura para trabalhar a questão da raça, do racismo no esporte. Bem… Há outras atividades que podem ser Sobre a rede CLACSO… A CLACSO é uma rede de estudo comparativo latinoamericana e a ideia é que investigadores, investigadoras e pessoas em formação estejam em contato para discutir diversos temas e assuntos que podem ser as questões de gênero, mas também discussão sobre políticas públicas. Aliás, este canal especificamente está bastante obstruído, pois nos custa muito chegar para contribuir e realizar políticas públicas concretas sobre determinados temas. E ainda sobre esse tema da política pública, que também está presente na CLACSO, sentimos na nossa própria pele os desafios quando se trata da questão da violência no futebol. Temos muito material elaborado sobre o tema, mas tudo muito fragmentado, entende? A rede tem isto: estão presentes discussões sobre gêneros, sexualidades e políticas públicas como carro chefe e ao longo do tempo foi-se somando pessoas de diferentes países. Acredito que em 1999 foi a primeira formação do grupo de trabalho dedicado às Ciências Sociais e esportes. E eu me lembro que nesse momento eram umas quinze pessoas mais ou menos, com países como Brasil, Argentina, Equador… Bom, eram muitos poucos países. Atualmente a rede tem setenta pessoas e os seguintes países: Argentina, Brasil, Chile, Bolívia, Colômbia, Porto Rico, Cuba, Equador, México, Paraguai, Peru e Uruguai. Mônica: E você, Luiz? O que eu quero dizer com isso é que podemos observar que há uma ampliação da incorporação de novos países que antigamente não participavam desses congressos que assistimos, onde se trabalha sobretudo o tema dos esportes. Ou seja, cresceu a produção a nível de outros países. E de toda maneira, eu chamo a atenção para as dificuldades, para o fato do quanto é complexo sustentar uma rede que funcione da forma como idealmente pensamos que deve funcionar. É muito complexo porque todas essas setenta pessoas estão trabalhando em pares. Algumas pessoas produziram algumas coisas como, por exemplo, o boletim dedicado à Copa América Feminina. Fizemos uma reunião na pandemia e, naquele momento, foi bom poder conectar pessoas de diferentes países e ter diálogos muito enriquecedores. Fizemos dois bate-papos muito interessantes: um sobre a formação de futebolistas e outro em que discutimos raça. Eu acho que a CLACSO, sendo um conselho latino americano, possui uma abertura para trabalhar a questão da raça, do racismo no esporte. Bem… Há outras atividades que podem ser 107 feitas como, por exemplo, o lançamento de boletins. Já a publicação de livros é um trabalho que demanda mais tempo e esforço. Temos essas reuniões para discutir assuntos pontuais, mas não podemos fazer muito mais por uma questão de tempo. Luiz Rojo: Bom, Verônica acabou focando bem nesse debate, até porque ela está na coordenação do nosso grupo da CLACSO. Eu acho que esse processo realmente é muito difícil porque construir conexões da forma como a gente trabalha, de forma muito isolada…Ou seja, acho que a gente ainda não conseguiu, pelo menos que eu saiba, produzir projetos mais comparativos, que é um salto que a gente tem que dar em equipe. Pensar como que nós podemos trabalhar em equipe para além dos encontros, dos boletins, dos livros, dos eventos. É um desafio que está posto. É bom quando a gente tem desafios pois temos mais coisas a enfrentar. E do ponto de vista da IUAES é um processo semelhante. Conversando isso algumas vezes com a Simone, a gente falava muito sobre a importância desses projetos de internacionalização. Tanto a Simone quanto o Pablo Alabarces fizeram esse trabalho forte da consolidação dos estudos sobre esportes na América Latina. Mônica: E você, Luiz? E, foi como a Verônica falou, desde 98, 99, não lembro exatamente o ano, houve a iniciativa do Pablo desse grupo da CLACSO e daí pra frente as viagens que fizeram juntos para a a Colômbia, México e em lugares para participarem de eventos. E agora eu me lembro de outro momento, de quando eu vi uma chamada de um congresso da IUAES que ia ter em Dubrovnik, na Croácia. Achei interessantíssimo e falei “poxa, nunca fui à Croácia!” e era aquele momento da vida em que, (ai que saudade!), a gente mandava um pedido de passagem, e de hospedagem, e de diária e vinha tudo. Passagem aérea, diária, hospedagem, inscrição… Tinha dinheiro para a gente investir em ciência, tecnologia, tinha dinheiro para a gente investir nessa parte, e eu acho que isso impulsionou muito a nossa possibilidade de avançar a nível internacional. Eu fui para aquele congresso e tinha lá o grupo formado sobre esportes. Ainda não havia um grupo organizado na IUAES, mas havia um grupo de trabalho. Quando cheguei lá eu tive uma surpresa gigantesca porque eram três sessões de trabalho, com quinze trabalhos no total. E tinham dois trabalhos, o meu e o de um doutorando da Finlândia… O dele sobre Maratonas Solidárias, sobre as pessoas se engajavam para arrecadar fundos para eventos específicos.Os nossos dois eram os únicos trabalhos de Antropologia Cultural. O resto era tudo Antropologia Física. “O impacto da lesão não sei o que…”, parecia que eu estava voltando ao mestrado assistindo aulas de anatomia, aquela coisa que eu acompanhei lá no trabalho de campo do mestrado. E eu lembro que a gente conversou, este finlandês e eu, e saímos de lá horrorizados pois ninguém 108 Pisani; Araujo fez pergunta para a gente, a gente não fez pergunta para ninguém, a não ser eu perguntar do trabalho dele e ele perguntar do meu. Não tinha nem ponte de contato. A gente ficou conversando sobre isso e, eu lembro que estava a Carmen Rial e a Miriam Grossi no congresso, elas já estavam à frente da IUAES participando ativamente, e elas me estimularam para “meter a mão nesta cumbuca”. Já no Congresso do Canadá, eu fiz uma proposta de grupo,eu comecei a conversar com todo mundo que estava, mandei e-mail e falei: “vamos construir o grupo dentro da IUAES”. Bem na cara e na coragem fomos construindo. Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Mônica: E você, Luiz? É uma infinidade tão grande de temáticas, Verônica… ica Moreira: Sim, é difícil sistematizar porque está em processo.O que ocorre na 109 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Interlocuções exportivas: uma dobradinha entre Brasil e Argentina CLACSO é que temos um perfil construído com foco no debate das desigualdades, justamente de norte a norte, e, a partir daí, nos organizamos sobre alguns assuntos como a desigualdade de gênero, a violência, políticas públicas. Há temas que norteiam e esse processo tem sido muito interessante. Por outro lado, tem toda uma dificuldade para lidar com as diferentes realidades, por exemplo, como abordar o racismo no Brasil, que é distinto da Bolivia, da Argentina,... Luiz Rojo: Há que se pensar que a CLACSO já tem uma história de vinte e três anos discutindo a questão do esporte. Nós somos descendentes, de descendentes, de descendentes do Pablo, da Simone, então isso já tem uma história, uma trajetória. No caso da IUAES, nós temos quatro anos de história. Então, é um movimento ainda muito embrionário que eu espero que vá se consolidar, mas que ainda é passo a passo. Verônica Moreira: Acredito que, se for pensar na pandemia, não há tanto diálogo na atualidade talvez porque não pudemos nos reunir presencialmente e continuar com as reuniões que para mim são um clássico do intercâmbio. Pontualmente, falo da RAM. A “RAM” começou, creio que com a primeira reunião em 2001, em Curitiba, com a coordenação da Simone e com Arlei Damo, que foi o primeiro congresso que eu me apresentei junto com José Fassheber. Foi o primeiro em tudo. Foi o primeiro congresso, primeiro congresso internacional, e a partir daí sempre, no meu caso, participei do grupo de Esportes e depois foi sendo construído uma mesa paralela, com um tema em particular. O que sinto é que a pandemia mudou algo, que acredito que possa ser revertido. Ficou algo pendente para mim também do que disse o Luiz, na questão de uma dimensão comparativa. Creio que Simone insistiu nisso e faz tempo que há um projeto para isso, com muitas ideias, mas com o intuito de se montar, por exemplo, grupos para escreverem sobre um tema pontual, mas fazê-lo com algumas pessoas de diferentes países. É difícil, às vezes, por uma questão de tempo material que não temos. Mônica: E você, Luiz? O Jerôme Soldani, da França, teve um papel fundamental de abrir o campo também na Europa, de trazer mais gente; Mariane Pisani participou depois aqui em Santa Catarina, uma série de pessoas foram se agregando. Se a Verônica fala da dificuldade da CLACSO, na IUAES a dificuldade é muito maior porque é um campo mundial. Hoje felizmente já tem gente dos cinco continentes, mas você imagina juntar pessoas dos Estados Unidos, da África do Sul, do Quênia, da índia, da Indonésia, do Japão, da Europa, da América do Sul, é uma loucura e ainda não está totalmente consolidado. Agora teremos o congresso na Índia, estamos trabalhando para isso e vai ser um momento muito delicado de passagem de bastão. Eu estarei saindo da coordenação, termino este meu mandato, o Jerôme irá continuar tendo uma pessoa o acompanhando, da República Tcheca, mas estaremos fazendo essa passagem e aí conseguindo avançar, mas é um processo lento, é um processo difícil porque envolve uma quantidade absurda de países, de momentos e de ritmos diferentes, de produção, de redes e de contatos dentro desse campo. Mas eu acho que é um desafio que estamos conseguindo colocar em movimento. Espero que para os próximos anos mais gente do Brasil se junte, mais gente da América Latina se junte para ocupar efetivamente esse espaço da IUAES que é uma conexão muito importante para gente. Verônica Moreira: Perdão. E de que temas tratam? Já sei que devem ser muito variados mas, que tipo de problemática colocam? Luiz Rojo: Nós sabemos - até em função do que já relatei sobre o congresso na Croácia - que alguns países a Antropologia do Esporte está muito vinculada à Antropologia da Saúde, à Antropologia Física, e uma das questões que nós colocamos é que nós não queremos ser um grupo de Antropologia Cultural dos Esportes. A gente nasceu assim, mas já incorporamos um indiano que trabalha, diria, na fronteira entre a Antropologia Cultural e a Antropologia Física. Então, a ideia é buscar ampliar ainda mais para poder ver esses diálogos, ver o que cada lado contribui, o que é difícil porque torna essa agenda ainda mais complexa. Mônica: E você, Luiz? Mas, também, há outros pontos: quem nos financia, quanto dinheiro nos dão para fazermos nosso trabalho de campo e para viajar, e eu acredito que aí o contexto político incide sobre o que fazemos, nos impacta. Na Argentina, toda essa questão de discutir gênero e sexualidades estão legitimadas porque há um Ministério de Mulheres e Diversidade, há um Ministério de Esportes que tem a agenda de gênero muito presente, tudo facilita isso, um monte de produções, há mais dinheiro circulando sobre isso. Eu, como diretora de um centro de formação de Gênero e Esportes na Universidade de Buenos Aires, tenho o apoio da Secretaria Esportes da Nação. Como o Luiz já tinha comentando, de que antes tinham a possibilidade de participar de um congresso onde te davam a passagem e todo o resto e hoje isso se encontra muito limitado… Então, o 110 Pisani; Araujo contexto político dita sim o que fazemos. Eu sempre vi que há um diálogo muito profundo, mas hoje vejo que isso diminuiu, creio eu, como produto da pandemia. A vontade é voltar a fazer os intercâmbios, então, agradeço a Mariane e Mônica por me convidar a participar disso, pois isso é o que eu entendo que temos que fazer e sair construindo entre todos. Tenho vontade de seguir estabelecendo diálogos e aprofundando os intercâmbios. Luiz Rojo: Mariane, essa questão que você colocou me fez lembrar do dia em que eu conheci a Verônica. Não sei se a Verônica se lembra que a gente se conheceu em Buenos Aires, em uma sala da Universidade de Buenos Aires, num desses encontros que a Simone e o Pablo organizavam e que foi um grupo daqui, algumas pessoas, para Buenos Aires, para um fim de semana de conversas. Em uma sala, foi a primeira ida para um evento assim. A Simone me convidou e eu fui; tava lá Garrica, tava lá Verônica, tava lá um grupo de pessoas e eu acho que isso, esses encontros, para além dos congressos, era algo que organizava, inclusive depois com a Simone indo fazer um pós-doutorado na Argentina, com o Nicolás Cabrera que veio aqui, pra cá, com o Davi Quitian, da Colômbia, que veio fazer um pós-doutorado aqui. Então, havia mais esse intercâmbio. Verônica Moreira: Qual é a tradução? Luiz Rojo: “Quanto mejor…” Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Mônica: E você, Luiz? Assim, como disse a Verónica a pandemia realmente teve um impacto nisso, mas mesmo antes a gente já sentia um recuo por conta da questão econômica e política, ou seja, a dificuldade de verba para viajar, para fazer as coisas. E eu acho que tem uma outra questão que temos que pensar, e aí é um ponto complicado, vou fazer uma brincadeira: tinha um bloco aqui em Niterói que dizia “se melhorar, afunda” e… Verônica Moreira: “Se hunde.” Luiz Rojo: Isso. E eu acho que uma parte disso também é fruto exatamente do nosso crescimento, do nosso sucesso. Porque quando nós éramos poucas pessoas lá em 2005, 2006, fundamentalmente Brasil, Argentina e uma pessoa daqui e uma outra pessoa de acolá era muito mais fácil se reunir, era muito mais fácil pensar projetos comuns dessa articulação. Nós tínhamos a RAM e a ABA, um congresso por ano, o que também dava encontros, mas dava tempo. Se a gente olhar a nossa agenda hoje, nós temos: todos os anos, a princípio, congresso da IUAES; a cada dois anos uma reunião da Associação Brasileira de Antropologia, acho que também lá do Congresso de Antropólogos da Argentina, uma reunião nacional; temos a reunião de Antropologia do Mercosul; temos a reunião da Associação Latinoamericana de Antropologia; então nós temos hoje uma sobrecarga de congresso. Além disso, ainda pensando que a gente praticamente não 111 participa da reunião de Antropologia Equatorial, como um grupo, como uma coisa organizada, e abandonamos praticamente ou totalmente a ANPOCS, no qual também pessoas da Argentina participavam, iam trocar. Se a gente pensar que em várias das nossas reuniões de antropologia do Brasil pesquisadores da Argentina vinham apresentar trabalho, e que muitos de nós íamos apresentar trabalho, olha a quantidade de congressos e eventos que nós temos. O que foi um crescimento e um fortalecimento da área também implicou, eu acho, em uma redução desses outros espaços de encontros mais próprios de sentar e debater mais profundamente, como fizemos na Argentina, acho que em 2005, 2006. Para conversar, trocar ideias e não para apresentar trabalho de quinze minutos, depois ter conferência, mesa redonda e seminário. Então, esses espaços foram se perdendo também. A gente se reúne muito, mas a gente se encontra pouco. E eu acho que a gente tem que pensar um pouco como a gente não vai abrir mão desses espaços. Como a Verónica falou - e eu concordo- , isso é importante para a visibilidade do campo, para o seu fortalecimento , mas como a gente consegue mediar? Talvez a tecnologia seja uma alternativa. Dá pra gente fazer… É ruim não ser presencial? Mas você veja, se a gente não tivesse esse espaço, como a gente estaria juntando Niterói, Teresina, Buenos Aires? Impossível! Então, usar mais a tecnologia para a gente trocar ideia e conversar, bater papo acadêmico e pensar projetos buscando recompor os espaços. Verônica Moreira: “Se hunde.” Essa possibilidade que a Verônica aponta lá da Argentina, a gente espera que no Brasil a partir do ano que vem comecem a surgir essas possibilidades, de mais bolsas e mais pesquisas para que a gente possa fazer doutorado sanduíche dos nossos orientandos e das nossas orientandas, pós doutorados entre a gente. Espaços também dessa circulação, que são tão importantes, para que a gente possa ir se fortalecendo. Verônica Moreira: Simplesmente isso do curso conseguir financiamento de alguma agência mundial, que não seja da Argentina ou do Brasil, que financie, que tenha dinheiro para essas reuniões presenciais com um dia, dois dias de discussão, de conversa, desses encontros que você menciona, que não são somente reuniões. Também vejo assim os congressos, como uma fábrica de salsichas (risos). Esta é uma metáfora aqui na Argentina para dizer quando vem uma coisa atrás da outra, e não há muito tempo para a discussão, para o diálogo, para que as coisas sejam melhor apuradas. E agora eu fico pensando nisso com pena, pois sinceramente nós perdemos essa questão do encontro, de estar de maneira presencial dialogando. Então há muito o que fazer. Pisani; Araujo Mônica: O Luiz descreveu o que viu no congresso da Croácia e só isso já daria um 11 Mônica: O Luiz descreveu o que viu no congresso da Croácia e só isso já daria um Mônica: O Luiz descreveu o que viu no congresso da Croácia e só isso já daria um 112 Pisani; Araujo artigo né (risos)... Já daria ali uma descrição bem interessante sobre os caminhos que são tomados a partir disso, uma nova realidade, uma expansão do campo que, por outro lado, traz um conjunto de desafios, uma complexidade que a gente tem que enfrentar. E o Luiz lembrando do papel da Simone e do Pablo na constituição desse campo, mas também em um espaço que transbordava. Espaço esse de diálogo, mas também um espaço de sociabilidade extra acadêmica. Isso me faz lembrar do papel do Nepess e nos eventos que eram liderado pela Leda Costa e pelo Martin Curi como, por exemplo, a visita a estádios, combinar saídas para assistir aos jogos… Essas coisas nos trazem um saudosismo em relação a essas outras atividades que tinham como horizontes, obviamente, os nossos temas de pesquisa, mas que extrapolava em termos de uma interação, da mobilização desses afetos. Verônica Moreira: “Se hunde.” Voltando para o nosso roteiro, a gente não tem como fazer uma entrevista dessa natureza sem falar do impacto da realização dos grandes eventos na cidade do Rio de Janeiro: Copa do Mundo de 2014 e depois os Jogos Olímpicos e Paralímpicos de 2016. Então, queria que vocês falassem um pouco sobre isso. Luiz Rojo: Respondendo a partir da minha própria vivência, eu acho que sem a realização dos jogos aqui no Rio de Janeiro, diante dos Jogos Paralímpicos que é o meu foco, é pouco provável que eu pudesse desenvolver o tipo de pesquisa que eu desenvolvi sobre a questão do esporte adaptado. Não apenas porque houve visibilidade gigantesca do tema, mas porque abriu um campo de interesse sobre essa temática. Tem uma série de análises, foram escritas coletâneas, livros, artigos sobre a questão do impacto político da Copa principalmente, mas também dos Jogos Olímpicos. Eu não tenho profundas divergências com a maioria deles, mas eu lembro de ter escrito um artigo em especial no qual dialogo com o nosso querido, saudoso e amigo, Gilmar Mascarenhas que tinha um olhar muito crítico para esses mega eventos. E eu falo assim: “ok mas, não por acaso, esse olhar crítico focava na Copa do Mundo e nos Jogos Olímpicos.” Em momento algum - e eu li a coletânea toda sobre o impacto dos mega eventos - há uma única citação à realização dos jogos paralímpicos e eu acho que esse evento trouxe um tipo de visibilidade. Falava-se tanto do legado, “qual o legado dos jogos?”, eu digo: a visibilidade dos jogos adaptados no Brasil”, pois é inegável a transformação que há pré jogos e pós jogos. Então, eu acho que esse é um tema que fala um pouco das nossas agendas. Voltando à questão feita anteriormente, sobre os conceitos utilizados… Metodologicamente, as questões que mais me impactaram foi a leitura do Magnani sobre a observação “de perto e de dentro”. Acho aquele texto de uma potência, de uma riqueza fantástica, e como todo bom texto, ele permite que você 113 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Interlocuções exportivas: uma dobradinha entre Brasil e Argentina se aproprie dele para além de somente ler. E uma das coisas que eu comecei a fazer há um bom tempo é partir para as considerações do Magnani para pensar a observação de perto e de dentro como uma alternativa a observação participante. Verônica Moreira: “Se hunde.” Mas não apenas para a questão urbana, do desenvolvimento, da forma como Magnani usa. Eu uso aquilo de uma forma um pouco diferente. E para pensar no que ele fala muito ali, do quanto que a dimensão urbana pouco olha para o ponto de vista das atribuições de significado nativos. E eu acho que esse olhar, do ponto de vista das pessoas que estavam ali vivenciando esses mega eventos, ainda faltou na nossa elaboração. Nós fomos de alguma forma apanhados por essa crítica aos mega eventos esportivos. Ela era importantíssima de ser feita, havia muitos aspectos indicados, mas ela conseguiu de alguma forma se impor como “a narrativa”. E de alguma forma ela prejudicou que outras narrativas pudessem aparecer porque parecia que outras narrativas poderiam legitimar a realização dos mega eventos. E o olhar crítico já tinha se colocado ali como uma vertente definitiva, podemos dizer assim. A Simone publicou um texto, tratando do recente contexto político brasileiro, no qual fala do “segundo sequestro da camisa verde e amarela”. E se ela foi sequestrada uma segunda vez é porque ela foi resgatada da primeira vez. A gente precisa de um resgate dos megaeventos esportivos, lançando outros olhares, outras perspectivas desses eventos, sem abrir mão da visão crítica. Precisamos procurar compreender o que eles significaram não apenas no macro mas, - nos apropriando do histórico e metodológico da nossa disciplina - impactos micro. Além disso, no que isto implica, em algum grau que seja, no fortalecimento da descentralização do monopólio do futebol, no suporte e na visibilidade de outras vivências e outras relações com a prática esportiva, sem contar as mudanças em relação às mídias. A maior questão que esses mega eventos trazem para a gente hoje é o reflexo inclusive sobre isso, sobre a nossa vivência, ou seja, cada um de nós deve ter percebido o quanto se tornou mais fácil publicar, mais fácil falar, o quanto dessa área ocupou um espaço, não apenas falando do nosso crescimento orgânico, mas porque o nosso crescimento orgânico enquanto grupo coincidiu com o fato de que a sociedade brasileira tava se debruçando sobre a questão do esporte como nunca se debruçou antes na vida. E para além disso, se debruçou simultaneamente sobre futebol em 2014 e sobre os esportes Olímpicos e Paralímpicos dois anos depois. Verônica Moreira: “Se hunde.” Então acho que a gente é herdeiro disso, eu sempre lembro a Mônica falando que tinha um projeto de doutorado sobre dança afro, se não me engano… Pisani; Araujo Mônica: Eu mesma mudei de projeto de doutorado em função de um grande evento 114 Mônica: Eu mesma mudei de projeto de doutorado em função de um grande evento Mônica: Eu mesma mudei de projeto de doutorado em função de um grande evento 114 Pisani; Araujo Pisani; Araujo esportivo. Luiz Rojo: Isso… E aí foi assistir uma prova de natação nos jogos parapanamericanos e mudou de tema. Isso é legado dos megaeventos. A tese de doutorado da Mônica é legado dos Jogos Parapanamericanos. Se não o houvesse, talvez nós tivéssemos mais uma tese muito boa sobre dança afrobrasileira, mas não teríamos a primeira tese de doutorado da história da Antropologia Brasileira sobre qualquer tipo de modalidade adaptada. Então a gente tem que pensar também qual é o impacto, isso também merecia um artigo, sobre os megaeventos esportivos na consolidação, diversificação e ampliação do campo da Antropologia dos Esportes no Brasil. Mônica: Então realmente a gente ficou muito refém de uma narrativa que é importante mas que foi pensada, posso estar sendo injusta, de uma maneira um pouco apressada, no sentido de dizer, de maneira muito categórica, chamar atenção apenas para os aspectos negativos como se colocássemos em jogo tudo aquilo que de positivo, de outros potenciais, a gente estivesse legitimando, de forma acrítica a realização desses eventos. E nós sabemos de todos os problemas, as questões das remoções, uma série de aspectos que foram muito complicados e que tiveram impacto concreto na vida de uma grande parte da população; ninguém está cego para isso, mas eu acho que tem outras camadas que não foram devidamente abordadas. Acho que ainda tem espaço e tempo para se fazer isso. Luiz, você começa a falar sobre isso no seu artigo sobre a questão da visibilidade como legado dos Jogos Paralímpicos, mas tem outra camada que tem a ver justamente com a produção do campo dos esportes que se amplia e diversifica.. Acho que também tem a questão da profusão de encontros, antes a gente tinha uma mesa, agora temos mais de um GT, mesas temáticas, ou seja, um aumento tem um aumento muito expressivo. Luiz Rojo: Para mim esse foi um momento muito bom para olhar para essa trajetória e analisar um pouco. . Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Verônica Moreira: “Se hunde.” E acho que o campo precisa disso, ocasionalmente, de fazer balanços como esse que acabamos de fazer, olhando para o que já foi feito, para as lacunas, para os ajustes possíveis, O Bordieu já dizia que a gente vai reconstruindo a memória e a significação dos eventos a partir do ponto que a gente está hoje para narrá- los, e eu acho que a gente hoje está em uma situação melhor para poder fazer essa leitura de forma mais crítica, no sentido mais amplo do termo, não crítica só negativa, mas crítica no sentido mais amplo, mais potente do termo, sobre esses eventos e sobre a própria construção do campo. Essa entrevista ajudou muito a contar não apenas trajetórias, mas caminhos futuros para a consolidação e desenvolvimento deste campo da Antropologia dos Esportes. Então, além de ser um prazer pessoal estar com vocês, 115 Interlocuções exportivas: uma dobradinha entre Brasil e Argentina Interlocuções exportivas: uma dobradinha entre Brasil e Argentina é um prazer também intelectual estar narrando, observando, pensando sobre. E, claro, sobre o meu papel nele. Já são dezessete anos estudando na Antropologia dos Esportes. É uma trajetória né. Legal as vezes parar e olhar para ela. Tem coisa aí construída. Mariane: Da minha parte eu só queria reiterar os agradecimentos, não só do Luiz e da Verônica, mas da Mônica também nessa parceria justamente porque no seio desse grupo das práticas esportivas que eu me constituí como Antropóloga. A primeira vez que nos encontramos eu estava apresentando um trabalho da graduação, depois do mestrado, depois do doutorado e depois como professora universitária. Então, praticamente para além das orientações das minhas professoras orientadoras, muito da antropóloga que me constitui hoje e dos meus interesses de pesquisa, nascem nestes grupos de trabalho, nessas trocas, nesse intercâmbio. A Verónica é uma parceira de trabalho maravilhosa, desde que eu a conheci a gente vai mantendo contato e a mesma coisa com Luiz, a mesma coisa com Mônica. Então eu acho que essa entrevista também é fruto de muita satisfação pessoal, de rever nessa história, dessa área, dessa temática de duas pessoas como você, Luiz, e Verônica, a consolidação e a possibilitação, a pavimentação de outras trajetórias como a minha, por exemplo.. É um prazer imenso ter estado junto com vocês três essa tarde. 116 Pisani; Araujo
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Who should Issue a Permit for the Memorial? Administrative Law as a Platform for the Conflict over the Construction of the Monument to the Victims of the Smoleńsk Tragedy in Warsaw
Politologija
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Received: 31/08/2023. Accepted: 15/12/2023 Copyright © 2023 Piotr Eckhardt. Published by Vilnius University Press. 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. Who should Issue a Permit for the Memorial? Administrative Law as a Platform for the Conflict over the Construction of the Monument to the Victims of the Smoleńsk Tragedy in Warsaw Who should Issue a Permit for the Memorial? Administrative Law as a Platform for the Conflict over the Construction of the Monument to the Victims of the Smoleńsk Tragedy in Warsaw Piotr Eckhardt University of Wrocław E-mail: piotr.eckhardt@uwr.edu.pl Piotr Eckhardt Abstract. Circles associated with the ruling Law and Justice party decided to build a mon- ument to the victims of the crash of a Polish government airplane in Smoleńsk on April 10, 2010 in Piłsudski Square in Warsaw. However, the authorities of that city, associated with the political opposition, were not positive about the project. Government bodies in- strumentally used (and even abused) existing institutions of administrative law to build the monument despite the opposition of the local self-government. First, control over Piłsudski Square was taken away from the city authorities. Then the square was declared a closed area of military importance so that the city authorities could not make it difficult to obtain permission to build the monument. Finally, the Polish parliament created special legislation to make it more difficult to remove the monument in the future. fi Keywords: Smoleńsk air disaster, Smoleńsk monument, instrumentalization of law, mem- ory laws, construction law. Kas turėtų išduoti leidimą statyti paminklą? Administracinė teisė kaip konflikto platforma: paminklo Varšuvoje Smolensko tragedijos aukoms atminti atvejis Politologija ISSN 1392-1681 eISSN 2424-6034 2023/4, vol. 112, pp. 108–138 DOI: https://doi.org/10.15388/Polit.2023.112.4 Contents lists available at Vilnius University Press Politologija ISSN 1392-1681 eISSN 2424-6034 2023/4, vol. 112, pp. 108–138 DOI: https://doi.org/10.15388/Polit.2023.112.4 Contents lists available at Vilnius University Press Contents lists available at Vilnius University Press ISSN 1392-1681 eISSN 2424-6034 DOI: https://doi.org/10.15388/Polit.2023.112.4 ISSN 1392-1681 eISSN 2424-6034 DOI: https://doi.org/10.15388/Polit.2023.112.4 Politologija 2023/4, vol. 112, pp. 108–138 Kas turėtų išduoti leidimą statyti paminklą? Administracinė teisė kaip konflikto platforma: paminklo Varšuvoje Smolensko tragedijos aukoms atminti atvejis Santrauka. Lenkijos valdančiosios partijos „Teisė ir teisingumas“ atstovai nusprendė Ju- zefo Pilsudskio aikštėje Varšuvoje pastatyti paminklą 2010 m. balandžio 10 d. Lenkijos vyriausybinio lėktuvo katastrofos Smolenske aukų atminimui. Tačiau su tuomete politine 108 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... opozicija sieta Varšuvos miesto valdžia projektą įvertino neigiamai. Nepaisant vietos savi- valdos pasipriešinimo, valstybinės valdžios institucijos pasinaudojo (ir net piktnaudžiavo) veikiančiomis administracinės teisės institucijomis, kad paminklas būtų pastatytas. Pir- miausia buvo apribotos miesto valdžios galimybės kontroliuoti Pilsudskio aikštę. Blokuo- jant miesto valdžios turimus įrankius ir siekiant apsunkinti leidimo statyti paminklą išda- vimą, ji buvo paskelbta uždara karinės reikšmės teritorija. Galiausiai Lenkijos parlamentas sukūrė specialius teisės aktus, apsunkinančius galimybę pašalinti paminklą ateityje. opozicija sieta Varšuvos miesto valdžia projektą įvertino neigiamai. Nepaisant vietos savi- valdos pasipriešinimo, valstybinės valdžios institucijos pasinaudojo (ir net piktnaudžiavo) veikiančiomis administracinės teisės institucijomis, kad paminklas būtų pastatytas. Pir- miausia buvo apribotos miesto valdžios galimybės kontroliuoti Pilsudskio aikštę. Blokuo- jant miesto valdžios turimus įrankius ir siekiant apsunkinti leidimo statyti paminklą išda- vimą, ji buvo paskelbta uždara karinės reikšmės teritorija. Galiausiai Lenkijos parlamentas sukūrė specialius teisės aktus, apsunkinančius galimybę pašalinti paminklą ateityje. Reikšminiai žodžiai: Smolensko lėktuvo katastrofa, Smolensko paminklas, įstatymo instrumentalizacija, atminties įstatymai. 1 Nikolai Koposov, Memory Laws, Memory Wars. The Politics of the Past in Europe and Russia (Cambridge: Cambridge University Press, 2018), 1. 2 Uladzislau Belavusau and Aleksandra Gliszczyńska-Grabias, “Introduction: Memory Laws: Mapping a New Subject in Comparative Law and Transitional Justice,” in Law and Memory. Towards Legal Governance of History, eds. Uladzislau Belavusau and Aleksandra Gliszczyńska-Grabias (Cambridge: Cambridge University Press, 2017), 1. 3 Belavusau and Gliszczyńska-Grabias, 1. 1 Nikolai Koposov, Memory Laws, Memory Wars. The Politics of the Past in Europe and Russia (Cambridge: Cambridge University Press, 2018), 1. 3 Belavusau and Gliszczyńska-Grabias, 1. 2 Uladzislau Belavusau and Aleksandra Gliszczyńska-Grabias, “Introduction: Memory Laws: Mapping a New Subject in Comparative Law and Transitional Justice,” in Law and Memory. Towards Legal Governance of History, eds. Uladzislau Belavusau and Aleksandra Gliszczyńska-Grabias (Cambridge: Cambridge University Press, 2017), 1. 3 B l d Gli ń k G bi 1 Introduction The interrelationship of law and social collective memory is usually investigated in the context of the creation and application of spe- cialized legal regulations in this area – so-called memory laws. This term was coined in France in 2000s as a name for legislation penaliz- ing i.a. Holocaust negationists.1 According to Uladzislau Belavusau and Aleksandra Gliszczyńska-Grabias “such laws enshrine state-ap- proved interpretations of crucial historical events. They commemo- rate victims of past atrocities as well as heroic individuals or events emblematic of national and social movements.”2 They explain, that “[m]emory laws affect us in various, often controversial ways. They sometimes impose criminal penalties on speech or conduct deemed offensive to the plight of heroes and victims. <…> Children every- where grow up reading state-approved texts designed to impact not merely a knowledge, but an interpretation of history. Governments everywhere designate national memorial ceremonies or authorize the construction of public monuments.”3 It is clear that the memory laws 109 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) quite often and thoroughly studied by scholars4 are specialized legal regulations created for the sole purpose of legal governance of his- tory. Marta Buholc names four areas of particular intense reciprocal relationship between law and memory in the context of memory ac- tivism: memory laws (defined as above), truth seeking initiatives, mnemonic mobilization in the struggles for historical justice, and constitutional memories.5 Also in the case of this broader area of reg- ulation, it is easy to see that their impact on social collective memory has had to be one of the contexts considered by the legislator. There are also such legal acts which do not have the primary in- tention of shaping collective memory, but it is easy to see that they can be used for this purpose. The laws regulating street naming can serve as an example. In the same procedure, a street can be given a name that is both completely historically neutral or that commemo- rates a certain person or event. This is being investigated by research- ers from various countries.6 However, there are situations where only in the practice of apply- ing the law it becomes apparent that some regulations are relevant to the implementation of certain projects of shaping social collective memory. 4 For state of research on memory laws see e.g.: Uladzislau Belavusau, “The Rise of Memory Laws in Poland an Adequate Tool to Counter Historical Disinformation?,” Security and Human Rights 29, Issue 1–4 (2018): 37–38. 5 Marta Buholc, “Law,” in The Routledge Handbook of Memory Activism, eds. Yifat Gutman and Jenny Wüstenberg (London and New York: Routledge, 2023), 150. 6 See e.g.: Michael Hebbert, “The Street as Locus of Collective Memory,” Environment and Planning D Society and Space 23: 581–596; Vasile Docea, “History, Ideology and Collective Memory. Reconstructing the Identities of Timisoara by Means of Monographies and Street Names during the Communist Regime (1947–1989),” Acta Universitatis Sapientiae European and Regional Studies 1, no. 1 (2010): 83–102; Bartłomiej Różycki, “Renaming Urban Toponomy as a Mean of redefining Local Identity: The Case of Street Decommunization in Poland,” Open Political Science 1, no. 1 (2017): 20–31. 4 For state of research on memory laws see e.g.: Uladzislau Belavusau, “The Rise of Memory Laws in Poland an Adequate Tool to Counter Historical Disinformation?,” Security and Human Rights 29, Issue 1–4 (2018): 37–38. 5 Marta Buholc, “Law,” in The Routledge Handbook of Memory Activism, eds. Yifat Gutman and Jenny Wüstenberg (London and New York: Routledge, 2023), 150. 6 See e.g.: Michael Hebbert, “The Street as Locus of Collective Memory,” Environment and Planning D Society and Space 23: 581–596; Vasile Docea, “History, Ideology and Collective Memory. Reconstructing the Identities of Timisoara by Means of Monographies and Street Names during the Communist Regime (1947–1989),” Acta Universitatis Sapientiae European and Regional Studies 1, no. 1 (2010): 83–102; Bartłomiej Różycki, “Renaming Urban Toponomy as a Mean of redefining Local Identity: The Case of Street Decommunization in Poland,” Open Political Science 1, no. 1 (2017): 20–31. Introduction An analysis of the content of legislation without the context of a particular case may lead to the conclusion that it has no relevance to the subject matter, but later in practice it nevertheless turns out that it is decisive. Examining the role of such legislation in the implemen- 110 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... tation of the politics of memory is only possible using the case study method. First, it is necessary to identify a specific conflict, and then analyze all the legal instruments that were used by both sides of the dispute. The results of such research make it possible to identify new areas (often specific to a particular country or region) in which there is an intense reciprocal relationship between law and memory. The installation of monuments in public space often becomes the topic of heated disagreements. Situations in which there is a seri- ous dissension in society about the appropriateness of commemo- rating a particular person or event (in general or in some specific way or place) are frequent. Usually these conflicts are analyzed from the perspective of politics, sociology or history. However, it should be remembered that in a democratic state under the rule of law, all major interventions in public space must take place on the basis of and within the limits of the law. That is why legal regulations can become a tool in the hands of those who want to press through the establishment of a certain monument. In turn, opponents of the same commemoration can use legal institutions to prevent the criticized initiative. Therefore, such conflicts can be a good subject for a case study on regulations whose significance for social collective memory is not obvious. This paper is a study of such a case from Poland. It analyzes the instrumental use of administrative law to build a Monument to the Victims of the Smoleńsk Tragedy on Piłsudski Square in Warsaw. Aside from the introduction and conclusion, the paper consists of five parts. First, relevant information about the Smoleńsk Tragedy, the place where it was to be commemorated and the monument itself is briefly gathered. Then the legal regulations governing the construc- tion of monuments in Poland are presented. 7 This was a war crime committed by the NKVD in the spring of 1940 – the Soviets executed then at least 21,768 Polish citizens (including many Polish Army officers). See: Anna M. Cienciala, Natalia S. Lebedeva and Wojciech Materski, eds., Katyn: A Crime Without Punishment. Annals of Communism Series (New Haven: Yale Univer- sity Press, 2008). 8 Agnieszka Bejma, „Od afery Rywina do katastrofy smoleńskiej – nowe (utrwalone) podziały społeczno-polityczne w Polsce,” Studia Politologiczne, nr 29 (2013): 127– 128. Introduction The following sections analyze how instrumental use of existing and newly created laws has been used by Poland’s ruling political forces to take control of the site of the intended commemoration, to authorize the construction of the monument despite the objections of local authorities, and to protect it from possible attempts to remove it in the future. 111 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) 9 Arkadiusz Nyzio, „Znacząca nieobecność? Katastrofa smoleńska w kampaniach wy- borczych 2015 roku,” in Oblicza kampanii wyborczych 2015, eds. Małgorzata Ku- łakowska, Piotr Borowiec and Paweł Ścigaj (Kraków: Wydawnictwo Uniwersytetu Jagiellońskiego, 2016), 436. 11 Halina Taborska, „Pomniki smoleńskie w Warszawie – lokalizacje, dzieła, kontrower- sje,” Zeszyty naukowe PUNO, nr 7 (2019): 15. 1.1. The Smoleńsk Tragedy Smoleńsk Tragedy is the name commonly used in Poland for the plane crash that took place at Smoleńsk North Airport near the city of Smoleńsk, Russia, on April 10, 2010. At the time, a Tupolev Tu- 154 M belonging to the Polish Air Force crashed while attempting to land. There were 96 people on board the machine, all of whom died. Among the delegation going to the ceremonies marking the seven- tieth anniversary of the Katyń massacre7 were the president of the Republic of Poland Lech Kaczyński and his wife Maria Kaczyńska, the last president of the Republic of Poland in exile Ryszard Kac- zorowski, deputy speakers of the Sejm and Senate, 18 members of parliament and the most important commanders of the Polish army.l The Smoleńsk Tragedy briefly united society and the political class. However, it soon proved to be a source of new conflicts and divisions. The first protests erupted after the announcement that the presidential couple would be buried at Wawel Castle. Subsequent tensions arose over the further fate of the cross spontaneously erect- ed by scouts in front of the Presidential Palace shortly after the ca- tastrophe, the investigation into the crash or the issue of returning the wreckage of the plane to Poland. Attitudes toward the disaster over- laid the lines of Poland’s long-standing political divisions, leading to an intensification of conflicts.8 The topic of the Smoleńsk catastrophe 112 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... continued to play an important role in the electoral campaign ahead of the 2015 presidential and parliamentary elections.9 Along with the catastrophe, the “Smolensk myth” constructed around the figure of the tragically deceased president was born. Its manifestations in- clude numerous films, books or exhibitions devoted to the Smoleńsk Tragedy, marches and happenings related to it or even recitals of “Smoleńsk songs.”10 This event had a very great impact on Polish social and political reality. Initiatives to commemorate it in the public space should therefore come as no surprise to anyone. 10 Paweł Sendyka, „Narodziny „mitu smoleńskiego”,” Prace Etnograficzne, nr 1 (2013): 49. 14 Portal Samorządowy, „Warszawa: Radni zdecydują o lokalizacji pomnika smoleń- skiego,” April 9, 2015. Accessed August 20, 2023, https://www.portalsamorzadowy. pl/komunikacja-spoleczna/warszawa-radni-zdecyduja-o-lokalizacji-pomnika- smolenskiego,69385.html 15 Dziennik Gazeta Prawna, „Sasin: Na początku przyszłego tygodnia podamy nowe lokalizacje pomników smoleńskich,” January 26, 2018. Accessed August 20, 2023, https://www.gazetaprawna.pl/wiadomosci/artykuly/1100549,jacek-sasin-na-poczat- ku-przyszlego-tygodnia-podamy-nowe-lokalizacje-pomnikow-smolenskich.html 13 Michał Wotjczuk, „3 mln zł za dwa pomniki ofiar katastrofy smoleńskiej. „Mają nie być okazałe, ale bardzo okazałe”,” Gazeta Wyborcza, April 13, 2017. Accessed August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,21631078,3-mln- zl-za-dwa-pomniki-ofiar-katastrofy-smolenskiej-maja.html#S.embed_link-K.C-B.1- L.2.zw 12 Anna Szulc, „Pomnik smoleński przed Pałacem. Co prezydent Duda zlecił w sekre- cie?”, Newsweek, March 21, 2016. Accessed August 20, 2023, https://www.newsweek. pl/polska/tajny-projekt-pomnika-lecha-kaczynskiego/ph1lknei 16 Wprost, „Ogłoszono miejsce postawienia warszawskiego Pomnika Ofiar Tragedii Smoleńskiej,” February 7, 2018. Accessed August 20, 2023, https://www.wprost. pl/kraj/10102659/ogloszono-miejsce-postawienia-warszawskiego-pomnika-ofiar- tragedii-smolenskiej.html 17 Eugeniusz Szwankowski, Ulice i place Warszawy (Warszawa: Państwowe Wydawnic- two Naukowe, 1970), 269. 18 Bartłomiej Kaczorowski (ed.), Encyklopedia Warszawy (Warszawa: Wydawnictwo Naukowe PWN, 1994), 638. 1.2. Piłsudski Square Regardless of any controversy surrounding the Smoleńsk catastro- phe, there was no doubt about the unprecedented magnitude of the tragedy. It is therefore not surprising that discussions about the need to commemorate it began shortly after the victims’ funerals. The de- bates focused on three potential locations. Two of them were speci- fied precisely from the beginning. The first was the crash site at the Smoleńsk North Airport, while the second was the section of the Powązki Military Cemetery in Warsaw, where 28 of the crash victims were buried. The third location was to be some open urban space in the Polish capital, suitable for a commemoration of this kind.11 Initially, there was even discussion of erecting a monument in front of the Presidential Palace on Krakowskie Przedmieście Street. It was supposed to commemorate only Lech Kaczyński, replacing the monument to Prince Poniatowski, that would have to be moved 113 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) to another location, which aroused great controversy.12 Later, loca- tions (already for two individual monuments: to the victims of the Smoleńsk catastrophe and separately to Lech Kaczyński) were also indicated on Krakowskie Przedmieście Street, but at a slightly great- er distance from the Presidential Palace. This variant was supported by the chairman of the Law and Justice party, Jarosław Kaczyński (brother of the president, who died in the crash), and Jacek Sasin – a Law and Justice party politician particularly involved in the con- struction of the monuments.13 However, the local government of Warsaw did not want to agree to this location, pointing out that it was not accepted by the city’s conservator of monuments. Instead, they proposed (in agreement with some of the families of the victims of the crash) to erect the monument at the corner of Trębacka Street and Focha Street, in the immediate vicinity of Krakowskie Przedmieście Street.14 In January 2018 Jacek Sasin rather unexpectedly announced that a new location for the monuments which would be “easier to carry out” would be announced soon, and according to him, no properties managed by the authorities of Warsaw can be considered in this con- text.15 On February 7, 2018, ‘Social Committee for the Construction of Monuments: The late President of the Republic of Poland Lech 114 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... 21 „Skład Komitetu,” Komitet Społeczny Budowy Pomników: Śp. Prezydenta RP Lecha Kaczyńskiego oraz Ofiar Tragedii Smoleńskiej 2010 roku. Accessed August 20, 2023, http://web.archive.org/web/20190121152818/http://komitetspolecznybudowypomni- kow.pl/sklad-komitetu.html 19 Rzeczpospolita, „Sondaż: Czy pomnik smoleński stawiać na placu Piłsudskiego,” February 14, 2018. Accessed August 20, 2023, https://www.rp.pl/spoleczenstwo/ art9934341-sondaz-czy-pomnik-smolenski-stawiac-na-placu-pilsudskiego 20 Michał Wojtczuk, „71 proc. warszawiaków w sondażu przeciwko budowie pomnika smoleńskiego na pl. Piłsudskiego,” Gazeta Wyborcza, November 22, 2017. Accessed August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22681241,71- proc-warszawiakow-w-sondazu-przeciwko-budowie-pomnika-smolenskiego.html 19 Rzeczpospolita, „Sondaż: Czy pomnik smoleński stawiać na placu Piłsudskiego,” February 14, 2018. Accessed August 20, 2023, https://www.rp.pl/spoleczenstwo/ art9934341-sondaz-czy-pomnik-smolenski-stawiac-na-placu-pilsudskiego 20 Michał Wojtczuk, „71 proc. warszawiaków w sondażu przeciwko budowie pomnika smoleńskiego na pl. Piłsudskiego,” Gazeta Wyborcza, November 22, 2017. Accessed August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22681241,71- proc-warszawiakow-w-sondazu-przeciwko-budowie-pomnika-smolenskiego.html 21 „Skład Komitetu,” Komitet Społeczny Budowy Pomników: Śp. Prezydenta RP Lecha Kaczyńskiego oraz Ofiar Tragedii Smoleńskiej 2010 roku. Accessed August 20, 2023, http://web.archive.org/web/20190121152818/http://komitetspolecznybudowypomni- kow.pl/sklad-komitetu.html 1.2. Piłsudski Square Kaczyński and the Victims of the 2010 Smoleńsk Tragedy’ has an- nounced that the Smoleńsk monument will be built in the immediate vicinity of Piłsudski Square.16 Marshal Józef Piłsudski Square (this is the full name) is located in Warsaw’s Śródmieście district, between the Saxon Garden and Moli- er, Królewska, Tokarzewski-Karaszewicz and Ossolińscy Streets. It was created as the courtyard of the Saxon Palace (built in 1712–1727 through a major expansion of the manor house that previously existed there). In the interwar period, the Tomb of the Unknown Soldier was located under the colonnade of the palace. The fragment of the colon- nade with this tomb is the only part of the Saxon Palace that survived after the structure was blown up by German troops in 1944 (measures have now been taken to rebuild it). During the People’s Poland peri- od, the square was called Victory Square.17 Piłsudski Square was the site of many events of a different nature: both the parades of the Ger- man occupiers during World War II, official celebrations in People’s Poland (such as the May Day parades), but also manifestations of the anti-communist opposition or the Mass celebrated by Pope John Paul II and the funeral ceremonies of Cardinal Stefan Wyszyński.18 Therefore, there is no doubt that this is a place of special significance for the history of Warsaw and Poland. It is worth mentioning that, according to public opinion research, the idea of building a Smoleńsk monument in Piłsudski Square has not gained widespread support. In a poll commissioned by the Rzec- zpospolita daily newspaper, 60.8% of respondents said that the mon- ument should not be erected in this location. Only 17.6% of peo- ple expressed support for its construction in this site. 21.8% had no 115 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) opinion.19 In a poll conducted only among Warsaw residents at the request of the capital’s City Hall, as many as 71% of people vot- ed against the construction of a Smoleńsk monument in Piłsudski Square.20 The location finally designated for the Monument to the Victims of the Smoleńsk Tragedy was therefore highly controversial not only among politicians, but also in society. 1.3. Monument to the Victims of the Smoleńsk Tragedy 22 Taborska, „Pomniki smoleńskie w Warszawie – lokalizacje, dzieła, kontrowersje,” 36. 23 Maria Czaputowicz-Głowacka, „Narracje heroiczne w przestrzeni miejskiej”, Stan Rzeczy, nr 19 (2020): 191. 24 „To nie są tylko schody do nieba”. Jerzy Kalina o pomniku smoleńskim, Polskie Radio 24. Accessed August 20, 2023, https://polskieradio24.pl/130/5927/artykul/2717701,to- nie-sa-tylko-schody-do-nieba-jerzy-kalina-o-pomniku-smolenskim 25 Ustawa z dnia 7 lipca 1994 r. Prawo budowlane (consolidated text: Dz.U. 2023 poz. 682). 1.3. Monument to the Victims of the Smoleńsk Tragedy The commemoration was initiated by the ‘Social Committee for the Construction of Monuments: The late President of the Republic of Poland Lech Kaczyński and the Victims of the 2010 Smoleńsk Trag- edy,’ established on April 26, 2016, which was also the organizer of the public fundraising for this purpose. It included many lead- ing Law and Justice party politicians, including Jarosław Kaczyński, Mariusz Błaszczak and Marek Kuchciński. It also included relatives of some of the victims of the crash and right-wing journalists, such as Bronisław Wildstein and Marcin Wolski.21 Therefore, this social organization cannot be considered apolitical. The social committee organized a competition to develop a de- sign for a Monument to the Victims of the Smoleńsk Tragedy. It was resolved on October 19, 2017 by a jury chaired by Prof. T. J. Żu- chowski, an art historian from Adam Mickiewicz University in Poznań. The chosen design was submitted by Jerzy Kalina, a gradu- ate of the Painting Department of the Academy of Fine Arts in War- 116 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... saw, sculptor, theater and film set designer, as well as creator of doc- umentary films and theater performances.22 The monument was unveiled on April 10, 2018, the eighth an- niversary of the catastrophe. It has the form of a black block 6 me- ters high. Its shape is reminiscent of an airplane passenger boarding stairs. On its front are 96 names of the victims in alphabetical order.23 The author of the monument said this about his intentions: “I wanted the usually empty square to resemble an airport waiting for the re- turn, and in this space there was a gangway with lights.”24 2. Polish legal regulations on the construction of monuments Before describing the case of the Monument to the Victims of the Smoleńsk Tragedy, it is necessary to clarify what legal regulations apply to the erection of monuments in Poland. The key legal act in this context should be considered the Construction Law.25 Its Article 3 point 3 puts the monuments in the category of structures. Accord- ing to Article 3 point 1, a structure is one of the types of construction structures. Article 3 point 7, on the other hand, states that the con- struction of a construction structure is construction work. According to Article 28 Section 1 of the Construction Law, construction work can only be started on the basis of a construction permit decision. The law provides for many exceptions to this rule, but the construction of a monument is not one of them. Therefore, an analysis of all these definitions leads to the conclusion that the erection of a monument in Poland requires a construction permit in the form of an adminis- 117 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) trative decision. Pursuant to Article 82 Section 2 in conjunction with Article 28 Section 1a, such a decision is issued by the relevant local self-government authorities at the level of the powiat.26 Warsaw (like other large cities in Poland) has the status of a city with the right of a powiat. This means that it is not part of any powiat, and its local government authorities perform all the tasks assigned in various laws to powiat authorities. Consequently, in Warsaw, as a rule, it is the mu- nicipal authorities that have the authority to issue decisions on con- struction permits. As will become immediately apparent, in order to obtain a permit it is necessary to dispose of the land for construction purposes. Art. 3 point 11 of the Construction Law defines this as the possession of a legal title arising from ownership, perpetual usufruct, management, limited right in rem or a contractual relationship pro- viding for the right to carry out construction work. This means that the entity authorized to obtain a construction permit is not always the owner of the land. In certain situations, the right to dispose of real estate for construction purposes may be held by someone else, based on one of the above-mentioned legal titles. 26 A powiat (sometimes translated as county) is the second of three levels of local government in Poland, located above a municipality and below a voivodeship. 26 A powiat (sometimes translated as county) is the second of three levels of local government in Poland, located above a municipality and below a voivodeship. 27 Ustawa z dnia 8 marca 1990 r. o samorządzie gminnym (consolidated text: Dz.U. 2023 poz. 40). 28 Beata Chanowska-Dymlang, „Rada gminy nie jest upoważniona do wyrażenia zgody na budowę pomnika,” Legalis administracja, August 23, 2017. Accessed August 20, 2023, https://gov.legalis.pl/rada-gminy-nie-jest-upowazniona-do-wyrazenia-zgody- na-budowe-pomnika/ 27 Ustawa z dnia 8 marca 1990 r. o samorządzie gminnym (consolidated text: Dz.U. 2023 poz. 40). 28 Beata Chanowska-Dymlang, „Rada gminy nie jest upoważniona do wyrażenia zgody na budowę pomnika,” Legalis administracja, August 23, 2017. Accessed August 20, 2023, https://gov.legalis.pl/rada-gminy-nie-jest-upowazniona-do-wyrazenia-zgody- na-budowe-pomnika/ 29 Tomasz Urzykowski, „Plac Piłsudskiego. Wojna wojewody z Zarządem Dróg Miej- skich o „serce stolicy”,” Gazeta Wyborcza, October 27 2017. Accessed August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22571263,plac-pilsudskiego- wojna-wojewody-z-zarzadem-drog-miejskich.html 30 Ustawa z dnia 21 sierpnia 1997 r. o gospodarce nieruchomościami (consolidated text: Dz.U. 2023 poz. 344). 31 Anna Trembecka, „Trwały zarząd jako forma władania nieruchomościami publicznymi na przykładzie miasta Krakowa,” Acta Scientiarum Polonorum. Administratio Locorum 16, nr 3 (2017): 216. 32 Leszek Bielecki, „Zarządzanie nieruchomościami a trwały zarząd nieruchomością,” Rocznik Administracji Publicznej, nr 1(2015): 10. 2. Polish legal regulations on the construction of monuments It is necessary to clarify here the meaning of Article 18 Section 2 point 3 of the Law on Municipal Self-Government,27 which stipu- lates that adopting resolutions on the erection of monuments is the exclusive competence of the municipal council (and therefore, in the case of urban municipalities, the city council). It should be pointed out that this provision is only related to the manner of exercising ownership rights in the event that the monument in question is to be located on land owned by the municipality.28 It does not give the municipal council the right to decide on the erection of monuments 118 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... on land that has other owners (i.e. private or state-owned). It should be understood as an indication that in the case of the construction of a monument on land owned by the municipality, it is the municipal council (and not, for example, the president of the city) that should make the decision. The entity erecting a monument on its own land is only required to obtain a construction permit. 32 Leszek Bielecki, „Zarządzanie nieruchomościami a trwały zarząd nieruchomością,” Rocznik Administracji Publicznej, nr 1(2015): 10. 29 Tomasz Urzykowski, „Plac Piłsudskiego. Wojna wojewody z Zarządem Dróg Miej- skich o „serce stolicy”,” Gazeta Wyborcza, October 27 2017. Accessed August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22571263,plac-pilsudskiego- wojna-wojewody-z-zarzadem-drog-miejskich.html 3. Struggle for control over Piłsudski Square As outlined above, in order to obtain a building permit, it is necessary to have the right to dispose of the property on which the project is to be located for construction purposes. Piłsudski Square is owned by the State Treasury.29 However, for many years it was the Warsaw authorities that held the right to dispose of this property for the con- struction purposes, as described above, necessary to build the monu- ment. This legal state of affairs requires clarification. The Law on Real Estate Management30 in its Article 43 intro- duced the institution of the so-called permanent management. This is a public-legal form of possession of national or municipal real estate by organizational units without legal personality, distinct from lim- ited rights in rem or civil law contracts.31 As a rule, state property can only be put under the management of a state organizational unit, and local government property only to a local government organi- zational unit.32 However, the political system reforms carried out in Poland in the 1990s created exceptions to this rule. The structure of 119 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) local government was then changed. In addition to communes and voivodships (the number of which was significantly reduced), a new, intermediate level of local self-government was introduced – powi- ats.33 As a result, it was necessary to adjust the categories of public roads. Until then, there were national, municipal and voivodeship roads, and powiat roads had to be introduced as well. According to Article 103 of the Introductory Provisions of the Laws Reforming Public Administration,34 national and provincial roads were listed in an ordinance of the Council of Ministers. The existing national and provincial roads not included in this list became powiat roads as of January 1, 1999. Powiat road authorities became the legal successors of the previous road authorities through the appropriate application of Section 2 of Article 49 of the Law on Real Estate Management. This provision stipulates that permanent management should be es- tablished over real estate in favor of the entities taking over the cor- responding tasks. 36 Tomasz Żółciak, „Wojna o Plac Piłsudskiego w Warszawie. Władze stolicy mają plan, jak go odzyskać,” October 31, 2017, Dziennik Gazeta Prawna. Accessed August 20, 2023, https://wiadomosci.dziennik.pl/wydarzenia/artykuly/561558,spor-plac-pilsudskiego- wladze-stolicy-kontra-wojewoda.html 33 See: Arkadiusz Ptak, „Territorial Self-government during Transformation in Poland. Significance, Evolution and Conclusions de lege ferenda,” in Transformacja polska – oczekiwania i rzeczywistość, eds. Joanna Dzwończyk and Jerzy Kornaś (Kraków: Wy- dawnictwo Uniwersytetu Ekonomicznego, 2010), 311–321. 34 Ustawa z dnia 13 października 1998 r. Przepisy wprowadzające ustawy reformujące administrację publiczną (Dz.U. nr 133 poz. 872). 35 „Wykaz dróg powiatowych w Warszawie,” Zarząd Dróg Miejskich w Warszawie. Ac- cessed August 20, 2023, https://zdm.waw.pl/wp-content/uploads/2018/07/2015-02-20_ DZP_5_PN_5_15_Wykaz_drog_powiatowych_w_Warszawie.pdf 36 Tomasz Żółciak, „Wojna o Plac Piłsudskiego w Warszawie. Władze stolicy mają plan, jak go odzyskać,” October 31, 2017, Dziennik Gazeta Prawna. Accessed August 20, 2023, https://wiadomosci.dziennik.pl/wydarzenia/artykuly/561558,spor-plac-pilsudskiego- wladze-stolicy-kontra-wojewoda.html 34 Ustawa z dnia 13 października 1998 r. Przepisy wprowadzające ustawy reformujące administrację publiczną (Dz.U. nr 133 poz. 872). 35 „Wykaz dróg powiatowych w Warszawie,” Zarząd Dróg Miejskich w Warszawie. Ac- cessed August 20, 2023, https://zdm.waw.pl/wp-content/uploads/2018/07/2015-02-20_ DZP_5_PN_5_15_Wykaz_drog_powiatowych_w_Warszawie.pdf 3. Struggle for control over Piłsudski Square Piłsudski Square is included in the list of powiat roads in Warsaw, as a city with rights of the powiat.35 According to the regulations ana- lyzed above, that is why the area had been under the permanent man- agement of the Warsaw City Road Authority since the late 1990s.36 According to Section 2 of Article 43 of the Law on Real Estate Man- agement, an entity to which real estate has been given into perma- nent management has the right to carry out construction work on the 120 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... property. Permanent management is one of the legal titles that are the basis for disposing of real estate for construction purposes according to Art. 3 point 11 of the Construction Law, discussed in the previous section. Therefore, in such a legal situation, the Warsaw Municipal Road Administration was the entity authorized to obtain a building permit for the investments planned in the area of Piłsudski Square, even though the owner of the property was the State Treasury. However, on October 25, 2017 the Minister of Infrastructure and Construction issued a decision to transfer Piłsudski Square into per- manent management to the Mazovian Voivode.37 It should be noted here that in the Polish administrative structure there is a kind of dual- ism at the voivodship level. In addition to local government (headed by a marshal of the voivodship appointed by the voivodship assem- bly coming from direct elections), there is also government adminis- tration, headed by a voivode (representative of the Council of Minis- ters in the voivodship, appointed by the Prime Minister). This means that, as a result of the decision of the Minister of Infrastructure and Construction, the management of Piłsudski Square was taken away from a local government unit (linked to the political opposition) and transferred to a body fully dependent on the parliamentary majority. It should be noted that in accordance with Article 46a Section 1 of the Law on Real Estate Management, as a rule, the Minister of Infrastructure and Construction had the right to issue a decision to terminate permanent management, and in accordance with Article 60 Section 3 in conjunction with Section 1, was allowed to subsequently transfer the property to permanent management for the needs of the voivodship office. Therefore, there is no obvious violation of the law here. 37 Urzykowski, „Plac Piłsudskiego.” 40 Patrycja Wieczorkiewicz and Paweł Gawlik, „Plac Piłsudskiego podzielony na nowo. Rzecznik ratusza: Nie było konsultacji,” Gazeta Wyborcza, January 5, 2018. Accessed August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22861523,plac- -pilsudskiego-podzielony-na-nowo-rzecznik-ratusza-nie.html 38 „Oświadczenie w sprawie placu Piłsudskiego w Warszawie,” Wojewoda Mazo- wiecki, October 27, 2017. Accessed August 20, 2023, https://web.archive.org/ web/20180210002409/https://www.mazowieckie.pl/pl/aktualnosci/komunika- ty/34763,Oswiadczenie-w-sprawie-placu-Pilsudskiego-w-Warszawie.html 39 Żółciak, „Wojna o Plac Piłsudskiego w Warszawie.” 38 „Oświadczenie w sprawie placu Piłsudskiego w Warszawie,” Wojewoda Mazo- wiecki, October 27, 2017. Accessed August 20, 2023, https://web.archive.org/ web/20180210002409/https://www.mazowieckie.pl/pl/aktualnosci/komunika- ty/34763,Oswiadczenie-w-sprawie-placu-Pilsudskiego-w-Warszawie.html 39 Żółciak, „Wojna o Plac Piłsudskiego w Warszawie.” 40 Patrycja Wieczorkiewicz and Paweł Gawlik, „Plac Piłsudskiego podzielony na nowo. Rzecznik ratusza: Nie było konsultacji,” Gazeta Wyborcza, January 5, 2018. Accessed August 20, 2023, https://warszawa.wyborcza.pl/warszawa/7,54420,22861523,plac- -pilsudskiego-podzielony-na-nowo-rzecznik-ratusza-nie.html 3. Struggle for control over Piłsudski Square However, it is worth to analyze the authorities’ communicated motives for this decision to assess whether the law was instrumental- ly used in this case to achieve political goals. In a statement published on October 27, 2017, the Mazovian Voivode stated that the decision to transfer to him Piłsudski Square 121 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) for permanent management was made at his request. He justified it by the fact that “it is a place that primarily serves the organization of state ceremonies and therefore should be under the supervision of the government administration.”38 On the other hand, the authorities of Warsaw pointed out that so far there have been no problems with the organization of state ceremonies at the site, and besides, the Tomb of the Unknown Soldier itself is still located on a separate plot still owned by the city, so any ceremonies that include the tomb will still have to be organized in consultation with the authorities of Warsaw. The local government also argued that taking the management of the property away from the Warsaw Municipal Road Administration is impossible as long as it includes powiat roads.39 It seems that the government administration in this case partially conceded to the city authorities. However, this did not involve returning the management of Piłsudski Square to the local self-government unit. Instead, an di- vision of the plot of land was made to exclude streets adjacent to the square.40 In the manner described above, the government authorities took control of Piłsudski Square from the local self-government. They used legitimate means to do so. However, it is significant that they were employed only at this moment, despite the existence of an unchanged legal status for many years. When asked by journalists whether taking control of the square was not a step towards building a monument there to the victims of the Smolensk catastrophe, the Mazovian Voivode replied that another location had been chosen for 122 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... it.41 Admittedly, Piłsudski Square was not officially designated as a place of commemoration until several months later, in early 2018. The issue of permanent management was the most important issue in the context of Piłsudski Square for only a short time. 41 Urzykowski, „Plac Piłsudskiego.” 42 Decyzja nr 231 Ministra Spraw Wewnętrznych i Administracji z dnia 31.10.2017 r. w sprawie ustalenia terenu zamkniętego. Accessed August 20, 2023, https://archiwum- bip.mswia.gov.pl/bip/komunikaty/25079,Decyzja-nr-231-Ministra-Spraw-Wewnetrz- nych-i-Administracji-z-dnia-31102017-r-w-s.html 43 Ustawa z dnia 17 maja 1989 r. Prawo geodezyjne i kartograficzne (consolidated text: Dz.U. 2023 poz. 1752). 3. Struggle for control over Piłsudski Square Just a few days later, further legally momentous events occurred that would eventu- ally lead to the construction of the Monument to the Victims of the Smoleńsk Tragedy there. 43 Ustawa z dnia 17 maja 1989 r. Prawo geodezyjne i kartograficzne (consolidated text Dz.U. 2023 poz. 1752). 4. “Militarization” of Piłsudski Square Taking over the management of Piłsudski Square from Warsaw’s lo- cal authorities was only the first stage of seizing effective control over the site by government authorities through legal measures. The decision issued on October 31, 2017 by the Minister of Internal Af- fairs and Administration is of the most momentous significance.42 It says that the Minister has declared plots of land encompassing Piłsudski Square a so-called closed area. The aforementioned decision was issued on the basis of Article 4, Section 2a of the Geodetic and Cartographic Law,43 which states that closed areas are established by the competent ministers and heads of central offices by decision. But what is this „closed area”? The Geo- detic and Cartographic Law, in its Article 2, contains a glossary con- sisting of definitions of terms used in the act. Its point 9 specifies that closed areas are understood to be areas of a restricted character for reasons of state defense and security, defined by the competent min- isters and heads of central offices. According to the jurisprudence of the Polish administrative courts, the very fact of recognizing an area as a closed area determines the designation of that area for purposes 123 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) related to national defense and security.44 This means that the Min- ister of Internal Affairs and Administration has recognized Piłsudski Square as an area of special military significance. The regulations on closed areas for the purposes of national de- fense and security are quite laconic, but an analysis of their content allows to understand quite well what was the aim of the legislator introducing these regulations. There is a number of solutions in the Geodetic and Cartographic Law that allow for the classification of information on technical infrastructure, plots of land, buildings and dwellings located in closed areas. Land and building records main- tained for an area where a closed area has been designated must im- mediately be brought into compliance with regulations on the pro- tection of classified information. The literature indicates that this re- quirement comes out of the need to ensure security and state defense readiness.45 It follows that the essence of closed areas should be a limited access to information about what is located within them. 44 Monika Ziniewicz, „Administracyjnoprawne ograniczenia procesu inwestycyjno-bu- dowlanego na terenach zamkniętych w Polsce,” Studia Iuridica Toruniensia, t. XXIX (2021): 490. 45 Mirosław Karpiuk, „Tereny zamknięte ze względu na obronność i bezpieczeństwo państwa ustanawiane przez organy administracji rządowej,” Ius Novum, nr 4 (2016): 199. 46 Rozporządzenie Ministra Obrony Narodowej z dnia 18 lipca 2003 r. w sprawie terenów zamkniętych niezbędnych dla obronności państwa (Dz.U. nr 141 poz. 1368). 44 Monika Ziniewicz, „Administracyjnoprawne ograniczenia procesu inwestycyjno-bu- dowlanego na terenach zamkniętych w Polsce,” Studia Iuridica Toruniensia, t. XXIX (2021): 490. 4. “Militarization” of Piłsudski Square This would be hard to achieve in the case of an open, publicly accessible space located in the heart of a large city, such as Piłsudski Square. The Ordinance of the Minister of Defense on Closed Areas Neces- sary for State Defense46 contains a list of closed areas where the Min- ister of Defense supervises surveying and mapping work. It includes, inter alia, command posts of the Armed Forces of the Republic in a state of threat to state security and war, facilities for radio reconnais- sance and combat and national air and anti-aircraft defense, telecom- munications facilities for the transmission of classified information constituting state secrets, war ports, military airports or ammunition depots and warehouses. It should be borne in mind that this is not a 124 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... complete enumeration of closed areas, because the supervision of the Minister of National Defense over surveying and mapping work has not been introduced for all of them, but it clearly comes out from this enumeration that the legislator was concerned with areas very direct- ly related to state defense, with strictly military use. There is no doubt that Piłsudski Square is not such an area. On November 17, 2017, a little more than two weeks after the decision discussed above was issued, the Ministry of Internal Affairs and Administration released a written statement,47 informing that Piłsudski Square will continue to be accessible to residents and tour- ists, and its area will not be fenced off. This was most likely to dispel doubts that may have come out of the colloquial understanding of the term closed area. The Ministry further wrote that “Piłsudski Square is a place where national holidays and major ceremonies are held.” It did not indicate what role the area has for state defense. It did not explain what connection the said state holidays and celebrations have with state defense. So what was the most likely real purpose of declaring Piłsudski Square a closed area? The answer must be sought in the already cited Construction Law. The key is Section 3 point 5 of Article 82, which stipulates that the architectural and construction administration body of first instance (i.e. the entity competent to issue decisions on con- struction permits) in the case of objects and construction work locat- ed in closed areas is the voivode. 47 „Oświadczenie MSWiA w sprawie placu Piłsudskiego,” Ministerstwo Spraw We- wnętrznych i Administracji. Accessed August 20, 2023, https://archiwum.mswia.gov. pl/pl/aktualnosci/16730,Oswiadczenie-MSWiA-w-sprawie-placu-Pilsudskiego.html 4. “Militarization” of Piłsudski Square This is an exception to the already mentioned general rule, according to which construction permits are issued in Poland by the head of the powiat (and in the case of cities with the rights of a powiat – such as Warsaw – by the president of the city). This means that the recognition of Piłsudski Square as a closed area automatically shifted the competence to issue building permits (as described above, required in the case of erecting a mon- ument) from a local self-government body, controlled by one side of 125 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) the dispute over the Smoleńsk monument, to an authority directly controlled by the government, coming from the political group that is the other side of that dispute. The matter of issuing building permits should be considered most important in the context of the construction of the Monument to the Victims of the Smoleńsk Tragedy, but it is worth to mention the sec- ond area in which the competencies of Warsaw’s local authorities have been drastically reduced in a result of the recognition of Piłsud- ski Square as a closed area. According to Article 3 Section 1 of the Law on Spatial Planning and Development,48 the shaping and con- ducting of spatial policy on the territory of the municipality, includ- ing the adoption of local spatial plans, is one of the municipality’s own tasks. However, this does not apply to closed areas. According to Article 4 Section 1 of this law, the determination of land use, the location of public purpose investments and the determination of the ways in which land is used and developed shall be made in a local spatial plan. However, Article 4 Section 2 point 2 stipulates that with regard to closed areas, only the boundaries of these areas are estab- lished in the local spatial plan. What is more, in the case of spatial planning and development, the recognition of a particular site as a closed area results in a transfer of authority similar to that of a building permit. According to Arti- cle 51 of the discussed law, in matters of determining the location of a public purpose investment, decisions are issued by the head of the municipality (i.e. the local government). However, if it is a pub- lic purpose investment in a closed area, the voivode (i.e. 48 Ustawa z dnia 27 marca 2003 r. o planowaniu i zagospodarowaniu przestrzennym (consolidated text: Dz.U. 2023 poz. 977). 4. “Militarization” of Piłsudski Square the rep- resentative of the government) is authorized to issue the decision. Importantly, such a decision is necessary precisely when the area in question is not covered by a spatial plan (and, as described above, such a plan is not drawn up for a closed area). Therefore, recognizing Piłsudski Square as a closed area not only made it impossible for the Warsaw authorities to determine the manner of its development in 126 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... the local spatial plan, but also deprived them of the authority to issue a decision to determine the location of a public purpose investment necessary in the absence of a plan. Referring the provisions of the Law on Spatial Planning and Development to the case of the Mon- ument to the Victims of the Smoleńsk Tragedy, it should be pointed out that the application for a decision establishing the location of a public purpose investment was submitted by Jacek Sasin on behalf of the social committee on January 29, 2018, and the Mazovian Voivode issued the decision on February 2. It became binding on February 5, 2018.49 It is worth recalling that the location of the monument was made public by the social committee on February 7, 2018, that is, when much of the paperwork required for its construction had al- ready been completed. Therefore, it can be considered that the recognition of Piłsudski Square as a closed area was another step towards the construction of a Monument to the Victims of the Smoleńsk Tragedy in Warsaw, in defiance of the local authorities of that city. After the “militarization” of the square, the state authorities could not only freely dispose of the property (which they ensured for themselves by taking over the man- agement of the square by the voivode), but also gained the certainty that there would be no problems with obtaining a building permit, since the competence to issue one was also given to the voivode. It seems that in the case of the decision to declare Piłsudski Square a closed area, legal measures were used in the political dispute in a much more instrumental way than in the matter of taking over the management of the square. 49 Portal Samorządowy, Wojewoda mazowiecki zatwierdził lokalizację Pomnika Ofiar Tragedii Smoleńskiej, February 7, 2018. Accessed August 20, 2023, https://www.por- talsamorzadowy.pl/polityka-i-spoleczenstwo/wojewoda-mazowiecki-zatwierdzil-lo- kalizacje-pomnika-ofiar-tragedii-smolenskiej,103790.html 53 Michał Wojtczuk, „Jest decyzja prokuratury w sprawie przejęcia placu Piłsudskiego przez rząd,” Gazeta Wyborcza, September 27, 2021. Accessed August 20, 2023, https:// warszawa.wyborcza.pl/warszawa/7,54420,27620065,plac-pilsudskiego-wziety-w- kamasze-jest-decyzja-prokuratury.html 50 Karpiuk, „Tereny zamknięte ze względu na obronność i bezpieczeństwo państwa usta- nawiane przez organy administracji rządowej,” 197. 52 Kamil Siałkowski, „Spór o pl. Piłsudskiego. Prokuratura musi jeszcze raz zba- dać, czy Mariusz Błaszczak nie przekroczył uprawnień,” Gazeta Wyborcza, Oc- tober 30, 2018. Accessed August 20, 2023, https://warszawa.wyborcza.pl/warsza- wa/7,54420,24111978,spor-o-plac-pilsudskiego-prokuratura-musi-jeszcze-raz-zba- dac.html 51 „Zawiadomienie o możliwości popełnienia przestępstwa,” Miasto Stołecz- ne Warszawa, Accessed August 20, 2023, https://um.warszawa.pl/document- s/39703/7003459/2018_03_27_m._st._warszawa_zawiadomienie.pdf/adb2c111-d- 0df-e4f0-ce39-83af5329713a?t=1634498830960 50 Karpiuk, „Tereny zamknięte ze względu na obronność i bezpieczeństwo państwa usta- nawiane przez organy administracji rządowej,” 197. 51 „Zawiadomienie o możliwości popełnienia przestępstwa,” Miasto Stołecz- ne Warszawa, Accessed August 20, 2023, https://um.warszawa.pl/document- s/39703/7003459/2018_03_27_m._st._warszawa_zawiadomienie.pdf/adb2c111-d- 0df-e4f0-ce39-83af5329713a?t=1634498830960 52 Kamil Siałkowski, „Spór o pl. Piłsudskiego. Prokuratura musi jeszcze raz zba- dać, czy Mariusz Błaszczak nie przekroczył uprawnień,” Gazeta Wyborcza, Oc- tober 30, 2018. Accessed August 20, 2023, https://warszawa.wyborcza.pl/warsza- wa/7,54420,24111978,spor-o-plac-pilsudskiego-prokuratura-musi-jeszcze-raz-zba- dac.html 53 Michał Wojtczuk, „Jest decyzja prokuratury w sprawie przejęcia placu Piłsudskiego przez rząd,” Gazeta Wyborcza, September 27, 2021. Accessed August 20, 2023, https:// b l/ /7 54420 27620065 l il d ki i t 4. “Militarization” of Piłsudski Square Indeed, the claim that in this situation a legal institution was used contrary to its intended purpose envisaged by the legislator is not groundless. The law in this case has become an instrument for achieving political goals. Similar doubts were ex- pressed by the authorities of Warsaw. 127 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) It should be noted that the decision to establish a closed area is not an administrative decision. This means that it cannot be appealed or challenged in an administrative court.50 In such a situation, the authorities of Warsaw took another option. On March 27, 2018, they filed a notice of possible commission of a crime by the Minister of Internal Affairs and Administration Mariusz Blaszczak of exceeding his powers to the prosecutor’s office. The Warsaw authorities indicat- ed that the recognition of Piłsudski Square as a closed area despite the absence of factual grounds related to defense and state security reasons is an abuse of legal institutions. The notice stated that the real purpose of these actions was to deprive the local authorities of the powers they are entitled to under the binding law related to de- cision-making in the field of spatial planning and development.51 However, the District Prosecutor’s Office in Warsaw refused to open an investigation, stating that no crime had been committed in this situation.52 The authorities of Warsaw filed a complaint against this decision with the competent court. The latter recognized the com- plaint and ordered the prosecutor’s office to launch an investigation. However, it was discontinued in 2021. The prosecutor’s office again cited the absence of the elements of a criminal act.53 It should be pointed out that the position of Attorney General at the time was held by Zbigniew Ziobro – one of the members of the ‘Social Committee 128 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... for the Construction of Monuments: The late President of the Repub- lic of Poland Lech Kaczyński and the Victims of the 2010 Smoleńsk Tragedy.’ The application of regulations created to protect military areas, such as firing ranges and naval bases, to an open, public space in the center of the Polish capital made it possible to build the Monument to the Victims of the Smoleńsk Tragedy at a site designated by a committee associated with the politicians of Law and Justice party. 54 Oficjalna strona Prezydenta Rzeczypospolitej Polskiej, „Prezydent podpisał deklarację o restytucji Pałacu Saskiego.” Accessed August 20, 2023, https://www.prezydent. pl/aktualnosci/polityka-historyczna/100-rocznica-odzyskania-niepodleglosci-rp/ aktualnosci/11-listopada---symboliczny-poczatek-odbudowy-palacu-saskiego,8259 4. “Militarization” of Piłsudski Square In this place it is worth reminding that Minister of Internal Affairs and Administration Mariusz Błaszczak, who issued the controversial decision, was one of the members of this committee. However, this was not the last situation in which regulations were creatively used in relation to this monument. The ruling majority decided to reach for such extraordinary legislative solutions that were designed to secure the monument for the future. 55 Tomasz Żółciak, „Lex Saski receptą na ewentualny opór władz Warszawy,” Dzien- nik Gazeta Prawna, 20 November 2018. Accessed August 20, 2023, https://www. gazetaprawna.pl/wiadomosci/artykuly/1356455,lex-saski-recepta-na-ewentualny- opor-wladz-warszawy.html 56 Druk nr 1388 Przedstawiony przez Prezydenta Rzeczypospolitej Polskiej projekt usta- wy o przygotowaniu i realizacji inwestycji w zakresie odbudowy Pałacu Saskiego, Pałacu Brühla oraz kamienic przy ulicy Królewskiej w Warszawie, July 7, 2021. Ac- cessed August 20, 2023, https://www.sejm.gov.pl/Sejm9.nsf/druk.xsp?nr=1388 57 Ustawa z dnia 11 sierpnia 2021 r. o przygotowaniu i realizacji inwestycji w zakresie odbudowy Pałacu Saskiego, Pałacu Brühla oraz kamienic przy ulicy Królewskiej w Warszawie (Dz.U. 2021 poz. 1551). 58 Ustawa z dnia 21 sierpnia 1997 r. o gospodarce nieruchomościami (consolitated text: Dz.U. 2023 poz. 344). 60 Katarzyna Żaczkiewicz-Zborska, „Odbudowa Pałacu Saskiego z poważnymi uster- kami w ustawie,” Prawo.pl, July 23, 2021. Accessed August 20, 2023, https://www. prawo.pl/samorzad/bledy-i-niedomowienia-w-ustawie-o-odbudowie-palacu-saskie- go,509608.html; Business Insider Polska, „Odbudowa Pałacu Saskiego może przebie- gać w atmosferze skandalu. Problematyczna specustawa,” August 16, 2021. Accessed August 20, 2023, https://businessinsider.com.pl/wiadomosci/odbudowa-palacu- saskiego-moze-przebiegac-w-atmosferze-skandalu/r7798pe 59 Katarzyna Domagała, „Ciąg dalszy kontrowersji wokół odbudowy Pałacu Saskiego. Eksperci piszą otwarty list sprzeciwu, projekt wraca do Komisji Kultury,” Architektu- ra i Biznes, July 22, 2021. Accessed August 20, 2023, https://www.architekturaibiznes. pl/odbudowa-palacu-saskiego-list-otwarty-ekspertow,8380.html 5. Monument protected by a special law In the section on the history and architecture of Piłsudski Square, it was mentioned that preparations are underway to rebuild the Saxon Palace, which was once located there. This project also has a legal dimension. Both the genesis and content of the regulations for the planned reconstruction are related to the history of the Monument to the Victims of the Smoleńsk Tragedy. The decision to reconstruct the Saxon Palace was made by Presi- dent Andrzej Duda when he made the solemn declaration on Novem- ber 11, 2018, as part of the celebration of the centennial of Polish in- dependence.54 Just a few days later, the newspaper Dziennik Gazeta Prawna, citing anonymous sources connected with the government, reported that the authorities were considering enacting a special law 129 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) separately regulating the rules for the implementation of only this one investment. According to unnamed ruling party politicians, such a solution was to be necessary because the Saxon Palace was to be rebuilt on land belonging to the city, and the story of the construction of the Monument to the Victims of the Smoleńsk Tragedy showed that the Warsaw authorities are unwilling to cooperate on govern- ment projects.55i A draft of the new legislation was submitted to the first chamber of the Polish parliament on July 7, 2021.56 Just over a month later, the Act of August 11, 2021 on the preparation and implementation of in- vestments in the reconstruction of the Saxon Palace, the Brühl Palace and the townhouses on Królewska Street in Warsaw was passed.57 The new law has ruthlessly resolved the problem of ownership of the land on which the Saxon Palace is to be reconstructed. According to its Article 37 Section 1, real estate in the area where the recon- struction will be carried out automatically becomes the property of the State Treasury by force of law, after the voivode issues a decision on determining the location of the investment. This is a special mode of property acquisition by the state. The provisions of the Real Es- tate Management Act58 allow expropriation of real estate for public purposes only after a separate procedure, to which the entire Chapter 4 of this law is dedicated. In the case of the reconstruction of the Saxon Palace, it was decided to speed up the proceedings not only 130 Piotr Eckhardt. 59 Katarzyna Domagała, „Ciąg dalszy kontrowersji wokół odbudowy Pałacu Saskiego. Eksperci piszą otwarty list sprzeciwu, projekt wraca do Komisji Kultury,” Architektu- ra i Biznes, July 22, 2021. Accessed August 20, 2023, https://www.architekturaibiznes. pl/odbudowa-palacu-saskiego-list-otwarty-ekspertow,8380.html 60 Katarzyna Żaczkiewicz-Zborska, „Odbudowa Pałacu Saskiego z poważnymi uster- kami w ustawie,” Prawo.pl, July 23, 2021. Accessed August 20, 2023, https://www. prawo.pl/samorzad/bledy-i-niedomowienia-w-ustawie-o-odbudowie-palacu-saskie- go,509608.html; Business Insider Polska, „Odbudowa Pałacu Saskiego może przebie- gać w atmosferze skandalu. Problematyczna specustawa,” August 16, 2021. Accessed August 20, 2023, https://businessinsider.com.pl/wiadomosci/odbudowa-palacu- saskiego-moze-przebiegac-w-atmosferze-skandalu/r7798pe 5. Monument protected by a special law Who should Issue a Permit for the Memorial? Administrative Law as a Platform... in terms of expropriating the necessary real estate. Procedures for determining compensation for their former owners were also simpli- fied, as well as those for the construction supervision of the ongoing investment. As a result, the law has stirred up controversy in various circles. Architectural historians have issued an open letter against it. Their concerns included the exclusion of the rebuilt Palace from the supervision of the monument protection service.59 Legal community criticized the law for drafting errors and ambiguities, in addition to severe restrictions on the powers of local government.60 Therefore, the reconstruction of the Saxon Palace involves a similar dispute between government authorities and local self-gov- ernment as the construction of the Monument to the Victims of the Smoleńsk Tragedy. However, the government learned from the first conflict and did not rely solely on already existing legal instruments. In this case, it has decided to create completely new regulations that will allow the implementation of the intended project without the possibility of resistance from local authorities. The dispute over the construction of the Monument to the Vic- tims of the Smoleńsk Tragedy was one of the reasons for the special law on the reconstruction of the Saxon Palace. At the same time, its provisions also directly regulate the legal situation of the monument itself. Article 36 of the analyzed act gave special legal protection to Marshal Józef Piłsudski Square with the following objects located there: Tomb of the Unknown Soldier, Monument to Józef Piłsudski, Papal Cross, Monument to Lech Kaczyński and Monument to the 131 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) Victims of the 2010 Smoleńsk Tragedy. According to this provision, the urban layout encompassing the square and these objects is invio- lable (of course, including the reconstructed Saxon Palace). This is a situation unprecedented in the Polish legal system, con- sisting of general and abstract norms as a rule, in which the legis- lator decided to secure the future of several specific monuments at the level of an act of statutory rank. This demonstrates the great im- portance attached to these objects by the political force that formed the parliamentary majority at the time the discussed law was passed. 5. Monument protected by a special law The legislation lists all the objects located in Piłsudski Square, but the presence there of the Tomb of the Unknown Soldier, the Papal Cross or the Monument to Józef Piłsudski does not raise any dispute in principle. Therefore, it can be presumed that the main purpose of introducing the discussed provision in the Law on the Reconstruc- tion of the Saxon Palace was to protect the controversial Monument to the Victims of the Smoleńsk Tragedy and the Monument to Lech Kaczyński. Conclusions On the basis of the analysis presented above, it can be concluded that the instrumental use of administrative law allowed the construction of a monument desired by the political forces controlling the gov- ernment administration in the very center of the city, whose local authorities expressed open opposition to commemoration at this par- ticular site. First, the voivode took control of the site where the monument was to be erected. He exercised his authority in this case, and there is no violation of the law in this case. However, the justification for this decision cannot be considered convincing. The claim that it was issued solely to facilitate the construction of the Monument to the Victims of the Smoleńsk Tragedy seems justified. Shortly thereafter, legal instruments created to ensure the national security and defense were used to circumvent the requirement to ob- 132 Piotr Eckhardt. Who should Issue a Permit for the Memorial? Administrative Law as a Platform... tain positive decisions from local authorities before building a monu- ment under construction law and spatial planning law. Finally, special provisions drafted to protect the Smolensk Trag- edy Victims Monument have been introduced into the newly creat- ed legislation, so that its removal will be difficult even if there is a change in the balance of political forces in the future. It is therefore clear that the instrumental use of the law can be a way to break the resistance of opponents to the implementation of a certain memory policy in the public space even when these oppo- nents are democratically elected local self-government authorities. l The pattern in which the conflict over the monument’s construc- tion revolves between the right-wing populist central government and the liberal local municipal authorities linked to the opposition to the forces establishing illiberal democracy can be observed not only in Poland. A very similar case took place in Hungary ruled by Viktor Orbán’s Fidesz. Right-wing state authorities intended to erect a new monument to the victims of the German occupation of Hungary in Liberty Square in Budapest. The city authorities originating from po- litical circles opposing Fides resisted against that project. Therefore, the Orbán government issued a decree declaring the project an issue of particular importance with regard to the national economy. 61 Ágnes Erőss, ““In Memory of Victims”: Monument and counter-monument in LibertySquare, Budapest,” Hungarian Geographical Bulletin 65, no. 3 (2016): 241. Conclusions As a result, construction of the monument could begin not only without the required permits, but also without a tender process.61 The story of the legal dispute over the Monument to the Victims of the Smoleńsk Tragedy proves that a democratic state needs mech- anisms to prevent the circumvention of the law and the extremely instrumental use of legal institutions contrary to their intended pur- pose by the legislator in order to achieve current political goals. Even the issue of building a monument in a certain square may be a sit- uation in which such mechanisms for protecting the rule of law as an independent prosecutor’s office, a constitutional judiciary or tools for enforcing compliance with the principles of good legislation will 133 ISSN 1392-1681 eISSN 2424-6034 Politologija 2023/4 (112) be crucial. 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https://openalex.org/W3007007446
https://europepmc.org/articles/pmc7063879?pdf=render
English
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Effects of Routine Checkups and Chronic Conditions on Middle-Aged Patients with Diabetes
Advances in preventive medicine
2,020
cc-by
5,657
Hindawi Advances in Preventive Medicine Volume 2020, Article ID 4043959, 8 pages https://doi.org/10.1155/2020/4043959 Hindawi Advances in Preventive Medicine Volume 2020, Article ID 4043959, 8 pages https://doi.org/10.1155/2020/4043959 Hindawi America E. McGuffee  , Kailyn Chillag, Amber Johnson, Regan Richardson, Hallie Williams, and Jessica Hartos epartment of Physician Assistant Studies, University of North Texas Health Science Center, Fort Worth, TX, USA Received 18 June 2019; Accepted 28 August 2019 Academic Editor: Gerardo E. Guillén Nieto Copyright © 2020 America E. McGuffee 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. Purpose. Middle-aged males and females with diabetes are more likely to have poor physical (PH) and mental health (MH); however, there is limited research determining the relationship between MH and PH and routine check-up in diabetic middle-aged adults, especially by gender. The purpose of this study was to determine whether PH and MH status differ by routine check-up in middle- aged (age 45–64) adults with diabetes in the general population. Methods. This cross-sectional analysis used data from the 2017 BRFSS conducted by the CDC for adults aged 45–64 who reported having diabetes in Florida (𝑁= 1183), Kentucky (𝑁= 617), Maryland (𝑁= 731), New York (𝑁= 593), and Ohio (𝑁= 754). Multiple logistic regression by state and gender was used to determine the relationship between MH and PH status and routine check-up while controlling for health-related, socioeconomic, and demographic factors. Results. Across states, up to one-half reported good PH (32–50%), over one-half reported good MH (46–67%), and most reported having a routine check-up (87–93%). Adjusted analysis indicated that MH and PH were not significantly related to routine check-up, but both were inversely related to having diabetes plus two other health conditions. Conclusions. Overall, routine check-up was not related to good PH and MH in this target population; however, a number of health conditions were inversely related to good PH and MH status. In a primary care setting for this target population, there may be a low to moderate prevalence of good PH and MH and a high prevalence of having a routine check-up and having multiple health conditions. It is recommended to automatically screen this target population for PH, MH, other chronic conditions, and physical activity and treat concurrently. 1. Introduction report having DM) [2]. Because this condition is chronic and progressive, it can lead to other physical and mental health complications over time [10–12, 14] . In addition, those with diabetes report lower HRQoL ratings than do individuals without chronic illnesses [10]. Thus, annual or more frequent checkups would be necessary for persons with diabetes as research indicates that preventative care decreases both the prevalence and progression of this condition [6]. Through utilization of preventative health examinations and routine checkups, the most common chronic physical and mental health conditions can be prevented, delayed, or treated more effectively [6, 11]. Visits of this type are linked with improved physical and mental health outcomes [4, 5, 14] as well as to improvements in health-related quality of life (HRQoL) and control over diseases [10]. However, research indicates that both engagement in preventative health checks and overall perception of one’s health differ based on demo- graphic factors, socioeconomic status, health insurance cover- age, lifestyle factors, and disease burden [4, 5, 9, 10, 12–14].i However, research for associations between routine check- ups and physical or mental health tends to focus on older adults/Medicare users [4–6], with no studies assessing these relations for differences by gender [9, 12–14] or by diabetes status [4, 7, 8]. Therefore, the purpose of this study is to assess whether physical and mental health differ by receiving a rou- tine checkup in middle-aged males and females with diabetes. Diabetes is a significant component of the disease burden in the US as it affects up to 30 million adults, and of those, up to 7 million may be undiagnosed (not aware of or did not Advances in Preventive Medicine 2 Table 1 (a): Participant characteristics by state: diabetic males. 1. Introduction Advances in Preventive Medicine 3 Table 1: Continued. (b): Participant characteristics by state: females with diabetes. 1. Introduction Variable Florida (𝑁= 516) Kentucky (𝑁= 236) Maryland (𝑁= 311) New York (𝑁= 300) Ohio (𝑁= 323) 푁 % 푁 % 푁 % 푁 % 푁 % Good mental health 516 100 236 100 311 100 300 100 323 100 Yes 333 65 131 56 207 67 199 66 209 65 No 183 35 105 44 104 33 101 34 114 35 Good physical health 516 100 236 100 311 100 300 100 323 100 Yes 232 45 87 37 154 50 141 47 142 44 No 284 55 149 63 157 50 159 53 181 56 Routine checkup 516 100 236 100 311 100 300 100 323 100 Yes 451 87 213 90 280 90 268 89 292 90 No 65 13 23 10 31 10 32 11 31 10 Health conditions 475 92 218 92 296 95 286 95 302 93 0 or 1 other health condition 101 21 34 16 67 23 84 29 55 18 2 other health conditions 374 79 184 84 229 77 202 71 247 82 Physical activity 461 89 214 91 270 87 248 83 300 93 Inactive 195 42 101 47 90 33 95 38 126 42 Insufficiently active 90 20 48 22 60 22 52 21 62 21 Active/Highly active 176 38 65 30 120 44 101 41 112 37 Weight status 487 94 230 97 295 95 287 96 315 98 Underweight or normal 53 11 27 12 34 12 32 11 34 11 Overweight 149 31 64 28 83 28 99 34 83 26 Obese 285 59 139 60 178 60 156 54 198 63 Tobacco use 495 96 229 97 296 95 277 92 315 98 Never 221 45 78 34 149 50 151 55 154 49 Former 182 37 82 36 90 30 85 31 113 36 Current 92 19 69 30 57 19 41 15 48 15 Alcohol use 495 96 228 97 298 96 293 98 313 97 None 299 60 157 69 146 49 138 47 182 58 Light 57 12 27 12 42 14 46 16 42 13 Moderate or excessive 139 28 44 19 110 37 109 37 89 28 Age 516 100 236 100 311 100 300 100 323 100 45–54 176 34 76 32 107 34 103 34 83 26 55–64 340 66 160 68 204 66 197 66 240 74 Ethnicity/Race 506 98 234 99 304 98 288 96 313 97 White 328 65 186 79 191 63 162 56 272 87 Other 178 35 48 21 113 37 126 44 41 13 Marital status 511 99 235 99 310 100 299 100 321 99 Married 292 57 130 55 187 60 145 48 190 59 Not married 219 43 105 45 123 40 154 52 131 41 Education level 515 100 233 99 310 100 297 99 321 99 Graduated college 126 25 56 24 209 33 93 31 75 23 Did not graduate college 389 76 177 76 101 67 204 69 246 77 Income level 464 90 182 77 272 87 272 91 287 89 $50,000 or more 142 31 65 36 164 60 103 38 123 43 Less than $50,000 322 69 117 64 108 40 169 62 164 57 Employment status 512 99 235 99 309 99 291 97 322 99 Employed 217 42 94 40 181 59 147 51 154 48 Other 295 58 141 60 128 41 144 49 158 52 (a): Participant characteristics by state: diabetic males. 1. Introduction Variable Florida (𝑁= 667) Kentucky (𝑁= 381) Maryland (𝑁= 420) New York (𝑁= 293) Ohio (𝑁= 431) 푁 % 푁 % 푁 % 푁 % 푁 % Good mental health 667 100 381 100 420 100 293 100 431 100 Yes 331 50 197 52 232 55 134 46 205 48 No 336 50 184 48 188 45 159 54 226 52 Good physical health 667 100 381 100 420 100 293 100 431 100 Yes 258 39 123 32 193 46 96 33 162 38 No 409 61 258 68 227 54 197 67 269 62 Routine checkup 667 100 381 100 420 100 293 100 431 100 Yes 580 87 353 93 372 89 267 91 391 91 No 87 13 28 7 48 11 26 9 40 9 Health conditions 605 91 355 90 398 95 274 94 395 92 0 or 1 other health condition 115 19 51 14 78 20 52 19 62 16 2 other health conditions 490 81 304 86 320 80 222 81 333 84 Physical activity 610 91 344 90 365 87 250 85 401 93 Inactive 294 48 189 55 150 41 107 43 198 49 Insufficiently active 116 19 872 21 74 20 5 22 83 21 Active/Highly active 200 33 83 24 141 39 88 35 120 30 Weight status 589 88 335 88 378 90 270 92 388 90 Underweight or normal 91 15 44 13 4343 11 41 15 31 8 Overweight 147 25 92 27 90 24 73 27 94 24 Obese 351 60 199 59 245 65 156 58 263 68 Tobacco use 643 96 375 98 398 95 275 94 422 98 Never 325 51 180 48 232 58 143 52 211 50 Former 166 26 108 29 105 26 78 28 111 26 Current 152 24$ 87 23 61 15 54 20 100 24 Alcohol use 656 98 379 99 410 98 284 97 420 97 None 473 72 303 80 227 55 143 60 307 73 Light 68 10 35 9^ 85 21 78 14 64 15 Moderate or excessive 115 18 41 11 98 24 54 26 49 12 Age 667 100 381 100 420 100 293 100 431 100 45–54 234 35 140 37 140 33 120 41 134 31 55–64 433 65 241 63 280 67 173 59 297 69 Ethnicity/Race 651 98 377 99 416 99 279 95 427 99 White 426 65 309 82 230 55 162 58 348 82 Other 225 35 68 18 186 44 117 42 79 19 Marital status 666 100 379 99 417 99 288 98 429 100 Married 300 45 196 52 200 48 118 41 205 48 Not married 366 55 183 48 217 52 170 59 224 52 Education level 667 100 380 100 420 100 291 99 429 100 Graduated college 137 21 83 22 142 34 92 32 95 22 Did not graduate college 530 79 297 78 278 66 199 68 334 78 Income level 544 82 268 70 357 85 256 86 372 86 $50,000 or more 130 24 94 35 179 50 86 34 117 31 Less than $50,000 414 76 174 65 178 50 170 66 255 69 Employment status 662 99 379 99 418 100 287 98 430 100 Employed 235 36 133 35 213 51 128 45 164 38 Other 427 65 246 65 205 49 159 55 266 62 Table 1: Continued. 1. Introduction (b): Participant characteristics by state: females with diabetes. Advances in Preventive Medicine Note. AOR = adjusted odds ratio; 95% CI = 95% confidence intervals; Ref = referent group; boldface indicates significance (AORs with 95% CI that do not include 1.00 are significant). All models controlled for ­physical activity, weight status, tobacco use, alcohol use, age, ethnicity/race, marital status, education level, income level and employment status. (a): Results of multiple logistic regression analyses across states: males. Predicting good mental health (yes vs. no) Florida Kentucky Maryland New York Ohio AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI Low High Low High Low High Low High Low High Routine check-up No Ref — — Ref — — Ref — — Ref — — Ref — — Yes 1.27 0.64 2.50 4.43 1.07 18.45 2.06 0.73 5.82 2.02 0.68 5.98 0.95 0.35 2.61 Health conditions 0 or 1 other health condition Ref — — Ref — — Ref — — Ref — — Ref — — 2 other health conditions 0.24 0.10 0.54 1.04 0.25 4.25 0.51 0.20 1.28 0.23 0.92 0.55 0.78 0 .33 1.84 Predicting good physical health (yes vs. no) Florida Kentucky Maryland New York Ohio AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI Low High Low High Low High Low High Low High Routine check-up No Ref — — Ref — — Ref Ref — — Ref — — Yes 0.59 0.29 1.18 2.39 0.53 10.77 1.39 0.50 3.86 2.55 0.84 7.76 1.48 0.54 4.03 Health conditions 0 or 1 other health condition Ref — — Ref — — Ref — — Ref — — Ref — — 2 other health conditions 0.18 0.09 0.37 0.08 0.01 0.48 0.41 0.18 0.96 0.39 0.18 0.88 0.95 0.42 2.11 Table 2 Note. AOR = adjusted odds ratio; 95% CI = 95% confidence intervals; Ref = referent group; boldface indicates significance (AORs with 95% CI that do not include 1.00 are significant). All models controlled for ­physical activity, weight status, tobacco use, alcohol use, age, ethnicity/race, marital status, education level, income level and employment status. (a): Results of multiple logistic regression analyses across states: males. Predicting good mental health (yes vs. 1. Introduction no) Florida Kentucky Maryland New York Ohio AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI Low High Low High Low High Low High Low High e check-up Ref — — Ref — — Ref — — Ref — — Ref — — 1.36 0.65 2.87 2.16 0.55 8.49 0.77 0.33 1.80 0.54 0.17 1.71 1.06 0.40 2.77 conditions other health condition Ref — — Ref — — Ref — — Ref — — Ref — — r health conditions 0.33 0.18 0.61 0.11 0.04 0.33 0.59 0.30 1.17 0.14 0.05 0.39 0.35 0.16 0.78 Table 2: Continued. (b): Results of multiple logistic regression analyses across states: females. Note. AOR = adjusted odds ratio; 95% CI = 95% confidence intervals; Ref = referent group; boldface indicates significance (AORs with 95% CI that do not include 1.00 are significant). Predicting good mental health (yes vs. no) Florida Kentucky Maryland New York Ohio AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI Low High Low High Low High Low High Low High Routine check-up No Ref — — Ref — — Ref — — Ref — — Ref — — Yes 1.39 0.71 2.73 1.05 0.31 3.61 0.56 0.22 1.41 4.58 1.24 16.91 0.85 0.34 2.10 Health conditions 0 or 1 other health condition Ref — — Ref — — — — Ref — — Ref — — 2 other health conditions 0.27 0.14 0.52 0.26 0.09 0.76 0.35 0.16 0.77 0.51 0.21 1.29 0.30 0.13 0.67 Predicting good physical health (yes vs. no) Florida Kentucky Maryland New York Ohio AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI Low High Low High Low High Low High Low High Routine check-up No Ref — — Ref — — Ref — — Ref — — Ref — — Yes 1.36 0.65 2.87 2.16 0.55 8.49 0.77 0.33 1.80 0.54 0.17 1.71 1.06 0.40 2.77 Health conditions 0 or 1 other health condition Ref — — Ref — — Ref — — Ref — — Ref — — 2 other health conditions 0.33 0.18 0.61 0.11 0.04 0.33 0.59 0.30 1.17 0.14 0.05 0.39 0.35 0.16 0.78 Table 2: Continued. (b): Results of multiple logistic regression analyses across states: females. Note. 1. Introduction no) Florida Kentucky Maryland New York Ohio AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI Low High Low High Low High Low High Low High Routine check-up No Ref — — Ref — — Ref — — Ref — — Ref — — Yes 1.27 0.64 2.50 4.43 1.07 18.45 2.06 0.73 5.82 2.02 0.68 5.98 0.95 0.35 2.61 Health conditions 0 or 1 other health condition Ref — — Ref — — Ref — — Ref — — Ref — — 2 other health conditions 0.24 0.10 0.54 1.04 0.25 4.25 0.51 0.20 1.28 0.23 0.92 0.55 0.78 0 .33 1.84 Predicting good physical health (yes vs. no) Florida Kentucky Maryland New York Ohio AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI Low High Low High Low High Low High Low High Routine check-up No Ref — — Ref — — Ref Ref — — Ref — — Yes 0.59 0.29 1.18 2.39 0.53 10.77 1.39 0.50 3.86 2.55 0.84 7.76 1.48 0.54 4.03 Health conditions 0 or 1 other health condition Ref — — Ref — — Ref — — Ref — — Ref — — 2 other health conditions 0.18 0.09 0.37 0.08 0.01 0.48 0.41 0.18 0.96 0.39 0.18 0.88 0.95 0.42 2.11 Table 2 5 Advances in Preventive Medicine 5 (b): Results of multiple logistic regression analyses across states: females. OR = adjusted odds ratio; 95% CI = 95% confidence intervals; Ref = referent group; boldface indicates significance (AORs with 95% CI that do not include 1.00 are significant). ting good mental health . no) Florida Kentucky Maryland New York Ohio AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI Low High Low High Low High Low High Low High e check-up Ref — — Ref — — Ref — — Ref — — Ref — — 1.39 0.71 2.73 1.05 0.31 3.61 0.56 0.22 1.41 4.58 1.24 16.91 0.85 0.34 2.10 conditions other health condition Ref — — Ref — — — — Ref — — Ref — — r health conditions 0.27 0.14 0.52 0.26 0.09 0.76 0.35 0.16 0.77 0.51 0.21 1.29 0.30 0.13 0.67 ting good physical (yes vs. 3. Results Because these responses were highly skewed toward 0 days in each state and because we wanted to predict “good” health, we reversed and dichotomized these values to represent “yes” (30 days of good health in the past 30 days) or “no” (fewer than 30 days of good health in the past 30 days) separately for “good mental health” and “good physical health.” The factor of interest, routine check-up, was measured as yes/no to having a checkup in the past year. 3.2. Participant Characteristics: Females with Diabetes. Table 1(b) lists participant characteristics for middle-aged females with diabetes. Most participants reported having a routine checkup within the past year (87–93%). About half of the participants reported good mental health (46–55%) and less than half reported good physical health (32–46%). Regarding health conditions, most participants had diabetes plus two or more chronic conditions (80–86%) and were obese (58–68%), and about one-third to one-half reported being inactive (41– 55%). Regarding health behaviors, the majority of participants reported no tobacco (48–58%) or alcohol use (55–80%). For demographics, a range of participants reported their race as white (55–82%) and around one half were married (41–52%). As for socioeconomic status, the majority of respondents had not graduated from college or technical school (66–79%) and earned an income of less than $50,000 (50–76%), while one- third to one-half of participants were employed (35–51%). 3.2. Participant Characteristics: Females with Diabetes. Table 1(b) lists participant characteristics for middle-aged females with diabetes. Most participants reported having a routine checkup within the past year (87–93%). About half of the participants reported good mental health (46–55%) and less than half reported good physical health (32–46%). Regarding health conditions, most participants had diabetes plus two or more chronic conditions (80–86%) and were obese (58–68%), and about one-third to one-half reported being inactive (41– 55%). Regarding health behaviors, the majority of participants reported no tobacco (48–58%) or alcohol use (55–80%). For demographics, a range of participants reported their race as white (55–82%) and around one half were married (41–52%). As for socioeconomic status, the majority of respondents had not graduated from college or technical school (66–79%) and earned an income of less than $50,000 (50–76%), while one- third to one-half of participants were employed (35–51%). All models controlled for physical activity, weight status, tobacco use, alcohol use, education level, income level, employment status, age, ethnicity/race, and marital status. 2. Methods interest. As such, similar results in three out of five states were considered reliable evidence for relations. Any observations with missing data for any variable were excluded from the adjusted analysis and all analyses were conducted in STATA Version 15.1 (Copyright 1985–2017 StataCorp LLC). 2.1. Design. This study is a cross-sectional analysis that used data from the 2017 Behavioral Risk Factor Surveillance System (BRFSS) conducted by the Centers for Disease Control and Prevention (CDC) [3]. BRFSS is an annual telephone survey system that uses random digit dialing techniques for both landlines and cell phones across all 50 states in the US and the District of Columbia. This survey gathers data about US adult residents’ health-related behaviors, chronic health conditions, and use of preventative services. The CDC compiles all BRFSS data and makes deidentified data available for secondary analysis by researchers. This study was given exempt status by the Institutional Review Board of The University of North Texas Health Science Center. 1. Introduction AOR = adjusted odds ratio; 95% CI = 95% confidence intervals; Ref = referent group; boldface indicates significance (AORs with 95% CI that do not include 1.00 are significant). Predicting good mental health (yes vs. no) Florida Kentucky Maryland New York Ohio AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI Low High Low High Low High Low High Low High Routine check-up No Ref — — Ref — — Ref — — Ref — — Ref — — Yes 1.39 0.71 2.73 1.05 0.31 3.61 0.56 0.22 1.41 4.58 1.24 16.91 0.85 0.34 2.10 Health conditions 0 or 1 other health condition Ref — — Ref — — — — Ref — — Ref — — 2 other health conditions 0.27 0.14 0.52 0.26 0.09 0.76 0.35 0.16 0.77 0.51 0.21 1.29 0.30 0.13 0.67 Predicting good physical health (yes vs. no) Florida Kentucky Maryland New York Ohio AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI AOR 95% CI Low High Low High Low High Low High Low High Routine check-up No Ref — — Ref — — Ref — — Ref — — Ref — — Yes 1.36 0.65 2.87 2.16 0.55 8.49 0.77 0.33 1.80 0.54 0.17 1.71 1.06 0.40 2.77 Health conditions 0 or 1 other health condition Ref — — Ref — — Ref — — Ref — — Ref — — 2 other health conditions 0.33 0.18 0.61 0.11 0.04 0.33 0.59 0.30 1.17 0.14 0.05 0.39 0.35 0.16 0.78 Table 2: Continued. 6 Advances in Preventive Medicine 3. Results 3.1. Participant Characteristics: Males with Diabetes. Table 1(a) lists participant characteristics for middle-aged males with diabetes. The majority of participants had attended a routine medical checkup within the past year (87–90%) and reported good mental health (56–67%), but less than half reported good physical health (37–50%). Regarding health conditions, most participants had diabetes plus two or more chronic illnesses (71–84%) and were obese (54–63%), yet less than half reported being inactive (33–47%). Regarding health behaviors, one-third to one-half of participants did not use tobacco products (34– 55%) or alcohol (47–69%). For demographics, the majority of participants were married (48–60%) and reported their race as white (56–87%). As for socioeconomic status, the majority of respondents had not graduated from college or technical school (67–77%), approximately half were employed (40–59%), and up to two-thirds earned an income of $50,000 or more (40–69%). 2.2. Sample. The samples in the study include males and females with diabetes between the ages of 45 and 64 in Florida (𝑁= 1183), Kentucky (𝑁= 617), Maryland (𝑁= 731), New York (𝑁= 593), and Ohio (𝑁= 754) that had data for mental health, physical health, and routine checkup. These states were chosen because they had a large diabetic population and higher rates of fair/poor health status when compared to the other states [1]. 2.3. Data. The original BRFSS variables for mental and physical health were determined by asking participants to self-report the number of “poor health days” in the past 30 days separately for mental health and physical health. Because these responses were highly skewed toward 0 days in each state and because we wanted to predict “good” health, we reversed and dichotomized these values to represent “yes” (30 days of good health in the past 30 days) or “no” (fewer than 30 days of good health in the past 30 days) separately for “good mental health” and “good physical health.” The factor of interest, routine check-up, was measured as yes/no to having a checkup in the past year. 2.3. Data. The original BRFSS variables for mental and physical health were determined by asking participants to self-report the number of “poor health days” in the past 30 days separately for mental health and physical health. 3. Results Health conditions were measured as the number of “yes” responses to whether participants had any of the following: heart attack, coronary heart disease, stroke, asthma, skin can- cer, cancer, COPD, arthritis, depression, kidney disease, and diabetes. The resulting numbers were then categorized as “dia- betes only,” “diabetes plus one other chronic condition,” and “diabetes plus two other chronic conditions.” Alcohol use was measured in BRFSS as number of drinks per day and we cat- egorized the numbers as “none,” “light” (<1), and “moderate or excessive” (1–4+ females, 1–5+ males). All variables and their categories are shown in Table 1(a). 3.3. Mental Health: Males. As shown in Table 2(a), the results of multiple logistic regression analysis for middle-aged males with diabetes indicated that after controlling for all other variables in the model, good mental health was significantly related to having had routine checkups in only 1 out of 5 states, which was not considered a reliable finding across states as was defined in the methods section. 2.4. Analysis. Frequency distributions by state were used to describe the samples. Multiple logistic regression was conducted by state and gender to determine the relationship between mental and physical health status and routine check- up while controlling for health-related, socioeconomic, and demographic factors. The state and gender data were analyzed separately to determine the relationship between the variables across multiple similar samples within our population of 3.4. Physical Health: Males. Also shown in Table 2(a), the results of multiple logistic regression analysis for middle- aged males with diabetes indicated that after controlling for all other variables in the model, good physical health was not significantly related to routine checkups across in any state. However, those who reported having diabetes plus two or 7 Advances in Preventive Medicine (instead of “general” health) and separately for males and females (instead of together), which allowed us to determine whether patterns in variable relations were similar for different facets of health and by gender. In addition, BRFSS also provided current information, given that our dependent variables (mental and physical health) were measured within the last 30 days. 4. Discussion The purpose of this study was to determine whether physical and mental health status differ by routine checkup in mid- dle-aged males and females with diabetes. For this target popu- lation, both good mental and physical health did not significantly differ related to having routine checkups across states. These results differ from prior research which showed that preventative care is related to both improved depressive symptoms and the perception of good overall health [4, 5, 11]. The differences in findings may be due to differing target populations. While our results focus on patients with diabetes, previous research focused on the general population as a whole. Therefore, it is possible that prevention efforts were in place as most of the patients were already under medical care. Thus, to our knowledge, our study is the first to focus only on middle-aged patients with diabetes as related to regular checkups. Conflicts of Interest The authors declare that they have no conflicts of interest. However, the results of this study did show that for mid- dle-aged males and females with diabetes, good physical and mental health were inversely related to having diabetes plus two or more other health conditions. This is generally consist- ent with prior research that showed chronic illnesses to be related to lower overall health in the general population [12]. As prior research focused primarily on the general population, our study focuses solely on middle-aged people with diabetes. For this target population, the comanagement and treatment of multiple chronic conditions may have a significant impact on their mental and physical health, and the assessment of comorbid conditions should be a focus for their care. 5. Conclusions Because this study used population-based data, the results may generalize to males and females aged 45–64 with diabetes. Regarding the optimization of patient’s mental and physical health, we recommend automatic mental and physical health screening for adults aged 45–64 with diabetes as well as screen- ing for other chronic health conditions. General practitioners should assess comorbid conditions and treatments, refer to specialists as needed, and educate patients on the importance of proper management of diabetes in combination with any other chronic illnesses for maintaining good mental and phys- ical health. 3. Results However, BRFSS did not include variables that provided information about (1) current treatment and management of any mental or physical health condition, (2) current treatment and management of diabetes specifically, or (3) current management and severity of the chronic illnesses in addition to diabetes, all of which could have an impact upon mental and physical health. Future studies should include information about the current management and treatment of any mental and physical health conditions and should consider the influence of specific disease management and medication use in relation to its impact on mental and physical health in diabetics. more other chronic conditions were about 2.5–12.5 times less likely to report good physical health compared to those who reported diabetes only across states. 3.5. Mental Health: Females. As shown in Table 2(b), the results of multiple logistic regression analysis for middle-aged females with diabetes indicated that after controlling for all other variables in the model, good mental health was significantly related to having routine checkups in only 1 out of the 5 states, which was not considered a reliable finding across similar samples. However, compared to those with only diabetes, those who reported having diabetes plus two or more other chronic conditions were approximately three to four times less likely to report good mental health compared to those who reported having diabetes only in a majority of the states. 3.6. Physical Health: Females. Also shown in Table 2(b), the results of multiple logistic regression analysis for middle-aged females with diabetes indicated that after controlling for all other variables in the model, good physical health was not significantly related to routine checkup across states. However, those who reported having diabetes plus two or more other chronic conditions were about 3–9 times less likely to report good physical health compared to those who reported having diabetes only in the majority of the states. Data Availability BRFSS 2017 data is available online from the CDC at https://www.cdc.gov/brfss/annual_data/annual_2017.html. References [1]  Center for Disease Control and Prevention (CDC), “BRFSS prevalence and trends data,” 2017a, https://www.cdc.gov/brfss/ brfssprevalence/index.html. [2]  Centers for Disease Control and Prevention (CDC), “National diabetes statistics report,” 2017b, https://www.cdc.gov/diabetes/ data/statistics/statistics-report.html. [3]  Center for Disease Control and Prevention (CDC), “Behavioral risk factor surveillance system,” 2018, https://www.cdc.gov/ brfss/index.html. [4]  D. Culica, J. Rohrer, M. Ward, P. Hilsenrath, and P. Pomrehn, “Medical checkups: who does not get them?” American Journal of Public Health, vol. 92, no. 1, pp. 88–91, 2002. 4.1. Limitations. The use of BRFFS data provided large, multiple samples to evaluate both physical and mental health Advances in Preventive Medicine 8 [5]  R. Dryden, B. Williams, C. McCowan, and M. Themessl-Huber, “What do we know about who does and does not attend general health checks? Findings from a narrative scoping review,” BMC Public Health, vol. 12, no. 723, pp. 1–23, 2012, http://www. biomedcentral.com/1471-2458/12/723. [6]  H. Eyre, R. Kahn, and R. M. Robertson, “Preventing cancer, cardiovascular disease, and diabetes: a common agenda for the American cancer society, the American diabetes association, and the American Heart Association,” Diabetes Care, vol. 27, no. 7, pp. 1812–1824, 2004. [7]  I. Ganguli, J. Souza, and J. McWilliams, “Trends in use of the U.S. Medicare annual wellness visit, 2011–2014,” Journal of American Medical Association, vol. 317, no. 21, pp. 2233–2235, 2017. [8]  A. Mehrota, A. M. Zaslavsky, and J. Z. Ayanian, “Preventative health examinations and preventative gynecological examinations in the United States,” Archives of Internal Medicine, vol. 167, no. 17, pp. 1876–1883, 2007. [9]  A. Molarius, K. Berglund, C. Eriksson et al., “Socioeconomic conditions, lifestyle factors, and self-rated health among men and women in Sweden,” European Journal of Public Health, vol. 17, no. 2, pp. 125–133, 2006. [10]  R. R. Rubin and M. Peyrot, “Quality of life and diabetes,” Diabetes and Metabolism Research and Reviews, vol. 15, no. 3, pp. 205– 218, 1999, https://www.ncbi.nlm.nih.gov/pubmed/10441043. [11]  A. L. Siu, K. Bibbins-Domingo, D. C. Grossman et al., “Screening for depression in adults,” JAMA, vol. 315, no. 4, pp. 380–387, 2016. [12]  T. W. Strine, D. P. Chapman, L. S. Balluz, D. G. Moriarty, and A. H. Mokdad, “The associations between life satisfaction and health-related quality of life, chronic illness, and health behaviors among U.S. community-dwelling adults,” Journal of Community Health, vol. 33, no. 1, pp. 40–50, 2008. [13]  M. Tajvar, M. Arab, and A. References Montazeri, “Determinants of health- related quality of life in elderly Tehran Iran,” BMC Public Health, vol. 8, no. 323, 2008. [14]  P. E. Wandell, “Quality of life of patients with diabetes mellitus,” Scandinavian Journal of Primary Health Care, vol. 23, no. 2, pp. 68–74, 2005.
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Temperature Approach Optimization in the Double Pipe Heat Exchanger with Groove
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INTRODUCTION through internally grooved pipe. Sunu (2015) investigated increased pressure drop on internal wall surface in pipe with rectangular groove. Sunu et al (2015) revealed the effect of groove numbers on pressure drop in pipe flows. Investigation about pressure drop characteristics in a periodically grooved was conducted by Adachi et al (2009). The investigation on pipe bend with rough surface produced 4 % drag reduction (Nakao, 1995). Lee and Jang (2005) studied v-shaped groove over curved body. Choi and Orchard (1997) reveal about turbulence management using passive device for momentum transfer. Ding et al (2009) present a correlation to predict frictional pressure drop of R410A-oil mixture inside internal spiral grooved microfin tube. Alam and Yong Kim (2012) conducted mixing analysis in microchannel with rectangular grooves. A number of studies have been carried out to optimize the enhancement the heat transfer of rough surface geometry. Investigation of turbulent channel flow conducted by Katoh et al (2000), reveal the relationship between drag and thermal enhancement by rough surface. Aroonrat et al (2013) investigated the relationship of heat transfer and flow characteristics in horizontal internally grooved tube made by stainless steel. The result showed the thermal enhancement factor is 1.4 to 2.2 for grooved tube. Graham et al (1999) studied of pressure drop and heat transfer in copper tube with axially grooved. Lorenz et al (1995) investigated the distribution of the heat transfer coefficient in a channel with periodic transverse grooves. A heat exchanger is a heat transfer device that exchange heat between two or more process fluids at different temperature. Heat exchangers have widespread applications in industrial such as industry process, petroleum transportation, power, heat recovery, RHVAC and many domestic applications. One of the simply heat exchanger is double pipe heat exchanger (DPHE). Their usual application is for small duties and they are suitable for high pressure and temperature. Another advantage is the design of DPHE serviceable easily than the other heat exchanger and can be connected in series or parallel. Heat exchangers have to fulfill some requirement such as effective temperature difference. The effective temperature driving force is a measure of the potential for heat transfer that exists at the design conditions. Effective temperature difference is defined by the log mean temperature difference (LMTD). Other simply method to measure thermal performance of heat exchanger is using temperature approach. ABSTRACT Heat transfer in double pipe heat exchanger with circumference-rectangular grooves has been investigated experimentally. The volume flowrate of cold and hot water were varied to determine its influence on the approach temperature of the outlet terminals. In this experimental design, the grooves were incised in annular room that is placed on the outside surface of the inner pipe. The shell diameter is 38.1 mm and tube diameter 19.4 mm with 1 m length, which is made of aluminum. The flow pattern of the two fluids in the heat exchanger is a parallel flow. The working fluid is water with volume flow rate of 27.1, 23.8 and 19.8 l/minute. The temperature of water on the inlet terminals are 50±10C for hot stream and 30±10C for cold stream. Temperature measurements conducted on each terminal of the inlet and outlet heat exchanger. The results showed that the grooves induced the approach temperature. The change of the approach temperature from the grooves compared to that of without grooves decreased by 37.9%. This phenomenon indicates an increase in heat transfer process and performance of the heat exchanger. Groove improves the heat surface area of the inner pipe, increasing the momentum transfer and in the other hand, reducing the weight of heat exchangers itself. Keywords: Approach temperature, groove, heat exchanger, optimization INTRODUCTION Temperature approach referred to difference of temperature between hot and cold outlet of heat exchanger. g The need for lightweight, space-saving, and economical heat exchangers has driven the development of compact surfaces. Many engineering techniques have been developed for enhancing the rate of heat transfer through the wall surface of heat exchanger. The enhanced of heat transfer accompanied by pressure drop and drag increase. One of the flow surface applications to increase heat transfer in turbulence flow is groove. Using grooves is well known as passive flow control. The passive flow control as concerned wide consideration as it need no auxiliary power, increase surface area, induced pressure drop, simplicity and hence give more benefits (Sunu et al., 2015). Changing the surface of pipe with circumference rectangular groove can be used to control flow separation. The groove provided as vortex generator and increased the boundary layer momentum. In the several paper describe above, most studies focus on heat transfer, flow characteristics and the both relationship inside/outside grooved tube. The studies of heat transfer through grooved pipe in a room between tube and shell has received little attention. Consequently, the objective of this present study is to optimize the temperature approach of double pipe heat exchanger with groove placed in annulus room. TEMPERATURE APPROACH OPTIMIZATION IN THE DOUBLE PIPE HEAT EXCHANGER WITH GROOVE Putu Wijaya Sunu, Daud Simon Anakottapary, Wayan G. Santika Department of Mechanical Engineering, Bali State Polytechnic, Badung-Bali, Indonesia. E-mail: wijayasunu@pnb.ac.id © The Authors, published by EDP Sciences. This is an open access article distributed under the terms of the Creative Co License 4.0 (http://creativecommons.org/licenses/by/4.0/). DOI: 10.1051/ conf/2016 matec 5804006 DOI: 10.1051/ conf/2016 matec 5804006 , Web of Conferences MATEC 58 04006 (2016) BISSTECH 2015 ished by EDP Sciences. This is an open access article distributed under the terms of the Creative Commons Attribution eativecommons.org/licenses/by/4.0/). © 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/). METHODOLOGY The flow pattern of the two fluids in a general heat exchanger can vary depending on the heat exchanger Over the years, numerous researchers have carried out experimental studies on flow characteristics DOI: 10.1051/ conf/2016 matec 5804006 , Web of Conferences MATEC 58 04006 (2016) BISSTECH 2015 outlet temperature of one stream and the outlet temperature of the other stream design. One of the flow patterns is a parallel flow, which is the hot fluid and cold fluid move in the same direction. This investigation used parallel flow in the flow direction. The hot side inlet temperature is in contact with the cold side inlet temperature, the two fluid progresses through the heat exchanger and at the other terminal point the cold side outlet temperature is in contact with the hot side outlet temperature. In a parallel flow heat exchanger, the approach temperatures are the difference between the The experiment was performed using the experimental apparatus shown schematically in Fig.1. The experiment installation consisted two centrifugal pump which was stabilized by electric stabilizer to circulate hot and cold water through a loop. The control valve used to vary flow rate through the test section and the water tank t h ld t f th t hold o hold approach temperatures are the difference between the to hold water from the system. Figure-1. Experiment set-up The hot water temperature was 50±10C and the cold water was 30±10C. The volume flow rate was varied by control valve set some distance from test section as 27.1, 23.8 and 19.8 l/minute respectively. The tube test outer diameter is 19.4 mm which has circumference rectangular groove 40 x 0.4 mm. While, the shell test section has 38.1 mm outer diameter. All of the tube made of aluminum pipes. to approach temperatures are the difference between the to hold water from the system. Figure-1. Experiment set-up Figure-1. Experiment set-up 19.4 mm which has circumference rectangular groove 40 x 0.4 mm. While, the shell test section has 38.1 mm outer diameter. All of the tube made of aluminum pipes. The hot water temperature was 50±10C and the cold water was 30±10C. The volume flow rate was varied by control valve set some distance from test section as 27.1, 23.8 and 19.8 l/minute respectively. The tube test outer diameter is Figure-2. Groove geometry Figure-2. METHODOLOGY Groove geometry Temperatures were measured by thermocouples placed in the inlet and outlet terminal of hot and cold water from the test section. A data logger digitalized signal from thermocouples before being recorded in a computer memory. The approach temperature (AT) was determined using the data point from hot and cold terminals of 750 s. The percentage of approach temperature (% AT) from the grooves was compared to that of a smooth pipe (without grooves) and estimated by using the equation bellow: ( ) ( ) % 100% ( ) smooth groove smooth AT AT AT x AT        Eq.1 Eq.1 2 DOI: 10.1051/ conf/2016 matec 5804006 , Web of Conferences MATEC 58 04006 (2016) , Web of Conferences MATEC 58 04006 (2016) BISSTECH 2015 RESULTS AND DISCUSSIONS The rate of approach temperature (a) Qhot= Qcold= 27.1 l/min; (b) Qhot= 27.1 l/min, Qcold= 23.8 l/min; (c) Qhot= 27.1 l/min, Qcold= 19.8 l/min; (d) Qhot= 23.8 l/min, Qcold= 27.1 l/min; (e) Qhot= 19.8 l/min, Qcold= 27.1 l/min higher momentum convection and energy transfer through interchange of fluid particles. The rate of approach temperature as a function of approach temperature is presented in figure 5. Marked with circle indicates the condition of smooth pipe (without groove) and marked with rectangular point represent with grooved pipe. Negative sign on ordinate axis, indicating the occurrence of a decrease in approach temperature and indicates greater of heat transfer process. For dT/dt grooved pipe, the rate of approach temperature for each approach temperature is more negative then that the smooth pipe. The greater the flow rate, the more negative the value dT/dt will be. Increased flowrate is accompanied by an increase in Re. Greater Re will increase the randomness of fluid motion, resulting in RESULTS AND DISCUSSIONS This data was then used as a comparison to the data from the double pipe heat exchanger with groove. The approach temperature data in DPHE are shown in fig. 3 and 4. Preliminary experiments were done on the double pipe heat exchanger without groove (smooth pipe) to establish the time series temperature and approach temperature. Figure-3. Average approach temperature for hot water flowrate variation. Figure-3. Average approach temperature for hot water flowrate variation. Figure-4. Average approach temperature for cold water flowrate variation. Figure-4. Average approach temperature for cold water flowrate variation. Fig. 3 shows the average value of approach temperature at various hot water flowrate with constant cold-water flowrate. While figure 4 shows the average value of approach temperature at various cold-water flowrate with constant hot water flowrate. The rectangular pointed denotes the average approach temperature in smooth pipe DPHE. The percentage values on the plot show percentage approach temperature estimated using equation 1. For variation in hot water supply 19.8, 23.8, 27.1 l/min, the approach temperature data of grooved DPHE indicates reduction of about 10.6%, 34.9%, and 37.9% respectively. For variation in cold water supply 19.8, 23.8, 27.1 l/min, the approach temperature data of grooved DPHE indicates reduction of about 28.9%, 37.2%, and 37.9% respectively. This phenomenon indicates the increases of heat transfer process between two fluids. It was observed that approach temperature decreased with increasing flow rate in all case. The approach temperature obtained from the circumference- rectangular grooved was lower than that those from the smooth pipe. This occurred because the grooved pipe provided the enhancement of heat transfer by increasing recirculation region of the flow. Groove produced swirl effect on the fluid near to the pipe surface in the annulus room which lacerating the boundary layer. The fluid thermal boundary layer became thinner and the increasing fluid mixing process increased the rate of heat transfer which represented by the rate of approach temperature. 3 DOI: 10.1051/ conf/2016 matec 5804006 , Web of Conferences MATEC 58 04006 (2016) , Web of Conferences MATEC 58 04006 (2016) BISSTECH 2015 BISSTECH 2015 Figure-5. The rate of approach temperature (a) Qhot= Qcold= 27.1 l/min; (b) Qhot= 27.1 l/min, Qcold= 23.8 l/min; (c) Qhot= 27.1 l/min, Qcold= 19.8 l/min; (d) Qhot= 23.8 l/min, Qcold= 27.1 l/min; (e) Qhot= 19.8 l/min, Qcold= 27.1 l/min Figure-5. CONCLUSIONS Heat transfer in double pipe heat exchanger with circumference-rectangular grooves was investigated using experimental method. The results showed that the grooves induced the approach temperature. Groove improves the heat surface area of the inner pipe (tube side), increasing the momentum transfer, produced swirl effect on the fluid near to the pipe surface in annulus room. The change of the approach temperature from the grooves compared to that of 4 DOI: 10.1051/ conf/2016 matec 5804006 , Web of Conferences MATEC 58 04006 (2016) BISSTECH 2015 Nakao, S.I. 1995. Effects of riblet bends on pipe flows. Applied Scientific Research 54: 237-247. without grooves decreased by 37.9%, which indicates an increase in heat transfer process and performance of the heat exchanger. Sunu P.W. 2015. The characteristics of increased pressure drop in pipes with grooved. Adv .Studies Theor. Phys. 9(2): 57-61. Sunu P.W. 2015. The characteristics of increased pressure drop in pipes with grooved. Adv .Studies Theor. Phys. 9(2): 57-61. http://dx.doi.org/10.12988/astp.2015.412152 REFERENCES Adachi Takahiro, Yamato Tashiro, Hirofumi Arima, Yasuyuki Ikegami. 2009. Pressure drop characteristics of flow in a symmetric channel with periodically expanded grooves. Chemical Engineering Science 64: 593-597 Sunu P.W., ING Wardana, A.A.Sonief, Nurkholis Hamidi. 2015. The effect of wall groove numbers on pressure drop in pipe flows. Int. J. Fluid Mech. Resch., 42(2): 119 - 130 Alam Afroz, Kwang-Yong Kim. 2012. Analysis of mixing in a curved microchannel with rectangular grooves. Chemical Engineering Journal 181–182: 708–716. Aroonrat, K., Jumpholkul, C., Leelaprachakul, R., Dalkilic, A.S., Mahian, O., Wongwises, S. 2013. Heat transfer and single-phase flow in internally grooved tube. International Communication in Heat and Mass Transfer 42: 62-68. Choi, K.S and Orchard D.M. 1997. Turbulence Management Using Riblets for Heat and Momentum Transfer. Experimental Thermal and Fluid Science 15: 109-124. Ding G., Haitao Hu, Huang X., Bin Deng, Yifeng Gao. 2009. Experimental investigation and correlation of two-phase frictional pressure drop of R410A–oil mixture flow boiling in a 5 mm microfin tube. International Journal of Refrigeration 32: 150– 161. Graham D., J.C. Chato, T.A. Newell. 1999. Heat transfer and pressure drop during condensation of refrigerant 134a in an axially grooved tube, International Journal of Heat and Mass Transfer 42: 1935–1944. Katoh K., Choi, K.S.,Azuma, T. 2000. Heat-transfer enhancement and pressure loss by surface roughness in turbulent channel flows. International Journal of Heat and Mass Transfer, 43: 4009-4017. Lee, S.J. and Jang, Y.G. 2005.Control of flow around a naca 0012 airfoil with a micro-riblet film. Journal of Fluid and Structure 20: 659-672. Lorenz S., Mukomilow D., Leiner W. 1995. Distribution of the heat transfer coefficient in a channel with periodic transverse grooves. Experimental Thermal and Fluid Science l1: 234-242 5
https://openalex.org/W3172085540
https://europepmc.org/articles/pmc8556635?pdf=render
English
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Clinic Time Required for Remote and In-Person Management of Patients With Cardiac Devices: Time and Motion Workflow Evaluation
JMIR cardio
2,021
cc-by
8,433
Corresponding Author: Corresponding Author: David Lanctin, MPH Medtronic 8200 Coral Sea Ct NE Mounds View, MN, 55112 United States Phone: 1 800 633 8766 Email: david.lanctin@medtronic.com Abstract Background: The number of patients with cardiac implantable electronic device (CIED) is increasing, creating a substantial workload for device clinics. number of patients with cardiac implantable electronic device (CIED) is increasing, creating a substanti clinics. Objective: This study aims to characterize the workflow and quantify clinic staff time requirements for managing patients with CIEDs. Objective: This study aims to characterize the workflow and quantify clinic staff time requirements for managing patients with CIEDs. Methods: A time and motion workflow evaluation was performed in 11 US and European CIEDs clinics. Workflow tasks were repeatedly timed during 1 business week of observation at each clinic; these observations included all device models and manufacturers. The mean cumulative staff time required to review a remote device transmission and an in-person clinic visit were calculated, including all necessary clinical and administrative tasks. The annual staff time to manage a patient with a CIED was modeled using CIED transmission volumes, clinical guidelines, and the published literature. Results: A total of 276 in-person clinic visits and 2173 remote monitoring activities were observed. Mean staff time required per remote transmission ranged from 9.4 to 13.5 minutes for therapeutic devices (pacemaker, implantable cardioverter-defibrillator, and cardiac resynchronization therapy) and from 11.3 to 12.9 minutes for diagnostic devices such as insertable cardiac monitors (ICMs). Mean staff time per in-person visit ranged from 37.8 to 51.0 and from 39.9 to 45.8 minutes for therapeutic devices and ICMs, respectively. Including all remote and in-person follow-ups, the estimated annual time to manage a patient with a CIED ranged from 1.6 to 2.4 hours for therapeutic devices and from 7.7 to 9.3 hours for ICMs. Conclusions: The CIED patient management workflow is complex and requires significant staff time. Understanding process steps and time requirements informs the implementation of efficiency improvements, including remote solutions. Future research should examine heterogeneity in patient management processes to identify the most efficient workflow. (JMIR Cardio 2021;5(2):e27720) doi: 10.2196/27720 (JMIR Cardio 2021;5(2):e27720) doi: 10.2196/27720 Original Paper Original Paper JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 1 (page number not for citation purposes) Clinic Time Required for Remote and In-Person Management of Patients With Cardiac Devices: Time and Motion Workflow Evaluation Amber Seiler1, NP, MSN, FHRS, CEPS, CCDS; Eliana Biundo2, MSc; Marco Di Bacco3, PharmD, MS; Sarah Rosemas3, MPH; Emmanuelle Nicolle3, MSc, MD; David Lanctin3, MPH; Juliette Hennion2, MSc; Mirko de Melis3, PhD; Laura Van Heel4, BSN 1Cone Health Medical Group, Greensboro, NC, United States 2Deloitte, Brussels, Belgium 3Medtronic, Mounds View, MN, United States 4Centracare, St. Cloud, MN, United States https://cardio.jmir.org/2021/2/e27720 JMIR CARDIO JMIR CARDIO Seiler et al Data Collection The number of patients receiving and living with cardiac implantable electronic devices (CIEDs), including permanent pacemakers, implantable cardioverter-defibrillators (ICD), cardiac resynchronization therapy (CRT) devices, and insertable cardiac monitors (ICMs), has increased significantly in the past several years [1-3]. Accordingly, the burden for device clinics to manage follow-up visits has increased. Such follow-up visits, consisting of device interrogation and subsequent care changes (ie, reprogramming device settings and acting upon clinical findings), have traditionally been performed in person. Their frequency, essentially based on clinical guidelines, may vary depending on the facility, physician and patient preferences, and available resources [4]. As an alternative or complement to in-person visits, remote monitoring (RM) has become a guideline-recommended method for managing patients with CIEDs [5,6]. RM capabilities are a standard feature of modern CIEDs, and data are continuously transmitted through landlines or mobile networks, which supplies health care providers with critical clinical (eg, arrhythmias) and device-related (eg, battery longevity) information that allows them to adjust and optimize patient treatment accordingly. In the 2015 Heart Rhythm Society (HRS) Consensus Statement on remote interrogation and monitoring for CIEDs, endorsed by European Heart Rhythm Association and other international societies, RM combined with an annual in-person visit is recommended rather than in-person evaluation alone, with the strongest (class I) recommendation and the highest level of evidence (A) [5]. This recommendation is primarily because of earlier detection of clinical events, including atrial fibrillation, ventricular arrhythmias, and pause arrhythmias, to which RM enables faster clinical response and appropriate medical action [7-9]. Several studies have confirmed the clinical and economic benefits of RM, including improved patient outcomes and reduced health care use [5,9-13]. A time and motion workflow evaluation was performed in 11 CIED clinics internationally to characterize the discrete activities and associated time required for all tasks related to managing patients with CIEDs. Among the participating clinics, 6 were located in the United States, and 5 were located in Europe (3 in the United Kingdom, 1 in France, and 1 in Germany). Participating clinics were actively managing an average of 5758 (range: 870-22,000) patients with CIEDs, an average of 4217 patients in the United States and 7606 in Europe. All 11 clinics used guideline-recommended RM in combination with in-person device follow-up. Half (3) of the US clinics were located within academic institutions, and 3 of the 5 European clinics were academic. KEYWORDS rdiac implantable electronic devices; remote monitoring; patient management; clinic efficiency; digital he cardiac implantable electronic devices; remote monitoring; patient management; clinic efficiency; digital health; mobile phone JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 1 (page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 JMIR CARDIO Seiler et al Data Collection A third-party observer prospectively collected data for one business week (5 days) at each clinic, recorded the tasks performed by the staff, and measured each task's duration with a stopwatch. Workflow measurements included all CIED types (permanent pacemaker, ICD, CRT, ICM) across any device manufacturer found within the clinic during the study week (Abbott, Biotronik, Boston Scientific, Medtronic, and Microport). The observations included all activities related to managing patients with CIEDs and were categorized into 3 groups of activities: in-person clinic visits, remote transmission review, and other patient management activities not attributable to a specific patient device check (eg, patient triage and scheduling, identifying patients lost to follow-up, and telephone communication with patients). Owing to insufficient data collection on remote transmission review workflow activities at the German site, these observations were excluded from the analysis. Staff Time Per Device Check for Remote and In-Person Device Follow-ups Furthermore, the literature has shown that the review of an RM transmission requires less staff time than an in-office interrogation, and RM is associated with greater patient adherence to device follow-up checks and a reduction in scheduled, often nonactionable in-office visits [10,14,15]. However, implementation in clinical practice of an overall management process for patients with CIEDs, incorporating both RM and in-person visits, can be challenging because of the scarcity of information on organizational models and requirements. The specific steps involved and the health care professional time required for these activities are poorly understood, which may hinder the implementation of optimal follow-up strategies, including remote solutions. Multimedia Appendix 1 lists all observed workflow steps occurring within each activity category (in-person clinic visit, remote transmission review, and other patient management activities). The differences in observed steps between categories are because of differences in device check scope; for example, assessing patient vitals or reprogramming device therapy are specific to in-person clinic visits. These lists are comprehensive of all possible steps observed, but all steps may not have occurred during each device check or in sequence as listed, as practices and workflow vary widely. Thus, to quantify the workload associated with an average patient device check (remote or in-person), the unit steps were weighted based on each step's likelihood of occurring in a given device check. The weighting factors are listed in Multimedia Appendix 2 [5,14,16-21] and were based on study observations where possible, supplemented by data from the literature. The mean time per remote and in-person device checks was calculated, including all clinical tasks and any administrative tasks related Statistical Analysis Staff Time Per Device Check for Remote and In-Person Device Follow-ups JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 2 (page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 Annual Staff Time for Other Patient Management Activities The annual time spent on other patient management activities not attributable to a specific patient device check was calculated based on observed clinic norms for performing tasks (eg, weekly identification of patients with disconnected monitors), whereas the frequency of telephone calls between the clinic and patient was based on a previous workflow study [21]. The per-patient workflow for in-person clinic visits, remote transmission review, and other patient management activities were extrapolated to the clinic level based on the average size of the clinics participating in the study (5758 patients). Annual Staff Time Per Patient for Remote and In-Person Device Follow-ups Annual Staff Time Per Patient for Remote and In-Person Device Follow-ups A total of 54 distinct workflow steps were observed and timed during the management of patients with CIEDs: 31% (17/54) for remote transmission review, 39% (21/54) for in-person clinic visits, and 30% (16/54) for other patient management activities such as patient phone calls and patient triage. The average time associated with each step is reported in Multimedia Appendices 3-5. During 11 total business weeks of data collection, observations included 276 in-person clinic visits (124/276, 44.9% the United States and 152/276, 55.1%, Europe), 1948 (1269/1948, 65.14% the United States and 679/1948, 34.86% Europe) individual remote transmission review tasks (not every step could be observed for each given transmission, as they often did not occur sequentially), and 440 other patient management tasks (the United States only). Considering all individual time recordings, approximately 50.21% (2424/4828) of the observations were in patients using pacemakers, 17.13% (827/4828) were in patients using ICD, 20.89% (1009/4828) were in patients using CRT, and 11.76% (568/4828) were in patients using ICM. On the basis of the calculated mean time per activity category, the annual staff time required to manage each patient with a CIED was modeled. The volume of remote transmissions per patient per year was based on real-world device transmissions from the calendar year 2016-2017 and included routine and alert-driven transmissions (Multimedia Appendix 2). For in-person clinical visits, it was assumed that each patient would have a routine visit per year according to clinical guidelines [6] and a number of unscheduled visits (ie, device alert or symptom-driven) based on the frequencies reported in the remotely monitored arm of published RM trials for each CIED type [16-20]. Objective This study aims to characterize the workflow processes and clinic staff time required for remote and in-person device follow-up of patients with CIEDs. https://cardio.jmir.org/2021/2/e27720 XSL•FO RenderX JMIR CARDIO Seiler et al programmer was used versus visits in which a tablet programmer was not used. to that device check (eg, software access, documentation, scheduling follow-up, and sending information for billing). For remote transmission review tasks, consideration of the transmission type and review process enabled further analyses. Transmissions were classified as nonactionable versus actionable (ie, requiring clinical follow-up because of either abnormal device functioning or a clinical patient event, such as an arrhythmia). It was assumed that 27% of transmissions would be actionable, based on a previously published time and motion evaluation [14]. Scenario analyses were performed to test the sensitivity of this parameter using additional literature-derived estimates [14,22,23]. We also estimated staff time spent on first- and second-line review of remote transmission data, considering that transmissions sometimes require escalation to more experienced staff for review and clinical decision-making. We assumed that 8.2% of transmissions would be sent for second-line review based on the aforementioned time and motion study [14]. For in-person clinic visits, 21.8% (27/124) of the visits were actionable based on study observations. Ethical Considerations As this study was a workflow process evaluation that collected no patient or clinical data and only collected staff time measurements, the study protocol did not require approval from a local ethics committee or institutional review board. This study adhered to the General Data Protection Regulation and Health Insurance Portability and Accountability Act data privacy guidelines in Europe and the United States, respectively. The included sites consented to participate in the data collection process in accordance with their privacy requirements. Participating sites were required to have more than one employee of any given type (eg, nurse, physiologist, and physician) to preserve employee privacy, with all workflow data pooled across a staff of the same type. Staff Time per Device Check for Remote and In-Person Device Follow-ups Mean cumulative staff time required to review a remote device transmission ranged from 9.4 to 13.5 minutes (16.1-21.7 minutes for actionable and 6.1-11.2 minutes for nonactionable transmissions) for therapeutic devices (pacemaker, ICD, or CRT) and 11.3 to 12.9 minutes (17.3-20.3 minutes for actionable and 8.0-11.3 minutes for nonactionable transmissions) for ICMs. https://cardio.jmir.org/2021/2/e27720 JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 3 (page number not for citation purposes) Predictors of Clinic Efficiency Prespecified subanalyses were performed to identify efficient clinical practices. Leveraging the same approach described above for modeling staff time per remote and in-person device check, the staff time per device check was modeled separately for the 3 US clinics in which vendor-neutral CIED management software (Medtronic Paceart Optima) was used during on-site observations, in comparison with 3 US clinics without management software. Similarly, the staff time per in-person visit was modeled separately for observations in which a tablet Participating clinics generally used a two-level transmission-review process. A nurse or device technician performed a preliminary review (first-line review) to determine if the transmission requires the intervention of an advanced practitioner (second-line review performed by a nurse practitioner, physician assistant, or medical doctor). The staff time for a first-line review ranged from 11.9 to 13.0 minutes in the United States and 9.63 to 11.1 minutes in Europe, depending on device type. A second-line review ranged from 7.2 to 7.9 XSL•FO RenderX Seiler et al JMIR CARDIO minutes in US clinics and 6.72 to 9.23 minutes in European clinics (Table 1). minutes in US clinics and 6.72 to 9.23 minutes in European clinics (Table 1). observations (n=165) were performed by clinical staff, including nurses, physiologists, and other advanced practitioners (Table 2). Cumulative staff time per in-person clinic visit ranged from 37.8 to 51.0 minutes and 39.9 to 45.8 minutes for therapeutic devices and ICM, respectively (Table 1). For both remote transmission review and in-person clinic visits, the overall percentage of labor performed by each staff type (nurses, technician or medical assistants, medical doctors, physician assistants, or nurse practitioners, administrative assistants, and physiologists) is characterized by country in Table 2. Furthermore, the staff performing administrative tasks differed by site and region. In the United States, 46.3% (348/751) of all administrative workflow observations were performed by medical and administrative assistants, whereas 53.7% (403/751) of administrative tasks were performed by clinical practitioners. In the United Kingdom, all administrative workflow Given that the estimated time to review an average remote transmission was dependent on the likelihood of a transmission being actionable, a series of scenario analyses were performed to test the sensitivity of this parameter. JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 4 (page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 Predictors of Clinic Efficiency On the basis of the range of available literature-derived estimates (ranging from 8% to 27%), the time to review a transmission in the United States ranged from 11.9 to 13.5 minutes for patients with pacemakers, 10.8 to 12.7 minutes for patients with ICDs, 10.8 to 11.9 minutes for patients with CRTs, and 11.7 to 12.9 minutes for patients with ICMs. In Europe, the time ranged from 7.7 to 9.4 minutes for patients with pacemakers, 9.8 to 11.6 minutes for patients with ICDs, 10.7 to 12.4 minutes for patients with CRTs, and 9.6 to 11.3 minutes for patients with ICM. Table 1. Mean cumulative staff time required per remote transmission review and in-person clinic visit. Table 1. Mean cumulative staff time required per remote transmission review and in-person clinic visit. Europe United States Workflow activity ICM CRT ICD PM ICMd CRTc ICDb PMa Remote device transmission review 11.3 12.4 11.6 9.4 12.9 11.9 12.7 13.5 Staff time per average transmissione, minutes 35.6 5.9 5.1 3.6 38.9 5.1 4.6 3.7 Number of transmissions per year (both scheduled and unscheduled transmissions)f 6.7 1.2 1.0 0.6 8.4 1.2 1.0 0.8 Annual staff time for remote transmissions per patient, hours In-person clinic visits 39.9 40.9 37.8 41.2 45.8 43.4 51.0 50.1 Staff time per visit, minutes 1.3 1.7 1.7 1.5 1.3 1.7 1.7 1.5 Number of visits per year (both routine and event-driven visits) 1.0 1.1 1.1 1.0 1.0 1.2 1.4 1.3 Annual staff time for clinic visits per patient, hours 7.7 2.4 2.0 1.6 9.3 2.4 2.4 2.1 Total annual per patient staff time, hours Type of remote device transmission Staff time required to review actionable versus nonactionable transmissions, minutes 20.3 21.7 20.6 18.3 17.3 16.1 20.1 19.8 Staff time per actionable transmission 8.0 9.0 8.3 6.1 11.3 10.3 9.9 11.2 Staff time per nonactionable transmission Distribution of staff time for first-line versus second-line review of remote transmissions, minutes 10.7 11.1 10.4 9.6 12.5 11.9 12.2 13.0 Staff time for first-line transmission review (relevant for all trans- missions) 8.0 9.2 6.7 8.0 7.8 7.2 7.9 7.8 Staff time for second-line transmission review (required for only 8.2% of transmissions) https://cardio.jmir.org/2021/2/e27720 XSL•FO RenderX XSL•FO RenderX JMIR CARDIO Table 2. Annual Staff Time for Other Patient Management Activities In-person clinic visit staff time was modeled separately for visits in which a tablet-based CIED programmer was used (n=599 total observations) compared with visits in which a legacy programmer—which is large and cumbersome—was used (n=794). A tablet-based programmer was associated with an average of 5.2 minutes lower staff time (54 vs 49 minutes; 9.6% reduction) for a clinic visit, driven by reduced time for programmer device transport to a patient room and improved data connectivity with the electronic health record. The staff time required for other patient management tasks such as calling patients, troubleshooting device connectivity issues, identifying loss to follow-up, and triaging patients or transmissions (full task list provided in Multimedia Appendix 5) was estimated to be 17.3 minutes per patient annually. At the clinic level (based on the average 5758-patient clinic size of participating clinics), this translates to 1659.2 hours of staff time per year (31.9 hours per week). Predictors of Clinic Efficiency Percentage of cardiac implantable electronic devices management workload by staff type and region.a Physiologistb, n Administrative assis- tant, n Medical doctor, physi- cian assistant, or nurse practitioner, n Technician or medi- cal assistant, n Nurse, n Staff type and region In-person clinic visits 0 2 45 29 24 United States 52 0 46 0 2 United Kingdom Remote transmission review 0 3 35 10 53 United States 100 0 0 0 0 United Kingdom Other patient management (eg, calls and connectivity troubleshooting)c 0 1 0 51 48 United States Time contribution by staff type: overall 0 2 34 20 44 United States 80 0 19 0 1 United Kingdom aLabor share was calculated in the United States and the United Kingdom due to having multiple clinics observed in each country (6 and 3, respectively). As only one clinic was observed in Germany and France, there were insufficient data to perform this analysis in these countries. bClinical cardiac physiologists in the United Kingdom carry out procedures and investigations on patients related to diagnosis, monitoring, and treatment. cThe Other Patient Management data were only collected in the United States. Table 2. Percentage of cardiac implantable electronic devices management workload by staff type and region.a aLabor share was calculated in the United States and the United Kingdom due to having multiple clinics observed in each country (6 and 3, respectively). As only one clinic was observed in Germany and France, there were insufficient data to perform this analysis in these countries. bClinical cardiac physiologists in the United Kingdom carry out procedures and investigations on patients related to diagnosis, monitoring, and treatment. cThe Other Patient Management data were only collected in the United States. aLabor share was calculated in the United States and the United Kingdom due to having multiple clinics observed in each country (6 and 3, respectively). As only one clinic was observed in Germany and France, there were insufficient data to perform this analysis in these countries. bClinical cardiac physiologists in the United Kingdom carry out procedures and investigations on patients related to diagnosis, monitoring, and treatment. cThe Other Patient Management data were only collected in the United States. Annual Staff Time Per Patient for Remote and In-Person Device Follow-ups The staff time required per remote and in-person device check was modeled separately for the 3 US clinics in which vendor-neutral CIED management software (Medtronic Paceart Optima) was used during on-site observations in comparison with the 3 US clinics without management software. On average, the total staff time to review a remote transmission was 2.1 minutes lower at sites with management software (11.5 vs 13.6 minutes). The staff time associated with an in-clinic visit was 2.2 minutes lower at clinics with management software (50.4 vs 52.6 minutes). For both remote transmission review and in-person clinic visits, the time savings were driven by the steps involved in electronic health record documentation. When extrapolated to an average clinic size of 5758 patients, the use of such software was associated with an estimated 10.1 cumulative staff hours saved during a clinic day (50.7 hours per week) based on 171 weekly clinic visits and 1335 weekly remote transmissions. Annually, this translates to 2639 hours of staff time saved, equivalent to 1.4 annual full-time equivalents. The mean number of transmissions per year per patient (including scheduled and unscheduled transmissions) ranged from 3.6 to 5.9 for therapeutic devices and 35.6 to 38.9 for ICMs (Table 1). In contrast, the number of expected in-person clinic visits per year ranged from 1.3 to 1.7 per patient. Although we seek to model time for an average clinic, the frequency of in-person and remote device checks will vary significantly between clinics depending on device programming practices, patient indications, and patient education. Multiplying the staff time for each expected remote and in-person device check by the annual frequencies of device checks per year yielded an estimated total annual staff time of 1.6 to 2.4 hours to manage a patient with a therapeutic device and 7.7 to 9.3 hours for a patient with an ICM (Table 1). The higher staff time to manage a patient with an ICM was attributed to the increased transmission volume observed. https://cardio.jmir.org/2021/2/e27720 JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 5 (page number not for citation purposes) Principal Findings Similar to most sites in this study, a two-tiered remote transmission review structure was leveraged, in which nurses (or other similar practitioners) performed the initial transmission review and escalated critical events to a physician. However, this model may not apply to all device clinics, depending on the size, RM infrastructure, and staff resources available. Our study observed a significant workload associated with fielding patient calls and troubleshooting connectivity, which is consistent with a recent study that found that more than 40% of patient calls received by CIED clinics pertain to troubleshooting RM equipment and transmission status [21]. Strategies to improve device connectivity—for instance, Bluetooth-enabled, smartphone-paired, or widespread use of other wireless monitors—could alleviate this significant workload burden on CIED clinics. Furthermore, optimizing the appropriate staffing types for each activity (eg, administrative tasks performed by administrative staff) could help clinics balance operational costs and resource availability. Although different organizational models, staff types, and workflows may exist in practice depending on the setting and available resources, the essential tasks required to manage patients with CIEDs remain similar. This evaluation sets a baseline by describing the essential activities performed by clinical staff to manage a population of patients with CIEDs and the time required to execute it. It also underscores the complexity of the current management of patients with CIEDs, identifying 54 distinct workflow tasks across three categories (remote transmission review, in-person clinic visits, and other patient management activities, such as patient phone calls and triaging). A number of studies have previously estimated the time to perform remote and in-person device checks, yielding a wide range of time estimates, suggesting that there may be significant clinic-to-clinic variability [14,31-33]. To our knowledge, this study is the first multicenter, multinational study to describe comprehensive work requirements for managing patients with CIEDs. Considering the significant time-consuming activities related to follow up patients with CIEDs, appropriate funding needs to be in place to ensure that this crucial part of the patient care pathway is not overlooked. As RM is considered a guideline-recommended standard of care for all patients with CIEDs, hospital or clinic budget holders, payers, and reimbursement authorities should financially support its implementation and day-to-day practice. Funding and reimbursement of RM are variable and remain a challenge in many geographies today, as all stakeholders involved in this continuous service provision are often not remunerated or insufficient. Principal Findings This study characterized the staffing resources necessary for cardiac device clinics to manage patients with CIEDs, including detailed time associated with each workflow step and breakdowns by device, geographic region, and staffing types. Although differences were observed across device types and geographic regions, the overall workload was found to be consistently substantial, regardless of CIED type and region. As revealed by the predictors of efficiency analysis described above, even small improvements in the efficiency of CIED clinics can have a significant positive impact on time savings. Although our study observed meaningful time savings associated with the use of patient management software and tablet-based programmers, further research is needed to identify other strategies for optimal patient follow-up. For instance, the growing number of technologies capable of transmitting patient data to CIED clinics represents a challenge for data management [25,26]. Further innovation on solutions for integrating and storing data from this multitude of sources could enhance the efficient management of patients with CIEDs. This software also presents an opportunity for closer clinical care and patient safety; previous studies using the triaging and analytic capabilities of the PaceArt Optima system showed an improved enrollment of patients in RM [27] and identification and successful interventions for patients with suboptimal ICD programming [28] and low CRT pacing [29,30]. As CIED technology advances, so do device data capabilities to inform and optimize patient care. The benefits of RM have been illustrated in several clinical studies, including faster event detection, improved patient outcomes, and reduced health care use. However, data alone will not result in clinical and economic benefits unless timely clinical action is taken. Clinical workflows must be optimized to capture the value of the device data. The HRS consensus statement on RM outlined the importance of implementing a streamlined organization with clear roles and responsibilities to manage RM data in parallel with in-person follow-ups [5]. However, there is limited literature on how patients with CIEDs are managed in practice, including the workflow steps and the staffing requirements associated with each task, creating implementation challenges for new RM users. Protocols for remote management of patients with CIEDs have been developed, including the HomeGuide registry study [24], which implemented a dedicated nurse-physician team strategy. Predictors of Clinic Efficiency A series of prespecified subanalyses were conducted to identify the predictors of clinic efficiency. JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 5 (page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 XSL•FO RenderX JMIR CARDIO Seiler et al devices) because of increased device transmissions both for routine data review and programmable automatic device alerts. However, it should be noted that the magnitude of the device transmission frequency with ICMs is highly dependent on the alert programming settings, patient indications, and patient education. The overall annual time required to follow and manage a patient with a CIED is lower for a patient with a therapeutic device (1.6-2.4 hours) than a patient with a diagnostic device (ICM: 7.7-9.3 hours). JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 6 (page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 Principal Findings Such a barrier affects RM adoption and its implementation as a standard of care. For this time and motion Mean staff time required per remote transmission review and in-person clinic visit ranged from 9.4 to 13.5 minutes and 37.8 to 51.0 minutes, respectively, depending on device type. This validates previous research demonstrating the efficiency opportunities for RM [14]. The annual time per patient required for in-person device checks was relatively consistent across device types (1.0-1.4 hours), perhaps because of the low frequency of office visits required for patients being continuously monitored with RM. The annual time per patient for RM was higher in patients with diagnostic devices (ICMs: 6.7-8.4 hours per year vs only 0.6-1.2 hours for therapeutic JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 6 (page number not for citation purposes) XSL•FO RenderX JMIR CARDIO Seiler et al different device populations and staffing resources is unknown. However, this is the first attempt at characterizing cardiac device clinic workflow in full and provides a first step in filling the knowledge gap around patient management practices and resource requirements. evaluation, countries where RM reimbursement is available were selected to avoid the influence of this lack of financial incentives on patient management organizations, which could be reflected in time measures. However, local reimbursement challenges persist, including limitations on specific cardiac devices, settings, and health care professionals in France and Germany. RM may not be suitable for every patient for different reasons (technical, clinical, or patient preference) but should be proposed to all eligible patients, in line with the medical recommendations and considering the current environment [34,35]. With the COVID-19 pandemic, RM benefits have been reinforced, also underlining the need to establish an appropriate infrastructure to manage patients remotely, which requires human, time, and financial investment. In addition, as the time and motion methodology was designed as a clinic-perspective workflow characterization and did not follow patients longitudinally, we were unable to measure patient clinical metrics, such as device connectivity success and patient adherence to follow-ups. Finally, extrapolations were made using externally published data (eg, proportion of device checks requiring second-line assessment) and HRS guidelines for patient follow-up, and these assumptions may not be generalizable to all clinics. A series of sensitivity analyses were performed to test the impact of our assumption on transmission actionability. Acknowledgments Acknowledgments The authors would like to thank each of the 11 participating clinics for permitting observation of their workflow. Data collection and analysis were funded by Medtronic. Conflicts of Interest MDB, SR, EN, DL, and MM are Medtronic employees and shareholders. Data collection for this study, performed by Deloitte, was funded by Medtronic. Multimedia Appendix 1 Workflow steps observed during the management of cardiac implantable electronic devices patients. [DOCX File , 46 KB-Multimedia Appendix 1] Multimedia Appendix 2 Modeling inputs. [DOCX File , 17 KB-Multimedia Appendix 2] Multimedia Appendix 3 Mean staff time required per instance for remote transmission review steps. [DOCX File , 38 KB-Multimedia Appendix 3] JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 7 https://cardio.jmir.org/2021/2/e27720 (page number not for citation purposes) FO erX The authors would like to thank each of the 11 participating clinics for permitting observation of their workflow. Data collection and analysis were funded by Medtronic. The authors would like to thank each of the 11 participating clinics for permitting observation of their workflow. Data collection and analysis were funded by Medtronic. Principal Findings Although device check-level and annual resource use will be dependent on individual workflow practices, individual workflow step measurements can readily be used to create a workflow framework that is highly customizable to individual centers and circumstances. Although it is widely acknowledged today that RM is a valuable tool for optimal follow-up of patients with CIEDs, to achieve this objective, infrastructure investments are required, including equipment (eg, additional computer or monitors) and setting up a specific clinic workflow organization involving sufficient human resources. As this infrastructural investment might not be an option in all settings, outsourcing remote patient management to other clinics or third-party arrhythmia review services could be an alternative to in-house implementation, as has been shown previously [36]. Conclusions This observational study confirmed the complexity of the management of patients with CIEDs. The associated workflows require significant clinical and administrative staff time across in-person clinic visits, remote transmission review, and other patient management tasks. RM is an efficient component of managing patients with CIEDs, allowing for continuous follow-up of patients with reduced staff time required per device check. Detailed recommendations on organizational models for managing patients with CIEDs are warranted to ensure homogeneous follow-up, support RM implementation, and enable optimal patient care. Limitations This study had several limitations. Owing to the real-world observational nature of this analysis, study measurements were reliant on the workflow taking place during the data collection week and were not systematically controlled for patient or center characteristics. This study describes the workflow observed at 11 centers in the United States and Europe, but the generalizability of these observations to other centers with Conflicts of Interest MDB, SR, EN, DL, and MM are Medtronic employees and shareholders. Data collection for this study, performed by Deloitte, was funded by Medtronic. Multimedia Appendix 1 Workflow steps observed during the management of cardiac implantable electronic devices patients. [DOCX File , 46 KB-Multimedia Appendix 1] JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 7 (page number not for citation purposes) Multimedia Appendix 2 Modeling inputs. Modeling inputs. [DOCX File , 17 KB-Multimedia Appendix 2] g p [DOCX File , 17 KB-Multimedia Appendix 2] Multimedia Appendix 3 Mean staff time required per instance for remote transmission review steps. [DOCX File , 38 KB-Multimedia Appendix 3] Multimedia Appendix 3 Mean staff time required per instance for remote transmission review steps. [DOCX File , 38 KB-Multimedia Appendix 3] Multimedia Appendix 3 JMIR Cardio 2021 | vol. 5 | iss. 2 | e27720 | p. 7 (page number not for citation purposes) https://cardio.jmir.org/2021/2/e27720 https://cardio.jmir.org/2021/2/e27720 XSL•FO RenderX Seiler et al JMIR CARDIO Multimedia Appendix 4 Mean staff time required per instance for in-person clinic visit steps. [DOCX File , 42 KB-Multimedia Appendix 4] Multimedia Appendix 5 Mean staff time required per instance for other patient management activities. [DOCX File , 37 KB-Multimedia Appendix 5] References 1. Mond HG, Irwin M, Ector H, Proclemer A. 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JMIR Cardio 2019 Dec 18;3(2):e9815 [FREE Full text] [doi: 10.2196/cardio.9815] [Medline: 31845898] https://cardio.jmir.org/2021/2/e27720 Abbreviations ©Amber Seiler, Eliana Biundo, Marco Di Bacco, Sarah Rosemas, Emmanuelle Nicolle, David Lanctin, Juliette Hennion, Mirko de Melis, Laura Van Heel. Originally published in JMIR Cardio (https://cardio.jmir.org), 15.10.2021. 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 Cardio, is properly cited. The complete bibliographic information, a link to the original publication on https://cardio.jmir.org, as well as this copyright and license information must be included. https://cardio.jmir.org/2021/2/e27720 XSL•FO RenderX XSL•FO RenderX
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Usability and Utility Needs of Mobile Applications for Business Management among MSEs: A Case of Myshop in Uganda
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To cite this version: Rehema Baguma, Marko Myllyluoma, Nancy Mwakaba, Bridget Nakajubi. Usability and Utility Needs of Mobile Applications for Business Management among MSEs: A Case of Myshop in Uganda. 14th International Conference on Human-Computer Interaction (INTERACT), Sep 2013, Cape Town, South Africa. pp.764-773, ￿10.1007/978-3-642-40480-1_54￿. ￿hal-01501817￿ Distributed under a Creative Commons Attribution 4.0 International License HAL Id: hal-01501817 https://inria.hal.science/hal-01501817v1 Submitted on 4 Apr 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 Usability and Utility Needs of Mobile Applications for Business Management among MSEs: A case of Myshop in Uganda Rehema Baguma1, Marko Myllyluoma2, Nancy Mwakaba2 and Bridget Nakajubi3 1 College of Computing & Information Sciences, Makerere University rbaguma@cit.mak.ac.ug 2 Nokia Research Centre Nairobi [marko.myllyluoma, ext-nancy.mwakaba]@nokia.com 3 Grameen Applab-Uganda Office bridget@applab.org 1 College of Computing & Information Sciences, Makerere University rbaguma@cit.mak.ac.ug 2 Nokia Research Centre Nairobi [marko.myllyluoma, ext-nancy.mwakaba]@nokia.com 3 Grameen Applab-Uganda Office bridget@applab.org Abstract. This paper discusses the usability needs of mobile applications for basic business management for Micro and Small Scale Enterprises (MSEs) in developing countries. This is based on results from a user study carried out in Uganda on 30 MSEs. The study was carried out on MyShop, an easy to use mobile business management application for cash transactions and book keeping designed for micro-entrepreneurs. The study investigated learning to use MyShop, the support MyShop gives to the user and its usefulness, and value addition to users. The study also covered the pleasure and stimulation MyShop gives to users. Results from the study show that MSE owners/shopkeepers would like an application that is easy to use such as have an intuitive navigation and a simple and clear language. They would also like an applica- tion that supports their unique context like multiple people operating a shop, selling goods on credit, ownership of multiple businesses, use of low end phones and regular load shedding. In terms of value addition, MSEs would like the application to assist them in managing the daily operations and developing the business in the long term such as marketing, time saving and control over business. Keywords: Usability, mobile applications, utility, MSEs, MyShop, business manage- ment. Keywords: Usability, mobile applications, utility, MSEs, MyShop, business manage- ment. 1 Introduction Micro and Small Scale Enterprises (MSEs) play important roles in the economic growth and sustainable development of every nation (Moore et al., 2008). The devel- opment and growth of MSEs can provide solutions to the problem of high unemploy- ment facing many countries especially developing countries. Maseko and Manyani (2012) noted that MSEs have low start-up costs, low risk and can exploit untapped knowledge bases of creativity in the population for new product development. Ac- cording to East African Community (EAC) (2010), MSEs are often considered a key source of productivity, growth and job creation. They promote equitable distribution of income because they are owned by relatively low income entrepreneurs, most of whom are women. MSEs are therefore important instruments for both income distri- bution and equitable participation in the process of economic development. For gov- ernments, well-managed and healthy MSEs are a source of revenue in form of taxes. Uganda has 0.8 million MSEs that contribute 20% to GDP and employ over 1.5 mil- lion people (EAC, 2010). In Uganda, MSEs are categorized according to number of employees, value of capital investments and turn over as follows: Table 1: MSE Definition used in Uganda Number of Em- ployees (Max) Capital Investments (Max in UGX) Revenue (Max in UGX) Micro 4 12m (USD 4800) 12m (USD 4800) Small 50 360m (USD 144000) 360m (USD 4800) From EAC (2010) As mobile phones are multiplying in the developing world, many social economic services and applications are being innovated by Mobile Network Operators (MNOs), not for profit and for profit organizations. Hellstrom (2010) noted that in a region where the vast majority have limited resources among other constraints, mobile phone solutions provide a means of extending a number of services to the poor who are in rural and remote areas. However, Corbett (2008) remarked that as sales, access, and coverage continue to grow, it is yet to be seen whether the mobile phone technology will play a significant, sustained role in alleviating poverty in the developing world. In most developing countries such as Uganda, while operators’ focus has been people with a high disposable income and revenue generating services like urban youth and entertainment, services and development oriented applications have not been priori- tised. Therefore the number of relevant applications for economic and social devel- opment is still limited. 1 Introduction p On the other hand, efforts to develop mobile applications for banking and manag- ing business internationally have been focused on applications for high end phones such as iPhone (e.g. Mint and Splash Money), Android (Xero) and ipad (quickbooks mobile). These sophiscated mobile applications are out of reach for MSEs in develop- ing countries due to their high cost, hi-tech nature (most MSE owners are computer illiterate), energy efficiency (battery consumption) and data dependency (online con- nection). As a result there is need for applications that can run on low end phones that most MSEs in developing countries use. In addition, most available applications are mainly about personal financial activities such as banking than managing business activities of a business. For example iPhones’s Ledger Docs is used for digital captur- ing of ledger receipts. Mint, another iPhone application, updates account balances, transmits real-time alerts to the phone for low account balances, over-budget, and tracks strange buying and selling activity. Android’s Xero keeps the user updated about business finances and cashflow, creates real time reports as well as integrated invoicing for precision management. To-date, most research on MSEs and mobile phone usage has been focused on the communication function of the phone and mobile commerce. Examples of such in- clude; Kwaka (2012) who reports about mobile phone usage by MSEs in semi-rural Ghana; Melchioly and Aebø (2010) reports about added value concerning economic growth and entrepreneurship to SMEs in terms of communication with suppliers and customers, market solicitation, social cohesion and operational cost reduction; Es- selaar et al (2008) reports on ICT usage and its impact on profitability of SMEs in 13 African Countries. Others are Escobari and Donner (2009), Matambalya and Sussana (2012), Dorflinger et al (2009), Edim and Muyingi (2010) and Giridher et al (2009). selaar et al (2008) reports on ICT usage and its impact on profitability of SMEs in 13 African Countries. Others are Escobari and Donner (2009), Matambalya and Sussana (2012), Dorflinger et al (2009), Edim and Muyingi (2010) and Giridher et al (2009). Hence little so far has been done about using mobile phones for business manage- ment. Palsey (2011) reports about a mobile book keeping application developed as part of her Honours studies to enable MSEs keep records of their business transac- tions and automatically generate financial reports. However, the application in ques- tion is not available in the public domain. 1 Introduction Therefore it is not clear whether it went beyond the university laboratory to be used by the target users. Business management for MSEs like other business types is important for plan- ning, budgeting and forecasting, taxation, access to finance among other functions. EAC (2010) noted that the quality of information that a firm produces and maintains determines its access to finance. However, EAC (2010) found out that majority of Micro and Small Scale Enterprises do not keep proper records due to lack of appro- priate skills. Therefore efforts to provide simple business management tools tailored to the needs and characteristics of MSEs are greatly needed. This paper discusses attributes for an easy to use and beneficial (utility) mobile ap- plication for business management among MSEs in developing countries. This is based on results of a user study carried out in Uganda on MyShop. MyShop is mobile business application for cash transactions and book keeping designed for micro- entrepreneurs. The study covered ease of use and utility evaluation of MyShop. It investigated learning to use MyShop and the phone (Nokia c3-01), support MyShop gives to the user, the pleasure and stimulation MyShop gives to users and the useful- ness, and value addition of MyShop to users. y Nielsen (2012) refers to usability as a quality attribute that assesses how easy the user interfaces are to use. According to Schumacher and Lowry (2010), usability is the effectiveness, efficiency and satisfaction with which specified users can achieve specified goals in a particular environment. Utility on the other hand refers to the design's functionality i.e. whether a product or service does what users need (Nielsen, 2012). Ease of use and utility are equally important and together determine whether something is useful. Nielsen (2012) noted that it matters little that something is easy to use if it is not what you want and it is also no good if the system can hypothetically do what you want, but you cannot make it happen because the user interface is too difficult. Therefore the attributes discussed in this work are concerned with ease of use and utility needs of mobile applications for business management among MSEs. In particular, this is discussed in the perspective of the MyShop application. 2 Methodology The ease of use and utility evaluation of MyShop was carried out on a sample of 30 MSEs dealing in products and services in and around Kampala city, Uganda. The study was conducted between November 2011 to March 2012. The study areas in- cluded one urban location and three peri-urban areas namely: Kampala city centre, Kawempe trading centre, Kyaliwajjala trading centre and Natete trading centre. The rationale for selecting one urban location versus 3 peri-urban ones was because most MSEs in Uganda operate in peri-urban and rural areas. g p p The 30 participants were chosen purposively based on the following attributes: p p p p y g ability to read and write in English. The minimum requirement was completion of Ordinary Level (Middle School) but completion of Advanced Level (High School) was preferred. This attribute was important because the application was in English. The second requirement was ability to use Short Message Service (SMS) or mobile money service. This gave an indication of experience with data applications. In addi- tion, some individual user characteristics were preferred in order to be sure that the participant would perform and fulfill all expected tasks. These included: able to at- tend trainings, willingness to use the application in day to day business, willingness to commit at least 1 hour daily to update information and commitment to meet data col- lection requirements. Other desired attributes included: located 10 - 15 kms from central Kampala, small scale dealing in products and services, 1+ years of operation; 10+ transactions/day, owner operated or employing not more than 5 people and be- tween 200 and 2000 USD start up capital. p p Three weeks to the beginning of the study, participants were trained (half day) in using the application and phone. After the training, they were given phones loaded with the application to use for three weeks before beginning of interviews. In addi- tion, they were given a user guide covering using the main menu and application set- tings, and a summary of how each of the application’s functions work. The study was conducted through weekly field visits to the study sites during which, the study team observed how participants were using the application in their cash and book keeping activities. In addition, 3 questionnaires on ease of use, reliability and enjoyment, and utility were administered to participants to elicit quantitative and more detailed qualitative data. 2 Methodology There was no requirement for approval from an Institu- tional Review Board before running the study. 3.1 About MSEs that Participated The study covered one urban area and three peri-urban areas around Kampala city. The study population was 30 MSEs dealing in products and services. Of the 30 partic- ipants, 53% were male and 47% female. Fifty percent had a degree or diploma, 33% had completed Advanced Level (High School) while 17% had completed Ordinary Level (Middle School). All the participants could read and write in English and could use SMS or mobile money. The business premises were located 10-15 KMs from central Kampala and 83% had been in operation for 1+ years. All participating busi- nesses had 10 + transactions/day, were owner operated or employing not more than 5 people and 59% of the businesses were worth 10 million Uganda Shillings and above (approximately $4,200 USD). In the findings discussed below, the names given are not actual names of participants for purposes of protecting the identity and businesses of participants. 3.1 Usability and Utility Needs of Mobile Applications for Business Management among MSEs: A case of Myshop in Uganda This section discusses ease of use and utility needs of mobile applications for business management among MSEs in developing countries. This is based on results from a user evaluation study of MyShop. MyShop was developed by Nokia and has four main functionalities: selling stock (called “Sell”), recording sales and expenses (called “Records”), purchases and inventory management (called “Stock”), and monitoring of business performance over time (called “Reports”). It is available for free in Nokia’s online store on http://store.ovi.com/content/249179. p The needs discussed are categorized into: ease of use, support to the user, usefulness and value addition to MSE owners/shopkeepers and the pleasure, and stimulation to the user. According to the Webster online dictionary, ease of use is the property of a product or thing that a user can operate without having to overcome a steep learning curve. High ease of use makes products or systems intuitive to use to the average user. In the context of computer/mobile applications, ease of use simply means an applica- tion that is effortless to understand, find what is needed and do what one wants to do. In addition, the user’s context such as characteristics of the environment, language preference, cultural or community practices, unique business characteristics, etc., need to be understood and supported for better usability. These attributes are catego- rized as support to the user in this work. 3.1 About MSEs that Participated Further more, for a product, service or sys- tem to be useful, it should be both easy to use and of value to the users (Nielsen, 2012). Hence value attributes are also important and are classified as value to the users in this work. Besides ease of use, supporting users’ context and being of value, a product, service or system should be pleasing and motivating to users to succeed. 3.1.1 Ease of Use This subsection discusses attributes that can make mobile applications for business management effortless to use for MSE owners/shopkeepers. These include: Using the application as transactions happen: MSE owners/shopkeepers prefer to use the application as transactions happen. In the MyShop usability evaluation study, 80% of the shopkeepers interviewed preferred to use the application as transactions happen. They noted that this helps them avoid forgetting details of transactions per- formed as Mariam, a shopkeeper from Kyaliwajjala trading centre remarked: “I use it as I transact my business throughout the day because I need to ensure that all records have been entered”. In line with this need, developers of mobile applications for business management among MSEs need to focus on making it easier and faster to record transactions because efficiency is very important to shopkeepers. Auto computation of tasks such as profits and losses: MSE owners like the auto computation of tasks by computer/mobile applications. This is much easier and less error prone compared to manual computations on paper. Jolly a shopkeeper in Kawempe trading centre equipped: “auto calculation of sales, profits and losses makes my life easy”. Intuitive navigation: MSE owners want a well organized interface that they can easily navigate and find functions needed. Participants in the MyShop study found it easy to use the simple navigation structure of MyShop (4 items at the first level and 3- 6 items inside each of the screens on the second level). Betty a saloon operator in Kawempe trading centre said: “I like the fact that it is easy to navigate through the application and know where to find what function when I need it”. 6 items inside each of the screens on the second level). Betty a saloon operator in Kawempe trading centre said: “I like the fact that it is easy to navigate through the application and know where to find what function when I need it”. Simple and clear language: MSE owners/shopkeepers would like mobile applica- tions written in simple and clear business management language. This is preferred because most of them have low levels of education and do not have formal training in book keeping. In the MyShop study, 68% strongly agreed that the language used in MyShop is clear and simple which made the application easy to use. 3.1.1 Ease of Use Violet, a drug shop attendant in Kawempe trading centre noted: “the application uses simple busi- ness language and the English is clear”. g g g Representative icons: Using icons that are a clear representation of intended function makes such applications easy to use for MSEs. In the MyShop study, most partici- pants found the icons used meaningful in relation to the intended function. Jumba, an operator of a crafts shop in Kyaliwajjala trading centre said: “the icons explain well what function they represent e.g. using a symbol of money notes to mean sell clearly shows that whatever is under that function is money coming in”. A key thing about the understandability of the icons is that they are not global abstract metaphors but tangible everyday items. For example, instead of a shopping cart, there is a basket and for stock, the initial metaphor of a delivery truck, was replaced with a pile of boxes. Easy to learn: MSEs find applications that are easy to learn easy to use. In the MyShop research study, 24% strongly agreed and 48% agreed that learning MyShop was easy which made use of the application easy. This was attributed to the ease of finding functions, simple and clear language, representative icons and an easy to op- erate phone. 3.1.2 Support to the User This subsection discusses usability attributes that address contextual needs of MSEs from mobile applications for business management. These include; Multiple user accounts: Some MSE owners have employees hence it is important for the mobile application to support multiple user accounts with varying privileges. This will enable shop owners/managers to restrict access to information on certain aspects such as reports. In the MyShop study, 80% of the participants preferred using the application alone (which meant running a parallel manual system) because the version used did not support multiple user accounts. Portability: MSEs prefer the mobile application to a computer application due to its portability. This helps them carry out offsite business management activities like re- stocking more easily. In the MyShop study, 35% strongly agreed and 57% agreed that they enjoy using MyShop in business partly due to its portability. Agnes, a grocery shop attendant in Kampala city centre noted: “I go with it when shopping for new stock and I use it to remind me about restocking needs”. Easy to operate phone: The phone(s) on which the application works must be easy to operate. In the MyShop study, 28% strongly agreed and 40% agreed that the phone on which MyShop was loaded, was easy to use. This was attributed to the semi-touch screen phone (small touch screen and large physical keys) and participants’ previous experience with other Nokia models. Isaac, a video library operator in Kawempe trad- ing centre noted that: “It is very easy to find functions with the touch screen”. This finding is not isolated because White (2010) noted that less educated and less tech- nology savy mobile phone users find touch screens easier to use because they directly manipulate interface objects rather than using third party interaction aids like a mouse and keyboard. y Short introduction to bookkeeping: EAC (2010) in a study about MSEs in E. Afri- can countries found that majority of micro and small enterprises do not keep proper records due to lack of appropriate skills. In the MyShop study, the “Reports” module was used less because most participants confused the “Records” module to offer simi- lar functions to “Reports” and or did not understand how it works. 3.1.2 Support to the User For example Chris- tine, a beverages shop operator in Kyaliwajjala trading centre said: “I really did not understand how the reports function works and since I can assess the business per- formance with records then I do not need to use reports”. The user manual in the version of MyShop used did not cover book keeping. Including an introduction to book keeping in the help module, can benefit those new to book keeping concepts. Provide cloud or local backup storage: To prevent against data loss in case of loss of the phone or a problem with the hardware or software, it is important to provide for data back up locally or in the cloud. The MyShop version that was used in the study did not have this provision. p Device independence: It is important to make such applications compatible with low end phones so that users are not limited on device choice. In the study, the Nokia c3- 01 used had a short battery life (which was a problem to participants due to regular load shedding). In addition, Nokia c3-01 costs approximately USD 200 hence is ex- pensive for most MSE owners but the current version of MyShop runs on lower end Nokia devices that cost as low as USD 50. Provide for selling services: The MSE sector has both product and service business- es with varying operational procedures. Therefore it is important for such applications to provide for both. One way is to have a product and service version with services offered and details of offering in the place of stock. The MyShop version used was only applicable to MSEs dealing in physical products such as retail shops. Therefore it was a challenge using it on businesses dealing in services like video libraries. g g g Provide for credit transactions: Selling on credit is a common practice especially for retail shops in Uganda and other African countries. The MyShop version used in the study did not have this provision and participants expressed a need for it. Betty, a cosmetics shop operator in Kawempe trading centre said: “It is very difficult to keep track of items sold on credit, yet we sometimes offer goods to on credit”. f y ff g Local language version: Most MSE owners are not comfortable with English due to low levels of education. 3.1.2 Support to the User UNESCO (2007) reported that one of the challenges of deliv- ering mobile phone based services is that 41% of the population in developing coun- tries is non-literate and even the literate among the poor are typically novice users of computer technologies. Due to this limitation, the study purposively selected partici- pants whose level of education ranged from Ordinary Level (Middle School) and above. Therefore for this application to succeed in the market like Uganda there is need for it to have a version in a language. In the study, participants requested for a version in Luganda, the most dominant local language in Uganda. Use one install for two or more businesses: Multiple business ownership is common among business people in Uganda and Africa. Ronald, a video library operator in Natete trading centre said: “I have a video library and a phone accessories shop hence I would prefer being able to use one copy of MyShop for both businesses”. Therefore it is important to make it possible for one install to be used for two or more businesses for example through a multi business edition. p g Link application to mobile money: Like other business people, MSEs make a lot of financial transactions such as paying suppliers, utilities, employees, receiving pay- ments from customers, etc. However, the banking infrastructure in Uganda like other developing countries is still severely limited and very few people can meet require- ments of banking institutions (FinScope, 2007). Participants in the study revealed that some of the payments they make in their businesses such as paying suppliers, rent, and receiving payment from some customers are settled using mobile money. There- fore such a function would make the application more useful and relevant for MSEs. 3.1.3 This subsection discusses attributes that address relevancy and value addition attrib- utes MSEs desire from mobile applications for business management. Marketing function: MSEs would like an application that can on top of basic book keeping, perform related functions such as marketing. This can be achieved through mass dissemination of marketing information via Short Message Service (SMS) or multimedia messaging. During the study, some participants used the phone camera to take pictures of their stock for marketing to potential customers. Moses, an operator of an arts and crafts shop in Kyaliwajjala trading centre noted: “I take pictures of current stock and sold out items to show to potential customers”. Reduction of workload: MSEs would like an application that reduces their work load thereby making work easier. 60% of the study participants agreed that using MyShop had made work easier in their business such as in stock taking and tracking profits and losses. Deborah, a supermarket operator in Kyaliwajjala remarked: “I track the stock automatically within the application which less tiresome”. y pp Time saving: MSEs desire applications that help them save time in the management of their businesses creating more efficiency. In the study, over 60% agreed that MyShop saves time in business management because of automated functions. Joshua an airtime supplier from city centre remarked that: “MyShop has promoted efficiency in business information recording/book keeping”. f g p g Safe keeping of business information: MSEs would like an application that keeps their business information safe and secure. Katende, a shopkeeper in Kawempe trad- ing centre remarked: “My business is individual therefore I like it that MyShop keeps my business information away from third parties”. Therefore it is important for such applications to restrict access to some information like reports. Control over business: MSEs would like the mobile application to help them better control their business such as keeping track when away and easy assessment of per- formance. Jackson, a mobile video and disco operator in Natete trading centre noted: “the business’ performance is easily assessed since everything is automated“. This can be further enhanced by making the app an online service that syncs across multi- ple shopkeepers so that the business owner can monitor while away. 3.1.4 Pleasure and Stimulation to the User This subsection discusses attributes that will make mobile applications for business management pleasing and motivating to use for MSE owners/shopkeepers. g p g g p p Exciting experience: MSE would be attracted to an application that gives them an exciting experience. This can be achieved through adaptation of the application to their business needs. In the MyShop usability study, 17% had an extremely exciting experience while 62% had an exciting experience. This was attributed to relevancy of MyShop and the semi-touch screen phone which most of them were using for the first time. Miriam a shopkeeper in Kyaliwajjala trading centre said: “MyShop helps me make business decisions based on facts e.g. every day, I look at MyShop to find out what needs restocking before I restock”. g f Enjoy using the application: MSEs would like an application that they enjoy using. To achieve this, the application must be relevant to their needs and context. In the MyShop study, 35% strongly agreed and 57% agreed that they enjoy using MyShop in business due to its portability and auto computation of tasks. Doris, a mini super- market operator in Kyaliwajjala said: “I go with it when shopping for new stock and I use it to remind me about restocking needs”. Conclusion The potential value of Mobile applications for business management among MSEs is enormous but for this to be realized such applications must be usable and have high utility to the target MSEs. For MSEs in developing countries such as Uganda, such applications must be effortless to use, relevant to the needs and context of MSEs add value to their businesses and be pleasurable and stimulating to use. Future efforts on such applications should focus on usability and utility for the target market segments. References 1. Donner, J. & Escobari, M. (no date). A review of the research on mobile use by micro and small enterprises (MSEs) ICTD 2009, Qatar, 17-19 April. p p 2. Dorflinger, J. et al (2009). Mobile Commerce in Rural South Africa-Proof of Concept of Mobile Solutions for the Next Billion Mobile Consumers. Proc. WOWMOM’09. \ 3. Dim, A. E. & Muyingi, H., N., A. (2010). Mobile Commerce Application for Rural Economy Development: A case study for Dwesa. Proc. SAICSIT’10. ACM Press (2010). 4. Esselaar, S., Stork, C., Ndiwalana, A. & Een-Swarray, M. (2008). ICT Usage and Its Im- pact on Profitability of SMEs in 13 African Countries. 5. Faris, S. (2012). Bookkeeping Made Easy…And Mobile With The Help Of Some Great New Apps. Retrieved on 13th June 2012 from http://www.smallbiztechnology.com/archive/2012/03/bookkeeping-made-easy-and- mobile-with-the-help-of-some-great-new-apps.html/ p g pp 6. Gilbert, C. (2012). Usability Evaluation. In: Soegaard, Mads and Dam, Rikke Friis (eds.). "Encyclopedia of Human-Computer Interaction". Aarhus, Denmark: The Interac- tion Design Foundation. Available online at http://www.interaction- design.org/encyclopedia/usability_evaluation.html 7. Giridher, T. et al. (2009). Mobile Applications for Informal Economies. Proc.IMCSIT'09. IEEE (2009). 7. Giridher, T. et al. (2009). Mobile Applications for Informal Economies. Proc.IMCSIT'09. IEEE (2009). 8. Hellström, J. (2010). The Innovative Use of Mobile Applications in East Africa, Sida Review 2010:12, published by Edita 2010. 9. Kwakwa, A. P. (2012). Mobile Phone Usage by Micro and Small Scale Enterprises in Semi-Rural Ghana, International Review of Management and Marketing Journal, Vol. 2, No.3, 2012. 10. Melchioly, R. S. & Sæbø, Ø. (2010). ICTs and Development: Nature of Mobile Phones usage for SMEs Economic Development - An Exploratory Study in Morogoro, Tanzania. IFIP, Technical Commission 9 – Relationship between Computers and Society. Work- shop at Makerere University, Uganda. 22-23 March 201. 11. Maseko, N. & Manyani, O. (2012). Accounting practices of SMEs in Zimbabwe: An in- vestigative study of record keeping for performance measurement (A case study of Bin- dura). Journal of Accounting and Taxation Vol. 3(8), pp. 171-181, Dec. 2011. 12. Moore et al. (2008). Managing small business: An entrepreneurial emphasis, 14th ed. 13. Nielsen, J. (2012). Usability 101: Introduction to Usability retrieved on 1st October 2012 from: http://www.useit.com/alertbox/20030825.html 14. Schumacher, R. M. & Lowry, S. Z. (2010).NIST Guide to the Processes Approach for Improving the Usability of Electronic Health Records, National Institute of Standards and Technology. 15. SMEs get productivity from mobile applications. Retrieved on 25th September from: http://www.computerweekly.com/news/2240088236/SMEs-get-productivity-from- mobile-applications. 16. References The East African Community (EAC), (2010). Study on the Promotion of Micro, Small and Medium Enterprises (MSMEs) in the East African Region, consolidated report by Ernst and Young. Retrieved on 30th June from: www.ugandainvest.go.ug. 17. UNESCO (2007). UNESCO Institute of Statistics Data Centre, regional literacy rates. Retrieved on 12th June 2012 from http://stats.uis.unesco.org/unesco/TableViewer/tableView.aspx?ReportId=y201. http://stats.uis.unesco.org/unesco/TableViewer/tableView.aspx?ReportId=y201. 18. Wamuyu, E.& Maharaj (2011). Usage of mobile technologies in Kenya, The African Journal of Information Systems. 19. Webster Online Dictionary. Retrieved on 2nd October 2012 from: http://www.websters- online-dictionary.org. 20. White, G. (2010). Designing Mobile services for the Non-literate communities. In the Proceedings of the 2nd International Conference on M4D 2010, Kampala, Uganda. 21. Xero Accounting Software. Retrieved on 20th September from; http://www.getapp.com/xero-application Acknowledgements We extend our sincere thanks to Nokia that allowed us to use results from an original- ly non-academic usability evaluation study on MyShop in Uganda. We also extend thanks to Grammeen Applab-Uganda Office in particular Sean Paavo Krepp, the Country Director and Annete Bogere, the Content and Services Manager. Grammen- Applab coordinated the study in Uganda as a local partner on behalf of Nokia. Our since thanks also go to Gabriel White who worked as a User Experience Consultant and Richard Nuwagaba, and Andrew Gagwera who worked as Research Assistants on the study.
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Retraction Note to: MiR-143-3p functions as a tumor suppressor by regulating cell proliferation, invasion and epithelial–mesenchymal transition by targeting QKI-5 in esophageal squamous cell carcinoma
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He et al. Molecular Cancer (2022) 21:170 https://doi.org/10.1186/s12943-022-01639-0 Open Access Publisher’s Note Publisher’s Note Retraction note to: Mol Cancer 15, 51 (2016) https://doi.org/10.1186/s12943-016-0533-3 Retraction note to: Mol Cancer 15, 51 (2016) https://doi.org/10.1186/s12943-016-0533-3 Publisher s Note Springer Nature remains neutral with regard to jurisdictional claims in pub- lished maps and institutional affiliations. The Editor in Chief has retracted this article because of significant concerns regarding a number of Figures presented in this work, which question the integrity of the data. The Editor-in-Chief therefore no longer has confidence in the integrity of the data in this article. All authors agree to this retraction. Retraction Note to: MiR‑143‑3p functions as a tumor suppressor by regulating cell proliferation, invasion and epithelial– mesenchymal transition by targeting QKI‑5 in esophageal squamous cell carcinoma Zhenyue He1†, Jun Yi2†, Xiaolong Liu2†, Jing Chen1, Siqi Han1, Li Jin1, Longbang Chen1* and The original article can be found online at https://​doi.​org/​10.​1186/​s12943-​ 016-​0533-3 †Zhenyue He, Jun Yi and Xiaolong Liu contributed equally to this work. *Correspondence: chenlongbang@yeah.net; songhaizhu@163.com 1 Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, 305 Zhongshan East Road, Nanjing, Jiangsu 210002, People’s Republic of China Full list of author information is available at the end of the article The original article can be found online at https://​doi.​org/​10.​1186/​s12943-​ 016-​0533-3 †Zhenyue He, Jun Yi and Xiaolong Liu contributed equally to this work. †Zhenyue He, Jun Yi and Xiaolong Liu contributed equally to this work. *Correspondence: chenlongbang@yeah.net; songhaizhu@163.com *Correspondence: chenlongbang@yeah.net; songhaizhu@163.com 1 Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, 305 Zhongshan East Road, Nanjing, Jiangsu 210002, People’s Republic of China Full list of author information is available at the end of the article © The Author(s) 2022. 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 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. Author details 1D f 1 Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, 305 Zhongshan East Road, Nanjing, Jiangsu 210002, People’s Republic of China. 2 Department of Cardiothoracic Surgery, Jinling Hospital, Medical School of Nanjing University, 305 Zhongshan East Road, Nanjing, Jiangsu 210002, People’s Republic of China. © The Author(s) 2022. 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 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.
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On the double-deck transportation of large-tonnage containers: start of work, suspension of the program, measures for its prolongation
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О двухъярусной перевозке крупнотоннажных контейнеров: начало работ, приостановка программы, мероприятия по ее пролонгации Ю. М. Лазаренко, Д. Н. Аршинцев, В. В. Семерханов, Е. А. Митина, Е. В. Капускина Акционерное общество «Научно-исследовательский институт железнодорожного транспорта» (АО «ВНИИЖТ»), Москва, 129626, Россия ных контейнерных перевозок активизировали в нача- ле 2000-х гг. освоение такого способа перевозок и на железных дорогах России. ных контейнерных перевозок активизировали в нача- ле 2000-х гг. освоение такого способа перевозок и на железных дорогах России. Аннотация. В начале XXI в. с целью повышения конкурен- тоспособности контейнерных перевозок на железных дорогах России были проведены комплексные исследования по воз- можности перевозки крупнотоннажных контейнеров, погру- женных в два яруса. В отличие от мирового опыта в освоении такого способа перевозок, где они осуществляются на линиях с тепловозной тягой, возможность перевозки контейнеров, по- груженных в два яруса, на электрифицированных отечествен- ных магистралях определяется наличием контактного прово- да, что создает дополнительное ограничение для увеличения высоты груза. р Условия перевозок на российских железных до- рогах существенно отличаются от действующих в указанных странах. Протяженность электрифици- рованных линий составляет более 50 % общей экс- плуатационной длины. Из-за наличия контактного провода имеется дополнительное ограничение для двухъярусной перевозки по высоте груза [1, 2, 3, 4, 5]. Тем не менее в 2001 г. ВНИИЖТ было поручено провести комплексные исследования по созданию спе- циализированной платформы для перевозки крупно- тоннажных контейнеров с погрузкой в два яруса. В ре- зультате этих исследований учеными и специалистами института были разработаны технические требования к платформе, а в 2003 г. на Брянском машиностроитель- ном заводе (ОАО «БМЗ-вагон») впервые в отечествен- ной практике был создан опытный образец специали- зированной колодцевой платформы (модель 13-3124) на типовых грузовых тележках модели 18-100 для двухъ­ ярусной перевозки крупнотоннажных контейнеров. Условия перевозок на российских железных до- рогах существенно отличаются от действующих в указанных странах. Протяженность электрифици- рованных линий составляет более 50 % общей экс- плуатационной длины. Из-за наличия контактного провода имеется дополнительное ограничение для двухъярусной перевозки по высоте груза [1, 2, 3, 4, 5]. В статье рассматриваются результаты многолетних ком- плексных исследований по созданию специализированной колодцевой платформы и разработке технологии перевозки в ней крупнотоннажных контейнеров с погрузкой в два яруса, выполненных ВНИИЖТ в начале 2000-х гг. Представлены осо- бенности конструкции колодцевой платформы, схемы раз- мещения в ней контейнеров, виды проведенных испытаний и данные об опытной перевозке платформы, груженной кон- тейнерами в два яруса. Приведены сведения о приостановке работ по внедрению двухъярусной перевозки контейнеров и предложены мероприятия, которые необходимо выполнить в случае возобновления работ по внедрению на сети российских железных дорог такого способа перевозок. Тем не менее в 2001 г. ВНИИЖТ было поручено провести комплексные исследования по созданию спе- циализированной платформы для перевозки крупно- тоннажных контейнеров с погрузкой в два яруса. E-mail: lazarenko_um@list.ru (Ю. М. Лазаренко) © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2 224 Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 224 О двухъярусной перевозке крупнотоннажных контейнеров: начало работ, приостановка программы, мероприятия по ее пролонгации Ю. М. Лазаренко, Д. Н. Аршинцев, В. В. Семерханов, Е. А. Митина, Е. В. Капускина Акционерное общество «Научно-исследовательский институт железнодорожного транспорта» (АО «ВНИИЖТ»), Москва, 129626, Россия 224 – 229 Параметры контейнеров Тип контейнеров 1АА 1А 1СС 1С 1ААА Длина, фут мм 40 12 192 40 12 192 20 6058 20 6058 40 12 192 Высота, мм 2591 2438 2591 2438 2896 Ширина, мм 2438 2438 2438 2438 2438 Масса брутто, т 30,48 30,48 24,0 24,0 30,48 Высота двух ярусов, мм 5182 4876 5182 4876 5792 Т а б л и ц а 1 Размерно-весовые параметры контейнеров T a b l e 1 Dimensions and weight parameters of containers • грузоподъемность при применении тележки модели 18-100 — 67 т; О двухъярусной перевозке крупнотоннажных контейнеров: начало работ, приостановка программы, мероприятия по ее пролонгации Ю. М. Лазаренко, Д. Н. Аршинцев, В. В. Семерханов, Е. А. Митина, Е. В. Капускина Акционерное общество «Научно-исследовательский институт железнодорожного транспорта» (АО «ВНИИЖТ»), Москва, 129626, Россия В ре- зультате этих исследований учеными и специалистами института были разработаны технические требования к платформе, а в 2003 г. на Брянском машиностроитель- ном заводе (ОАО «БМЗ-вагон») впервые в отечествен- ной практике был создан опытный образец специали- зированной колодцевой платформы (модель 13-3124) на типовых грузовых тележках модели 18-100 для двухъ­ ярусной перевозки крупнотоннажных контейнеров. Проведенные учеными и специалистами ВНИИЖТ исследо- вания по внедрению перевозок крупнотоннажных контейнеров типа 1АА, 1А, 1СС и 1С с погрузкой в два яруса на колодцевой платформе показали высокую эффективность разработанной технологии перевозки. Она по-прежнему сохраняет свою ак- туальность и может быть внедрена в настоящее время. Пере- численные в статье мероприятия, подлежащие реализации для возобновления работ по внедрению данной технологии, пред- лагается включить в программу внедрения такого вида пере- возок. При выполнении указанных работ учитывались размерно-весовые параметры контейнеров четырех типов (табл. 1). Типаж крупнотоннажных контейнеров: Типаж крупнотоннажных контейнеров: 40-футовые (длина 12 192 мм) — 1АА, 1А; 20-футовые (длина 6058 мм) — 1СС, 1С. Ключевые слова: крупнотоннажный контейнер; колод- цевая платформа; двухъярусная перевозка; габариты погрузки; технология перевозки Характеристики колодцевой платформы модели 13-3124 для двухъярусной перевозки крупнотоннажных контейнеров. Платформа конструируется без хребто- вой балки. Рама вагона формируется из продольных боковых балок, которые образуют в межтележечном пространстве колодец для размещения контейнера. Продольные балки изготавливаются из двух профи- лей: двутавра со срезами в консольных частях и при- варенного к нему Z-образного профиля (рис. 1, 2). На нижние полки Z-образного профиля укладываются листы пола, стягивающие балки. О О пыт применения двухъярусной перевозки крупно- тоннажных контейнеров за рубежом, основания для начала работ. Положительный опыт зарубежных железных дорог США, Канады, Китая, Австралии, Индии и других стран по перевозке крупнотоннажных контейнеров, погруженных в два яруса, на линиях с тепловозной тягой, а также возросшая актуальность повышения конкурентоспособности железнодорож- Платформа модели 13-3124 имеет следующие основные параметры: © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 224 следовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. • грузоподъемность при применении тележки модели 18-100 — 67 т; Размерно-весовые параметры контейнеров ; • масса тары — 27,6 т; • грузоподъемность при применении новых пер- спективных тележек с нагрузкой на ось 25 т — 72 т; • нагрузка на ось — 23,5 т на тележках модели 18-100; • погонная нагрузка — 4,65 кН/м для тележек мо- дели 18-100, 4,95 кН/м — для новых тележек. На колодцевую платформу в два яруса может быть погружено: На колодцевую платформу в два яруса может быть погружено: • четыре 20-футовых контейнера типа 1С (высота 2438 мм) или 1СС (высота 2591 мм), имеющих загруз- ку до 17 т каждый (среднесетевая загрузка — 14 – 15 т) (рис. 3); Примечание. Контейнеры типа 1ААА были исключены из подготовки к двухъярусной перевозке, так как они использовались только в транзитных перевозках и возможность их перевозки в два яруса потребовала бы подъема контактной сети на высоту не менее 6400 мм, что сопряжено с ростом рас- ходов на реконструкцию устройств подвески контактной сети и сделало бы двухъярусную перевозку экономически нецелесообразной. • два 40-футовых контейнера типа 1А (высота 2438 мм) или 1АА (высота 2591 мм), имеющих полную загрузку и массу брутто каждого 30,48 т (рис. 4). Параллельно с разработкой конструкции и изготов- лением опытного образца колодцевой платформы была проработана конструкция межъярусного крепления кон- тейнеров. Все известные способы крепления для контей- неров первого и второго ярусов были неприемлемы. Рис. 1. Колодцевая часть платформы: 1 — двутавровый профиль; 2 — Z-образный профиль; 3 — ме- таллическая стенка колодца; 4 — направляющий металлический элемент; УГР — уровень головки рельса; пунктирная линия — внешний контур контейнера Fig. 1. Well part of the platform: 1 — I-profile; 2 — Z-shaped profile; 3 — metal plate of the well; 4 — guiding metal element; УГР — rail head level; dashed line — outer contour of the container 280 17 1071 310 130 10 20 791 1 2 3 4 13,5 10 50 2438 12 13 1325 УГР 224 УГР 254 УГР 280 17 1071 310 130 10 20 791 1 2 3 4 13,5 10 50 2438 12 13 1325 УГР 224 УГР 254 УГР 280 17 1071 310 130 10 20 791 1 2 3 4 13,5 10 50 2438 12 13 1325 УГР 224 УГР 254 УГР Номинальное габаритное пространство инфра- структуры характеризуется следующими нормативами: • габарит приближения строений С (ГОСТ 9238–83 «Габариты приближения строений и подвижного со- става железных дорог колеи 1520 (1524) мм»); 791 • высота подвески контактного провода — 5750 мм. • грузоподъемность при применении тележки модели 18-100 — 67 т; Основные варианты размещения контейнеров в два яруса. Основные варианты размещения контейнеров в два яруса. Первый вариант — размещение в пределах высоты, допускаемой габаритом погрузки (5300 мм). Первый ярус: высота строго 2438 мм: один контей- нер типа 1А или два типа 1С . Второй ярус: а) высота 2438 мм — один контейнер типа 1А, при высоте 2591 мм — один контейнер типа 1АА; б) высота 2438 мм — два контейнера типа 1С . Общая высота 5130 или 5283 мм с учетом высоты площадки Z-образного профиля (254 мм). Второй вариант — размещение с превышением высоты, допускаемой габаритом погрузки. Первый ярус: высота 2591 мм — один контейнер типа 1АА или два типа 1СС. Второй ярус: высота 2591 мм — один контейнер типа 1АА или два типа 1СС . Рис. 1. Колодцевая часть платформы: 1 — двутавровый профиль; 2 — Z-образный профиль; 3 — ме- таллическая стенка колодца; 4 — направляющий металлический элемент; УГР — уровень головки рельса; пунктирная линия — внешний контур контейнера Fig. 1. Well part of the platform: 1 — I-profile; 2 — Z-shaped profile; 3 — metal plate of the well; 4 — guiding metal element; УГР — rail head level; dashed line — outer contour of the container Рис. 1. Колодцевая часть платформы: 1 — двутавровый профиль; 2 — Z-образный профиль; 3 — ме- таллическая стенка колодца; 4 — направляющий металлический элемент; УГР — уровень головки рельса; пунктирная линия — внешний контур контейнера Fig. 1. Well part of the platform: 1 — I-profile; 2 — Z-shaped profile; 3 — metal plate of the well; 4 — guiding metal element; УГР — rail head level; dashed line — outer contour of the container Общая высота составляет 5436 мм. На железных дорогах еще имеются объекты ин- фраструктуры, не отвечающие габариту приближения строений С и высоте подвески контактного провода (5750 мм). В связи с этим специалистами ВНИИЖТ и железных дорог были проведены обследования указан- ных объектов и сделана оценка, приведенная ниже. g. . p p : 1 — I-profile; 2 — Z-shaped profile; 3 — metal plate of the well; 4 — guiding metal element; УГР — rail head level; dashed line — outer contour of the container плекса было проведено натурное обследование факти- ческих габаритов сооружений и устройств и прочности пути на маршруте Москва — Владимир — Чепца — Оценка технических возможностей железных дорог по пропуску вагонов с двухъярусной погрузкой контейнеров. В 2005 г. 22 © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 По второму варианту погрузки Наличие ограничений: • по осевой нагрузке — нет; • по габаритам сооружений — в двух тоннелях верхний угол второго яруса будет задевать обделку: Керакский тоннель Забайкальской железной дороги (7344 км), Облученский тоннель Дальневосточной железной дороги (8193 км); • по габаритам сооружений — в двух тоннелях верхний угол второго яруса будет задевать обделку: Керакский тоннель Забайкальской железной дороги (7344 км), Облученский тоннель Дальневосточной железной дороги (8193 км); Рис. 2. Продольный вид платформы: 1 — первый ярус; 2 — второй ярус Fig. 2. Longitudinal view of the platform: 1 — first deck; 2 — second deck • по контактному проводу — на большинстве мо- стов, тоннелей, путепроводов высота контактного про- вода менее 5750 мм. Ориентировочные расходы в ценах 2005 г. на проведение работ по устранению ограниче- ний по контактному проводу приведены в табл. 2. • по контактному проводу — на большинстве мо- стов, тоннелей, путепроводов высота контактного про- вода менее 5750 мм. Ориентировочные расходы в ценах 2005 г. на проведение работ по устранению ограниче- ний по контактному проводу приведены в табл. 2. Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС на колодцевую платформу модели 13-3124 Рис. 3. Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС на колодцевую платформу модели 13-3124 Fig. 3. Double-deck loading of four 20-foot containers 1C or 1СС on a well platform model 13-3124 Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС на колодцевую платформу модели 13-3124 Испытания платформы. Колодцевая четырехосная платформа модели 13-3124 успешно прошла прочност- ные, тормозные и динамические испытания на Экс- периментальном кольце ВНИИЖТ, после чего были проведены ее комплексные динамические ходовые и по воздействию на путь и стрелочные переводы испы- тания на Скоростном испытательном полигоне (СП) ВНИИЖТ Белореченская — Майкоп. Основанием для проведения испытаний платфор- мы являлось указание МПС России от 16.10.2003 г. № П-107у. Испытания проводились со скоростями до 135 км/ч в прямых участках пути, до 120 км/ч — в кривой радиусом 650 м, до 80 км/ч — в кривой радиусом 350 м и до 50 км/ч — на боковое направление стрелочных пере- водов марки 1/11. При движении по кривым участкам пути реализовывались положительные поперечные не- погашенные ускорения величиной до 0,7 – 0,8 м/с2. Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1С на колодцевую платформу модели 13-3124 Рис. 3. Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС на колодцевую платформу модели 13-3124 Fig. 3. По второму варианту погрузки Наличие ограничений: Double-deck loading of four 20-foot containers 1C or 1СС on a well platform model 13-3124 Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1С на колодцевую платформу модели 13-3124 Рис. 4. Двухъярусная погрузка двух 40-футовых контейнеров 1АА на колодцевую платформу модели 13-3124 Номинальное габаритное пространство инфраструктуры ис. 4. Двухъярусная погрузка двух 40-футовых контейнеров 1АА на колодцевую платформу модели 13-3124 Рис. 4. Двухъярусная погрузка двух 40-футовых контейнеров 1А или 1АА на колодцевую платформу модели 13-3124 Fig. 4. Double-deck loading of two 40-foot containers 1A or 1AA on a well platform model 13-3124 В качестве ходовых частей платформы использова- ны две двухосные тележки модели 18-100. Конструкция верхнего строения пути на опытных участках СП: рель- сы типа Р65, сваренные в плети, шпалы железобетонные количеством 1840 – 2000 шт. на 1 км, балласт щебеноч- ный. Фактическое состояние рельсовой колеи в период проведения испытаний определялось по данным прохо- да путеизмерительного вагона № 247 от 11.11.2003 г. На всех опытных участках отступлений в содержании рель- совой колеи выше 2-й степени обнаружено не было. В прямом участке преобладали отступления по уровню величиной от 9 до 12 мм и длиной от 2 до 17 м. с. 4. Двухъярусная погрузка двух 40-футовых контейнеров 1АА на колодцевую платформу модели 13-3124 минальное габаритное пространство инфраструктур 4. Двухъярусная погрузка двух 40-футовых контейнеров 1АА на колодцевую платформу модели 13-3124 Рис. 4. Двухъярусная погрузка двух 40-футовых контейнеров 1А или 1АА на колодцевую платформу модели 13-3124 Fig. 4. Double-deck loading of two 40-foot containers 1A or 1AA on a well platform model 13-3124 По результатам испытаний были рекомендованы следующие допускаемые в эксплуатации скорости дви- жения: в прямых — до 90 км/ч, в кривых — скорости при непревышении непогашенного ускорения 0,3 м/с2. Важным этапом в создании новой специализи- рованной платформы и перспективной технологии двухъярусной перевозки крупнотоннажных контей- неров стало проведение эксплуатационных испыта- ний — опытной перевозки погруженных в два яруса 20- и 40-футовых контейнеров с реальным грузом. По результатам испытаний были рекомендованы следующие допускаемые в эксплуатации скорости дви- жения: в прямых — до 90 км/ч, в кривых — скорости при непревышении непогашенного ускорения 0,3 м/с2. Важным этапом в создании новой специализи- рованной платформы и перспективной технологии двухъярусной перевозки крупнотоннажных контей- неров стало проведение эксплуатационных испыта- ний — опытной перевозки погруженных в два яруса 20- и 40-футовых контейнеров с реальным грузом. Называевская — Мариинск — Юрты — Петровский завод — Архара — Хабаровск — Находка — Москва. • грузоподъемность при применении тележки модели 18-100 — 67 т; ВНИИЖТ с помощью диагностического ком- 225 © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 I Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Рис. 2. Продольный вид платформы: 1 — первый ярус; 2 — второй ярус Fig. 2. Longitudinal view of the platform: 1 — first deck; 2 — second deck 7 . Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС на колодцевую платформу модели 13-3124 Рис. 3. Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС на колодцевую платформу модели 13-3124 Fig. 3. Double-deck loading of four 20-foot containers 1C or 1СС on a well platform model 13-3124 7 Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС на колодцевую платформу модели 13-3124 2 1 12 500 1040-1080 14 950 17 950 19 170 254 Рис. 2. Продольный вид платформы: 1 — первый ярус; 2 — второй ярус Fig. 2. Longitudinal view of the platform: 1 — first deck; 2 — second deck 7 3. Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС на колодцевую платформу модели 13-3124 Рис. 3. Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС на колодцевую платформу модели 13-3124 Fig. 3. Double-deck loading of four 20-foot containers 1C or 1СС on a well platform model 13-3124 7 Двухъярусная погрузка четырех 20-футовых контейнеров 1С или 1СС на колодцевую платформу модели 13-3124 По второму варианту пог Наличие ограничений: • по осевой нагрузке — • по габаритам сооруж верхний угол второго ярус Керакский тоннель Забайк (7344 км), Облученский т железной дороги (8193 км); • по контактному прово стов, тоннелей, путепроводо вода менее 5750 мм. Ориенти 2005 г. на проведение работ ний по контактному проводу Испытания платформы. платформа модели 13-3124 у ные, тормозные и динамич периментальном кольце ВН проведены ее комплексные по воздействию на путь и ст тания на Скоростном испы ВНИИЖТ Белореченская — Основанием для проведе мы являлось указание МП № П-107у. Испытания пров 135 км/ч в прямых участках п радиусом 650 м, до 80 км/ч — до 50 км/ч — на боковое нап водов марки 1/11. При движ 2 1 12 500 1040-1080 14 950 17 950 19 170 254 По второму варианту погрузки Наличие ограничений: © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 226 • производительность выше на 30 %; • производительность выше на 30 %; • себестоимость перевозок контейнеров ниже на 24 %; • среднегодовой дисконтированный доход на одну платформу — 211,3 тыс. руб.; • повышение веса поезда на 800 – 1000 т в преде- лах существующих длин станционных путей. ВНИИЖТ совместно с ЦЭ ОАО «РЖД» провел анализ габаритных характеристик сооружений и вы- соты подвески контактного провода на указанных на- правлениях и установил, что для отработки практики эксплуатации платформы 13-3124 при перевозке кон- тейнеров в два яруса из всех указанных маршрутов целесообразно принять два маршрута: Вместе с тем в 2006 г. при рассмотрении итогов опыт- ной перевозки на одном из совещаний в ОАО «РЖД», несмотря на положительные результаты исследова- ний и перспективность внедрения новой двухъярус- ной технологии перевозок контейнеров, работы по проекту были приостановлены, так как двухъярусная перевозка не учитывала контейнеры типа 1ААА. первый: Койты — Микунь — Низовка — Коноша —  Вологда-2 — Кошта — Волховстрой-2 — Мга — Обу- хово — Автово — Новый порт — Санкт-Петербург- Варшавский; Перспективы внедрения технологии перевозок кон- тейнеров с двухъярусной погрузкой, отмеченные в 2006 г. В связи с возникшей проблемой учета 40-футовых контейнеров типа 1ААА для двухъярусной перевозки и решением совещания у первого вице-президента ОАО «РЖД» В. Н. Морозова от 29.09.2006 г. протокол №ВМ-98 «О целесообразности завершения разработ- ки и внедрения в эксплуатацию специализированной платформы модели 13-3124 с двухъярусной погрузкой контейнеров» ОАО «Трансконтейнер» определило следующие направления для организации перевозок контейнеров типа 1С, 1СС, 1А и 1АА с погрузкой в два яруса на платформу модели 13-3124 [6, 7]: второй: Архангельск-город — Исакогорка — Коно- ша — Вологда-2 — далее по первому маршруту. второй: Архангельск-город — Исакогорка — Коно- ша — Вологда-2 — далее по первому маршруту. Наиболее подготовленным был первый маршрут, на котором находились шесть сооружений, где вы- сота подвески контактного провода ниже норм на 40 – 75 мм (эти отклонения могли быть устранены регулировкой подвески контактного провода в не- большие сроки при стоимости работ ориентировоч- но 12 млн руб.). При этом для первого маршрута было учтено, что по еще имеющемуся на нем одному пре- пятствию (негабаритный мост на участке Мга — Обу- хово) Октябрьская железная дорога уже ведет строи- тельные работы, и оно будет устранено. • Москва — Екатеринбург — Новосибирск и обратно; • Койты — Низовка — Исакогорка — Архангельск- город — Санкт-Петербург-Варшавский — Автово — Новый порт. 227 © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 По второму варианту погрузки Наличие ограничений: Результаты обследования: По первому варианту погрузки Наличие ограничений: • по осевой нагрузке 25 тс — нет; • по габаритам сооружений — нет; • по контактному проводу — нет. теризуется следующими нормативами: р р р фр ру ур ризуется следующими нормативами: Называевская — Мариинск — Юрты — Петровский завод — Архара — Хабаровск — Находка — Москва. Результаты обследования: По первому варианту погрузки Наличие ограничений: • по осевой нагрузке 25 тс — нет; • по габаритам сооружений — нет; • по контактному проводу — нет. теризуется следующими нормативами: р р р фр ру ур еризуется следующими нормативами: Московская, Юго-Восточная и Приволжская же- лезные дороги для проведения эксплуатационных испы- таний подготовили маршрут Лесок — Рязань — Ряжск — • по габаритам сооружений — нет; • по контактному проводу — нет. Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Железная дорога Расходы, млн руб. Октябрьская 210 Московская 108 Горьковская 39 Северная 20 Юго-Восточная 30 Приволжская 80 Свердловская 15 Западно-Сибирская 24 Красноярская 30 Восточно-Сибирская 50 Забайкальская 259 Дальневосточная 385 Всего: 1250 Т а б л и ц а 2 Ориентировочные расходы на проведение работ по устранению ограничений по контактному проводу для пропуска двухъярусной погрузки с контейнерами 1АА и 1СС T a b l e 2 Estimated costs of work to eliminate restrictions on the overhead wire for passing double-decker loading with containers 1AA and 1СС Кочетовка — Анисовка — Саратов — Астрахань — Ку- тум. Ученые и специалисты ВНИИЖТ и ВНИИАС провели эксплуатационные испытания платформы модели 13-3124 с двухъярусной погрузкой контейне- ров типов 1АА и 1СС. Результаты — положительные. Успешная опытная перевозка контейнеров типа 1АА и 1СС, погруженных в два яруса, по маршруту протяженностью около 3000 км и относительно невы- сокие расходы на устранение ограничений по контакт- ному проводу (1,25 млрд руб.) свидетельствовали о том, что разработанная новая технология двухъярусной пе- ревозки может быть рекомендована для сетевого вне- дрения. Целесообразность такого решения подтверж- далась высокой экономической эффективностью двухъярусной перевозки, полученной в выполненных ВНИИЖТ расчетах и характеризуемой следующими данными по сравнению с одноярусной: • производительность выше на 30 %; Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Лельма — Шалакуша Северной железной дороги (ориентировочная стоимость 30 млн руб.). бы стать одним из важнейших направлений техни- ческого прогресса на железнодорожном транспорте. Это следует из того, что более половины перевозок крупнотоннажных контейнеров включают перевозку контейнеров типа 1А, 1С, 1АА и 1СС, возможность двухъярусной перевозки которых уже доказана. Опытный образец платформы 13-3124 в то время должен был пройти на Экспериментальном кольце ВНИИЖТ ресурсные испытания. К сожалению, после пробега 2000 км ресурсные испытания были прекра- щены из-за разрушения сварных швов в скругляемых местах перехода консольных площадок к несущей раме колодца. Заключение. Проведенные учеными и специалиста- ми ВНИИЖТ исследования по внедрению перевозок крупнотоннажных контейнеров типа 1АА, 1А, 1СС и 1С с погрузкой в два яруса на колодцевой платформе по- зволяют сделать вывод, что для железных дорог Россий- ской Федерации создана высокоэффективная техно- логия перевозки крупнотоннажных контейнеров. Она по-прежнему сохраняет свою актуальность и может быть внедрена в настоящее время. Перечисленные в статье мероприятия, подлежащие реализации для во­ зобновления работ по внедрению данной технологии, предлагается включить в программу внедрения такого вида перевозок. Мероприятия, подлежащие реализации для во­зоб­ новления работ по внедрению технологии перевозки крупнотоннажных контейнеров типа 1А, 1С, 1АА и 1СС, погруженных в два яруса 1. Разработка проекта модернизации колодцевой платформы модели 13-3124 с целью улучшения сопря- жения консольной части платформы и боковых стен ее колодца и устранения других недостатков конструкции. 2. Актуализация данных по габаритной характери- стике сооружений и высоте подвески контактного про- вода на всех железных дорогах. Разработка программы подготовки сети железных дорог к эксплуатации мо- дернизированной колодцевой платформы, загружен- ной в два яруса контейнерами типа 1А, 1С, 1АА и 1СС. СПИСОК ЛИТЕРАТУРЫ Как было сказано выше, не- возможность применения данной технологии пере- возки к контейнеру типа 1ААА стала одной из причин отказа от ее внедрения. Другая причина заключается, видимо, в том, что технология двухъярусной перевозки более сложная по сравнению с одноярусной. Однако с учетом высокой эффективности двухъярусной пере- возки этот вопрос может найти решение при возобнов- лении программы внедрения перевозок такого вида. 7. Ла з арен ко Ю. М., А рш и н цев Д. Н., Морозов Э. Н. О вне­дрении высокоэффективной технологии перевозки крупнотон- нажных контейнеров в два яруса на железных дорогах Российской Федерации // Промышленный транспорт XXI век. 2013. № 1. С. 21. СПИСОК ЛИТЕРАТУРЫ 1. Современные габаритные возможности железных дорог / Ю. М. Лазаренко [и др.] // Железнодорожный транспорт. 1978. № 4. С. 61 – 66. 1. Современные габаритные возможности железных дорог / Ю. М. Лазаренко [и др.] // Железнодорожный транспорт. 1978. № 4. С. 61 – 66. 3. Изготовление двух опытных образцов модерни- зированной колодцевой платформы, межъярусных замков. Проведение комплекса необходимых испыта- ний и сертификации платформы. 2. Лазаренко Ю. М. Нестандартные решения для нестан- дартных грузов // РЖД-Партнер. Спец. выпуск: Контрейлерные перевозки. 2012. С. 31. 3. Богданов В. М. Использование габаритных возможностей сети для повышения провозной способности // Увеличение габа- ритов и повышение погонных нагрузок грузовых вагонов: сб. науч. тр. ВНИИЖТ. М.: Транспорт, 1983. Вып. 660. С. 4 – 17. 4. Разработка технических требований к испытаниям. 5. Изготовление партии (сто единиц) модернизи- рованных колодцевых платформ и поставка их в вы- бранные вагонные депо. тр. ВНИИЖТ. М.: Транспорт, 1983. Вып. 660. С. 4 – 17. 4. Лазаренко Ю. М. Лесным грузам — увеличенный габарит погрузки // Железнодорожный транспорт. 1980. № 5. С. 20 – 23. 6. Разработка технологической инструкции по двухъярусной погрузке и выгрузке крупнотоннажных контейнеров и технических условий размещения и крепления контейнеров 1А, 1С, 1АА и 1СС в два яруса на модернизированной колодцевой платформе. 5. Лазаренко Ю. М., Богданов В. М. Совершенствование габаритов на железных дорогах ОСЖД // Бюллетень ОСЖД. 1980. № 4. С. 9 – 13. 6. Лисицын А. Л., Лазаренко Ю. М., Вологин В. А. Пере- возки крупнотоннажных контейнеров в два яруса // Железнодо- рожный транспорт. 2002. № 8. С. 33 – 35. Приведенные мероприятия предусматривают ре- шение технических вопросов, но в них не учтен еще один важнейший аспект: необходимо положительное отношение к двухъярусной перевозке крупных кон- тейнерных операторов, транспортно-логистических компаний, для которых важно обеспечить перевозку контейнеров всех типов. Как было сказано выше, не- возможность применения данной технологии пере- возки к контейнеру типа 1ААА стала одной из причин отказа от ее внедрения. Другая причина заключается, видимо, в том, что технология двухъярусной перевозки более сложная по сравнению с одноярусной. Однако с учетом высокой эффективности двухъярусной пере- возки этот вопрос может найти решение при возобнов- лении программы внедрения перевозок такого вида. Приведенные мероприятия предусматривают ре- шение технических вопросов, но в них не учтен еще один важнейший аспект: необходимо положительное отношение к двухъярусной перевозке крупных кон- тейнерных операторов, транспортно-логистических компаний, для которых важно обеспечить перевозку контейнеров всех типов. © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 228 • производительность выше на 30 %; Дополнительно были указаны также направления для организации кольцевых маршрутов: По второму рекомендуемому маршруту дополни- тельно к указанным работам необходимо было произ- вести регулировку подвески контактного провода на двух мостах Северной железной дороги (866 и 856 км), где ее высота ниже нормы на 75 мм (ориентировоч- ная стоимость работ 5 млн руб.), и заменить пролетное строение на мосту через реку Недзюга — 848 км участка Дополнительно были указаны также направления для организации кольцевых маршрутов: • Санкт-Петербург-Варшавский — Сегежа —  Санкт-Петербург-Варшавский; • Санкт-Петербург-Варшавский — Автово — Новый порт — Соликамск — Санкт-Петербург-Варшавский; С С Санкт-Петербург-Варшавский — Автово — Новый порт — Соликамск — Санкт-Петербург-Варшавский; • Соликамск — Новороссийск — Соликамск. порт — Соликамск — Санкт-Петербург-Варшавский; • Соликамск — Новороссийск — Соликамск. • Соликамск — Новороссийск — Соликамск. 227 © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 REFERENCES Valeriy V. SEMERKHANOV, Senior Researcher, JSC “VNIIZhT” 1. Lazarenko Yu. M., Bogdanov V. M., Ostrov A. B., Vol'ko­vich Yu. N. Sovremennye gabaritnye vozmozhnosti zheleznykh dorog [Mo­ dern overall dimension capacities of railways]. Zheleznodorozhnyy transport, 1978, no. 4, pp. 61 – 66. Elena A. MITINA, Leading Engineer, JSC “VNIIZhT” p pp 2. Lazarenko Yu. M. Nestandartnye resheniya dlya nestandart­ nykh gruzov [Non-standard solutions for non-standard freight]. 2. Lazarenko Yu. M. Nestandartnye resheniya dlya nestandart­ nykh gruzov [Non-standard solutions for non-standard freight]. Elena V. KAPUSKINA, Leading Engineer, JSC “VNIIZhT” E-mail: lazarenko_um@list.ru (Yu. M. Lazarenko) On the double-deck transportation of large-tonnage containers: start of work, suspension of the program, measures for its prolongation Yu. M. LAZARENKO, D. N. ARSHINTSEV, V. V. SEMERKHANOV, E. A. MITINA, E. V. KAPUSKINA Sovershenstvovanie ga­ baritov na zheleznykh dorogakh OSZhD [Improvement of dimen- sions on the OSJD railways]. Byulleten' OSZhD [OSJD Bulletin], 1980, no. 4, pp. 9 – 13. yy p pp 5. Lazarenko Yu. M., Bogdanov V. M. Sovershenstvovanie ga­ baritov na zheleznykh dorogakh OSZhD [Improvement of dimen- sions on the OSJD railways]. Byulleten' OSZhD [OSJD Bulletin], 1980, no. 4, pp. 9 – 13. 6. Lisitsyn A. L., Lazarenko Yu. M., Vologin V. A. Perevozki krup­ notonnazhnykh konteynerov v dva yarusa [Transportation of large- tonnage containers in two decks]. Zheleznodorozhnyy transport, 2002, no. 8, pp. 33 – 35. 7. Lazarenko Yu. M., Arshintsev D. N., Morozov E. N. O vnedre­ nii vysokoeffektivnoy tekhnologii perevozki krupnotonnazhnykh konteynerov v dva yarusa na zheleznykh dorogakh Rossiyskoy Fede­ratsii [On the introduction of highly efficient technology for the transportation of large-capacity containers in two decks on the railways of the Russian Federation]. Promyshlennyy transport XXI vek [Industrial transport XXI century], 2013, no. 1, p. 21. 7. Lazarenko Yu. M., Arshintsev D. N., Morozov E. N. O vnedre­ nii vysokoeffektivnoy tekhnologii perevozki krupnotonnazhnykh konteynerov v dva yarusa na zheleznykh dorogakh Rossiyskoy Fede­ratsii [On the introduction of highly efficient technology for the transportation of large-capacity containers in two decks on the railways of the Russian Federation]. Promyshlennyy transport XXI vek [Industrial transport XXI century], 2013, no. 1, p. 21. Research carried out by scientists and specialists of the VNIIZhT on the implementation of transportation of large-capacity containers of the 1AA, 1A, 1CC and 1C types with loading in two decks on a well platform have shown the high efficiency of the developed transportation technology. It still retains its relevance and can be implemented at the present time. The measures listed in the article to be implemented to resume work on the implementation of this technology are proposed to be included in the program for the in- troduction of this type of transportation. Информация об авторАХ ЛАЗАРЕНКО Юрий Михайлович, канд. техн. наук, консультант, АО «ВНИИЖТ» ЛАЗАРЕНКО Юрий Михайлович, канд. техн. наук, консультант, АО «ВНИИЖТ» АРШИНЦЕВ Дмитрий Николаевич, канд. техн. наук, руководитель группы, АО «ВНИИЖТ» СЕМЕРХАНОВ Валерий Викторович, старший научный сотрудник, АО «ВНИИЖТ» СЕМЕРХАНОВ Валерий Викторович, старший научный сотрудник, АО «ВНИИЖТ» МИТИНА Елена Алексеевна, ведущий инженер, АО «ВНИИЖТ» МИТИНА Елена Алексеевна, ведущий инженер, АО «ВНИИЖТ» КАПУСКИНА Елена Владимировна, ведущий инженер, АО «ВНИИЖТ» КАПУСКИНА Елена Владимировна, ведущий инженер, АО «ВНИИЖТ» Авторы данной статьи стремятся еще раз обратить внимание на существование полностью разработан- ной, но не внедренной высокоэффективной техно- логии перевозок, которая и в настоящее время могла Статья поступила в редакцию 03.05.2020 г., актуализирована 17.07.2020 г., принята к публикации 22.07.2020 г. Статья поступила в редакцию 03.05.2020 г., актуализирована 17.07.2020 г., принята к публикации 22.07.2020 г. © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731 228 Ю. М. Лазаренко и др. /Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229 Для цитирования: О двухъярусной перевозке крупнотоннажных контейнеров: начало работ, приостановка программы, мероприятия по ее пролонгации / Ю. М. Лазаренко [и др.] // Вестник ВНИИЖТ. 2020. Т. 79. № 4. С. 224 – 229. DOI: https:// doi.org/10.21780/2223-9731-2020-79-4-224-229. Yuriy M. LAZARENKO, Yuriy M. LAZARENKO, Cand. Sci. (Eng.), Consultant, JSC “VNIIZhT” Keywords: large-capacity container; well platform; double- deck transportation; loading dimensions; transportation technology Cand. Sci. (Eng.), Consultant, JSC “VNIIZhT” Dmitriy N. ARSHINTSEV, Cand. Sci. (Eng.), Head of the Group, JSC “VNIIZhT” On the double-deck transportation of large-tonnage containers: start of work, suspension of the program, measures for its prolongation Yu. M. LAZARENKO, D. N. ARSHINTSEV, V. V. SEMERKHANOV, E. A. MITINA, E. V. KAPUSKINA Joint Stock Company “Railway Research Institute” (JSC “VNIIZhT”), Moscow, 129626, Russia RZhD-Partner, Spets. vypusk: Kontreylernye perevozki [Specialist. issue: Piggyback transportation], 2012, p. 31. RZhD-Partner, Spets. vypusk: Kontreylernye perevozki [Specialist. issue: Piggyback transportation], 2012, p. 31. Abstract. At the beginning of the XXI century in order to in- crease the competitiveness of container transportation on the railways of Russia, comprehensive studies were carried out on the possibility of transporting large-capacity containers loaded in two decks. In contrast to the world experience in the development of this method of transportation, where they are carried out on lines with diesel traction, the possibility of transporting containers loaded in two decks on electrified domestic mainlines is determined by the presence of an overhead wire, which creates an additional restric- tion for increasing the height of the freight. 3. Bogdanov V. M. Ispol'zovanie gabaritnykh vozmozhnostey seti dlya povysheniya provoznoy sposobnosti [Using the overall capacity of the network to increase the carrying capacity]. Uveli- chenie gabaritov i povyshenie pogonnykh nagruzok gruzovykh vagonov. Sb. nauch. tr. VNIIZhT [Increasing the dimensions and increasing the running loads of freight cars. Proc. of articles of scientific works of the VNIIZhT]. Moscow, Transport Publ., 1983, no. 660, pp. 4 – 17. 4. Lazarenko Yu. M. Lesnym gruzam — uvelichennyy gaba­ rit pogruzki [Increased loading gauge for the forest freights]. Zheleznodorozhnyy transport, 1980, no. 5, pp. 20 – 23. 4. Lazarenko Yu. M. Lesnym gruzam — uvelichennyy gaba­ rit pogruzki [Increased loading gauge for the forest freights]. Zheleznodorozhnyy transport, 1980, no. 5, pp. 20 – 23. The article discusses the results of many years of comprehen- sive research on the creation of a specialized well platform and the development of a technology for transporting large-capacity containers in it with loading in two decks, carried out by the VNIIZhT in the early 2000s. The article provides the features of the structure of the well platform, the layout of containers in it, the types of tests carried out and data on the experimental trans- portation of the platform loaded with containers in two decks. Information on the suspension of work on the introduction of double-deck container transportation is provided and measures are proposed that must be performed in case of resumption of work on the introduction of this method of transportation on the Russian railways network. yy p pp 5. Lazarenko Yu. M., Bogdanov V. M. E-mail: lazarenko_um@list.ru (Yu. M. Lazarenko) For citation: Lazarenko Yu. M., Arshintsev D. N., Semerkhanov V. V., Mitina E. A., Kapuskina E. V. On the double-deck transportation of large-tonnage containers: start of work, suspension of the program, measures for its prolongation // VNIIZhT Scientific Journal. 2020. 79 (4): 224 – 229 (In Russ.). DOI: https://doi.org/10.21780/2223-9731-2020-79-4-224-229. 229 © Вестник Научно-исследовательского института железнодорожного транспорта (Вестник ВНИИЖТ), 2020 ISSN 2223 – 9731
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Figure S3 from Inhibition of HER2 Increases JAGGED1-dependent Breast Cancer Stem Cells: Role for Membrane JAGGED1
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CD24 - PE CD24 - PE CD44 - APC CD44 - APC + Control MDA-MB-231 - Control MDA-MB-468 SORTED LAPATINIB JAGGED1 HIGH CD24 - PE CD24 - PE UNSTAINED UNSORTED DMSO UNSORTED LAPATINIIB UNSTAINED SORTED VEHICLE JAGGED1 LOW CD44 - FITC CD24 - PE CD44 - FITC CD24 - PE CD44 - APC CD44 - APC HCC1954 ementary Figure 7. Expression of CD44 and CD24 in response to lapatinib. A. HCC1954 cells were treated with DMSO (Vehicle) or 2M lapatinib ays and stained for expression of CD44 and CD24 by flow cytometry. B. Cells were treated as described in A. and then sorted based on Jagged1 sion by flow cytometry. The sorted cells were then stained for CD44 and CD24 expression by flow cytometry. C. MDA-MB-231 and MDA-MB-468 were stained for expression of CD44 and CD24 followed by flow cytometry. The MDA-MB-231 cells served as positive controls while MDA-MB-468 erved as negative controls for CD44 high and CD24 low expressing cells. C. CD24 - PE CD24 - PE CD44 - APC CD44 - APC + Control MDA-MB-231 - Control MDA-MB-468 SORTED LAPATINIB JAGGED1 HIGH CD24 - PE CD24 - PE UNSTAINED UNSORTED DMSO UNSORTED LAPATINIIB UNSTAINED SORTED VEHICLE JAGGED1 LOW CD44 - FITC CD24 - PE CD44 - FITC CD24 - PE CD44 - APC CD44 - APC HCC1954 ementary Figure 7. Expression of CD44 and CD24 in response to lapatinib. A. HCC1954 cells were treated with DMSO (Vehicle) or 2M lapatinib ays and stained for expression of CD44 and CD24 by flow cytometry. B. Cells were treated as described in A. and then sorted based on Jagged1 sion by flow cytometry. The sorted cells were then stained for CD44 and CD24 expression by flow cytometry. C. MDA-MB-231 and MDA-MB-468 were stained for expression of CD44 and CD24 followed by flow cytometry. The MDA-MB-231 cells served as positive controls while MDA-MB-468 erved as negative controls for CD44 high and CD24 low expressing cells. C. UNSTAINED UNSORTED DMSO CD24 - PE CD44 - APC CD APC A. HCC1954 CD24 - PE CD44 - APC + Control MDA-MB-231 CD24 - PE UNSTAINED UNSORTED DMSO UNSORTED LAPATINIIB CD24 - PE CD44 - APC CD44 - APC A. HCC1954 C. CD24 - PE CD24 - PE CD44 - APC CD44 - APC + Control MDA-MB-231 - Control MDA-MB-468 C. CD24 - PE CD44 - APC + Control MDA-MB-231 C. UNSTAINED A. HC CD24 PE UNSORTED LAPATINIIB CD44 - APC A. C. B. CD24 - PE CD44 - APC CD44 APC + Control MDA-MB-231 SORTED LAPATINIB JAGGED1 HIGH CD24 - PE CD24 - PE UNSTAINED UNSORTED DMSO UNSORTED LAPATINIIB UNSTAINED SORTED VEHICLE JAGGED1 LOW CD44 - FITC CD24 - PE CD44 - FITC CD24 - PE CD44 - APC CD44 - APC A. HCC1954 C. B. LAPA UNSTAINED SORTED VEHICLE JAGGED1 LOW CD44 - FITC CD24 - PE CD44 - FITC B. UNSTAINED SORTED VEHICLE JAGGED1 LOW CD44 - FITC CD24 - PE B. SORTED LAPATINIB JAGGED1 HIGH CD24 - PE CD44 - FITC CD44 - FITC CD44 - FITC CD44 - FITC ementary Figure 7. Expression of CD44 and CD24 in response to lapatinib. A. HCC1954 cells were treated with DMSO (Vehicle) or 2M lapatinib ays and stained for expression of CD44 and CD24 by flow cytometry. B. Cells were treated as described in A. and then sorted based on Jagged1 ssion by flow cytometry. CD24 - PE CD24 - PE CD44 - APC CD44 - APC + Control MDA-MB-231 - Control MDA-MB-468 SORTED LAPATINIB JAGGED1 HIGH CD24 - PE CD24 - PE UNSTAINED UNSORTED DMSO UNSORTED LAPATINIIB UNSTAINED SORTED VEHICLE JAGGED1 LOW CD44 - FITC CD24 - PE CD44 - FITC CD24 - PE CD44 - APC CD44 - APC HCC1954 ementary Figure 7. Expression of CD44 and CD24 in response to lapatinib. A. HCC1954 cells were treated with DMSO (Vehicle) or 2M lapatinib ays and stained for expression of CD44 and CD24 by flow cytometry. B. Cells were treated as described in A. and then sorted based on Jagged1 sion by flow cytometry. The sorted cells were then stained for CD44 and CD24 expression by flow cytometry. C. MDA-MB-231 and MDA-MB-468 were stained for expression of CD44 and CD24 followed by flow cytometry. The MDA-MB-231 cells served as positive controls while MDA-MB-468 erved as negative controls for CD44 high and CD24 low expressing cells. C. The sorted cells were then stained for CD44 and CD24 expression by flow cytometry. C. MDA-MB-231 and MDA-MB-468 were stained for expression of CD44 and CD24 followed by flow cytometry. The MDA-MB-231 cells served as positive controls while MDA-MB-468 erved as negative controls for CD44 high and CD24 low expressing cells.
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Telomere shortening and accelerated aging in COPD: findings from the BODE cohort
Respiratory research
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Abstract Background: Chronic Obstructive Pulmonary Disease (COPD) may be associated with accelerated aging. Telomere shortening is a biomarker of aging. Cross-sectional studies describe shorter telomeres in COPD compared with matched controls. No studies have described telomere length trajectory and its relationship with COPD progression. We investigated telomere shortening over time and its relationship to clinical and lung function parameters in a COPD cohort and smoker controls without COPD. Methods: At baseline leukocyte telomere length was measured by qPCR in 121 smokers with COPD and 121 without COPD matched by age (T/S0). The measurements were repeated in 70 of those patients with COPD and 73 non-COPD smokers after 3 years of follow up (T/S3). Results: At initial measurement, telomeres were shorter in COPD patients when compared to smoker controls (T/S = 0. 68 ± 0.25 vs. 0.88 ± 0.52, p = 0.003) independent from age and sex. During the follow-up period, we observed an accelerated telomere shortening in individuals with COPD in contrast to smoker controls (T/S0 = 0.66 ± 0.21 vs. T/S3 = 0.46 ± 0.16, p < 0.001, for the patients with COPD and T/S0 = 0.83 ± 0.56 vs. T/S3 = 0.74 ± 0.52, p = 0.023 for controls; GLIM, p = 0.001). This shortening was inversely related to the baseline telomere length (r = −0.49, p < 0.001). No significant relationship was found between the rate of change in telomere length and change in lung function in the patients with COPD (p > 0.05). Conclusions: Compared with smokers, patients with COPD have accelerated telomere shortening and this rate of attrition depends on baseline telomere length. Furthermore, the telomere length and its rate of shortening did not relate to clinical and lung function parameters changes over 3 years of follow-up. Keywords: COPD, Telomeres, Aging It has been suggested that COPD is a disease of accel- erated aging [4, 5] and telomere length has been pro- posed as a biomarker of aging [6, 7]. Telomeres consist of stretches of repetitive hexanucleotides (5´-TTAGGG-3´) that protect the end of chromosomes from being recog- nized as double-strand breaks and avoid truncation. Because the DNA cannot be duplicated at the end of the chromosome, each duplication results in its shortening. Thus, telomeres get progressively shorter as cells divide, an event that is known as the end-replication process. © The Author(s). 2017 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 Other mechanisms may also account for the accelerated loss of telomeres, such as the DNA damage induced by oxidative stress [8]. Telomere shortening and accelerated aging in COPD: findings from the BODE cohort Córdoba-Lanús Elizabeth1* , Cazorla-Rivero Sara1, Espinoza-Jiménez Adriana1, Juan P. de-Torre Pajares María-José4, Aguirre-Jaime Armando1, Celli Bartolomé5 and Casanova Ciro1,2 * Correspondence: elizabeth-cordoba@hotmail.com 1Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. del Rosario 145, 38010 Santa Cruz de Tenerife, Spain Full list of author information is available at the end of the article Elizabeth et al. Respiratory Research (2017) 18:59 DOI 10.1186/s12931-017-0547-4 Elizabeth et al. Respiratory Research (2017) 18:59 DOI 10.1186/s12931-017-0547-4 Open Access RESEARCH Open Access Telomere shortening and accelerated aging in COPD: findings from the BODE cohort Córdoba-Lanús Elizabeth1* , Cazorla-Rivero Sara1, Espinoza-Jiménez Adriana1, Juan P. de-Torres3, Pajares María-José4, Aguirre-Jaime Armando1, Celli Bartolomé5 and Casanova Ciro1,2 Telomere length measurement Venous blood was obtained at baseline and at the third- year post enrollment. DNA was extracted from leuko- cytes using the QIAamp DNA Mini Kit (GE Healthcare). Telomere length was measured using a qPCR based protocol previously published [21, 22]. Briefly, DNA samples were quantified using the Nanodrop lite spec- trophotometer (Thermo Scientific, Wilmington, DE, USA). Telomere length measurement was performed in triplicate using 20 ng of DNA. Intra-plate coefficients of variance (CV) were calculated between the replicates and samples with CV > 5% were excluded from further analysis. As a reference DNA sample with shorter telo- meres we used the DNA from MCF-7 cells. For longer telomeres, we assayed a DNA from a young control indi- vidual. These calibrator samples were assayed in tripli- cate on each PCR plate to control for variation between plates. Inter-assay variability was controlled by measur- ing two control DNA samples per run as a normalizing factor. Inter-plate CV for the calibrator sample was cal- culated to be <9%. Standard curves were derived from serially diluted reference DNA. Albumin, being a single copy gene, was used as a reference gene. The primer sequences and cycling conditions for the measurement of telomere length were the same used by others [22]. qPCR reactions were performed in 20 μL reactions for each individual: 10 μL SYBRGreen PCR Master Mix (BioRad), 0.9 μM of Telg and Telc and 0.6 μM of Albu and Albd. All the reactions were performed on tripli- cates of the telomere and reference gene assays on the iQ Cycler Real-Time PCR Instrument (BioRad). The aim of the present study was to investigate if telo- mere shortening occurs over time in patients with COPD and if this shortening is related to clinical and lung function parameters. Background Chronic obstructive pulmonary disease (COPD), a major cause of morbidity and mortality throughout the world, is thought to result from the interaction of environmen- tal agents such as tobacco smoking or exposure to biomass fuel and inherited genetic factors [1]. COPD is a multidimensional disease that frequently coexists with other age-related co-morbidities such as osteoporosis, cardiovascular disease, lung cancer, depression and dia- betes [2, 3]. There is no uniform acceptance of the interaction be- tween telomere length and COPD. However, some studies Page 2 of 8 Elizabeth et al. Respiratory Research (2017) 18:59 have shown that patients with COPD exhibit shorter telo- meres in circulating leukocytes compared to age matched smokers without COPD [9, 10]. Some authors have pro- posed that telomere shortening might be accelerated in patients with COPD and serve as a biomarker of disease progression [11], a theory that has some clinical support because the telomere length in peripheral leukocytes of patients with COPD has been related to important health outcomes such as all-cause and cancer mortality [12]. comparison (Fig. 1). From these subjects, 70 patients with COPD age-matched with 73 control smokers returned for all follow-up evaluations over 3-years and were analyzed in the longitudinal study. The indi- viduals included in the final analysis did not have any relevant clinical difference with the ones that did not complete the 3-year study (see Additional files 1 and 2). The study was approved by the institutional review board at both hospitals. All participants provided written in- formed consent. The unanswered question fueling the debate about the meaning of telomere shortening in patients with COPD is that all of the studies performed have been cross- sectional in design, not informing whether there are changes in length over time and whether there is any re- lationship between those changes and outcomes. That this is possible in COPD is highlighted by a recent study that analyzed leukocyte telomere trajectory in a cohort of individuals with coronary artery disease and found that this is powerfully influenced by baseline telomere length in a pattern suggestive of negative feedback regu- lation [13]. Baseline findings The clinical characteristics and lung function data of the 121 COPD patients and 121 controls at baseline, are summarized in Table 1. The range of airflow ob- struction distributed by GOLD stages in COPD was as follows: 1 (19.8%), 2 (43%), 3 (28.9%) and 4 (8.3%). As expected, patients with COPD had worse lung function and a higher BODE index than controls. However, the two groups were similar in age, sex, BMI and Charlson co-morbidity score. Although the total pack years smoking was higher in COPD pa- tients, there were more current smokers in the con- trol group. Telomere length measured by the T/S ratio inversely correlated with age in COPD (r = −0.21; p = 0.02) and in smoker controls (r = −0.19; p = 0.02). Given this relationship, all subsequent analyses were adjusted by age. For the longitudinal analysis, telomere length changes were calculated as the difference between baseline (T/S0) and the third year (T/S3) of the telo- mere length measure. Individuals analyzed for follow- up were categorized as follows: subjects showing a steeper rate of telomere shortening in contrast to subjects with a lower telomere shortening rate, main- tenance or lengthen of their telomeres (defined by the median telomere length change). g g A t-Student, ANOVA, Chi2 and Paired Sample T test were used to test differences in means and pro- portions of baseline and follow-up characteristics between groups. The association between baseline telomere length (T/S) or telomere length change with clinical and/or pulmonary function variables was ex- plored using Pearson’s correlation coefficients. A mul- tiple logistic regression was performed to test the association of telomere length with COPD susceptibil- ity adjusting for age, sex and pack years. By using a general linear modelling for repeated measures (GLIM) we tested the telomere dynamics difference between patients with COPD and smokers without COPD, or within these groups between current and former smokers. We also conducted a longitudinal analysis to evaluate the progression of the disease of clinical and pulmonary function variables using change in telomere length as comparative factor (GLIM). SPSS 20.0 IBM Co software was used for all statistical analyses and two-tailed p-values < 0.05 were consid- ered significant. COPD patients had significant shorter telomeres than smokers without COPD (T/S = 0.68 ± 0.25 vs. Methods Subjects j A total of 422 subjects were screened for this study at the Hospital Universitario La Candelaria, Tenerife and the Clinica Universitaria de Navarra, Pamplona, Spain. From these, the control group of 165 smokers without COPD had a smoking history of > 15 pack-years and normal lung function (FEV1 > 80%; FEV1/FVC ≥0.70). There were 257 smokers with COPD followed annually as part of the BODE study [14]. Inclusion criteria: age > 40 years, smoking history >15 pack-years and post- bronchodilator FEV1/FVC ratio < 0.70 measured 20 min after administration of 400 mg of albuterol. Pulmonary function test, spirometry lung volumes and exercise cap- acity were measured according to ATS-ERS guidelines [15–17] using the European Community for Steel and Coal as reference values [18]. Dyspnea was evaluated by mMRC scale [19]. The BODE Index was calculated as previously described [14]. Co-morbidity was quantified using the Charlson index [20]. Patients were clinically stable (no exacerbation for at least 6 weeks) at the time of evaluation. Repeated determinations of the complete blood count revealed similar values at all visits. Exclu- sion criteria: uncontrolled co-morbidities such as malig- nancy at baseline, asthma or other pulmonary conditions than COPD. From the screened group, 121 patients with COPD were matched with 121 smokers without COPD and were included in the present study for baseline Telomere length was calculated as a ratio of telomere to albumin as previously described [22]. The T/S ratio for an experimental DNA sample is T, the number of nanograms of the Standard DNA that matches the ex- perimental sample for copy number of the telomere template, divided by S, the number of nanograms of the standard DNA that matches the experimental sample for copy number of the albumin single copy gene. The telo- mere length standardized to the reference single copy gene (T/S) was calculated using the “ΔΔCp with effi- ciency correction” calculation method [23]. Elizabeth et al. Respiratory Research (2017) 18:59 Page 3 of 8 Fig. 1 Consort diagram illustrating the selection and assessment of patients and control smokers included in the study Fig. 1 Consort diagram illustrating the selection and assessment of patients and control smokers included in the study Results For the cross-sectional analysis, patients with COPD were categorized in three groups by telomere length ratio (T/S) tertiles at baseline: shorter, medium or longer telomeres. Baseline findings 0.88 ± 0.52, p < 0.0001) even after adjusting for age, sex and pack-years (95% CI: 0.11–0.64, p = 0.003), (Table 1 and Fig. 2). There were no significant differ- ences between males (0.68 ± 0.28) and females (0.66 ± 0.20) within the COPD group or in the smokers (0.82 ± 0.53 vs. 0.96 ± 0.49 for males and females, respectively). There was no relationship between telomere length and the clinical and lung function parameters (Table 2) or between patients with less and more severe COPD (GOLD 1–2 vs. GOLD 3–4 or BODE ≤2 vs. BODE > 2) (p > 0.05). In addition, no significant associations were found between comorbidities such as cardiovascular events, diabetes, hypertension or cancer and relative telomere length in patients with COPD. Elizabeth et al. Respiratory Research (2017) 18:59 Page 4 of 8 Page 4 of 8 Table 1 Baseline characteristics of COPD patients and smokers without COPD included in the study Variable COPD cases (N = 121) Smokers (N = 121) p-value Sex (male%) 66 62 N.S. Age (years)a 57 ± 8 57 ± 8 N.S. BMI (Kg/m2)a 27 ± 5 28 ± 4 N.S. Smoking habitc (pack-yrs)ac 60 ± 25 44 ± 22 <0.0001 Active smoking (%) 50 64 0.027 T/S ratioa 0.68 ± 0.25 0.88 ± 0.52 <0.0001 FEV1 (L)a 1.66 ± 0.7 2.9 ± 0.7 <0.0001 FEV1 (% pred)a 59 ± 21 101 ± 14 <0.0001 FVC (% pred)a 89 ± 22 108 ± 15 <0.0001 FEV1 / FVC (%)a 53 ± 12 76 ± 5 <0.0001 PaO2 (mmHg)a 72.3 ± 14.3 78.7 ± 10 <0.001 KCO (%) 79.6 ± 25.1 97.3 ± 21.3 0.001 IC/TLC (%) 36 ± 9 45 ± 8 <0.001 6MWD (m)a 523 ± 89 551 ± 76 0.03 mMRC dyspneab 1 (0–2) 0 (0–0) 0.006 BODE indexb 1 (0–3) 0 (0–1) <0.001 Charlson indexb 0 (0–1) 0 (0–0) N.S. Data are presented as amean ± SD and bmedian (25th-75thpc) and compared by Student’s t-test or Chi2 test. cNumber of packs of cigarettes smoked per day x number of years smoking. Percentage BMI body mass index, T/S ratio relative telomere length, FEV1 forced expiratory volume in one second, FVC forced vital capacity, % pred per cent predicted. PaO2 partial oxygen tension, KCO diffusion capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio, 6MWD six-min walk distance test. Baseline findings N.S non-significant Table 1 Baseline characteristics of COPD patients and smokers without COPD included in the study Telomere length dynamics This difference in telomere length remained significant after 3 years between the 70 patients with COPD age matched with 73 smoker controls that presented the follow-up (T/S3 = 0.46 ± 0.16 vs. 0.74 ± 0.52, p < 0.001); even after adjusting for age, sex and smoking habit in a logistic regression analysis (95% CI: 0.12–0.90), p = 0.03). The telomere length ratio in the control group of smokers without COPD, decreased significantly (T/S0 = 0.83 ± 0.56 vs. T/S3 = 0.74 ± 0.52, p = 0.002) after the follow-up period. The same occurred in the group of pa- tients with COPD (T/S0 = 0.66 ± 0.21 vs. T/S3 = 0.46 ± 0.16, p < 0.001). However, when we compared the telo- mere trajectory between these groups over the follow-up period, we observed an accelerated telomere shortening in individuals with COPD in contrast to the control group (GLIM, general lineal model for repetitive mea- sures, p = 0.001) (Fig. 3). Relation of telomere length change and clinical variables We found a strong relationship between baseline telo- mere length and change in telomere length (r = −0.49, p < 0.001; adjusted by age) (Fig. 4). Compared with COPD patients that did not change, lengthened or had a low rate of telomere shortening, those patients with a more rapid shortening of their telo- meres had similar lung function characteristics (Table 3). By using correlation matrices, we were not able to find any significant relationship between the rate of change in telomere length and change in lung function in the patients with COPD (see Additional file 3). This lack of association was seen whether we compared current vs. former smokers, number of comorbidities or mortality (Chi2, p > 0.05). Compared with COPD patients that did not change, lengthened or had a low rate of telomere shortening, those patients with a more rapid shortening of their telo- meres had similar lung function characteristics (Table 3). Data are presented as amean ± SD and bmedian (25th-75thpc) and compared by Student’s t-test or Chi2 test. cNumber of packs of cigarettes smoked per day x number of years smoking. Percentage BMI body mass index, T/S ratio relative telomere length, FEV1 forced expiratory volume in one second, FVC forced vital capacity, % pred per cent predicted. PaO2 partial oxygen tension, KCO diffusion capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio, 6MWD six-min walk distance test. Telomere length dynamics N.S non-significant By using correlation matrices, we were not able to find any significant relationship between the rate of change in telomere length and change in lung function in the patients with COPD (see Additional file 3). This lack of association was seen whether we compared current vs. former smokers, number of comorbidities or mortality (Chi2, p > 0.05). Fig. 2 Average telomere length and SE relative telomere length (T/S) in COPD patients (n = 121) vs. age-matched smokers without COPD (n = 121) Elizabeth et al. Respiratory Research (2017) 18:59 Page 5 of 8 Page 5 of 8 Table 2 Pulmonary function characteristics of the three groups of patients with COPD defined by their baseline telomere length Variable Short T/Sa (n = 40) Medium T/Sa (n = 41) Long T/Sa (n = 40) p-value T/S ratiob 0.44 ± 0.09 0.66 ± 0.07 1.09 ± 0.21 <0.001 Sex (male%) 65 66 67 N.S. Age (years)b 59 ± 7 58 ± 8 55 ± 9 N.S. BMI (Kg/m2)b 28 ± 6 27 ± 5 27 ± 5 N.S. Smoking habitd (pack-yrs)bd 62 ± 28 63 ± 24 57 ± 23 N.S. Active smoking (%) 42 56 52 N.S. FEV1 (L)b 1.70 ± 0.71 1.64 ± 0.67 1.66 ± 0.74 N.S. FEV1 (% pred)b 61 ± 23 59 ± 21 58 ± 21 N.S. FVC (% pred)b 89 ± 24 92 ± 22 87 ± 21 N.S. FEV1 / FVC (%)b 55 ± 12 51 ± 13 53 ± 12 N.S. PaO2 (mmHg)b 71.1 ± 15.7 71.9 ± 15.8 73.5 ± 11.5 N.S. Kco (%) 74.1 ± 25.6 75.5 ± 24.1 75.2 ± 21.1 N.S. IC/TLC (%) 37 ± 6 36 ± 8 35 ± 10 N.S. 6MWD (m)b 517 ± 77 537 ± 95 513 ± 92 N.S. mMRC dyspneac 1 (0–2) 1 (0–2) 1 (0–2) N.S. BODE indexc 1 (0–2) 1 (0–3) 1 (0–3) N.S. Charlson indexc 0 (0–1) 0 (0–1) 0 (0–1) N.S. aGroups defined by telomere length (T/S) tertiles: <0.54, 0.54–0.73 and >0.73. Data are presented as bmean ± SD and cmedian (25th-75thpc) and compared by ANOVA test or Chi2 test. dNumber of packs of cigarettes smoked per day x number of years smoking. BMI body mass index, T/S ratio relative telomere length, FEV1 forced expiratory volume in one second, FVC forced vital capacity, % pred per cent predicted. Telomere length and change over time Telomere length and change over time In our study, at baseline, telomere length was shorter with older age, both in the COPD patients and the smokers without COPD. However, COPD patients pre- sented shorter telomeres than the control group inde- pendent of age and sex. Other studies evaluating the relation between telomere length and COPD have shown discordant results. Morla et al. [24] failed to find a differ- ence in telomere length between COPD patients and smokers, whereas some other studies have reported shorter telomeres in subjects with COPD compared to smokers and healthy individuals [8, 10]. These discord- ant results may have been due to differences in sample size in the studies or by technical bias or defects in study design, some of which lacked of appropriate controls. We found no relationship between telomere length and clinical or lung function parameters in our COPD co- hort in the cross-sectional analysis. This is in agreement with the results of Savale et al. [9] who described a bor- derline correlation between PaO2 and PaCO2 and telo- mere length but strangely not to lung function parameters. However, Rode et al. [25] in a study of more than 45.000 individuals in a Danish population reported a modest correlation between telomere length and the lung function expressed by the FEV1. More recently, Rutten et al. studying several markers of aging in pa- tients with COPD, found telomere length to be the only one associated with lung function [26]. All these studies aGroups defined by telomere length (T/S) tertiles: <0.54, 0.54–0.73 and >0.73. Data are presented as bmean ± SD and cmedian (25th-75thpc) and compared by ANOVA test or Chi2 test. dNumber of packs of cigarettes smoked per day x number of years smoking. BMI body mass index, T/S ratio relative telomere length, FEV1 forced expiratory volume in one second, FVC forced vital capacity, % pred per cent predicted. PaO2 partial oxygen tension, KCO diffusion capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio, 6MWD six-min walk distance test. N.S non-significant Telomere length dynamics PaO2 partial oxygen tension, KCO diffusion capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio, 6MWD six-min walk distance test. N.S non-significant Table 2 Pulmonary function characteristics of the three groups of patients with COPD defined by their baseline telomere length with COPD have shorter telomeres than smokers who do not have COPD. However, there were no associations between telomere length and clinical and lung function parameters at baseline or between changes in telomere length and change in those parameters overtime. To our knowledge, this is the first study reporting the course of telomere length change in a well-characterized cohort of patients with COPD and smoker controls. Telomere length and clinical variables were cross-sectional in design and in consequence not adequate to evaluate the possible relationship between telomere length and COPD progression. In addition, the only lung function parameter evaluated was FEV1 and patients with comorbidities were excluded. Previous cross-sectional studies have concentrated pri- marily on the relationship between telomere length and the FEV1. We expanded on those studies relating not only FEV1, but also lung hyperinflation (IC/TLC), diffu- sion capacity (KCO) and gas exchange to telomere length. Disappointingly, we were unable to document any asso- ciation between telomere length in COPD patients with any clinical or functional expression of the disease or presence of any comorbidities at baseline. This is in gen- eral agreement with most of the published studies that have reported poor associations, if any, between the ac- tual telomere length and the FEV1. Of interest, the stud- ies that have described an association between telomere shortening and lower FEV1 have included larger sample size, thus facilitating a statistical significance to those The current report is the first one to document that COPD patients have an accelerated rate of telomere shortening in contrast to smoker controls, and this dif- ference was more marked in those individuals with lon- ger baseline telomeres. In our study, 85% of the COPD patients showed telomere length shortening after 3 years of follow-up, a proportion that is similar to that ob- served in general population studies [27–29], however, the rate of decline is significantly lower in those normal individuals. It is important to compare our findings with that of other populations including different pathologies. Discussion This longitudinal study shows that COPD patients experience an accelerated telomere shortening process compared with smokers without COPD and this telomere attrition occurs in close relation to baseline telomere length. The study also confirms that patients Fig. 3 Telomere length (relative T/S ratio) dynamics in COPD patients (n = 70) vs. age-matched smokers without COPD (n = 73) after 3 years’ follow-up (p = 0.001, using GLIM - general lineal model for repetitive measures; T/S differences between groups p(T/Sxgroups)=0.002) Elizabeth et al. Respiratory Research (2017) 18:59 Page 6 of 8 Page 6 of 8 Fig. 4 Correlation between baseline telomere length and the rate of change in telomere shortening in COPD patients after 3 years’ follow-up (r = −0.49, p = 0.001, adjusted by age) Fazarneh et al. [13] analyzed leukocyte telomere trajec- tory over 5 years in a cohort of individuals with coronary artery disease and found, as we have, that telomere shortening rate is powerfully influenced by baseline telo- mere length. Our results support a pattern suggestive of negative feedback regulation in the telomere shortening dynamics, as has been proposed by others [29]. It may be that once a critical telomere length has been reached, activation of certain mechanisms in the cells occur to prevent telomere shortening over years accounting for less attrition per replication or maintenance of viable telomere lengths in subjects with shorter telomeres. The exact reason why telomeres shorten faster in pa- tients with COPD was beyond the scope of this study. However, oxidative stress and inflammation are the most important factors thought to be responsible for the loss of telomeric DNA [8], which in turn may favor the de- velopment of structural tissue damage [30]. Studies on mouse models of accelerated aging and lung dysfunc- tion, suggested that this process might enhance suscepti- bility to COPD [5]. Fig. 4 Correlation between baseline telomere length and the rate of change in telomere shortening in COPD patients after 3 years’ follow-up (r = −0.49, p = 0.001, adjusted by age) Data are presented as mean ± SD and were compared by Paired Sample T-Test. FEV1 forced expiratory volume in one second, FVC forced vital capacity, % pred per cent predicted, PaO2 partial oxygen tension, KCO diffusion capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio. aSubjects consider to analysis in each group (n = 17). bBelow the median of telomere length rate of change. cUpper the median telomere length rate of change Additional files Additional file 1: Baseline characteristics of COPD patients with and without three-year follow-up included in the study. (DOCX 14 kb) Additional file 2: Baseline characteristics of smokers without COPD with and without three-year follow-up included in the study. (DOCX 75 kb) Additional file 3: Correlations between the rate of change in telomere length and the change in pulmonary function variables in patients with COPD after three years of follow-up. (DOCX 68 kb) Additional file 1: Baseline characteristics of COPD patients with and without three-year follow-up included in the study. (DOCX 14 kb) Additional file 2: Baseline characteristics of smokers without COPD with and without three-year follow-up included in the study. (DOCX 75 kb) Additional file 3: Correlations between the rate of change in telomere length and the change in pulmonary function variables in patients with COPD after three years of follow-up. (DOCX 68 kb) Additional file 1: Baseline characteristics of COPD patients with and without three-year follow-up included in the study. (DOCX 14 kb) Additional file 1: Baseline characteristics of COPD patients with and without three-year follow-up included in the study. (DOCX 14 kb) Additional file 2: Baseline characteristics of smokers without COPD with and without three-year follow-up included in the study. (DOCX 75 kb) Additional file 2: Baseline characteristics of smokers without COPD with and without three-year follow-up included in the study. (DOCX 75 kb) Additional file 3: Correlations between the rate of change in telomere length and the change in pulmonary function variables in patients with COPD after three years of follow-up. (DOCX 68 kb) This study has several limitations. Telomere length was measured on circulating leukocytes and therefore our findings may not reflect the process occurring in the whole lung. Interestingly, telomere length in blood cor- relates well with telomere length in lung tissue of COPD [31] and rates of telomere shortening are similar in dif- ferent tissues [32]. We used qPCR relative telomere length measures rather than absolute ones which may result in a loss of precision, however qPCR results were reported to be strongly correlated those obtained with southern blot technique [22]. Leukocyte telomere length is also considered a marker of oxidative stress and in- flammation, and both contribute to COPD development. Telomere length is determined by environmental as well as genetic factors. There is a large inter-individual vari- ability in telomere length in humans of the same age that makes difficult any cross-sectional comparisons. Conclusions In summary, in this longitudinal observational study we found that compared with smoker controls, an acceler- ated telomere shortening occurs in patients with COPD, even if they had shorter telomeres at baseline. Interest- ingly, the speed of shortening relates inversely to base- line telomere length. However, the telomere length and its rate of shortening did not relate to clinical and lung function parameters and their change over time, making telomere length change an unlikely useful biomarker of COPD progression. Because the value of a biomarker resides primarily in its capacity to reflect association to prognosis or to change in disease progression, we followed patients and controls over 3 years. We observed no correlation be- tween the rate of shortening of telomeres and the change in lung function, or for that matter with any other clinical variable, rendering those findings difficult to interpret of to apply clinically. Perhaps, a longer period of observation or a larger sample may be neces- sary to evaluate these clinical and physiological variables or other patient related outcomes such as exacerbations, cardiovascular events and all-cause mortality. On the other hand, these findings suggest that the rate of telo- mere shortening may not be a viable surrogate marker of disease progression of major clinical utility. Funding Th d The study was supported by the Instituto de Salud Carlos III (PI 12/00355); European Regional Development Funds, ERDF, and Spanish Respiratory Society, SEPAR (PI 13/007). Acknowledgments We will like to thank Angela Montejo-de-Garcini, Hilaria González Acosta and Delia Mayato for their excellent technical assistance. We are also thankful to Antonio Gonzalez Biorganic Institute (Tenerife, Spain) for their kindly donation of the MCF-7 cells line. Telomere length and clinical variables Table 3 Pulmonary function variables over time and telomere length rate of change in COPD patients Variable High rate of shorteningb (n = 35) Low rate of shortening maintenance or lengtheningc (n = 35) Baseline 3-years p-value Baseline 3-years p-value FEV1 (L) 1.66 ± 0.72 1.59 ± 0.68 0.04 1.60 ± 0.5 1.52 ± 0.5 0.15 FEV1(%pred) 59 ± 20 58 ± 20 0.63 59 ± 19 58 ± 19 0.54 FVC (L) 3.01 ± 0.99 2.95 ± 0.98 0.35 3.15 ± 0.94 3.01 ± 0.97 0.12 FEV1/FVC 54 ± 10 53 ± 11 0.21 52 ± 12 52 ± 13 0.77 PaO2 (mmHg) 73.5 ± 7.9 70.9 ± 9.6 0.04 72.1 ± 12.9 68.8 ± 11.6 0.09 KCO (%)a 77.3 ± 23.7 74.9 ± 23.4 0.21 74.4 ± 19.1 70.6 ± 20.4 0.16 IC/TLC (%) 35 ± 9 31 ± 10 0.03 36 ± 8 32 ± 8 0.02 Data are presented as mean ± SD and were compared by Paired Sample T-Test. FEV1 forced expiratory volume in one second, FVC forced vital capacity, % pred per cent predicted, PaO2 partial oxygen tension, KCO diffusion capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio. aSubjects consider to analysis in each group (n = 17). bBelow the median of telomere length rate of change. cUpper the median telomere length rate of change Data are presented as mean ± SD and were compared by Paired Sample T-Test. FEV1 forced expiratory volume in one second, FVC forced vital capacity, % pred per cent predicted, PaO2 partial oxygen tension, KCO diffusion capacity of carbon monoxide, IC/TLC inspiratory to total lung capacity ratio. aSubjects consider to analysis in each group (n = 17). bBelow the median of telomere length rate of change. cUpper the median telomere length rate of change Elizabeth et al. Respiratory Research (2017) 18:59 Page 7 of 8 Page 7 of 8 findings. This is important when attempting to relate statistical associations to practical the clinical application of those findings. Availability of data and materials Any requests for data and material should be directed to the corresponding author. Competing interests p g The authors declare that they have no competing interests. Additional files Our control smokers presented a shorter tobacco exposure history than the cohort of patients with COPD. However, analysis between current vs. former smokers in both cohorts did not show significantly differences. Another limitation is that the sample size or duration of observation (3 years) may not have been large or long enough to find significant associa- tions between telomere shortening and lung function parameters. In this context, we cannot discard that our findings may be affected by regression towards the mean. Further studies with a larger follow-up period with many time points of measurements are needed to validate these findings. However, for imple- mentation of precision medicine, biomarkers need to have clinical applicability in small numbers, if not in individuals. Lastly, we did not investigate other markers of aging; however, other authors who have done so, and have found telomere length to be the most relevant of all [26]. Abbreviations 6MWD: 6-min walk distance; BMI: Body mass index; COPD: Chronic obstructive pulmonary disease; FEV1: Forced expiratory volume in one second; FVC: Forced vital capacity; GLIM: General linear modelling for repeated measures test; GOLD: Global initiative for chronic obstructive lung disease; IC/TLC: Inspiratory to total lung capacity ratio; KCO: Diffusion capacity of carbon monoxide; N.S.: Non-significant; PaO2: Partial oxygen tension; pPCR: Quantitative real time polymerase chain reaction; SD: Standard deviation; T/S: Relative telomere length ratio; T/S0: Relative telomere length ratio at baseline; T/S3: Relative telomere length ratio at the third year of follow-up Authors´ contributions E.C.L. and C.C. participated in conception and design; analysis and interpretation and drafting the manuscript for important intellectual content. S.C.R., A.E.J. and A.A.J. participated in analysis and interpretation. B.C. participated in the interpretation of the results and helped draft the manuscript for important intellectual content. All authors read and approved the final manuscript. Ethics approval and consent to participate Ethical approval was obtained from Hospital Universitario La Candelaria, Tenerife and the Clinica Universitaria de Navarra, Pamplona, Spain. Written informed consent was obtained from all participants. Page 8 of 8 Page 8 of 8 Page 8 of 8 Page 8 of 8 Elizabeth et al. Respiratory Research (2017) 18:59 Author details 1 24. Morlá M, Busquets X, Pons J, et al. Telomere shortening in smokers with and without COPD. Eur Respir J. 2006;27:525–8. 1Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. del Rosario 145, 38010 Santa Cruz de Tenerife, Spain. 2Pulmonary Division, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain. 3Pulmonary Division, Clínica Universitaria de Navarra, Pamplona, Spain. 4Centro de Investigación Médica Aplicada (CIMA), UNAV, Pamplona, Spain. 5Pulmonary and Critical Care Department, Brigham and Women’s Hospital, Boston, MA, USA. 25. Rode L, Bojesen SE, Weischer M, et al. Short telomere length, lung function and chronic obstructive pulmonary disease in 46,396 individuals. Thorax. 2013;68:429–35. 26. Rutten EP, Gopal P, Wouters EF, Franssen FM, Hageman GJ, Vanfleteren LE, Spruit MA, Reynaert NL. Various mechanistic pathways representing the aging process are altered in COPD. Chest. 2016;149:53–61. 5Pulmonary and Critical Care Department, Brigham and Women’s Hospital, Boston, MA, USA. 27. Gardner JP, Li S, Srinivasan S, et al. Rise in insulin resistance is associated with escalated telomere attrition. Circulation. 2005;111:2171–7. Received: 3 February 2017 Accepted: 7 April 2017 28. Masi S, D'Aiuto F, Martin-Ruiz C, et al. Rate of telomere shortening and cardiovascular damage: a longitudinal study in the 1946 British Birth Cohort. Eur Heart J. 2014;35:3296–303. 29. Epel ES, Merkin SS, Cawthon R, et al. The rate of leukocyte telomere shortening predicts mortality from cardiovascular disease in elderly men. Aging (Albany NY). 2008;1:81–8. Publisher’s Note 22. Cawthon RM. Telomere length measurement by a novel monochrome multiplex quantitative PCR method. Nucleic Acids Res. 2009;37, e21. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 23. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29, e45. RT-PCR. Nucleic Acids Res. 2001;29, e45. 24. Morlá M, Busquets X, Pons J, et al. Telomere short and without COPD. Eur Respir J. 2006;27:525–8. References 1. Vestbo J, Hurd SS, Agustí AG, et al. Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease: GOLD executive summary. Am J Respir Crit Care Med. 2013;187:347–65. 30. Lee MS, Yaar M, Eller MS, et al. Telomeric DNA induces p53-dependent reactive oxygen species and protects against oxidative damage. J Dermatol Sci. 2009;56:154–62. GOLD executive summary. Am J Respir Crit Care Med. 2013;187:347–6 y 2. Barnes PJ, Celli BR. Systemic manifestations and comorbidities of COPD. Eur Resp J. 2009;33:1165–85. 2. Barnes PJ, Celli BR. Systemic manifestations and comorbidities of COPD. Eur Resp J. 2009;33:1165–85. 31. Saferali A, Lee J, Sin DD, et al. Longer telomere length in COPD patients with α1-antitrypsin deficiency independent of lung function. PLoS One. 2014;9, e95600. 3. Divo M, Cote C, de Torres JP, et al. Comorbidities and risk of mortality in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2012;186:155–61. 3. Divo M, Cote C, de Torres JP, et al. Comorbidities and risk of mortality in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2012;186:155–61. 32. Daniali L, Benetos A, Susser E, Kark JD, Labat C, Kimura M, Desai K, Granick M, Aviv A. Telomeres shorten at equivalent rates in somatic tissues of adults. Nat Commun. 2013;4:1597. 4. Ito K, Barnes PJ. COPD as a disease of accelerated lung aging. Chest. 2009; 135:173–80. 4. Ito K, Barnes PJ. COPD as a disease of accelerated lung aging. Chest. 2009; 135:173–80. 5. Maciewicz RA, Warburton D, Rennard SI. Can increased understanding of the role of lung development and aging drive new advances in chronic obstructive pulmonary disease? Proc Am Thorac Soc. 2009;6:614–7. 5. Maciewicz RA, Warburton D, Rennard SI. Can increased understanding of the role of lung development and aging drive new advances in chronic obstructive pulmonary disease? Proc Am Thorac Soc. 2009;6:614–7. 6. Mather KA, Jorm AF, Parslow RA, et al. Is telomere length a biomarker of aging? A review. J Gerontol A Biol Sci Med Sci. 2011;66(2):202–13. 6. Mather KA, Jorm AF, Parslow RA, et al. Is telomere length a biomarker of aging? A review. J Gerontol A Biol Sci Med Sci. 2011;66(2):202–13. 7. Armanios M. Telomeres and age-related disease: how telomere biology informs clinical paradigms. J Clin Invest. 2013;123:996–1002. 7. Armanios M. Telomeres and age-related disease: how telomere biology informs clinical paradigms. J Clin Invest. 2013;123:996–1002. 8. References Houben JM, Moonen HJ, van Schooten FJ, et al. Telomere length assessment: biomarker of chronic oxidative stress? Free Radic Biol Med. 2008;44:235–46. 9. Savale L, Chaouat A, Bastuji-Garin S, et al. Shortened telomeres in circulating leukocytes of patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2009;179:566–71. 10. Mui TS, Man JM, McElhaney JE, et al. Telomere length and chronic obstructive pulmonary disease: evidence of accelerated aging. J Am Geriatr Soc. 2009;57:2372–4. 11. Houben JM, Mercken EM, Ketelslegers HB, et al. Telomere shortening in chronic obstructive pulmonary disease. Respir Med. 2009;103:230–6. 12. Lee J, Sandford AJ, Connett JE, et al. The relationship between telomere length and mortality in chronic obstructive pulmonary disease (COPD). PLoS One. 2012;7, e35567. 13. Farzaneh-Far R, Lin J, Epel E, et al. Telomere length trajectory and its determinants in persons with coronary artery disease: longitudinal findings from the heart and soul study. PLoS One. 2010;5, e8612. 14. Celli BR, Cote C, Marin JM, Casanova C, et al. 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Evaluation of clinical methods for rating dyspnea. Chest. 1988;93:580e6. 19. Mahler D, Wells C. Evaluation of clinical methods for rating dyspnea. Chest. 1988;93:580e6. 20. Charlson M, Szatrowski T, Peterson J, et al. Validation of a combined comorbidity index. J Clin Epidemiol. 1994;47:1245e51. 20. Charlson M, Szatrowski T, Peterson J, et al. Validation of a combined comorbidity index. J Clin Epidemiol. 1994;47:1245e51. 21. Cawthon RM. Telomere measurement by quantitative PCR. Nucleic Acids Res. 2002;30, e47. 21. Cawthon RM. Telomere measurement by quantitative PCR. Nucleic Acids Res. 2002;30, e47.
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Development of a RP-HPLC method for determination of glucose in Shewanella oneidensis cultures utilizing 1-phenyl-3-methyl-5-pyrazolone derivatization
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PLOS ONE PLOS ONE RESEARCH ARTICLE Development of a RP-HPLC method for determination of glucose in Shewanella oneidensis cultures utilizing 1-phenyl-3- methyl-5-pyrazolone derivatization Norberto M. GonzalezID1*, Alanah Fitch1, John Al-Bazi2 1 Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States of America, 2 Department of Chemistry, Northeastern Illinois University, Chicago, IL, United States of America * ngonzalez7@luc.edu * ngonzalez7@luc.edu OPEN ACCESS Citation: Gonzalez NM, Fitch A, Al-Bazi J (2020) Development of a RP-HPLC method for determination of glucose in Shewanella oneidensis cultures utilizing 1-phenyl-3-methyl-5-pyrazolone derivatization. PLoS ONE 15(3): e0229990. https:// doi.org/10.1371/journal.pone.0229990 Editor: Tommaso Lomonaco, University of Pisa, ITALY Received: November 12, 2019 Accepted: February 18, 2020 Published: March 12, 2020 Copyright: © 2020 Gonzalez 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: © 2020 Gonzalez 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 A method was developed and validated for low-level detection of glucose. The method involves quantitation of glucose though derivitization with 1-phenyl-3-methyl-5-pyrazolone (PMP) and HPLC-DAD analysis. The developed method was found to be accurate and robust achieving detection limits as low as 0.09 nM. The applicability of the method was tested against microbial samples with glucose acting as a carbon fuel source. The method was shown to be able to accurately discriminate and quantify PMP-glucose derivatives within Shewanella oneidensis MR-1 samples. The method proved capable at examining glu- cose usage during the early hours of microbial growth, with detectable usage occurring as early as two hours. S. oneidensis cultures were found to grow more effectively in the pres- ence of oxygen which coincided with more efficient glucose usage. Glucose usage further increased in the presence of competing electron acceptors. The rate at which S. oneidensis reached exponential growth was affected by the presence of ferric iron under microaerobic conditions. Such samples reached exponential growth approximately two hours sooner than aerobic samples. Introduction Microorganisms can utilize organic material to facilitate culture growth, which can include simple organic carbons such as acetate, lactate, fumarate and, to a lesser extent, carbohydrates such as glucose [1–3]. Understanding the relative use of these substances may be important in a wide range of fields, one example of which is the use of a carbon source by bacteria for micro- bial fuel cell development. Data Availability Statement: https://doi.org/ Data Availability Statement: https://doi.org/10. 6084/m9.figshare.10062095.v1; https://doi.org/10. 6084/m9.figshare.11741700.v1; https://doi.org/10. 6084/m9.figshare.11741703.v1. Most methods are individual to the carbon source and may involve a wide number of strat- egies. In the case of glucose common methods include glucose assays [4], copper-iodometric methods [5], mass spectrometry [6], and chromatographic methods to include gas chromatog- raphy and high-performance liquid chromatography (HPLC) [7–9]. Glucose assays are among the fastest and simplest forms of analysis. They suffer, however, from high cost with numerous Funding: The authors received no specific funding for this work. Competing interests: The authors have declared that no competing interests exist. 1 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures samples and are limited to one or only a few reducing sugars. Furthermore, a survey of glu- coses assays available from leading manufacturers showed method sensitivities as low as 1 μM limiting their use for biological detections [10–13]. HPLC methods allow for a decrease in cost when testing numerous samples and for quanti- tation of various reducing sugars either individually or simultaneously. An increasing popular LC method involves the use of derivatizing reducing sugars like glucose with 1-phenyl- 3-methyl-5-pyrazolone (PMP) (Fig 1). First proposed by Honda et al. [14] the method involves directly reacting PMP with a reducing sugar under basic conditions to form a PMP-reducing sugar derivative that can be used for observing multiple reducing sugars simultaneously in the ultraviolet spectrum. While the method has been refined by various research groups [15–17] to include unicellular algae [18], the usefulness of the method for analysis of bacterial cultures has not been examined. Many current methods of PMP derivatization suffer from long reten- tion times exceeding 25 minutes and inconsistent reaction times ranging from 30–120 min- utes. Further, many methods suffer from a lack of full validation for LC methods set by such governing agency as the International Council on Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) [19,20]. Proper method validation would improve method robustness and repeatability. In this study, a modified PMP method was developed for examining glucose. The method focuses on achieving decreased run times, improved method robustness through method vali- dation, and achieving lower detection limits not previously seen in similar works. The applica- bility of the method was tested using the microorganism Shewanella oneidensis MR-1 and examines the rate of glucose consumption by the microbe over time. Data Availability Statement: https://doi.org/ Several publications attempted to address the ability of Shewanella to utilize glucose utilizing different instrumental Fig 1. A reaction scheme for the formation of PMP-Glucose. One equivalent of glucose reacts with two equivalents of PMP to form one equivalent of PMP-Glucose under basic conditions. Fig 1. A reaction scheme for the formation of PMP-Glucose. One equivalent of glucose reacts with two equivalents of PMP to form one equivalent of PMP-Glucose under basic conditions. Fig 1. A reaction scheme for the formation of PMP-Glucose. One equivalent of glucose reacts with two equivalents of PMP to form one equivalent of PMP-Glucose under basic conditions. n of PMP-Glucose. One equivalent of glucose reacts with two equivalents of PMP to form one equivalent of PMP-Glucose https://doi.org/10.1371/journal.pone.0229990.g001 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 2 / 13 PLOS ONE Determination of glucose in Shewanella oneidensis cultures determinations of glucose. Work conducted by Nakagawa et al. [21] utilized a genetically altered Shewanella strain and enzymatic assays for glucose measurements. Howard et al. [22] also utilized a mutated Shewanella strain, however, the group incorporated LC method with refractive index (RI) detection for glucose detection. Likewise, Choi et al. [23] also incorpo- rated the use of LC and RI detection of glucose used by a mutated Shewanella strain. Rosen- baum et al. [24] used a wild type from of Shewanella and HPLC with pulsed amperometric detection (PAD) for quantifying glucose in growth cultures. Although these works have dem- onstrated that refractive index detectors can detect glucose in growth media, RI detectors suf- fer from limited sensitivity and gradient incompatibilities that reduces their ability to achieve low detection limits. S. oneidensis was chosen as the model for three reasons. Firstly, the organism, in general, is of intense interest due to its utilization in microbial fuel cells [25–29]. S. oneidensis is a faculta- tive anaerobe used in microbial fuel cells (MFC), and has been shown to be well adapted at using small carbon compounds as a fuel source [30,31]. The microbe has shown difficulty uti- lizing larger carbon compounds like glucose primarily due to a lack of key enzymes required for glycolysis [22,32–36]. However, some research has suggested Shewanella can utilize glucose when the microbe is allowed to condition in a glucose containing solution, or when the microbe has adapted it metabolism to an oxygenated environment prior to growth [37]. Instrumentation The method development and validation experiments were performed using an Agilent Tech- nologies 1100 Series HPLC system equipped with a quaternary pump, auto sampler, and a diode array detector. The chromatographic data were obtained using Agilent Technologies ChemStation for LC Rev.A10.02[1757] software. The column used was a YMC-Pack ODS-AQ with a column length of 150 mm, an inside diameter of 4.6 mm and a particle size of 3 microns. Standards and reagents The mobile phase organic solvent acetonitrile was purchased from Fisher Chemical and was of HPLC grade. Potassium phosphate dibasic was purchased from Sigma-Aldrich and was of ACS grade. The glucose standard was purchased from Fisher Chemical and was of ACS grade. The derivatizing reagent 1-phenyl-3-methyl-5-pyrazolone (PMP) was purchased from Sigma- Aldrich and was of ACS grade. The tryptic soy broth (TSB) growth medium was purchased from Sigma-Aldrich and was of microbiology grade. Iron oxide and iron chloride were pur- chased from Fisher Chemical and were of reagent grade. The Shewanella oneidensis MR-1 microbe were purchased from ATCC as a frozen culture. Data Availability Statement: https://doi.org/ Sec- ondly, the use of PMP derivatization and HPLC analysis has not been previously seen for tracking carbohydrate utilization by S. oneidensis. Finally, current literature has focused on the utilization of glucose over an extended growth window. Few publications have focused on examining the use of glucose during early (0–15 hours) microbial growth and at which point glucose utilization begins. Preparation of standard solutions and samples Stock solutions. Solutions of PMP were prepared by dissolving 87 mg of PMP in 1 mL of methanol to yield a 0.5 M stock solution of PMP-methanol. Glucose stock solutions were pre- pared by dissolving 0.125 g of glucose in 50 mL of deionized water to yield a 0.0139 M stock solution of glucose. The appropriate aliquot of 0.0139 M glucose stock was used for all other PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 3 / 13 PLOS ONE Determination of glucose in Shewanella oneidensis cultures stock solution preparations. Solutions of TSB were prepared by dissolving 30 g of TSB in 1 L of deionized water. All TSB solutions were autoclaved after preparation. For TSB containing fer- ric iron, both soluble and insoluble iron was first dissolved in the TSB prior to incubation. Standard solutions. Standards of PMP-glucose were prepared by combining 800 μL of a 0.0139 M solution of glucose with 800 μL each of 0.5 M NaOH and 0.5 M solution of PMP in methanol to yield a solution at a pH of 13. The reaction was carried out at 70˚C with agitation every 30 minutes. After derivatization, the solution was neutralized at 4˚C with 800 μL 0.5 M HCl. Reaction impurities were extracted using 2 mL of dichloromethane. The solution was mixed vigorously for 30 seconds and centrifuged at 4˚C and 5000 rpm for 5 mins. The dichlor- omethane extraction was repeated twice more for a total of 3 extractions. The upper aqueous layer containing the PMP-glucose was removed for analysis. Sample solutions. The TSB was prepared by autoclaving 80 mL of the growth media. Media designated as microaerobic was purged with nitrogen gas as the media cooled to room temperature. Media designed as aerobic was saturated with oxygen gas for 10 minutes. The samples were prepared by adding 1 mL of a S. Oneidensis MR-1 containing solution to the 80 mL of autoclaved TSB. The microaerobic flasks were sealed with a septa cap to prevent addi- tional oxygen exposure while aerobic flasks were covered with foil. Samples were placed in an incubator set at a temperature of 30˚C and a shake speed of 150 rmp. The samples were set to grow for 15 hours with sampling occurring throughout the growth period. S. oneidensis samples. The analysis of glucose occurred utilizing a single growth culture. Preparation of standard solutions and samples Samples extracted from a single culture over a 15-hour incubation period exhibited greater reproducibility when compared to sampling a new culture for every hour of analysis. Addi- tionally, utilizing a single growth culture allowed for samples to be collected every 15–30 min- utes when samples exhibited exponential growth. All results were replicated with a second growth culture. Microbial growth was normalized, and the glucose utilization was averaged. Samples extracted from a single culture over a 15-hour incubation period exhibited greater reproducibility when compared to sampling a new culture for every hour of analysis. Addi- tionally, utilizing a single growth culture allowed for samples to be collected every 15–30 min- utes when samples exhibited exponential growth. All results were replicated with a second growth culture. Microbial growth was normalized, and the glucose utilization was averaged. Microbial samples were inoculated in 80 mL of TSB and allowed to incubate under microaero- bic and aerobic conditions for 15 hours at 30˚C. At various intervals over the growth period, the growth of the microbe was determined by examining its turbidity at 650 nm, and 1 mL of growth media was collected for analysis by HPLC. Growth media samples were derivatized and examined by HPLC in the same manner as the method development and validation samples. Preparation steps included centrifugation of the samples and extraction of the sample supernatant. Microbial samples were inoculated in 80 mL of TSB and allowed to incubate under microaero- bic and aerobic conditions for 15 hours at 30˚C. At various intervals over the growth period, the growth of the microbe was determined by examining its turbidity at 650 nm, and 1 mL of growth media was collected for analysis by HPLC. Growth media samples were derivatized and examined by HPLC in the same manner as the method development and validation samples. Preparation steps included centrifugation of the samples and extraction of the sample supernatant. PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 Optimization of chromatographic parameters Peak area of PMP-Glucose as a function of derivatization reaction time. The peak area of PMP-Glucose remains that the reaction has reached completion. https://doi.org/10.1371/journal.pone.0229990.g002 https://doi.org/10.1371/journal.pone.0229990.g002 3 μm) column was selected which provided a uniform peak with adequate resolution. A 3 μm YMC guard column with a 4.0 mm inside diameter was used to prolong the life of the column. Gradient selection. The separation of PMP-glucose from the corresponding matrix was of interest. This was achieved utilizing a segmented gradient which consisted of 15 mM potas- sium phosphate dibasic buffer at a pH of 7.2 (Eluent A) and ACN (Eluent B) (Table 1). This gradient provided a reasonable retention time of 16.7 min with significant resolution between the peak of interest and the sample matrix (Fig 3A and 3B). Optimization of chromatographic parameters Wavelength selection. The wavelength used for the detection of PMP-glucose was selected by the analysis of glucose, PMP, and PMP-glucose on an offline UV detector. The λmax for PMP- glucose was selected to be 245 nm. The UV spectrum of PMP-glucose using a DAD was used as further evidence for the location of the PMP-glucose peak in sample chromatograms. g g g by the analysis of glucose, PMP, and PMP-glucose on an offline UV detector. The λmax for PMP- glucose was selected to be 245 nm. The UV spectrum of PMP-glucose using a DAD was used as further evidence for the location of the PMP-glucose peak in sample chromatograms. Reaction optimization. The optimal reaction time for the derivatization was performed by multiple reactions ranging from 30 to 150 min. Reaction mixtures were injected and the peak areas were determined and plotted against the reaction time (Fig 2). The optimal reaction time was determined to be 90 minutes, when an increase in the PMP-glucose peak area was no longer observed, indicating that the reaction was complete. Reaction optimization. The optimal reaction time for the derivatization was performed by multiple reactions ranging from 30 to 150 min. Reaction mixtures were injected and the peak areas were determined and plotted against the reaction time (Fig 2). The optimal reaction time was determined to be 90 minutes, when an increase in the PMP-glucose peak area was no longer observed, indicating that the reaction was complete. Column selection. Both reversed-phase and normal-phase columns were tested for method development using a mobile phase consisting of 15 mM potassium phosphate dibasic pH 7.2 and ACN. Selection of the appropriate column was determined by injecting a sample of PMP-glucose and observing the overall separation and peak characteristics. Based on the anal- ysis of six C18, two amino, and two phenyl columns, a YMC-Pack ODS-AQ (150 x 4.6 mm, 4 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures Fig 2. Peak area of PMP-Glucose as a function of derivatization reaction time. The peak area of PMP-Glucose remains constant after 90 minutes indicating that the reaction has reached completion. Fig 2. Peak area of PMP-Glucose as a function of derivatization reaction time. The peak area of PMP-Glucose remains constant after 90 minutes indicating that the reaction has reached completion. Fig 2. PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 Method validation System suitability. To ensure reliability of the developed method, five injections of an 8.33 mM PMP-glucose sample were performed. The separation parameters were evaluated for each injection to ensure the resolution and reproducibility of the system was adequate (Table 3). Based on the acceptance criteria for each parameter, it was determined that the selected method parameters were acceptable. Specificity. Specificity studies were performed to ensure no co-eluting impurities with the peak of PMP-glucose. Forced degradation was performed as part of the peak purity studies [19,20,38]. Samples of 1 mL PMP-glucose were subjected to acid and base degradation using 1 mL of various concentrations of HCl and NaOH. The degraded solutions were neutralized with the appropriate acid or base. Oxidation degradation was assessed using l mL of various percentages of hydrogen peroxide. Additionally, l mL of PMP-glucose was subjected to heat and UV degradation. The percent degradation for PMP-glucose was assessed utilizing HPLC. The results showed the greatest degradation occurring under both 3 M NaOH and HCl as well as 0.001% hydrogen peroxide. The determination of peak purity was conducted by combining 100 μL of the samples sub- jected to 0.001% H2O2, 3 M NaOH, and 3 M HCl degradation and injecting this mixture into the HPLC system. Successive scans of the PMP-glucose peak were conducted and overlaid to determine the purity. From these scans, PMP-glucose peak was determined to have a purity of 99.9%. This value is well within the acceptance criteria of 99%. These results indicate that impurities within the reaction mixture will not interfere with the PMP-glucose peak. Robustness. The robustness of the method was tested to measure its capacity to remain unaffected by small variations in the method parameters. Robustness was particularly focused on the resolution of PMP-glucose from adjacent peaks. Small variations in the method param- eters were studied by deliberately changing the wavelength, flow rate, buffer pH and ionic strength, and the temperature of the column. Acceptance criteria for method robustness have not been set by the ICH, therefore a lower specification limit (LSL) of 1.5 (baseline resolution) Table 3. System suitability study. Method development 6 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures Table 2. Summery of method parameters. Column YMC Pack ODS-AQ (150 x 4.6 mm, 3 μm) Injection Volume 5 μL Mobile Phase Eluent A: 15 mM Potassium Phosphate Dibasic pH 7.2 Eluent B: 100% ACN Flow Rate 1 mL/min Column Temperature 29.5˚C Wavelength 245 nm Run Time 35 min Equilibration Time 10 min https://doi.org/10.1371/journal.pone.0229990.t002 Method development Development of the method focused on maximizing the peak area and theoretical plates while achieving adequate resolution. Optimization of the method parameters examined the effect of varying injection volume, flow rate, temperature, and buffer pH and ionic strength. Based on these studies, the optimal method parameters were selected (Table 2). The method showed a substantial decrease of 10–15 minutes in run time when compared to many other PMP methods. Table 1. Segmented gradient profile. Percent composition Time (Min) Eluent A Eluent B 0 90 10 9 86 14 30 36 64 35 36 64 https://doi.org/10.1371/journal.pone.0229990.t001 Table 1. Segmented gradient profile. 5 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures The decrease in retention time can be attributed to two factors. The column used was 100 h t d h d ll ti l i th th d b th k [15 18] M Fig 3. Representative chromatograms for a) blank TSB growth media and b) TSB supernatant extracted from a S. oneidensis culture. https://doi.org/10.1371/journal.pone.0229990.g003 LOS ONE Determination of glucose in Shewanella oneidensis cultures Fig 3. Representative chromatograms for a) blank TSB growth media and b) TSB supernatant extracted from a S. oneidensis culture. Fig 3. Representative chromatograms for a) blank TSB growth media and b) TSB supernatant extracted from a S. oneidensis culture. https://doi.org/10.1371/journal.pone.0229990.g003 The decrease in retention time can be attributed to two factors. The column used was 100 mm shorter and had a smaller particle size than those used by other works [15–18]. More importantly, the mobile phase was changed to a phosphate buffer as opposed to the commonly seen acetate buffer. The result is a weaker interaction between PMP-glucose with the stationary phase due to an increase in mobile phase pH. Increasing the mobile phase pH consequently decreased the retention time of PMP-glucose. The decrease in retention time can be attributed to two factors. The column used was 100 mm shorter and had a smaller particle size than those used by other works [15–18]. More importantly, the mobile phase was changed to a phosphate buffer as opposed to the commonly seen acetate buffer. The result is a weaker interaction between PMP-glucose with the stationary phase due to an increase in mobile phase pH. Increasing the mobile phase pH consequently decreased the retention time of PMP-glucose. Method validation Parameter Acceptance Criteria Mean Values (n = 5) Plate Number  2000 399586 ± 39.7 Tailing Factor (Tf) 0.9  Tf  2 1.242 ± 0.00242 Resolution  1.5 7.213 ± 0.0004 % RSD Retention Time  2% 0.0299 ± 0.0005 % RSD Peak Area  2% 1.97 ± 0.0835 % Drift Peak Area  2% 1.09 ± 0.0604 https://doi.org/10.1371/journal.pone.0229990.t003 7 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 7 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures was established as the acceptance criteria. After testing each condition in triplicates, the study showed the method was unaffected by small variations in method parameters and therefore is considered robust (S1 Table). Limit of quantitation and detection. The limit of quantitation (LOQ) and the limit of detection (LOD) for the method were determined by measuring the magnitude of the PMP- glucose peak height to the magnitude of the baseline noise (S/N). A S/N ratio of 10 is accept- able for the LOQ and 3 for the LOD. The LOQ was found to be 0.2 nM with a S/N ratio of 9.8, and the LOD was found to be 0.09 nM with a S/N ratio of 3.7. The values for LOQ and LOD were performed in triplicates. The limit of detection of was found to be an order of magnitude lower than the lowest known LOD for glucose utilizing similar instrumentation [39]. The lower detection limit can be attributed to the use of a column with a particle size of 3 microns when compared to the 5 microns used for other works. Reducing the particle size resulted in an increase in theoretical plates and sharper PMP-glucose peak. Linearity and range. Linearity studies were conducted to measure how well a calibration plot of peak area versus concentration approximates a straight line. Several glucose concentra- tions covering the range of 16.65 mM to 0.2 nM (the LOQ) were tested. The expected maxi- mum glucose concentration within a sample was 13.87 mM (2.5 g/L). The upper range corresponds to 120% of the maximum glucose concentration within TSB while the lower limit was set to the limit of quantitation, 0.2 nM. A linear regression equation was then processed along with a correlation coefficient (S1 Fig). The correlation coefficient of 0.999 meets the acceptance criteria of  0.999. Method validation The calculated percent bias was determined to be 0.65% meet- ing the ICH guideline of NMT ± 3% indicating the results are not forced though the origin. Accuracy. The accuracy of the method was determined by investigating how closely the test results reflect the true value. The accuracy was conducted by preparing 3 samples of PMP- glucose in the range of 0.5 to 2.5 g/L. All 3 samples were performed in triplicates. Based on the linear regression equation, the recovered concentrations were calculated. The percent recovery fell within the acceptance range of 98–102% (S2 Table). Precision. The injection precision for the method was tested to measure how similar the results are with repeated injections. A 2.5 g/L sample of PMP-glucose was prepared and injected six times. After averaging the peak areas, a percent RSD of 0.093% was calculated. This value is within the acceptance criteria range of a %RSD  1.5% (S3 Table). The method precision was conducted to measure how similar the results are among sepa- rate stock solutions. Six samples of PMP-glucose were prepared from separate stock solutions at a concentration of 2.5 g/L and diluted to 1.5 g/L. After injecting each sample, the peak areas were average together and a percent relative standard deviation of 0.16% was calculated (S3 Table). This value meets the acceptance criteria of a percent RSD  1.5%. PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 Method application The applicability of the method was investigated through the quantitation of glucose con- sumed by S. oneidensis during early growth development. Cell cultures were grown for 15 hours. The turbidity of the cultures was measured at 30 to 60 minute intervals. The optical density achieved was dependent on the growth conditions (Fig 4A). The maximum growth was highest under aerobic compared to microaerobic conditions with oxygen rich cultures exhibiting 5 times the turbidity achieved by their oxygen deficient counterparts. The optical density disparity between the microaerobic and aerobic cultures correlates to the use of glucose by S. oneidensis (Fig 4B). Aerobic cultures utilized the most glucose after 15 hours. The addi- tion of oxygen in the growth media resulted in a 2-fold increase in glucose utilization com- pared to microaerobic cultures. Microaerobic cultures containing Fe(III) as the predominate 8 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures E | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 9 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 9 / 13 PLOS ONE Determination of glucose in Shewanella oneidensis cultures Fig 4. A comparison of a) S. oneidensis growth to b) the microbe’s utilization of glucose after 15 hours and c) after 2 hours of initial growth. Glucose usage increases with increasing oxygen concentration and upon the addition of ferric iron. Fig 4. A comparison of a) S. oneidensis growth to b) the microbe’s utilization of glucose after 15 hours and c) after 2 hours of initial growth. Glucose usage increases with increasing oxygen concentration and upon the addition of ferric iron. electron acceptor exhibited a more rapid onset of exponential growth compared to all other growth conditions (Fig 5A). These results agree with S. oneidensis’s ability to use various termi- nal electron acceptors to sustain growth [39–41]. Additionally, this early onset correlates to the time at which glucose begins to be utilized (Fig 5B). The strength of the method is apparent when examining culture samples grown for two hours. Of the six culture types, the method could detect glucose across all but the microaerobic culture (Fig 4C). Measured glucose usage after five hours ranges between 9 to 40 mg/L. Comparable utilization times have not been reported in previous glucose studies [21–23]. Fig 5. Conclusions An accurate and robust method was developed for analysis of glucose by derivatization with 1-phenyl-3-methyl-5-pyrazolone (PMP). The developed method focused on achieving low detection limits and reduced run times when compared to similar works. The applicability of the method was tested on microbial samples and was shown to be capable in determining the levels of glucose throughout the growth of Shewanella oneidensis MR-1. The developed method was sensitive and capable quantify glucose usage in microbial cultures after only two hours. Supporting information S1 Fig. Linearity of PMP-glucose with increasing the LOQ (0.2 nM) while the upper limit correspond (3 g/L). (TIF) S1 Table. Robustness study. (DOCX) S2 Table. Accuracy study. (DOCX) S3 Table. Precision studies. (DOCX) S1 Fig. Linearity of PMP-glucose with increasing concentration. The lower limit represe the LOQ (0.2 nM) while the upper limit corresponds to 120% of the expected glucose in T (3 g/L). (TIF) S1 Table. Robustness study. (DOCX) S2 Table. Accuracy study. (DOCX) S3 Table. Precision studies. (DOCX) S1 Fig. Linearity of PMP-glucose with increasing concentration. The lower limit represents the LOQ (0.2 nM) while the upper limit corresponds to 120% of the expected glucose in TSB (3 g/L). S1 Fig. Linearity of PMP-gluco the LOQ (0.2 nM) while the upp (3 g/L). (TIF) S1 Table. Robustness study. (DOCX) S2 Table. Accuracy study. (DOCX) S3 Table. Precision studies. (DOCX) Method application Normalized results for a) optical density and b) glucose usage. The onset of exponential growth appears sooner for microaerobic samples containing ferric iron in the growth media, which also correlates to the time at which glucose utilization becomes more rapid. https://doi.org/10.1371/journal.pone.0229990.g005 Fig 5. Normalized results for a) optical density and b) glucose usage. The onset of exponential growth appears sooner for microaerobic samples containing ferric iron in the growth media, which also correlates to the time at which glucose utilization becomes more rapid. https://doi.org/10.1371/journal.pone.0229990.g005 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 10 / 13 PLOS ONE Determination of glucose in Shewanella oneidensis cultures Interestingly, the method revealed an ability of S. oneidensis to utilize a combination of elec- tron acceptors to facilitate both microbial growth and consumption of glucose. These results agree with those proposed by Choi et al. [23] and Serres and Riley [32] indicating that S. onei- densis can grow in the presence of glucose only once oxygen is present within the media envi- ronment. When oxygen is limited, S. oneidensis exhibited stunted growth regardless of the presence of ferric iron. Further evidence for stunted growth comes when examining the two- hour growth cultures. Microaerobic cultures, except for those cultures containing iron chlo- ride, did not register glucose usage suggesting the microbe has difficulty using glucose under these conditions. These results may indicate that oxygen is the preferred electron acceptor, and that the use of glucose when iron chloride is present may occur though a separate metabolism. Acknowledgments We are grateful to the Department of Chemistry at Northeastern Illinois University for provid- ing resources critical to sample analysis. We are grateful to the Department of Chemistry at Northeastern Illinois University for provid- ing resources critical to sample analysis. References 1. Lovley DR, Phillips EJP. Novel Mode of Microbial Energy Matabolism: Organic Carbon Oxidation Cou- pled to Dissimilatory Reduction of Iron or Manganese. Appl Environ Microbiol 1988; 54(6):1472–1480. PMID: 16347658 2. Myers CR, Myers JM. 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Isr J Chem 2016:1–5. 17. Author Contributions Conceptualization: Norberto M. Gonzalez. Formal analysis: Alanah Fitch, John Al-Bazi. Investigation: Norberto M. Gonzalez. Methodology: Norberto M. Gonzalez. Supervision: Alanah Fitch, John Al-Bazi. Validation: John Al-Bazi. Conceptualization: Norberto M. Gonzalez. Conceptualization: Norberto M. Gonzalez. Formal analysis: Alanah Fitch, John Al-Bazi. Investigation: Norberto M. Gonzalez. Methodology: Norberto M. Gonzalez. Supervision: Alanah Fitch, John Al-Bazi. Validation: John Al-Bazi. 11 / 13 PLOS ONE | https://doi.org/10.1371/journal.pone.0229990 March 12, 2020 PLOS ONE Determination of glucose in Shewanella oneidensis cultures Writing – original draft: Norberto M. Gonzalez, Alanah Fitch, John Al-Bazi. Writing – original draft: Norberto M. Gonzalez, Alanah Fitch, John Al-Bazi. Writing – original draft: Norberto M. Gonzalez, Alanah Fitch, John Al-Bazi. Writing – review & editing: Norberto M. Gonzalez, Alanah Fitch, John Al-Bazi. 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Solving Steady-State Wave Responses of One-Dimensional Multi-Degree-of-Freedom Lattices with Strong Nonlinearities Based on an Improved Incremental Harmonic Balance Method
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Solving Steady-State Wave Responses of One- Dimensional Multi-Degree-of-Freedom Lattices with Strong Nonlinearities Based on an Improved Incremental Harmonic Balance Method Hongyu Wang  Dalian University of Technology Xuefeng Wang  (  xwang201@eng.ua.edu ) Peking University https://orcid.org/0000-0002-9071-6322 Jian Zhao  Dalian University of Technology Jian Zhang  Dalian University of Technology Yu Huang  Dalian Ocean University Hongyu Wang  Dalian University of Technology Xuefeng Wang  (  xwang201@eng.ua.edu ) Peking University https://orcid.org/0000-0002-9071-6322 Jian Zhao  Dalian University of Technology Jian Zhang  Dalian University of Technology Yu Huang  Dalian Ocean University Research Article Keywords: strong nonlinearity, incremental harmonic balance method, wave problem, delay differential equation Posted Date: May 25th, 2022 DOI: https://doi.org/10.21203/rs.3.rs-1589885/v1 * Jian Zhao, Email: jzhao@dlut.edu.cn * Xuefeng Wang, Email: wang_xf@pku.edu.cn * Jian Zhao, Email: jzhao@dlut.edu.cn * Xuefeng Wang, Email: wang_xf@pku.edu.cn DOI: https://doi.org/10.21203/rs.3.rs-1589885/v1 DOI: https://doi.org/10.21203/rs.3.rs-1589885/v1 License:   This work is licensed under a Creative Commons Attribution 4.0 International License. License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Abstract The nonlinearity plays an important role in modulation of wave propagation characteristics, such as the adjustment of band structures by media nonlinearities. When strong nonlinearities are involved in a multi-degree-of-freedom (multi-DoF) wave propagation problem, traditional methods have difficulties to solve it accurately and efficiently due to the growth of dimensions. An algorithm based on an improved incremental harmonic balance (IHB) method is developed in this work to obtain steady-state solutions of a general wave problem with complex nonlinearities. A multi-DoF wave problem is firstly transformed to a delay differential equation (DDE), and Jacobian matrices of a harmonic balanced residual of the DDE can be directly constructed by conducting fast Fourier transform of the residual without any numerical integration. The algorithm decouples wave vectors from basis functions to significantly reduce the number of the functions, and it is more efficient than that based on a traditional IHB method of solving a wave problem, especially for the case that high-order basis functions are involved to handle strong nonlinearities. Moreover, the nonlinear wave problem can be solved when frequencies are given and wave vectors unknown, which is a challenge of a traditional IHB method. In this work, one- dimensional diatomic lattices with Hertz contact law and cubic spring models are studied as examples, where dispersion curves and bandgap properties are generated. Results show that it is necessary to use high-order Fourier functions to obtain accurate steady-state responses when strong nonlinearities exist. Results also show that the convergence rate of the method with use of a fixed frequency is faster than that of a fixed wave vector. Keywords: strong nonlinearity, incremental harmonic balance method, wave problem, delay differential equation Keywords: strong nonlinearity, incremental harmonic balance method, wave problem, delay differential equation Solving Steady-State Wave Responses of One- Dimensional Multi-Degree-of-Freedom Lattices with Strong Nonlinearities Based on an Improved Incremental Harmonic Balance Method1 Hongyu Wang a, Xuefeng Wang b, *, Jian Zhao a, *, Jian Zhang a, Yu Huang c a State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian, China. b Department of Advanced Manufacturing and Robotics, College of Engineering, Peking University, Beijing, China. c College of Ocean and Civil Engineering, Dalian Ocean University, Dalian, China. c College of Ocean and Civil Engineering, Dalian Ocean University, Dalian, China. 1. Introduction Dispersion is an important characteristic of wave propagation, which attracts attentions of many researchers. Interesting phenomena of dispersion were found in previous studies, such as stop-bands, pass-bands, adjustable band gaps, etc., and these phenomena can be influenced by materials and media structures [1], e.g., band structures can be significantly varied by changing media nonlinearities [2, 3]. Many devices were implemented in different applications with use of dispersion characteristics, such as vibration/noise reductions and acoustic modulators [4-6]. Wave propagation problems are usually modeled as linear systems when media are weakly excited, where wave properties, such as dispersion, can be analytically studied [7]. The linear assumption is an appropriate approach to describe wave motions under small excitations, but it is inaccurate to calculate general wave motions under strong excitations that generate strong nonlinearities. To understand wave propagation in general cases and develop effective methods to control wave characteristics, many researchers paid attentions to obtain dynamic responses of nonlinear wave problems. The nonlinearity of a wave propagation system can be caused by medium structures (e.g. the cubic spring [8]), contact models (e.g. Hertz contact law [9]), external excitations (e.g. electrostatic [10] and electromagnetic forces [11]), etc. Periodic responses of wave problems with nonlinearities can be solved by linearization methods, numerical and experimental methods, perturbation methods, and incremental harmonic balance (IHB) methods. For the case of complex wave propagation problems with strong nonlinearities, it is usually difficult to calculate steady-state solutions accurately and effectively. In some studies, propagation characteristics were obtained by linear approximation, where effects of nonlinear interactions were ignored [12]. Numerical methods, such as Runge-Kutta methods and numerical simulations [13-18], were used to verify dispersion properties. Perturbation and incremental harmonic balance (IHB) methods are semi-analytical methods to study nonlinear differential equations. Perturbation methods were used in solving weakly nonlinear wave problems [19-23]. Vakakis et al. [8, 24] used a multi-scale perturbation method to study a nonlinear periodic system with external excitations. In the work, a spatial multi-scale method was used to study a single-coupled periodic system with cubic nonlinearities, and amplitude-dependent nonlinear wave propagation characteristics were obtained [8]. An asymptotic method was developed to study nonlinear standing waves, which is suitable for problems with weak nonlinearities under small vibrations [24]. Sreelatha et al. [25] used the perturbation method to study propagations of nonlinear waves in a two-dimensional heterogeneous lattice. 1. Introduction In this work, three cases of quadratic, cubic, and quadratic-cubic-combined nonlinearities were involved, and solutions with weak nonlinearities were obtained. Narisetti et al. [26, 27] used a perturbation method to study wave propagations in discrete nonlinear structures, where amplitude-dependent characteristics were obtained. This method was extended to wave propagation problems in a two-dimensional periodic lattice with weak nonlinearities. However, the perturbation method will be inaccurate when complex and strong nonlinearities are introduced [28]. At this time, the IHB method can be employed to solve such strong nonlinear problems. The IHB method was first proposed by Lau and Cheung, which is a combination of Newton's method and Galerkin process [29, 30]. The IHB method was mainly used to obtain steady-state solutions of vibrations in past works [31-33]. Since dispersion is the characteristic of steady-state waves, the IHB method was used to study the nonlinear filtering characteristics of a 1D atomic chain in a low-frequency range [34]. It was found that the movements of the band-gap depends on the degree of nonlinearities. A general IHB method was proposed in [9] to study propagations of plane waves in periodic media with strong nonlinearities, and the method was verified by comparing dispersion curves with a numerical method. In the work [35], the IHB method was used in the study of nonlinear elastic waves, and diode effects were observed through experiments. In the above IHB methods, wave responses are obtained only if wave vectors are given, which cannot hold for many cases. When wave responses are expected to be controlled at a certain external excitation frequency, the wave vector is unknown and has to be calculated as a variable. On the other hand, the number of basis functions used in the above IHB methods for wave problems is much larger than that of harmonic terms of wave responses, since the basis functions are made of many sets of harmonic functions with different phases that are multiples of wave vectors. Practically, to avoid complex and time-consuming Galerkin integration calculations, low-order trigonometric functions were usually used as basis functions in a traditional IHB method, which will reduce the accuracy when strong nonlinearities are involved. Based on the original IHB method, Wang [36] developed a new IHB method to solve wave problems of 1D nonlinear single-degree-of-freedom (single-DoF) systems. 1. Introduction The key of this method is to transform the governing equation of a nonlinear wave problem into a delayed differential equation (DDE) with multiple delays and advances [37], and then the DDE can be solved by an improved IHB method [28]. It was proved that steady-state solutions of the original wave problem are the same as those of the transformed DDE. The advantage of this transformation approach is that the wave vector will be decoupled from basis functions and it can be served as a variable in the DDE. Thus, this method significantly reduces the number of basis functions, as well as the dimension of general coordinates, in a IHB method, and is capable to solve wave responses at a given excitation frequency. The method was used to calculate wave responses of 1D single-DoF systems [36]. Multi-degree-of-freedom (multi-DoF) systems are more general and complicated due to coupling of DoFs. The expression of the Jacobian matrix is more complicated and cannot be obtained directly by the above method. Thus, a method for solving multi-DoF wave problems will be derived here. The method will be extended to solve steady- state responses of wave propagations at a fixed frequency, and its performance will be studied. There are three main contributions in this paper. First, a general method to obtain steady-state solutions of multi-DoF wave propagation problems is developed. The method can be more efficient than traditional IHB methods of solving wave problems when high-order basis functions are involved to handle strong nonlinearities. Second, results of this work show that it is necessary to use high-order Fourier functions to obtain accurate steady-state wave responses when strong nonlinearities exist, which was not been explicitly recognized in past works since only low-order Fourier functions were used to solve wave problems. Third, the method can be used to calculate steady-state wave responses and wave vectors simultaneously when excitation frequencies are given, and results also show that the convergence rate of solving steady-state responses at a fixed frequency is faster than that at a fixed wave vector. This article consists of four sections. In the next section, the IHB method is developed by transforming multi-DoF wave propagation problems into multi-DoF DDEs when frequencies or wave vectors are given. 1. Introduction In the third section, two examples, including a 1D diatomic lattice model with a Hertz contact law and a cubic-stiffness spring, are used to show the results and performance of the proposed IHB method. The fourth section summarizes outcomes of this work. 2.1 Transformation of Multi-DoF Wave Problems to DDEs (1), the number i can be set to zero to simplify the expression: ( ( ) ) ( , , , , , ) 0 n n L R F U U U U t − +   = (3) ( ( ) ) ( , , , , , ) 0 n n L R F U U U U t − +   = (3) ( ( ) ) ( , , , , , ) 0 n n L R F U U U U t − +   = (3) and the steady-state solution of the j-th unit can be written as and the steady-state solution of the j-th unit can be written as and the steady-state solution of the j-th unit can be written as ( ) ( ) j j U U t T  = − (4) ( ) ( ) j j U U t T  = − (4) ( ) ( ) j j U U t T  = − (4) where Tj represents the j-th time-delay term where Tj represents the j-th time-delay term where Tj represents the j-th time-delay term where Tj represents the j-th time-delay term , , , j L R T j j n n  = = − + (5) (5) n which μ represents the value of the wave vector in the 1D medium. Thus, the DDE can be written as ( ( ) ) ( , , , , , , ) 0 n n L R F U U U U t  − +   = (6) ( ( ) ) ( , , , , , , ) 0 n n L R F U U U U t  − +   = (6) It is noted that in Eq. (6), both time-lag and time-advance terms are included. It is noted that in Eq. (6), both time-lag and time-advance terms are included. 2.1 Transformation of Multi-DoF Wave Problems to DDEs Suppose that when a traveling wave reaches a steady state in an infinite periodic medium, each particle vibrates with a specific phase difference from adjacent particles, and motions of all particles are periodic in space. Therefore, steady-state solutions of a 1D multi-DoF wave problem can be obtained by solving periodic solutions of a multi-DoF DDE. First, the construction of the DDE is shown as follows. The governing equation of the 1D multi-DoF wave problem with a general nonlinearity can be written as ( ) ( ) ( ) ( ) ( , , , , , ) 0 i n i n i i L R F U U U U t − +   = (1) (1) where ( ) F  is a nonlinear function to describe the wave propagation, t is the time variable, the prime represents the time derivative, ( )i U represents motions of particles in the i-th period unit in the medium, and nL and nR represent numbers of units on the left and right, respectively, which have effects on the unit i. For a 1D medium with n particles appearing periodically, the number of particles in a period unit of the wave shape is n, and ( )i U is an n-dimensional vector: represents the time derivative, ( )i U represents motions of particles in the i-th period unit in the medium, and nL and nR represent numbers of units on the left and right, respectively, which have effects on the unit i. For a 1D medium with n particles appearing periodically, the number of particles in a period unit of the wave shape is n, and ( )i U is an n-dimensional vector: ( ) ( ) ( ) ( ) 1 2 , , , i T i i i n U u u u   =   (2) (2) where ( ) i k u is the motion of the k-th particle in the i-th period unit with k=1, …, n. Thus, function ( ) F  has n components 1 [ , , ]T n F F F = . has n components 1 [ , , ]T n F F F = . In Eq. (1), the number i can be set to zero to simplify the expression: In Eq. 2.2 Construction of Multi-DoF Delayed Variables The steady-state solution of the DDE in Eq. (6) can be derived by modifying the method in [37]. First, a dimensionless time variable can be defined as imensionless time variable can be defined as t   = (7) t   = (7) t   = (7) The first and second derivative of U can be expressed as The first and second derivative of U can be expressed as dU dU d U dt d dt    = = (8) dU dU d U dt d dt    = = (8) 2 2 2 ( ) ( ) d U d d d U U U dt d dt dt        = = = (9) (8) 2 2 2 ( ) ( ) d U d d d U U U dt d dt dt        = = = (9) (9) respectively, where the over-dot represents the derivative with respect to τ. The time-delay variable is expressed as ( ) ( ) j j U U T  = − (10) (10) Substituting Eq. (7) to Eq. (10) into Eq. 2.2 Construction of Multi-DoF Delayed Variables (6) yields ( ( ) ) ( , , , , , , , ) 0 n n R L F U U U U  + − = (11) (11) The steady-state periodic solution U(τ) can be approximated by the Fourier series: 1 , T T T S S n U C q C q   =   , (12) 1 , T T T S S n U C q C q   =   , (12 (12) where the superscript T represents the transposition of the vector, CS is a set of truncated Fourier basis functions where the superscript T represents the transposition of the vector, CS is a set of truncated Fourier basis functions   1, cos , , cos , sin , , sin T S C M M     = (13) (13) in which M is the truncated order, and qk with k=1, …, n are coefficient vectors of CS for the k-th particle in a unit, which can be expressed as particle in a unit, which can be expressed as 1 1 1 1 1 1 0 1 1 0 1 1 [ , , , , , , ] [ , , , , , , ] T M M n n n n n T n M M q a a a b b q a a a b b = = (14) (14) m U C Q = (15) m U C Q = (15) (15) where Cm is a n × n(2M+1) matrix (2 1) 1 (2 1) 1 (2 1) 1 (2 1) 1 (2 1) 1 (2 1) 1 0 0 0 0 0 0 T S M M T m M S M T M M S C C C C +  +  +  +  +  +          =         (16) (16) and Q is a n(2M+1) ×1 vector nd Q is a n(2M+1) ×1 vector 1 2 [ , , , ] T T T T n Q q q q = (17) 1 2 [ , , , ] T T T T n Q q q q = (17) (17) The first and second derivatives of the steady-state solution U can be expressed as The first and second derivatives of the steady-state solution U can be expressed as 1 2 m m U CG Q U CG Q = = (18) 1 2 m m U CG Q U CG Q = = (18) where Gm1 and Gm2 are both n(2M+1)-dimensional square matrices: where Gm1 and Gm2 are both n(2M+1)-dimensional square matrices: 1 (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) 1 (2 1) (2 1) 1 (2 1) (2 1) (2 1) (2 1) 1 0 0 0 0 0 0 M M M M M M M M m M M M M H H G H +  + +  + +  + +  + +  + +  +         =         (19) (19) 2 (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) 2 (2 1) (2 1) 2 (2 1) (2 1) (2 1) (2 1) 2 0 0 0 0 0 0 M M M M M M M M m M M M M H H G H +  + +  + +  + +  + +  + +  +         =         (20) (2 1) (2 1) 2 (2 1) (2 1) 2 (2 1) (2 1) (2 1) (2 1) 2 0 0 0 0 M M M M m M M M M H G H +  + +  + +  + +  +       =         (20) (20) in which H1 and H2 are the first-order and second-order derivative operator matrices, respectively: 1 0 0 0 0 0 0 0 T T M M M M M M M M H S S       =     −   , 2 2 2 0 0 0 0 0 0 0 T T M M M M M M M M H S S       = −     −   with 1 0 0 S M     =       (21) (21) where 0M is an M-dimensional zero vector and 0M×M is an M-dimensional zero matrix. 2.2 Construction of Multi-DoF Delayed Variables In Eq. (11), the time-delay variable can be expressed as: In Eq. (11), the time-delay variable can be expressed as: ( ) 1 j m U C Q = (22) (22) where Cm1 is a n × n(2M+1) matrix: where Cm1 is a n × n(2M+1) matrix: (2 1) 1 (2 1) 1 1 (2 1) 1 (2 1) 1 (2 1) 1 (2 1) 1 0 0 0 0 0 0 T ST M M T m M ST M T M M ST C C C C +  +  +  +  +  +          =         (23) (23) in which CST is a set of basis functions with a phase difference Tj, i.e., the value of the wave vector of the j-th unit: [1, cos( ), ,cos ( ), sin( ), , sin ( )] T ST j j j j C T M T T M T     = − − − − (24) (24) In previous IHB methods for solving multi-DoF wave problems, CST were directly used as basis functions, so that the number of the basis functions is 1 2( ) R L n n M + + , which is much larger than M, the order of harmonic functions of the response. The basis functions were also directly integrated in the harmonic balance procedure and information of Tj was lost. Thus, it is necessary to decouple Tj and the basis functions: the trigonometric functions in Eq. (24) can be transformed as cos ( ) cos cos sin sin , 1 , , sin ( ) cos sin sin cos , 1, , j j j j j j M T M MT M MT M M M T M MT M MT M M       − = + = − = − + = (25) (25) and Eq. (22) can be written as and Eq. (22) can be written as and Eq. 2.2 Construction of Multi-DoF Delayed Variables (22) can be written as ( ) ( ) j j m m U C D Q = (26) ( ) ( ) j j m m U C D Q = (26) ( ) ( ) j j m m U C D Q = (26) (26) where ( ) j m D is n(2M+1) square matrix: where ( ) j m D is n(2M+1) square matrix: where ( ) j m D is n(2M+1) square matrix: re ( ) j m D is n(2M+1) square matrix: where ( ) j m D is n(2M+1) square matrix: (2 1) (2 1) (2 1) (2 1) ( ) (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) 0 0 0 0 0 0 j M M M M j M M j M M m M M M M j D D D D +  + +  + +  + +  + +  + +  +         =         (27) (27) in which Dj, the delay matrix operator, is in which Dj, the delay matrix operator, is in which Dj, the delay matrix operator, is 0 0 1 0 0 0 cos sin cos sin 0 0 sin cos sin cos 0 j j j j j j j j j T T MT MT D T T MT MT     −       − =             (28) (28) Therefore, the basis functions are still CS and information of Tj is in Dj. Substituting Eq. (15), Eq. (18), and Eq. (26) into Eq. (11) yields Therefore, the basis functions are still CS and information of Tj is in Dj. Substituting Eq. (15), Eq. (18), and Eq. (26) into Eq. (11) yields 2 1 ( , , , , , , , ) 0 L R n n m m m m m m m m F C G Q C G Q C D Q C D Q   − + = ( ) ( ) (29) (29) 2.3 Newton Method to Solve Steady-State Responses If a guess of the solution U is not equal to the steady-state solution, there is a nonzero residual r that If a guess of the solution U is not equal to the steady-state solution, there is a nonzero residual r that can be written as 2 1 ( , , , ) ( , , , , , , , ) L R n n m m m m m m m m r Q F C G Q C G Q C D Q C D Q      − + = ( ) ( ) (30) (30) which is an n-dimensional vector for a multi-DoF wave problem. Its harmonic balanced residual R is 2 2 0 1 ( , , ) ( , , , ) m R Q C r Q d       =  (31) (31) where Cm2 is a n × n(2M+1) matrix: 1 (2 1) 1 (2 1) 1 2 (2 1) 1 1 (2 1) 1 (2 1) 1 (2 1) 1 1 0 0 0 0 0 0 S M M m M S M M M S C C C C +  +  +  +  +  +          =         (32) (32) in which Cs1 is a set of basis functions orthogonal to Cs: in which Cs1 is a set of basis functions orthogonal to Cs: 1 1 , cos , , cos , sin , , sin 2 T S C M M       =     (33) (33) Newton's method is used to solve Q to make R in Eq. (31) vanish. Newton’s iterative formula is Q J Q J J R     + + = − Q J Q J J R     + + = − (34) (34) where R represents the harmonic balanced residual, JQ, Jω, and Jμ represent Jacobian matrices of variables Q, ω, and μ, respectively, and Q , , and  are increments of the variables. The numerical integration method to obtain R from Eq. (31) is usually time-consuming. The following method can be used to improve the efficiency. 2.3 Newton Method to Solve Steady-State Responses Let the residual r be where R represents the harmonic balanced residual, JQ, Jω, and Jμ represent Jacobian matrices of variables Q, ω, and μ, respectively, and Q , , and  are increments of the variables. The numerical integration method to obtain R from Eq. (31) is usually time-consuming. The following method can be used to improve the efficiency. Let the residual r be 1 [ , , ]T n r r r = (35) (35) where , 1, , kr k n = are residuals of n particles in a unit. The harmonic balanced residual 1 2 [ , , , ] T T T T n R R R R = (36) 1 2 [ , , , ] T T T T n R R R R = (36) (36) can be efficiently computed by the Fast Fourier Transform (FFT) method [34], where Rk with k=1, …, n, is the FFT of rk: can be efficiently computed by the Fast Fourier Transform (FFT) method [34], where Rk with k=1, …, n, is the FFT of rk: can be efficiently computed by the Fast Fourier Transform (FFT) method [34], where Rk with k=1, …, i h FFT f can be efficiently computed by the Fast Fourier Transform (FFT) method [34], where Rk with k=1, …, n, is the FFT of rk: 1 1 1 1 1 1 0 1 1 2 2 2 2 2 2 0 1 1 0 1 1 [ , , , , , ] [ , , , , , ] [ , , , , , ] T M M T M M n n n n n T n M M R p p p l l R p p p l l R p p p l l = = = (37) (37) in which k m p and k ml denote the values of the real and imaginary parts of the m-th order Fourier function of the k-th particle, respectively. in which k m p and k ml denote the values of the real and imaginary parts of the m-th order Fourier function of the k-th particle, respectively. Jacobian matrices in Eq. 2.3 Newton Method to Solve Steady-State Responses (34) can be calculated by exchanging the sequence of partial derivative and integral: 2 2 0 1 Q m R r J C d Q Q      = =    (38) 2 2 0 1 m R r J C d         = =    (39) 2 2 0 1 m R r J C d         = =    (40) (38) (39) (40) In this work, the method proposed in [35] is extended to construct a semi-analytical formula of JQ: 1 1 1 ( ) 2 1 R L n j Q m DD m m m D m m m j m m j n J L f L G L f L G L f L D − − − =− = + +  (41) (41) where m L and 1 m L− are n(2M+1) square matrices: where m L and 1 m L− are n(2M+1) square matrices: where m L and 1 m L− are n(2M+1) square matrices: 1 (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) 1 (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) 1 0 0 0 0 0 0 M M M M M M M M m M M M M L L L L +  + +  + +  + +  + +  + +  +         =         (42) 2 (2 1) (2 1) (2 1) (2 1) 1 (2 1) (2 1) 2 (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) 2 0 0 0 0 0 0 M M M M M M M M m M M M M L L L L +  + +  + − +  + +  + +  + +  +         =         (43) (42) (43) in which L1 and L2 are 2M+1 square matrices: in which L1 and L2 are 2M+1 square matrices: 1 0 0 1 0 0 1 0 1 1 0 1 0 0 L j j j j           =     − −       −   (44) 1 0 0 1 0 0 1 0 1 1 0 1 0 0 L j j j j           =     − −       −   (44) 2 0 1 0 1 1 2 0 0 0 0 2 0 1 0 1 j j L j j           =     −       −   (45) fDD is 1 (2 1) (2 1) 0 dd M M f f +  +     (46) 2 0 1 0 1 1 2 0 0 0 0 2 0 1 0 1 j j L j j           =     −       −   (45) 2 0 1 1 2 0 0 0 0 2 0 1 0 1 j L j j     =     −       −   (45) 2 0 1 1 2 0 0 0 0 2 0 1 0 1 j L j j     =     −       −   (45) (45) 0 1 j   −   fDD is 1 (2 1) (2 1) (2 1) (2 1) 0 0 dd M M DD n M M dd f f f +  + +  +     =       (46) 1 (2 1) (2 1) (2 1) (2 1) 0 0 dd M M DD n M M dd f f f +  + +  +     =       (46) 1 (2 1) (2 1) (2 1) (2 1) 0 0 dd M M DD n M M dd f f f +  + +  +     =       (46) (46) in which k dd f , k=1, …, n is Toeplitz form of 0 [ ] k k k M M f f f − that is a coefficient vector of M-order in which k dd f , k=1, …, n is Toeplitz form of 0 [ ] k k k M M f f f − that is a coefficient vector of M-order Fourier functions of kF U   , which can be simply calculated by FFT of kF U   : Fourier functions of kF U   , which can be simply calculated by FFT of kF U   : Fourier functions of kF U   , which can be simply calculated by FFT of kF U   : 0 0 0 0 0 k k M k k k k dd M M k k M f f f f f f f f − −         =         (47) (47) fD and fj are 1 (2 1) (2 1) (2 1) (2 1) 0 0 d M M D n M M d f f f +  + +  +     =       and 1,1 1, ,1 , n j n n n f f f f f     =       (48) (48) respectively, in which k df , k=1, …, n and 1 2 , k k jf , k1, 2=1, …, n are Toeplitz forms of coefficient vectors of kF U   and ( ) k j F U   with , , L R j n n = − , respectively, which can be obtained by FFT of kF U   and ( ) k j F U   . 2.3 Newton Method to Solve Steady-State Responses The Jacobian matrices with respect to the frequency ω and wave vector μ can be obtained by FFTs of r    and r   , where FFTs of r    and r   , where 2 ( , , ) m m r F C G Q    =  (49) 2 ( , , ) m m r F C G Q    =  (49) (49) and ( ) ( ) ( , , , , ) j j m m m m m m r F C Q C D Q C D D Q    =  (50) and ( ) ( ) ( , , , , ) j j m m m m m m r F C Q C D Q C D D Q    =  (50) ( ) ( ) ( , , , , ) j j m m m m m m r F C Q C D Q C D D Q    =  (50) (50) respectively, in which m D is an n(2M+1) square matrix: respectively, in which m D is an n(2M+1) square matrix: respectively, in which m D is an n(2M+1) square matrix: (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) (2 1) 0 0 0 0 0 0 M M M M M M M M m M M M M D D D D +  + +  + +  + +  + +  + +  +         =         (51) (51) and D is a partial derivative matrix operator of the wave vector: and D is a partial derivative matrix operator of the wave vector: and D is a partial derivative matrix operator of the wave vector: 0 0 0 0 0 0 0 0 0 0 0 0 0 j D jM j jM     −       = −             (52) 0 0 0 0 0 0 0 0 0 0 0 0 0 j D jM j jM     −       = −             (52) 0 0 0 0 0 0 0 0 0 0 0 0 0 j D jM j jM     −       = −             (52) (52) There are two cases when solving Eq. 2.3 Newton Method to Solve Steady-State Responses of kF U   and ( ) k j F U   with , , L R j n n = − , respectively, which can be obtained by FFT of kF U   and ( ) k j F U   . 3.1.1 Model Description and Calculation In this work, the proposed method is used to study a 1D diatomic lattice model under the Hertz contact law [9]. A unit of the diatomic chain model consists of two different masses, m1 and m2, as shown in Fig. 2. Both ends of the chain are subjected to an initial compression force of F0, and the initial compression displacement of two adjacent particles is δ0, which is given by F0 and the particle stiffness. The nonlinearity of the 2-DoF system is strong when the compression force is large. The nonlinearity of the 2-DoF system is strong when the compression force is large. Figure. 2 Schematic diagram of a 1D diatomic lattice under Hertz contact law Figure. 2 Schematic diagram of a 1D diatomic lattice under Hertz contact law As shown in Fig. 2, u1 and u2 denote dynamic displacements of the two particles with masses of m1 and m2, respectively. These displacements are relative to their static positions under the initial compression F0. 2.3 Newton Method to Solve Steady-State Responses (34). One is that when the wave vector μ is fixed, Eq. (34) can be written as Q J Q J R  + = − (53) (53) and Newton method can be used to solve Q and ω iteratively. In the other case, when the frequency ω is given, Eq. (34) can be written as and Newton method can be used to solve Q and ω iteratively. In the other case, when the frequency ω is given, Eq. (34) can be written as Q J Q J R  + = − (54) (54) In the same way, Q and μ can be iteratively solved by the Newton method. In the same way, Q and μ can be iteratively solved by the Newton method. The procedure to calculate steady-state wave solutions used in this work is summarized in Fig. 1. The procedure can be automatically implemented by a computer program and the only manual work is to give partial differentiations of the DDE, which is a much easier task than derivation of Jacobian matrices in traditional IHB methods. Figure. 1 The procedure of solving wave propagation problems with strong nonlinearities Figure. 1 The procedure of solving wave propagation problems with strong nonlinearities 3.1.1 Model Description and Calculation (56) can be expressed as 2 3 3 1 2 2 1 2 2 3 3 2 2 2 2 1 2 ( ) ( ) ( ) ( ) d u m dt d u m dt     + + + +  =  −   =  −  (62) (62) where 0 0 0     +    =     , 0 0 0     +    =     and 1 1 1 1 0 0 0     +    =     (63) (63) in which 1 0 1 2 ( ) u u   − = − − , 0 2 1 ( ) u u   = − − and 1 1 0 1 2 ( ) u u   = − − (64) (64) The diatomic chain is composed of aluminum balls and stainless steel balls in this example, where the parameters are E1=68.9 GPa, E2=193 Gpa, R1=R2=9.5025 mm, v1=0.35, v2=0.3, m1=9.73 g, m2=29.10 g, and F0=20 N. The diatomic chain is composed of aluminum balls and stainless steel balls in this example, where the parameters are E1=68.9 GPa, E2=193 Gpa, R1=R2=9.5025 mm, v1=0.35, v2=0.3, m1=9.73 g, m2=29.10 g, and F0=20 N. 3.1.1 Model Description and Calculation The system displacement vector of the i-th unit can be represented as ( ) ( ) ( ) 1 2 , i T i i U u u   =   (55) (55) The governing equation of the 1D diatomic lattice under the Hertz contact law can be written as The governing equation of the 1D diatomic lattice under the Hertz contact law can be written as 2 3 3 1 2 2 1 2 2 3 3 2 2 2 2 1 2 ( ) ( ) ( ) ( ) i i i i i i d u m dt d u m dt     + + + + +  =  −   =  −  (56) (56) where where 0 0 0 i i i i     +    =     , 0 0 0 i i i i     +    =     and 1 1 1 1 0 0 0 i i i i     + + + + +    =     (57) (57) i  i  1 i+  in which in which 1 0 1 2 ( ) i i i u u   − = − − , 0 2 1 ( ) i i i u u   = − − and 1 1 0 1 2 ( ) i i i u u   + + = − − (58) 1 0 1 2 ( ) i i i u u   − = − − , 0 2 1 ( ) i i i u u   = − − and 1 1 0 1 2 ( ) i i i u u   + + = − − (58) (58) Γ denotes the coefficient of nonlinear recovering forces: nd Γ denotes the coefficient of nonlinear recovering forces: 1 2 1 2 1 2 2 2 2 1 1 2 1 1 4 ( ) 3[ (1 ) (1 )] E E R R E E   − + = − + − (59) 1 2 1 2 1 2 2 2 2 1 1 2 1 1 4 ( ) 3[ (1 ) (1 )] E E R R E E   − + = − + − (59) (59) in which E1, E2, ν1, and ν2 denote the elastic modulus and Poisson's ratio of masses m1 and m2, respectively, and R1 and R2 denote radii of the particles, respectively. 3.1.1 Model Description and Calculation The initial compression displacement can be expressed as in which E1, E2, ν1, and ν2 denote the elastic modulus and Poisson's ratio of masses m1 and m2, respectively, and R1 and R2 denote radii of the particles, respectively. The initial compression displacement can be expressed as 1 2 2 2 0 1 2 1 2 3 0 1 2 9 ( ) ( ) 16 F k k R R R R   + + =( ) (60) 1 2 2 2 0 1 2 1 2 3 0 1 2 9 ( ) ( ) 16 F k k R R R R   + + =( ) (60) (60) where 2 1 1 1 1 k E   − = and 2 2 2 2 1 k E   − = (61) where 2 1 1 k  − = and 2 2 1 k  − = (61) where 2 1 1 1 1 k E   − = and 2 2 2 2 1 k E   − = (61) (61) Without loss of generality, i can be set to 0, and Eq. (56) can be expressed as Without loss of generality, i can be set to 0, and Eq. 3.1.1 Model Description and Calculation Thus, the residual r can be expressed as 3 3 2 + + 2 2 1 1 2 1 3 3 2 + + 2 2 2 2 2 2 1 ( , , , ) ( ) ( ( , , , ) ( ) T g S g T g S g r Q m C G q r Q m C G q            = − +    = − +   ) ( ) (68) (68) where 0 2 1 ( ) T T S g S g C q C q   = − − and 1 0 1 1 2 ( ) T T S g S g C D q C q   = − − (69) 0 1 1 2 ( ) T T S g S g C q C D q   − = − − , 0 2 1 ( ) T T S g S g C q C q   = − − and 1 0 1 1 2 ( ) T T S g S g C D q C q   = − − (69) (69) Based on the procedure in Fig. 1, harmonic balance residuals R1 and R2 can be calculated by FFTs of r1 and r2, respectively. The Jacobian matrix JQ, Jω, and Jμ can be calculated by following the procedure given in Eq. (38) to Eq. (41), as shown in Appendix A. 3.1.1 Model Description and Calculation The initial guess of the solution Ug can be expressed as g m g U C Q = (65) g m g U C Q = (65) where (65) g m g U C Q = (65) where 1 2 [ , ] T T T g g g Q q q = (66) where 1 2 [ , ] T T T g g g Q q q = (66) 1 2 [ , ] T T T g g g Q q q = (66) (66) is a guess of 1 2 [ , ] T T T g g g Q q q = , in which is a guess of 1 2 [ , ] T T T g g g Q q q = , in which s a guess of 1 2 [ , ] T T T g g g Q q q = , in which 1 1 1 1 1 2 1 2 2 2 2 2 2 1 2 1 [0 , , , , , , ] [0 , , , , , , ] T g M M T g M M q A a a b b q a a a b b = = (67) 1 1 1 1 1 2 1 2 2 2 2 2 2 1 2 1 [0 , , , , , , ] [0 , , , , , , ] T g M M T g M M q A a a b b q a a a b b = = (67) (67) and A represents a presetting amplitude of the first-order cosine function of u1, which controls the nonlinearity strength. Vibrations of the two particles make the constant components of qg1 and qg2 equal to zero, which are dropped in the following calculation. Thus, the residual r can be expressed as and A represents a presetting amplitude of the first-order cosine function of u1, which controls the nonlinearity strength. Vibrations of the two particles make the constant components of qg1 and qg2 equal to zero, which are dropped in the following calculation. 3.1.2 Steady-State Responses with Given Wave Vectors When the wave vector of a wave problem is given, Newton’s iterative formula shown in Eq. (53) can be used to find solutions of q1, q2, and ω. Since the coefficient of the 1st-order cosine function of u1, i e the first element of Q is given as A and the frequency is unknown the formula is converted to be used to find solutions of q1, q2, and ω. Since the coefficient of the 1st-order cosine function of u1, i.e. the first element of Q, is given as A and the frequency is unknown, the formula is converted to (70) xJ x R = − (70) where x are variables consisting of the frequency and coefficients of the rest of the basis functions: sisting of the frequency and coefficients of the rest of the basis functions: 1 1 1 2 2 2 2 1 1 1 [ , , , , , , , , , ] T M M M M x a b b a a b b  = (71) (71) in which the first element of the coefficient vector Q, is replaced by the frequency ω, Jx is the Jacobian matrix of x, in which the first column vector of JQ is replaced by Jω, and an increment of x is denoted by Δx. Convergence analysis of basis functions is carried out for the proposed IHB method at different strengths of nonlinearities. Frequencies of steady-state wave responses with different wave vectors and A=0.99δ0 are calculated by different orders of basis functions, as shown in Table 1. The amplitude A is used to control nonlinearity strength, and A=0.99δ0 yields a strong nonlinearity. Results show that frequencies calculated with low orders of basis functions (M less than seven) cannot converge in some cases. When M is higher (M = 7 and 9), frequencies of all cases will converge and the resultant responses can be accurate. Convergence rates are different with wave vectors. For example, the difference between frequencies with M=5 and M=7 is 3.8 Hz when μ=0.3, and the value is 0.1 Hz when μ=0.6. To secure convergence for all wave vectors, it is necessary to use high-order basis functions. Table 1. Frequencies (kHz) of steady-state waves with different orders M when A=0.99δ0. Table 1. Frequencies (kHz) of steady-state waves with different orders M when A=0.99δ0. 3.1.2 Steady-State Responses with Given Wave Vectors μ 0.3 0.6 0.9 1.2 1.5 2.1 M=1 0.6002 1.1932 1.7706 2.3245 2.8259 3.5886 M=3 0.6127 1.2231 1.8160 2.3721 2.8852 3.5776 M=5 0.6192 1.2265 1.8162 2.3732 2.8898 3.5994 M=7,9 0.6230 1.2266 1.8163 2.3733 2.8899 3.6047 Computing efficiency of the improved IHB method is compared with that of traditional IHB methods. At the same condition (A=0.99δ0 and μ=0.9), values of calculation time in MATLAB with use of different orders as M=1, 3, 5, 7 are shown in Table 2. Results show that calculation time of a traditional IHB method and that of the improved IHB method are close when a low order of basis functions (M =1) is used. With the order increasing, calculation time of the improved IHB method is almost unchanged and still short (less than 0.4s). However, calculation time of the traditional IHB method increases exponentially, since the number of integration increases exponentially with the order of basis functions. For example, calculation time of the improved IHB method with M =7 is 0.35s, and that of the traditional IHB method is 66.81s. A nonlinear multi-DoF wave problem requires high-order truncated Fourier series to obtain converged steady-state responses. Thus, the method shown in the work has the advantage of dealing with the complex multi-DoF wave problems. Table 2. Time (s) of calculation with different orders M when A=0.99δ0 and μ=0.9 M 1 3 5 7 Improve IHB 0.366949 0.343543 0.302675 0.357626 Traditional IHB 0.752322 3.917901 8.157872 66.81462 Table 2. Time (s) of calculation with different orders M when A=0.99δ0 and μ=0.9 Table 2. Time (s) of calculation with different orders M when A=0.99δ0 and μ=0.9 Dispersion curves are shown in Fig. 3 when different truncated orders of Fourier series are used for weak nonlinearity (A= 0.1δ0) and strong nonlinearity (A= 0.99δ0) cases. When A= 0.1δ0, dispersion curves with M=5 and M=9 are overlapped but are different from the curve with M=1. Moreover, when the wave vector is large (μ>2.7), no solution can be calculated with use of low-order basis functions with M=1 and M=5, since the calculation does not converge. For the strong nonlinearity case, the region where solutions cannot be calculated with low-order basis functions is even larger (μ>2.1). Thus, it is also important to use high-order basis functions to ensure existence of solutions. Dispersion curves with weak and strong nonlinearities are different. 3.1.2 Steady-State Responses with Given Wave Vectors When the value of the wave vector is small (lower than 1.5), frequencies at different nonlinearities are very close. When the value is large, dispersion curves are separated, where the frequency decreases as the nonlinearity increases. Figure 3. The dispersion curves with different orders M when A=0.1δ0 and A=0.99δ0 Figure 3. The dispersion curves with different orders M when A=0.1δ0 and A=0.99δ0 Dispersion curves of optical (higher) and acoustic (lower) waves together constitute the bandgap of the system, which are shown in Fig. 4 for weak nonlinearity (A= 0.1δ0) and strong nonlinearity (A= 0.99δ0) cases. The shaded part is the stopband, where waves cannot travel when their frequencies are those in the region. Red dashed lines form the stopband for the strong nonlinearity case and blue dashed lines form that for the weak nonlinearity case. As the nonlinearity increases, the stopband will move to the lower-frequency region. Meanwhile, the stronger the nonlinearity is, the larger the region of the stopband is. Figure 4. Bandgap properties of 1D diatomic lattice in the Hertz contact model Figure 4. Bandgap properties of 1D diatomic lattice in the Hertz contact model 3.1.3 Steady-state Responses with Given Frequencies When the frequency of a wave problem is fixed, Eq. (54) is used as Newton's iterative formula. Similarly, with A given as the first element of Q, the formula is changed to xJ x R = − (72) (72) where 1 1 1 2 2 2 2 1 1 1 [ , , , , , , , , , ] T M M M M x a b b a a b b  = (73) (73) in which the first element of the coefficient vector Q, is replaced by the wave vector 𝜇, and Jx is the Jacobian matrix of x, in which the first column vector of JQ is replaced by Jμ. At different frequencies, wave vectors of steady-state responses of acoustic waves with a strong nonlinearity (A=0.99δ0) are calculated with use of different orders of basis functions, which are shown in Table 3. Results show that wave vectors can converge when the order of basis functions is larger than or equal to 3, which means that steady-state wave responses solved with fixed frequencies can converge faster (M ≥3) than those solved with fixed wave vectors (M ≥7). Table 3. Wave vectors of steady-state waves with the different orders as M=1,3,5,7 when A=0.99δ0 f (kHz) 0.5 1 1.5 2 2.5 3 3.5 4 M=1 0.25 0.50 0.76 1.02 1.30 1.61 2.02 2.45 M=3 0.24 0.49 0.74 1.00 1.27 1.57 1.96 2.76 M=5,7 0.24 0.49 0.74 1.00 1.27 1.57 1.96 2.76 Table 3. Wave vectors of steady-state waves with the different orders as M=1,3,5,7 when A=0.99δ0 Dispersion curves of acoustic waves obtained by fixed wave vectors and fixed frequencies are compared in Fig. 5 for weak nonlinearity (A= 0.1δ0) and strong nonlinearity (A= 0.99δ0) cases. Results from the two methods are the same, which verifies the accuracy of the new method that solves the wave problem with fixed frequencies, and the new method has a faster convergence rate. Figure 5. Comparison between dispersion curves of acoustic waves solved with fixed wave vectors Figure 5. Comparison between dispersion curves of acoustic waves solved with fixed wave vectors and fixed frequencies 3.2.1 Model Description and Calculation In this work, the proposed method is used to study a 1D diatomic lattice model with a cubic spring [38]. A unit of the diatomic chain model consists of two different masses, m1 and m2 (Fig. 6). The nonlinearity of the 2-DoF system gets stronger as displacements of particles get larger. Figure 6. Schematic diagram of a 1D diatomic lattice with cubic spring. Figure 6. Schematic diagram of a 1D diatomic lattice with cubic spring. In Fig. 6, k1 and k2 denote stiffness coefficients of two types of linear springs in the diatomic chain, and Γ1 and Γ2 denote coefficients of third-order polynomials of two nonlinear springs. The system displacement can be written as ( ) ( ) ( ) 1 2 , i T i i j U u u   =   (74) ( ) ( ) ( ) 1 2 , i T i i j U u u   =   (74 (74) where i denotes the location of the unit. When i=0, the governing equation of the system can be expressed as where i denotes the location of the unit. When i=0, the governing equation of the system can be expressed as where i denotes the location of the unit. 3.2.1 Model Description and Calculation When i=0, the governing equation of the system can be expressed as as 1 1 1 1 ( , ) ( , , ) 0 L NL j j j j j j j j j mu Ku f u u f u u u − − + + + = (75) (75) where 1 2 0 0 m m m   =     , 1 2 1 2 1 2 k k k K k k k + −   =   − +   , 1 2 ( ) ( ) j u t u u t   =     , 1 1 1 1 2 1 2 ( ) ( , ) ( ) L j j j u t f u u k u t − −   = −     and 3 1 3 1 1 1 1 2 2 1 2 3 1 3 1 2 1 2 2 1 ( ) ( ) ( , , ) ( ) ( ) NL j j j j u u u u f u u u u u u u − −    − +  − =    − +  −   (76) 1 2 0 0 m m m   =     , 1 2 1 2 1 2 k k k K k k k + −   =   − +   , 1 2 ( ) ( ) j u t u u t   =     , 1 1 1 1 2 1 2 ( ) ( , ) ( ) L j j j u t f u u k u t − −   = −     and 3 1 3 1 1 1 1 2 2 1 2 3 1 3 1 2 1 2 2 1 ( ) ( ) ( , , ) ( ) ( ) NL j j j j u u u u f u u u u u u u − −    − +  − =    − +  −   (76) (76) With an initial guess 1 2 [ , ] T T T g g g Q q q = , the residual of the governing equation can be expressed as 2 3 3 1 1 2 1 1 2 1 1 2 2 1 2 1 1 2 2 1 1 2 2 3 3 2 2 2 2 1 2 2 1 1 2 1 1 1 2 1 2 2 1 1 ( ) ( ) ( ) ( ) ( ) ( ) T T T T T T T T S g S g S g S g S g S g S g S g T T T T T T T T S g S g S g S g S g S g S g S g r m C G q k k C q k C q k C D q C q C q C q C D q r m C G q k k C q k C q k C D q C q C q C q C D q   − −  = + + − − +  − +  − = + + − − +  − +  −  2 3 3 1 1 2 1 1 2 1 1 2 2 1 2 1 1 2 2 1 1 2 2 3 3 2 2 2 2 1 2 2 1 1 2 1 1 1 2 1 2 2 1 1 ( ) ( ) ( ) ( ) ( ) ( ) T T T T T T T T S g S g S g S g S g S g S g S g T T T T T T T T S g S g S g S g S g S g S g S g r m C G q k k C q k C q k C D q C q C q C q C D q r m C G q k k C q k C q k C D q C q C q C q C D q   − −  = + + − − +  − +  −  = + + − − +  − +  −  (77) Based on the procedure in Section 2.3, harmonic balanced residuals R1 and R2 can be calculated by FFTs Based on the procedure in Section 2.3, harmonic balanced residuals R1 and R2 can be calculated by FFT Based on the procedure in Section 2.3, harmonic balanced residuals R1 and R2 can be calculated by FFTs Based on the procedure in Section 2.3, harmonic balanced residuals R1 and R2 can be calculated by FFTs of r1 and r2, respectively. frequencies Bandgap properties of hardened spring (Γ=0.05), softened spring (Γ=-0.05), and linear spring (Γ=0) cases are shown in Fig. 8. Three curves at a low-frequency region are dispersion curves of acoustic waves, and the other three are those of optical waves. A part formed by two lines with the same color is a stopband region of a type of springs. Compared with a linear spring, the stopband region of the hardened spring is higher, and that of the softened spring is lower. Figure 8. Bandgap properties of different spring models Figure 8. Bandgap properties of different spring models 3.2.1 Model Description and Calculation Jacobian matrices JQ, Jω, and Jμ can be calculated by following the procedure given in Eq. (38)- Eq. (41), as shown in Appendix B. A set of the model parameters are given in Table 4, which will be used in the calculation and analysis of the diatomic chain system. The frequency ωn is a reference frequency that is given in [36], and the ratio of the system frequency to the reference frequency n    = is used as a dimensionless frequency in this problem. Table 4. Cubic spring model parameters [38] m1 m2 k1 k2 Γ1 Γ2 ωn 1 2 1 5 ±0.05 ±0.05 2.45 Table 4. Cubic spring model parameters [38] Table 4. Cubic spring model parameters [38] Steady-state responses of given wave vectors and frequencies with Γ1,2=0.05 are calculated with use of different orders of basis functions, which are shown in Table 5 and Table 6, respectively. Results show that the convergence rate of given frequencies is faster (M ≥3) than that of given wave vectors (M ≥5), which is consistent with that of the wave problem in Section 3.1. Table 5.  of steady-state waves with different orders M and different wave vectors μ when Γ=0.05 μ 0.3 0.6 0.9 1.2 1.5 1.8 2.1 M=1 0.0646 0.1299 0.1969 0.2675 0.3430 0.4837 0.6464 M=3 0.0646 0.1301 0.1967 0.2657 0.3397 0.4250 0.5638 M=5,7 0.0647 0.1302 0.1965 0.2640 0.3326 0.4040 0.4653 Table 6. Wave vectors of steady-state waves with different orders M and different  when Γ=0.05  0.1 0.3 0.5 0.7 0.9 1.1 1.3 1.5 M=1 0.19 0.56 0.83 1.30 1.67 2.03 2.41 2.79 M=3,5 0.19 0.56 0.83 1.30 1.67 2.03 2.41 2.79 Table 5.  of steady-state waves with different orders M and different wave vectors μ when Γ=0.05 Dispersion curves solved with fixed wave vectors and fixed frequencies are shown in Fig. 7 for hardened spring (Γ=0.05), softened spring (Γ=-0.05), and linear spring (Γ=0) cases. Results show that dispersion curves obtained by the two methods are the same. As wave vectors increase, frequencies of hardened and softened nonlinear springs are higher and lower than those of linear springs, respectively. Figure 7. Comparison between dispersion curves solved with fixed wave vectors and f i Figure 7. Comparison between dispersion curves solved with fixed wave vectors and frequencies Figure 7. Comparison between dispersion curves solved with fixed wave vectors and 4. Conclusion An algorithm based on an improved IHB method is developed to obtain steady-state solutions of general multi-DoF wave propagation problems with strong nonlinearities. In this algorithm, no numerical integration is needed to obtain residuals and Jacobian matrices, which are most time-consuming procedures in traditional IHB methods. Meanwhile, use of a delay matrix operator enables to decouple wave vectors from basis functions, which significantly reduces the number of basis functions, and high- order basis functions are able to be employed in this method to handle strong nonlinearities. Meanwhile, the method can solve a nonlinear wave problem when either the frequency or wave vector is given, which makes the method more adaptive to different applications. Results of examples show advantages of the method in calculation efficiency and accuracy when a wave problem with strong nonlinearities is solved. It is able to use the method to obtain dispersion curves for weak and strong nonlinearity cases, and results show that strong nonlinearities can significantly change bandgaps. Acknowledgments We gratefully acknowledge support from the National Natural Science Foundation of China (No. U1930206). Author Contributions All authors contributed to the concept development and manuscript editing. Hongyu Wang, Xuefeng Wang and Jian Zhao contributed to the development of the method, Jian Zhang contributed to method validation, and Yu Huang contributed to analysis of wave characteristics. Competing Interests The authors declare that they have no conflict of interest. Funding This work was supported by the National Natural Science Foundation of China (No. U1930206). under Hertz contact law Substituting the dimensionless time variable t   = into Eq. (62) yields 2 3 3 2 1 2 2 1 2 2 3 3 2 2 2 2 2 1 2 ( ) ( ) ( ) ( ) d u m d d u m d         + + + +  =  −   =  −  (A1) (A1) The vectors u1 and u2 and their first-derivative, second-derivative, and time-delay terms can be approximated by M-order Fourier functions: 1 1 2 2 ( ) ( ) T S T S u C q u C q    =  =  , 1 1 1 2 1 2 ( ) ( ) T S T S u C G q u C G q     =  =  , 1 2 1 2 2 2 ( ) ( ) T S T S u C G q u C G q     =  =  and 1 1 1 1 1 2 1 2 ( ) ( ) T S T S u C D q u C D q   − −  =  =  (A2) (A2) respectively, where CS, q1, and q2 are (2M+1) ×1 vectors, G1, G2, D-1, and D1 are 2M+1 square matrices. espectively, where CS, q1, and q2 are (2M+1) ×1 vectors, G1, G2, D-1, and D1 are 2M+1 square matrices. Substituting Eq. (A2) into Eq. (A1), the governing equation can be expressed as 3 3 2 + + 2 2 1 2 1 3 3 2 + + 2 2 2 2 2 1 ( ) ( 0 ( ) 0 T S T S m C G q m C G q        − +  =   − +  =  ) ( ) (A3) (A3) and ξ, η, and ξ1 in Eq. under Hertz contact law (A3) can be expressed as 0 1 1 2 ( ) T T S S C q C D q   − = − − , 0 2 1 ( ) T T S S C q C q   = − − and 1 0 1 1 2 ( ) T T S S C D q C q   = − − (A4) (A4) The Jacobian matrix JQ can be calculated by following the procedure of Eq. (41). To obtain JQ in this example, intermediate variables fDD, fD, and fj, j =-1, 0, 1 will be calculated first. For the second derivative of U: 1 (2 1) (2 1) 2 (2 1) (2 1) 0 0 dd M M DD M M dd f f f +  + +  +   =       (A5) (A5) the FFT of F U   is calculated first, where the FFT of F U   is calculated first, where the FFT of F U   is calculated first, where 2 1 2 2 0 0 m F U m      =      (A6 2 1 2 2 0 0 m F U m      =      (A6) (A6) Since every term in the matrix is a constant, 1 dd f and 2 dd f can be directly represented as 2 1 1 2 1 0 0 dd m f m       =       and 2 2 2 2 2 0 0 dd m f m       =       (A7) (A7) respectively. Since there is no first derivative of U, fD is a zero matrix. Data Availability The datasets generated during the current study are available from the corresponding author on reasonable request. under Hertz contact law (40): 2 1 1 1 0 2 2 2 1 0 1 1 s s r J C d r J C d             =      =      (A14) where 1 1 2 1 2 1 2 2 1 1 1 3 ( ) ( ) 2 3 ( ) ( ) 2 T S g T S g r C D Dq r C D Dq     −  = −    = −   (A15) 2 1 1 1 0 2 2 2 1 0 1 1 s s r J C d r J C d             =      =      (A14) 2 1 1 1 0 2 2 2 1 0 1 1 s s r J C d r J C d             =      =      (A14) (A14) where where 1 1 2 1 2 1 2 2 1 1 1 3 ( ) ( ) 2 3 ( ) ( ) 2 T S g T S g r C D Dq r C D Dq     −  = −    = −   (A15) 1 1 2 1 2 1 2 2 1 1 1 3 ( ) ( ) 2 3 ( ) ( ) 2 T S g T S g r C D Dq r C D Dq     −  = −    = −   (A15) (A15) nd Jμ can be obtained by FFT of Eq. (A15). and Jμ can be obtained by FFT of Eq. (A15). and Jμ can be obtained by FFT of Eq. (A15). under Hertz contact law (39): 2 1 1 1 0 2 2 2 1 0 1 1 s s r J C d r J C d             =      =      (A12) (A12) where where where 1 1 2 1 2 T S g r m C G q   = 1 1 2 1 2 2 2 2 2 2 T S g T S g r m C G q r m C G q      =   =  (A13) 1 1 2 1 2 2 2 2 2 2 T S g T S g r m C G q r m C G q      =   =  (A13) (A13) and Jω can be simply calculated by FFT of Eq. (A13). The Jacobian matrix 1 2 [ , ] T T T J J J    = can be calculated by the procedure in Eq. (40): and Jω can be simply calculated by FFT of Eq. (A13). The Jacobian matrix 1 2 [ , ] T T T J J J    = can be calculated by the procedure in Eq. under Hertz contact law Time delay terms fj, j= -1,0,1 are 1 (2 1) (2 1) 1 (2 1) (2 1) (2 1) (2 1) 0 0 0 M M T M M M M f f − +  + − +  + +  +   =       , 0 0 1 2 0 0 0 3 4 T T T T f f f f f   =     and (2 1) (2 1) (2 1) (2 1) 1 1 (2 1) (2 1) 0 0 0 M M M M T M M f f +  + +  + +  +   =     (A8) (A8) According to Section 2.3, 1 Tf −, 0 f and 1 Tf are Toplitz forms of coefficient vectors that are obtained by According to Section 2.3, 1 Tf −, 0 f and 1 Tf are Toplitz forms of coefficient vectors that are obtained by FFT of 1 F   , F   and 1 F   , respectively, where According to Section 2.3, 1 Tf −, 0 f and 1 Tf are Toplitz forms of coefficient vectors that are obtained by FFT of 1 F U −   , F U   and 1 F U   , respectively, where According to Section 2.3, 1 Tf −, 0 f and 1 Tf are Toplitz forms of coefficient vectors that are obtained by F  F  F  FFT of 1 F U −   , F U   and 1 F U   , respectively, where 1 2 1 3 0 ( ) 2 0 0 F U  −    −    =        (A9) 1 2 1 3 0 ( ) 2 0 0 F U  −    −    =        (A9) 1 1 1 2 2 2 1 1 1 2 2 2 1 3 3 3 ( ) ( ) ( ) 2 2 2 3 3 3 ( ) ( ) ( ) 2 2 2 F U          +  −       =    −   +      (A10) 1 1 2 0 0 3 ( ) 0 2 F U       =    −      (A11) 1 2 1 3 0 ( ) 2 0 0 F U  −    −    =        (A9) 1 1 1 2 2 2 1 1 1 2 2 2 1 3 3 3 ( ) ( ) ( ) 2 2 2 3 3 3 ( ) ( ) ( ) 2 2 2 F U          +  −       =    −   +      (A10) 1 1 2 0 0 3 ( ) 0 2 F U       =    −      (A11) (A9) 1 1 1 2 2 2 1 1 1 2 2 2 1 3 3 3 ( ) ( ) ( ) 2 2 2 3 3 3 ( ) ( ) ( ) 2 2 2 F U          +  −       =    −   +      (A10) 1 1 2 0 0 3 ( ) 0 2 F U       =    −      (A11) (A10) (A11) The Jacobian matrix 1 2 [ , ] T T T J J J    = can be calculated by the procedure in Eq. Appendix B: Jacobian matrices of 1D diatomic lattice with cubic springs Incorporating the dimensionless time variable t   = into Eq. (75) yields 2 2 1 3 1 3 1 1 1 2 1 1 2 2 2 1 1 2 2 1 2 2 2 2 1 3 1 3 2 2 1 2 2 1 1 2 1 1 2 1 2 2 1 2 ( ) ( ) ( ) 0 ( ) ( ) ( ) 0 d u m k k u k u k u u u u u d d u m k k u k u k u u u u u d     − −  + + − − +  − +  − =   + + − − +  − +  − =  (B1) (B1) Substituting Eq. (A2) into Eq. (B1), the governing equation can be expressed as Substituting Eq. (A2) into Eq. (B1), the governing equation can be expressed as 2 3 3 1 2 1 1 2 1 1 2 2 1 2 1 1 2 2 1 1 2 2 3 3 2 2 2 1 2 2 1 1 2 1 1 1 2 1 2 2 1 1 ( ) ( ) ( ) 0 ( ) ( ) ( ) 0 T T T T T T T T S S S S S S S S T T T T T T T T S S S S S S S S m C G q k k C q k C q k C D q C q C q C q C D q m C G q k k C q k C q k C D q C q C q C q C D q   − −  + + − − +  − +  − =  + + − − +  − +  − =  (B2) (B2) The Jacobian matrix of Q, JQ, can be calculated by the procedure in Eq. (41). Appendix B: Jacobian matrices of 1D diatomic lattice with cubic springs (39), where The Jacobian matrix of ω, Jω, can be calculated by the procedure in Eq. (39), where 1 1 2 1 2 2 2 2 2 2 T S g T S g r m C G q r m C G q      =   =  (B4) (B4) According to Section 2, the Jacobian matrix of ω can be calculated by the FFT of Eq. (B4). According to Section 2, the Jacobian matrix of ω can be calculated by the FFT of Eq. (B4). The Jacobian matrix of μ, Jμ, can be calculated by the procedure in Eq. (40), where 2 1 2 1 2 2 1 1 2 1 2 2 2 2 1 1 2 2 1 1 1 1 3 ( ) ( ) 3 ( ) ( ) T T T T S g S g S g S g T T T T S g S g S g S g r k C D Dq C q C D q C D Dq r k C D Dq C q C D q C D Dq   − − −  = − − −   = − − −  (B5) (B5) According to Section 2, the Jacobian matrix of μ can be calculated by the FFT of Eq. (B5). Appendix B: Jacobian matrices of 1D diatomic lattice with cubic springs The parameters can be expressed as 2 1 2 2 0 0 m F U m      =      , 1 2 2 2 1 2 1 0 3 ( ) 0 0 k u u F U − −   − − −  =      , 1 2 1 2 2 2 1 0 0 3 ( ) 0 F k u u U    =   − − −    and 1 1 2 1 2 2 1 2 1 2 1 1 2 2 1 2 1 1 1 2 2 2 1 2 2 2 1 1 2 1 1 2 1 2 1 2 2 1 1 2 3 ( ) 3 ( ) 3 ( ) 3 ( ) 3 ( ) 3 ( ) F F u u k k u u u u k u u F F F u k u u k k u u u u u u −           + +  − +  − − − −    = =        − − − + +  − +  −         (B3) 2 1 2 2 0 0 m F U m      =      , 1 2 2 2 1 2 1 0 3 ( ) 0 0 k u u F U − −   − − −  =      , 1 2 1 2 2 2 1 0 0 3 ( ) 0 F k u u U    =   − − −    F F     and 1 1 2 1 2 2 1 2 1 2 1 1 2 2 1 2 1 1 1 2 2 2 1 2 2 2 1 1 2 1 1 2 1 2 1 2 2 1 1 2 3 ( ) 3 ( ) 3 ( ) 3 ( ) 3 ( ) 3 ( ) F F u u k k u u u u k u u F F F u k u u k k u u u u u u −           + +  − +  − − − −    = =        − − − + +  − +  −         (B3) (B3) The Jacobian matrix of ω, Jω, can be calculated by the procedure in Eq. 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MOVING: A User-Centric Platform for Online Literacy Training and Learning
Progress in IS
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Claudia Koschtial Thomas Köhler Carsten Felden Editors e-Science e-Science Open, Social and Virtual Technology for Research Collaboration Progress in IS Progress in IS More information about this series at http://www.springer.com/series/10440 Progress in IS “PROGRESS in IS” encompasses the various areas of Information Systems in theory and practice, presenting cutting-edge advances in the field. It is aimed especially at researchers, doctoral students, and advanced practitioners. The series features both research monographs that make substantial contributions to our state of knowledge and handbooks and other edited volumes, in which a team of experts is organized by one or more leading authorities to write individual chapters on various aspects of the topic. “PROGRESS in IS” is edited by a global team of leading IS experts. The editorial board expressly welcomes new members to this group. Individual volumes in this series are supported by a minimum of two members of the editorial board, and a code of conduct mandatory for all members of the board ensures the quality and cutting-edge nature of the titles published under this series. More information about this series at http://www.springer.com/series/10440 Editors Claudia Koschtial TU Bergakademie Freiberg Freiberg, Germany Carsten Felden TU Bergakademie Freiberg Freiberg, Germany Thomas Köhler Media Center TU Dresden Dresden, Germany ISSN 2196-8705 ISSN 2196-8713 (electronic) Progress in IS ISBN 978-3-030-66261-5 ISBN 978-3-030-66262-2 (eBook) https://doi.org/10.1007/978-3-030-66262-2 © The Editor(s) (if applicable) and The Author(s) 2021. This book is an open access publication. Open Access This book is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribu- tion 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 license and indicate if changes were made. The images or other third party material in this book are included in the book’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the book’s Creative Commons license 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. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland This Springer imprint is published by the registered company Springer Nature Switzerland A The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Introduction This publication, e-science: The enhanced science, is a collection of conference papers, reviewed and selected in a double-blind review process by a distinguished reviewer committee. From the very beginning when John Taylor introduced the term, e-science did not only comprise infrastructure as an enabler of scientific discovery, but also “global collaboration in key areas of science” (Taylor 1999). As computer technologies and digital tools pervade the academic world, it is time to ask what changes are implied when an “e” is added to science. What is primarily discussed in Germany and Great Britain under the term e-science corresponds in the USA to the concept of cyber infrastructures and in Australia to the concept of e-research. More recently the discourse about e-science has been dealing with collaborative research that is based on a comprehensive digital infrastructure. This infrastructure both ultimately integrates all relevant resources for a research domain in a digital format and provides tools for processing such data. In computing-intensive research scenarios, e-science includes distribution of computing capacities, supporting collab- orative processes of a rather inter-institutional character, such as (inter)national networks. The open innovation approach creates new platforms for developing and publishing research results. For example the MOVING platform (http://moving- project.eu/moving-platform/ cf. Vagliano et al. 2018) supports new collaborative research practices and has become a resource for further research. In this sense and in addition to the technological aspect (virtualization of hard- ware),e-sciencealsohasasocialandpolitics-of-scienceaspect(cooperativeresearch, reusability of data and interoperability of digital tools). Although there is the will to expand e-science methods into the wider economy and society, this development is occurring slowly. New skill sets are being acquired in the e-humanities, virtual engineering or visual analytics (Redecker and Punie 2017; Köhler 2018). Yet e- science also comprises open access, e-learning and grid computing; these changes are enabled by state funding and public interest. As a result, the concept of e-science continues to generate new concepts for particular disciplines such as e-geography, e-humanities, e-medicine or e-engineering. The 2014 International Conference on Infrastructures and Cooperation in e- Science and e-Humanities reflected the broad ongoing discussion concerning the changesaffectingresearchandteachinginuniversitiesnowadays.Itaddressedcurrent v vi Introduction Section 3: IT perspectives Section 2: Organizational & sociotechnical perspectives Section 4: Cases & experiences Section 1: Definition and terms Section 5: Future prospects Fig. 1 Structure of “e-science: the enhanced science” Introduction vi Fig. 1 Structure of “e-science: the enhanced science” questionsandsolutionsrelatedtotechnologiesorapplicationsaswellastheirimplica- tionsfortheconductofscience.Itinvestigateddigitallyenhancedacademicinitiatives from technological and socio-scientific perspectives. Introduction This volume is subdivided into five sections representing different perspectives on e-science, as seen in the figure below. The first section introduces the book and reviews the literature concerning the definition of e-science. Section 2 provides orga- nizational and socio-technical perspectives, especially the use of web 2.0 tools from an individual viewpoint and the successful implementation of such tools from an organizational viewpoint. As e-science of course relates to information technology, Section 3 covers IT perspectives, and Section 4 presents domain-specific cases and experiences. Finally, the proceedings close with future prospects (Fig. 1). The introductory section of the proceedings Digital research infrastructure: an overview starts out with C. Koschtial’s contribution, an analysis of the terms covered by the field of digital research, that is, e-science itself, and related terms like cyber- science or science 2.0. As e-science is a socio-technical system, it can be approached from the perspective of the human user, the task or the technology, as identified by Heinrich (1993, pp. 8). The aim is to identify the dominant approach to e-science, to distinguish between the different terms and identify how the terms reflect changes in the prevailing research streams. Section 2 deals with individual usage of tools and organizational enablement of this. The first paper of the second section, authored by T. Köhler, C. Lattemann and J. Neumann, is entitled Organizing Academia Online: Organization models in e-learning Versus e-science Collaboration, identifies forms of organizational gover- nance enabling effective e-collaboration for scientists. Organizational governance Introduction vii captures (social, output or behavioural) controls that are suitable for effective e- collaborationinscientificcommunities.Basedonthreecasestudies,theauthoridenti- fies IT as a key factor in successful virtualization and concludes that there is a need for virtualized organization models which refer to processes and structure. The second contributionfrominthissectionbyB.MohamedandT.Köhlerinvestigatesindividual researchers and their will to use web 2.0 tools. In the third paper, focus on concep- tualizing and validating digital research collaboration between novice researchers. Based on the FISH model, an online survey of 140 novice researchers was carried out and analysed using Partial Least Squares for the analysis of the data. One main result is that successful usage of online tools enhances the belief in web 2.0 as a useful instrument. The second main result is that benefits experienced by sharing enhance motivation for collaboration. Introduction One of the most important elements in search content is metadata, which is shown to be useful for finding data and algorithms. Section 4 presents cases and experiences in the field of e-science. In the first paper, M. Heidari and O. Arnold show that fully digitalized scholarly activities such as online examinations can have a high variability, which presents a manageability challenge. The authors analyse the variability of legally analogue exam processes and prove the necessity for establishing management models. The authors of the second paper, Designing External Knowledge Communication in a Research Network: The Case of Sustainable Land Management, examine factors influencing the knowl- edge communication process. The aim is to find factors in successful communi- cation between researchers and stakeholders as a representation of collaboration. The authors describe steps that need to be taken to enable successful communica- tion: formulate the problem, analyse the situation, define communication objectives, identify target groups, formulate the message and develop a communication strategy and activities. S. Münster’s paper, Researching Scientific Structures Via Joint Author- ships: The Case of Virtual 3D Modelling in Humanities is the last in Section 4. This case study of scientific structures is an analysis of co-authoring for a defined set of conferences. The topics are interdisciplinarity, number of publications and co- authoring, and multipliers. The author identifies multipliers for knowledge in the field of 3D modelling. Finally, in Section 5, A. Skulimowski presents a Delphi study trying to shed some light on future developments in e-science, especially in selected IT technolo- gies. He focuses on two emerging systems, brain-computer interfaces and global expert systems that process databases, communication and unstructured formats like videos. These systems may lead to collective rather than collaborative research, as one researcher cannot manage the volume of information alone anymore. Another scenario based on the automated data analyses is that papers can be produced almost completely with minimal human intervention. In any case, Skulimowski paints an interesting picture of the future of science. We hope that you will find this an interesting collection of a wide range of perspectives, which contributes to your ideas and visions of e-science. Introduction Based on an online study comparing Germany as a whole with the federal state of Saxony, the final contribution of the second section authored by S. Albrecht, C. Minet, S. Herbst, D. Pscheida and T. Köhler presents research into the extent to which digital tools are adopted. One finding is that certain tools are now used by more than the half of the scientists in their daily professional life, but web 2.0 tools like microblogs and social networking sites are used far less often. In Section 3, the focus is on digital tools or information infrastructures, which have not been considered yet. The first paper contributed by O. Schonefeld, M. Stührenberg and A. Witt in this section discusses important guidelines for research infrastructures, which are used to support teaching, research and young researchers. Regarding IT, research infrastructures should be maintained in collaboration between organizations. To reduce costs, energy efficient or green, technologies should be considered, and secure networks are needed enabling to minimize risks. Concerning the aspect of information infrastructure, the authors stress the relevance of data repositories and publication servers in a format that allows the stored documents or data to be used in the long term. Further important considerations regarding research infrastructures include copyright laws with specific national regulations and personal data protection. Accordingly, the authors identify a need for an IT strategy and corresponding roles such as that of data protection officer in organizations providing a research infrastructure. The second paper authored by A. Apaolaza, T. Backes, S. Barthold, I. Bienia, T. Blume, C. Collyda, A. Fessl, S. Gottfried, P. Grunewald, F. Günther, T. Köhler, R. Lorenz, M. Heinz, S. Herbst, V. Mezaris, C. Nishioka, A. Pournaras, V. Sabol, A. Saleh, A. Scherp, U. Simic, A.M.J. Skulimowski, I. Vagliano, M. Vigo, M. Wiese and T. Zdolšek Draksler introduces MOVING: A User-Centric Platform for Online Literacy Training and Learning. The platform enables the usage of machine learning for searching, organizing and managing unstructured data sources. The data sources comprise but are not limited to publications, videos or social media. The contribution presentsthewebplatformfromauser-centredperspectiveinordertogiveanoverview of the functionalities. The final paper of Section 3 from G. Heyer and V. Boehlke presents a research infrastructure called CLARIN-D. This is a web-based platform for the e-humanities, used to collect and provide digital content, with the services needed to store the viii Introduction content. Acknowledgements First of all, the conference was part of the e-science Network of the Technische Universität Bergakademie Freiberg, Technische Universität Dresden and Leipzig University of Applied Sciences. This conference and the resulting publication have been enabled and financially supported by the European Social Fund ESF and the Saxon State Ministry of Science and Culture, whom we want to thank herewith. Additionally, we want to thank Dean Prof. Dr. Andreas Horsch for his financial support in order to make the book available as open access publication. The editors especially want to thank all the authors whose contributions give this volume its special quality, and for their patient support throughout the process ix Introduction of publication. Furthermore, we want to thank all reviewers for their helpful and progress enabling comments, enhancing the quality of all contributions. We want to thank Dominik Wuttke as well as Ilia Vershinin for their exact transfer of all the papers to LNCS. For the language correction, we want to thank Dr. Kate Sotejeff-Wilson for her support and quality assurance. We wish you, the readers, inspiring reading! We wish you, the readers, inspiring reading! Claudia Koschtial Thomas Köhler Carsten Felden Freiberg/Dresden, Germany Spring 2020 Freiberg/Dresden, Germany Spring 2020 Contents Understanding e-Science—What Is It About? . . . . . . . . . . . . . . . . . . . . . . . . 1 Claudia Koschtial Organising Academia Online . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 Thomas Köhler, Christoph Lattemann, and Jörg Neumann The Fish Model: When Do Researchers Collaborate Online? . . . . . . . . . . 29 Bahaaeldin Mohamed and Thomas Köhler The Use of Digital Tools in Scholarly Activities. Empirical Findings on the State of Digitization of Science in Germany, Focusing on Saxony . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 Steffen Albrecht, Claudia Minet, Sabrina Herbst, Daniela Pscheida, and Thomas Köhler Digital Research Infrastructure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 Maik Stührenberg, Oliver Schonefeld, and Andreas Witt MOVING: A User-Centric Platform for Online Literacy Training and Learning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 Aitor Apaolaza, Tobias Backes, Sabine Barthold, Irina Bienia, Till Blume, Chrysa Collyda, Angela Fessl, Sebastian Gottfried, Paul Grunewald, Franziska Günther, Thomas Köhler, Robert Lorenz, Matthias Heinz, Sabrina Herbst, Vasileios Mezaris, Chifumi Nishioka, Alexandros Pournaras, Vedran Sabol, Ahmed Saleh, Ansgar Scherp, Ilija Simic, Andrzej M.J. Skulimowski, Iacopo Vagliano, Markel Vigo, Michael Wiese, and Tanja Zdolšek Draksler CLARIN-D: An IT-Based Research Infrastructure for the Humanities and Social Sciences . . . . . . . . . . . . . . . . . . . . . . . . . . References Heinrich, L.J.: Wirtschaftsinformatik. Oldenbourg Verlag, München (1993) Köhler, T.: Research training for doctoral candidates in the field of education and technology. In: Drummer, J., Hakimov, G., Joldoshov, M., Köhler, T., Udartseva, S. (eds.) Vocational Teacher Education in Central Asia. Developing Skills and Facilitating Success. Springer, Berlin (2018) Redecker, C., Punie, Y.: European framework for the digital competence of educators DigCompEdu. Publications Office of the European Union Luxembourg (2017) Köhler, T.: Research training for doctoral candidates in the field of education and technology. In: Drummer, J., Hakimov, G., Joldoshov, M., Köhler, T., Udartseva, S. (eds.) Vocational Teacher Education in Central Asia. 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Claudia Koschtial Abstract Our daily life has experienced significant changes in the Internet age. The emergence of e-science is regarded as a dramatic one for science. Wikis, blogs, virtual social networks, grid computing and open access are just a brief selection of related new technologies. In order to understand the changes, it is necessary to define these aspects of e-science precisely. Right now, no generally used term or common definition of e-science exists, which limits the understanding of the true potential of the concept. Based on a well-known approach to science in terms of three dimensions—human, task and technology—the author provides a framework for understanding the concept which enables a distinctive view of its development. The concept of e-science emerged in coherence with the technological development of web 2.0 and infrastructure and has reached maturity. This is impacting on the task and human dimensions as in this context, the letter “e” means more than just electronic. Keywords e-Science · Open access · Grid computing · Science 2.0 Keywords e-Science · Open access · Grid computing · Science 2.0 1 Introduction The “e” in combination with a number of well-known terms implies a transfor- mation into online networks and the usage of information technologies, which has evolved in both private and professional life. Science, in its most general meaning as scholarship comprising all disciplines, has also been subject to this transformation. This development is being referred to as electronic/enhanced science, or e-science. The transformation may enable changes going beyond technology itself. According to Luskin, the big e means more than just electronic (Luskin 2012). Fausto et al. (2012) stated this more precisely: “Increasing public interest in science information in a digital and Science 2.0 era promotes a dramatically, rapid, and deep change in science itself”. The goal of this paper is to review research as work in progress. C. Koschtial (B) Technische Universität Bergakademie Freiberg, Freiberg, Germany e-mail: claudia.koschtial@web.de 1 1 © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_1 2 2 C. Koschtial The resulting literature analysis shows what and how science is changing due to the impact of using online networks and information technology. The change in science can be traced back to the 1990s, when the concept of collaborative laboratories (collaboratories) evolved (Bly et al. 1997, p. 1). In 1996, the term cyberscience was sharpened by Nentwich (1999) who refers cyberscience to research activity which scientists were increasingly carrying out in the developing information and communication space. Taylor (1999) produced a definition close to this one: “e-science is about global collaboration in key areas of science, and the next generation of infrastructure that will enable it” and “e-science will change the dynamic of the way science is undertaken”. The definitions mark just the beginning of an ongoing transformation. Most recent aspects of e-science contain open access or science 2.0, referring to the usage of web 2.0 technologies like social networks, blogs or wikis. The cited definitions share some elements: activity of research, scien- tists, infrastructure, collaboration, information and communication. Nevertheless, a common definition does not yet exist, and more diverse terms have emerged since the first occurrence of this concept. Understanding the potential and extent of the change requires an analysis of the concept itself. The present research is an initial step towards this, which can be used as a basis for designing a comprehensive framework of the concept of e-science in order to support the work of scientists. 1 Introduction The remainder of the paper is as follows: the second section presents related work and the research gap. The third section explains how the research has been carried out and how the concept is going to be analysed in order to derive a definition. In Sect. 4, the results of the analyses are presented, leading to a discussion in Sect. 5. 2 Related Work Science defines one possible way to make reality understandable. Leaving behind myth and religion, the ancient Greek philosophy represented an early systematic examination of the world. It dates from 2500 years ago, when the society transformed in the search for education and elucidation. Schools evolved, so science was (and still is) closely connected to teaching (Schülein and Reitze 2012, 31 p.) Nowadays, there is no common perception or description of the change comprised by the term e-science (Yahyapour 2018, p. 369). The literature often deals with open access or particular problems related to data availability. Shneiderman (2012, p. 1349) stresses the potential for understanding and rethinking how a phenomenon is analysed. He promotes methodologies that move away from laboratory to real- world conditions, especially to analyse areas like “secure voting, global environ- mental protection, energy sustainability, and international development” (Shnei- derman 2012, p. 1349). Eastman approaches the underlying process of e-science in terms of data analysis. He formulates an observational-inductive model in order to reflect on Knowledge Discovery in Databases and Data Sensor High-Performance Computing Models without a theoretical basis. His idea sounds promising, but he Understanding e-Science—What Is It About? 3 provides few arguments for it (Eastman et al. 2005, 67 p.). Work and related organisa- tional aspects of science like group learning and cooperative processes are addressed by Pennington (2011, 55 p.). The mentioned literature is exemplary of a search in three literature databases (see Sect. 3.1). No general analysis of this area of discourse exists yet, so the usage and definitions of the terms have not been analysed before. Scientific understanding dependsheavilyonthesepapers,however.Inordertosharpentheconceptandidentify discussed characteristics of e-science, the present authors performed the following literature analysis. 3 Research Approach This section introduces the area of discourse and describes the applied methodology in Sect. 3.1. The applied research framework is then proposed in Sect. 3.2. 3.1 Research Field and Methodology The research follows the method proposed by Fettke (2006, 257 p.). The research process itself demands that researchers have increasingly complex knowledge, which is usually beyond the borders of their own fields (Reinefeld 2005, p. 4). Two research challenges can be identified: • The Internet can be used to search for and communicate information, but success in identifying information is not guaranteed. • The vast amount of data is challenging to process in order to identify relevant content. The mentioned challenges appear as well for the field of e-science. A couple of terms being used in e-science comprise some or all the elements mentioned above. The ones which have been mentioned so far are: The mentioned challenges appear as well for the field of e-science. A couple of terms being used in e-science comprise some or all the elements mentioned above. The ones which have been mentioned so far are: • e-science itself meaning electronic or digitally enhanced science (Hiller 2005, p.5); • cyber infrastructure (Hey 2006); • e-research (University of Technology Sydney 2013); • cyberscience (Atkins 2005, 1 p.); and • science 2.0 (Leibnitz 2012). As these terms appear at different points in time, the meaning has to be reflected on and trends need to be considered in order to understand the circumstances in which they arose. Relevant literature was identified by searching the title, abstract and keywords for the terms “e-science”, “eScience”, “e-research”, “eResearch”, “science 2.0”, “cyberscience”, “cyberinfrasructure”, “grid computing” and “grid” 4 C. Koschtial Fig. 1 Heirich’s human—task—technology framework (Heinrich 1993, p. 8) and its adaption to the field of e-science 4 4 C. Koschtial Fig. 1 Heirich’s human—task—technology framework (Heinrich 1993, p. 8) and its adaption to the field of e-science togetherwith“e-science”inthreedatabases:EBSCOAcademicSearch,ACMDigital Library and IEEE XPlore. To increase the amount of results, Google Scholar was also searched for titles in the period from 1994 to 2005. Digital humanities were excluded as it refers solely to e-science in the field of humanities. 3.2 Research Framework A research framework is needed in order to identify the essence of the concept of e-science and differences between the terms being used. Science 2.0 includes a range of topics. Shneiderman (2012, p. 1349) identified research on sociotechnical systems as the basis for an increasing collaboration. Hein- rich (1993, p. 8) regards sociotechnical information systems as composed of human, task and technical dimensions; he sees such systems as open, complex and sophis- ticated. Figure 1 shows the general framework created by Heinrich (left-hand side) and its adaption to the context of e-science (right-hand side). Regarding the given definitions, some initial characteristics can be extracted: scientists, information and communication, infrastructure, collaboration and research. In order to reflect all aspects of e-science, collaboration is added to the framework, as this was inherent in all definitions. Figure 2 shows the framework used. 4 Results The literature search led to 148 definitions of the selected terms related to e- science. The most frequent definition was “e-science” (43%), followed by “grid” 5 5 Understanding e-Science—What Is It About? Fig. 2 E-science framework including collaboration Fig. 2 E-science framework including collaboration (32%), “science 2.0” (9%), “cyberinfrastructure” (8%), “e-research” (7%) and “cyberscience” (3%). Table 1 shows the number of definitions per year. Figure 3 shows the occurrence of these terms over time. In a second step, the authors analysed the development of the selected definitions over time and investigated whether the dimensions of the framework were mentioned in each definition. The following examples show key terms related to each dimension. • Technical dimension: • Technical dimension: – Web 2.0 technologies as a single technology; – Networks and infrastructure as a collaboration technology. • Task dimension: • Task dimension: • Human dimension: • Human dimension: – Researcher as human; – Virtual organisations like social networks. – Virtual organisations like social networks. The next step was to analyse the relations between the three dimensions, human, task and technology. • Task dimension: – Publishing, analysing or teaching as single tasks; – Collaborative projects which may have an interdisciplinary focus. Table 1 Number of definitions per year 1998–2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 5 5 5 16 17 15 14 12 10 17 11 11 10 Table 1 Number of definitions per year 1998–2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 5 5 5 16 17 15 14 12 10 17 11 11 10 6 C. Koschtial Fig. 3 Relative frequency of terms related to time 6 C. Koschtial Fig. 3 Relative frequency of terms related to time C. Koschtial 6 6 Fig. 3 Relative frequency of terms related to time Fig. 3 Relative frequency of terms related to time 5 Discussion of Initial Results Figure 3 shows that terms like cyberscience or cyberinfrastructure disappeared over time. The presence of the term e-science is relatively stable over the time, which can be seen as acceptance and establishment of this term. The frequency of the term grid is decreasing, which may hint that the technological side of the concept is already mature, established and needs no further development but that claim needs to be checked for the next years. Additionally, the funding period of the UK e-Science Core Programme stopped in 2006, resulting in a reduction of interest in the topic or at least resulting in a reduced amount of publications. Figure4showsthecontentanalysisofthedefinitions.Thehumandimensionhasan approximately stable occurrence over time. But technology is less often mentioned throughout the analysed period. Regarding technology, the number of definitions describing collaborative technology as a constitutive characteristic decreases over time. The term grid is also used less and less over time. Technology seems to be no longer a challenge, but an enabler. The single resource referring to web 2.0 tech- nologies is stable over time. In the task dimension, collaborative/interdisciplinary research projects do not play a significant role. The intention of financial supporting institutions to encourage collaborative research may play an increasing role—but such a trend is not visible, yet. Research as task is an increasing part of the defini- tions, which might be a further hint that the technology itself is mature and the usage is becoming more important. This allows the concept to be used in more different fields. Understanding e-Science—What Is It About? 7 7 7 Understanding e-Science—What Is It About? Understanding e-Science—What Is It About? Understanding e-Science—What Is It About? 7 Fig. 4 Results of the analysis of the human, task and technology dimensions of e-science Fig. 4 Results of the analysis of the human, task and technology dimensions of e-science Regarding the relations between the dimensions, an important link is emerging between task and technology. This may be understood as an indicator for increasing automation. Furthermore, the relation between human and task is the relation that is increasing most sharply. The use of the selected terms varied by geographical location and in relation to public funding programmes in the respective area. The term e-science itself has been used by the UK e-science Core Programme from 1999 until 2006. Cyberinfrastruc- ture comes from the USA, and e-infrastructure emerged in Europe. 5 Discussion of Initial Results A further term appeared in 2005 on an initiative of the Australian Research Councils, which was entitled e-research. The focus here however is not on geographical differences and funding; this issue requires further investigation. 6 Conclusion The aim of this paper was to show how the use of the term e-science is changing through a literature analysis. The initial results show that the concept of e-science changes over time. One aspect of the concept is technology, referring to infrastructure and single resources: • Grid computing is “an important new field, distinguished from conventional distributed computing by its focus on large-scale resource sharing, innovative applications, and, in some cases, high-performance orientation” (Foster et al. 2001, p. 200). 8 C. Koschtial C. Koschtial • Web 2.0 technologies are an evolutionary stage in Internet use. Examples are virtual communities, blogs or wikis (Nentwich 2009). • Web 2.0 technologies are an evolutionary stage in Internet use. Examples are virtual communities, blogs or wikis (Nentwich 2009). Furthermore, e-science is oriented to tasks: processing vast amounts of data, searching for information or publishing content. The task of establishing collab- orative projects is weakly represented in the analysed literature. • Open access refers to “The first is a change in the publishing model to one more suited to the age of the Web; the second, a change in how scientists connect with society – their major funders through taxation” (e-science talk 2012). • Open access refers to “The first is a change in the publishing model to one more suited to the age of the Web; the second, a change in how scientists connect with society – their major funders through taxation” (e-science talk 2012). Additionally, the scientist plays an important role in the concept of e-science in two ways: Additionally, the scientist plays an important role in the concept of e-science in two ways: • as a single researcher; • as virtual communities, which exist only in the Internet. They form for a limited period in time as interdisciplinary groups of regional segregated elements (Mosch 2005). The key characteristic of such units is collaboration. • as virtual communities, which exist only in the Internet. They form for a limited period in time as interdisciplinary groups of regional segregated elements (Mosch 2005). The key characteristic of such units is collaboration. The changes related to e-science are apparent in all three of Heinrich’s dimensions. Important concepts like open access or the grid have been attributed to the different dimensions. 6 Conclusion Therefore, the potential of e-science is not reduced to electronification, but expanded to include redesign of tasks, the emergence of virtual organisations and the rapidly increasing importance of collaboration. Right now, the technology dimension still dominates the concept, but it is maturing and this will form the basis for further changes. 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Informatik Spektrum (Informatik-Spektrum) 41, 369– 375 (2018) Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), 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 license and indicate if changes were made. g The images or other third party material in this chapter are included in the chapter’s Creative Commons license, unless indicated otherwise in a credit line to the material. References If material is not included in the chapter’s Creative Commons license 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. 1 Introduction The central aim of this article is to identify forms of organisational governance (social, output, or behavioural control) that are suitable for effective e-collaboration in scientific communities. Are “e-learning” and “e-science” fundamentally different things? Specifically, does e-learning concern teaching, and e-science, research? This is factually correct, but from an organisation theory perspective, not a sufficient criterion for differentiation. Above all, the clientele at issue here is the same: the teaching and research staff of universities. In addition, both activities are carried out within the same institution. In this respect, comparison is not only possible, it is mandatory. Our evaluation is based on both a review of the relevant literature and empirical studies, some of which were conducted by the authors. Following the classification of virtual organisations, the main characteristics of organising academic activities are presented and validated through suitable institutional examples. Thomas Köhler, Christoph Lattemann, and Jörg Neumann Thomas Köhler, Christoph Lattemann, and Jörg Neumann Abstract Research on organisational arrangements of scholarly networks in both e-learning and e-research is located at the intersection of different theoretical justifi- cations and developmental contexts such as organisational theory, computer science, education science and media informatics. However, there is still a lack of research on the organisational context of e-learning arrangements and its impact on collaboration inacademiccommunities.E-learningresearchshowsthattheintegrationofelectronic media in scientific communities negatively impacts their effectiveness and causes conflicts within communities. Research networks however are far less investigated as there is not direct didactic focus on how to collaborate. Recent theories on organi- sational design, virtual organisations and governance provide concepts for organising e-collaboration more effectively. Managerial instruments such as direct control of results and behaviours need to be supplemented or even replaced by concepts of social control; typically trust and confidence become the central mechanisms for the new forms of inter- and intra-organisational coordination. This paper starts with concepts. Then, to exemplify the organisational coordination mechanisms in schol- arly e-communities, the authors critically discuss and reflect on these organisational arrangements and managerial concepts for two higher education portals and one research network in Germany. The conclusion is that, just as previous research has confirmed for educational networks, governance within academic networks relies heavily on the functionality of social and communicative forms of control. Keywords Research network · Education portal · Virtual organisation · Governance · Social control · Science collaboration · Scholarly collaboration · Online community T. Köhler (B) Department of Education, Technische Universität Dresden, Dresden, Germany e-mail: thomas.koehler@tu-dresden.de C. Lattemann Department of Business and Economics, Jacobs University, Bremen, Germany e-mail: c.lattemann@jacobs-university.de J. Neumann Media Center, Technische Universität Dresden, Dresden, Germany e-mail: joerg.neumann@tu-dresden.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_2 T. Köhler (B) Department of Education, Technische Universität Dresden, Dresden, Germany e-mail: thomas.koehler@tu-dresden.de C. Lattemann Department of Business and Economics, Jacobs University, Bremen, Germany e-mail: c.lattemann@jacobs-university.de J. Neumann Media Center, Technische Universität Dresden, Dresden, Germany e-mail: joerg.neumann@tu-dresden.de J. Neumann Media Center, Technische Universität Dresden, Dresden, Germany e-mail: joerg.neumann@tu-dresden.de 11 11 © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_2 © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_2 T. Köhler et al. T. Köhler et al. 12 2.1 Online Technologies in Higher Education The integration of new media in educational settings has been intensively discussed in academic research and education for about 15 years. Various forms of online, distance, and blended learning have been implemented and tested. After a series of tentative, rather experimental tests to integrate new Internet technologies and electronic media in teaching processes, the management of students and eventu- ally the teaching itself, we now see the results in the forms of web-based tutorials (WBT), virtual learning environments (VLE) and more recently in massive open online courses (MOOC). With respect to developments in the online learning arena, in 1999 the German expert group on Higher Education Development by New Media predicted the higher education landscape would be as follows (cf. Köhler et al. 2010): 1. Global education providers and platforms offer worldwide accessible online courses. 1. Global education providers and platforms offer worldwide accessible online courses. 2. Traditional universities are in competition with private online providers, in partic- ular with corporate universities, and students use the opportunities of the global education market. 3. In order to survive in this competitive situation, many colleges have joined together in networks and offer common learning opportunities, while univer- sities are jointly offering their academic programs together under the umbrella of a virtual university. Organising Academia Online 13 4. Student services are provided by facilitators and tutors, and less by classical university teachers, because more than 50% of students study online. 4. Student services are provided by facilitators and tutors, and less by classical university teachers, because more than 50% of students study online. As of today, these predictions can only partly be confirmed. However, besides the established Open Universities like the British Open University or the German Fernuniversität Hagen, new global education providers such as the edX, Coursera or Udacity are emerging and become more relevant with the increasing need for lifelong learning and with growing numbers of students seeking for flexible online learning. Nevertheless, they still only play a niche role in higher education so far. But it is no surprise that the Centre for Higher Education Development (Hener and Buch 2006) concluded more than a decade ago that “[i]n academic education […] uses of digital media in teaching and learning and integration of information technology- based administrative services have become widely established. Key questions of the future are seen especially in the interlinking of different services” (p. 2). 2.2 Virtualisation in Higher Education Academic research has dealt with the use of Internet-based technology in teaching for many years (see, e.g., Lievrouw et al. 2000; Issing and Klimsa 2003, 2010). While initial claims were rather didactic (“classroom technology”), virtualised educational scenarios (VLEs, MOOCs, etc.) are of increasing interest nowadays. The concept of virtualisation is being used more and more often to describe the essential features and expectations of information and communication technologies (ICT) and multimedia, and to document the change. What exactly is behind it? Features of virtualisation described by Köhler et al. (2010) include the facts that students no longer meet their seminar leaders personally and that neither they nor the lecturers need to borrow books from the library. Researchers submit their conference abstracts, and expert opinions on other posts, via an Internet portal, while heads of research projects identify potential research partners in a database—without having ever met in person before. All in all, universities and virtual academies cooperate by uploading teaching content to a joint learning management system to be used by students from other institutions. In sum, such a far-reaching change in the educational landscape has established itself in less than 15 years and is on the verge of becoming the standard. However, acceptance by the teaching staff, especially at universities, is rather low; for example, professors in Toronto went on strike in 1997 and have managed to keep their teaching offline until today. Similarly, a study published by the Centro Nacional de Estadística, Geografía e Informática Mexico in 2004 (INEGI 2004) explained that 70% of professors in Mexico protested against the use of ICT in education. Their main reason was and perhaps still is the form of presentation of course content when using ICT in formats like PowerPoint and LaTeX. The distinctly reluctant behaviour of university staff is illustrated, for example, by the words of a professor from education sciences “you have to operate well didactically […] and a part of this is the whole computer nonsense” (Misoch and Köhler 2005, p. 1). In the same T. Köhler et al. 14 T. Köhler et al. 2.2 Virtualisation in Higher Education way, the dean of the engineering department at a leading German university stated in 2015 that “the nightmare is graduates who no longer draw without a computer, no more writing”.1 The prevailing opinion is that this leads to a very impersonal design of seminar rooms and lecture halls, whereby students may lose their communication and personal contact with each other. Respondents continue to believe ICT should only be used in education to communicate data and not to communicate between people, nor do they see it as a new academic format or alternative for formation, though it may be used in addition to a classroom setting. Hence, pivotal questions remain unanswered. What will the campus of 2025 look like? Which organisational models of e-learning and e-science collaboration will prevail? Despite the aforementioned reluctance in academia, other developments are observable. For example, online learning is proliferating in media-related disciplines; topics such as artificial intelligence, telemedicine and distance learning, MOOCs and open science are frequently and extensively discussed as powerful new opportunities for improving academic activity in general (Pscheida et al. 2014; Lattemann and Khaddage 2013). Our first conclusion is that ICT has changed (academic) education. As the above examples illustrate, this change is not limited to education, academic teaching and learning. This raises the question of what exactly the virtualisation of education means. As early as 1999, Landfried, then President of the German Rectors’ Confer- ence, described unlimited access to stocks of knowledge independent of time and space; yet this knowledge is disconnected (separated) from physical institutions and, in particular, individuals (Landfried 2009). What is meant by this double separation? To answer this, it is important to analyse what is virtualised, which is more than the learning objects or knowledge content. In fact, relations (micro- and macro-social, but also those between learners and learning object) can be virtualised as well as knowledge, sometimes both at the same time. 1This quotation was taken from an anonymised interview by the author. 3 Change of Organisational Theories and Paradigms What has been known from both management and operational practice for a long time (cf. Frindte et al. 2000) now also appears to apply to education: ICT is becoming more important in managing organisational processes, and these infrastructures are becoming permanent. But these processes vary significantly, raising the question of the ideal configuration of technology and organisation. The first research to address this issue introduced new ICT to control operational processes in knowledge coopera- tion.Munkvold(2003)setupsuchaheuristicthatcanbetransferredtotheeducational context almost directly. He divided the “implementation of collaboration technolo- gies” into four sub-areas, the (1) organisational context, (2) implementation project, 15 Organising Academia Online (3) technological context and (4) implementation phase. Similarly, with explicit refer- ence to the introduction of online learning in higher education when used as dimen- sions of change, Euler et al. (2004) proposed the following five dimensions: (1) economic dimension, (2) pedagogical-didactic (educational) dimension, (3) organ- isational/administrative dimension, (4) technical dimension and (5) sociocultural dimension. Are these theories based on economics or technology? Neither. Organisation and organisational culture are central to change. With this assessment, the authors align with a strand in the German educational research tradition (Neumann and Schütte 2008) that is gaining ground but still rather new. This broadens the academic perspec- tive on the use of media, which was previously dominated primarily by cognitive (psychology), teaching (pedagogy), education-oriented (educational science) or even technological (computer science, etc.) approaches. An organisational perspective adds a social and management science-based momentum, and macro-social perspec- tives. After 2005 more research programmes in Germany sought to meet the need for such an approach, including New Media in Education II or the later Digitisation Initiative (2014). In education and media studies, where approaches based on organ- isation studies, education science, or media economics are preferred, researchers are frequently challenged to take these approaches. Just after 2010, based on the concept of openness—used when coining the terms of OER and MOOC—many became convinced that the technology used for univer- sity operations would be revolutionised. Within the next decade, it is expected that students will no longer attend lectures or work in a lab, but will join professors’ research activities online, whenever and wherever they want. Academic knowledge will be tailored, or transferred from mass production to mass customisation. So what is the core of the “digitisation of teaching” or the “advent of information and commu- nication technologies in the university”? 3 Change of Organisational Theories and Paradigms Germany’s former Minister of Science, Bulmahn (2004, p. 5), argued that “the new media in the combination of computer andInternet[willpenetrate]allsocialandeconomicsectors[andwillrelease]afunda- mental structural change” combined with unprecedented speed of market globalisa- tion. Ortner and Nickolmann (1999) stressed that the success of open universities will force conventional universities to adopt innovations in teaching organisation, such as distance learning, on-campus students as independent learners, modular course structures and the enrolment of mature part-time students. This goes along with changing forms of social micro-study, from online learning communities (Kahnwald and Köhler 2005) to more complex flexible online knowledge organisations (Köhler et al. 2003). To speed up the new media restructuring of higher education, the Federal Ministry of Education and Research (BMBF) has targeted the existing New Media in Educa- tion Programme and the 2004 re-bid. The first phase of the programme from 2000 to 2004 aimed to develop high-quality e-learning content and concepts for mobile learning, and to put them into regular practice, particularly in undergraduate studies. These developments were intended to be available from 2005 and to be sustained and broadened by two conveyor lines. Conveyor line (A) was for projects in an inter- disciplinary and university-specific context, called “e-learning integration”. This is T. Köhler et al. T. Köhler et al. 16 about developing organisational infrastructure and about changing management to develop utilisation of the opportunities provided by ICT innovation potential in the field of teaching, learning, and exams to universities systematically and sustain- ably. Conveyor line (B), for projects in a university-wide and primarily subject- specific context, referred to as “e-learning transfer”, was to lead to new organisa- tional concepts and business models for services, related to the production and use of online learning primarily supporting professional and technical areas (cf. BMBF, 2004, all translations from German by the authors). By 2010, most of these projects were completed. What impact did the targeted re-organisation of online learning in German universities have? 3.1 The Research Framework: Virtual (Educational) Organisations In view of the different organisational theories applicable to online teaching and learning in a university context, including its structural and procedural commonali- ties, the following issues should be noted. At the institutional level, online learning is integrated into the organisational structure of the university. This requires suffi- cient integration of external service providers. Figure 1 presents the value chain of e-learning from a university perspective, including the internal and external partners at the Technische Universität Dresden in 2008. The e-learning value chain shows that teaching and learning in an electronically mediated environment is multifaceted and involves various stakeholders. Because of the various partners involved, the organisational concept shows many charac- teristics of a virtual organisation with loosely coupled partners (external content providers, platform providers, external and internal instructors and students, etc.). Hence, universities which provide online learning arrangements must also follow, or at least adopt, mechanisms of virtual organisations. They must change their struc- tures from their traditional departmental separation towards more process-oriented, open and collaborative organisational settings. These kinds of new virtual organisations are primarily shaped by their virtual char- acter and are limited by their lack of “real” organisational boundaries. This applies to all organisational aspects: the location, bonds and stability of the organisation. Such a virtual organisation is “multisite, multi-organisational and dynamic” (Snow et al. 1999). As shown by Köhler and Schilde (2003), virtual organisations can differ greatly in terms of size, durability or stability. Furthermore, various forms of virtual organisa- tion and cooperation are described in theory and can be observed in practice, under an equally large number of names (network, cluster, virtual team, virtual organisation, etc.). In order to make these phenomena comparable and assign experimental find- ings, a further differentiation of the term is required. Okkonen (2002) proposed one 17 Organising Academia Online Fig. 1 Organisational framework of online learning using the example of the Technische Universität Dresden (own figure after Neumann and Schütte 2008) Fig. 1 Organisational framework of online learning using the example of the Technische Universitä Dresden (own figure after Neumann and Schütte 2008) way of doing this, presented by Köhler et al. (2003) as an advanced systematisation of virtualised organisational forms (see the following Table 1). In the following, two case studies on online learning and one case study on online research are presented and critically discussed from the perspective of virtual organisations. able1 Differentiatedcharacteristicsofvirtualisedorganisationalforms(ownfigureafterOkkonen 002; Köhler et al. 2003) Table1 Differentiatedcharacteristicsofvirtualisedorganisationalforms(ownfigureafterOkkonen 2002; Köhler et al. 2003) We have chosen two case studies because the authors of this paper are involved in the projects and they have deep insights. A triangulation approach was utilised as this is “the most desired pattern for dealing with case study data” (Yin 2011). Seminal articles on the case study topics were selected for analysis (Yin 2013). For this particular example, differing sources have been consolidated to present a comprehensive case study summary, including scientific publications, research reports,andpublicdescriptionsonthewebsitesofthechoseninstitutions.Allmaterial was either available publicly or from internal sources. Figures used come from self- descriptions of those projects—the layout was not changed, but translated. 3.2 Research Methods This paper follows an inductive research approach in order to identify relevant organ- isational mechanisms in an e-learning institution, based on three case studies. The case study method is selected as it is a common and comprehensive investigative tool for exploring individual, group, organisational or social phenomena (Yin 2013; Bryman and Bell 2011). In this instance, the weaknesses in corporate data security are investigated, in order to reveal potential causes, as discussed in the analysis section. 18 T. Köhler et al. Case I: Online learning in academic education through the education portal of Saxony (since 2001) Since 2001, a university network has been supporting online teaching at public universities in the German federal state of Saxony. After an initial phase with the direct participation of the four universities which comprised this group since 2004, a system corporation, BPS Education Sachsen GmbH, was founded in 2006. In an evaluation of the state of development of online learning at Saxon universities for the Saxon Minister of Science and Art, the German National Centre for Higher Education Development (CHE), stated in 2006 that despite many years of funding by means of the country and the special commitment of many scientists concluded that online media is still used on a relatively small scale. Overall, however, acceptance is increasing among both university staff and students. But Hener and Buch (2006) noted a lack of liability for student usage, sustainability in higher education, and overall management of e-learning in higher education. This has been confirmed by further analyses (Köhler and Ihbe 2006) calling for a more systematic integration of online learning at Germany’s largest technical university, the Technische Universität Dresden. In 2007, control of the project passed to the newly established e-learning Organising Academia Online 19 Fig. 2 Model of the education portal of Saxony (cf. https://bildungsportal.sachsen.de/) Organising Academia Online 19 Fig. 2 Model of the education portal of Saxony (cf. https://bildungsportal.sachsen.de/) working group of the Rector’s Conference Saxony. Since then, all public universities in Saxony and two private universities have joined the network. The following Fig. 2 shows the distribution of the educational portal in Saxony as of 2008: T. Köhler et al. T. Köhler et al. Fig. 3 Model of the education portal of Thuringia (own figure after Schmidt 2002) ig. 3 Model of the education portal of Thuringia (own figure after Schmidt 2002) Fig. 3 Model of the education portal of Thuringia (own figure after Schmidt 2002) Case II: Online-supported continuous learning in the education portal of Thuringian universities (2000–2013) Based on analysis of the need for media-based academic training and organisa- tional structures at and between the universities of Thuringia, and to support more sustainable development of such online training, the (online) education portal for Thuringia was constructed in 2001 (www.bildungsportal-thueringen.de). As a conse- quence of the above tests, this portal aimed to serve institutional training seekers or their staff, that is, employees who want to selectively add to their skills profile according to their academic or equivalent qualifications or needs. There was already significant potential demand for this when the portal opened. An expert (Stifter- verband 2001) estimated that 20,000 of almost 60,000 students of the Distance University of Hagen alone are undergoing a hidden continuing professional devel- opment (CPD). The education portal of Thuringia competed with several private CPD providers. This fact should be mentioned because the expectations and attri- butions of training seekers were influenced by their experiences with these market leaders. Nevertheless, the participating universities have reconfigured themselves on the virtual organisation model, consisting of a core information broker and a network of partners meeting training needs, as in Fig 3. The education portal of the Thuringian universities remained at the project stage until 2013 and was then closed by the responsible Ministry of Science. 20 Case III: The e-Science Saxony Research Network as a virtual science organisation (since 2011) The e-Science Research Network project is a Saxony-wide comprehensive research network of all state universities created to explore approaches and methods in e-science (electronic science). The term e-science describes the different fields of scientific research and development related to the use of computer technologies. While this term is mainly used in Germany and the UK, comparable concepts include “cyber-infrastructure” in the United States or “e-research” in Australia. Currently, the slogan “Science 2.0” frames the discussion, in particular concerning cooperative digital scientific work (Weichselgartner 2010). The thematic range of infrastructures, application architectures, grid and cloud technologies extends to the educational technology known as e-learning. In addition, e-science systems support cooperative research between universities and with the private sector (cf. Ziegler and Diehl 2009). Research in e-science can be subdivided into disciplines such as e-humanities, e- medicine or e-engineering. In any case, it extends the scholarly process by integrating e-technologies and methods based thereon. The methodology was found to screen collaborative research activity, but knowledge organisation changed also dramati- cally and has been systematically underdeveloped by these e-disciplines. Even when research contexts are established or reused, it creates new paradigms, such as the concept of a “living lab”. This is user-centred research and open innovation practice, based on research work in multidisciplinary teams. One of the essential activities of these teams is co-creation, bringing together technological innovations and their applications through procedures such as crowdsourcing and crowdcasting. In these driven-by-research community practices, a variety of opinions, needs and knowledge exchanges can be used to brainstorm new scenarios, solutions and applications; yet these may be one-sided (Fig. 4). Overall, starting with a steady drop in the “half-life of knowledge”, the changing demands of industry and the economy, and social changes in the knowledge society, the network partners have developed a new type of research and the accompanying scientific activities. New information and communication technologies can be used in this context, especially to provide, disseminate and use research information, such as laboratory data from simulations using complex aggregate social science information. Thus, media-based networking researchers are characterised by a high degree of flexibility and variability; usage may translate into new contexts through the restructuring of data and their usage. Through the coordinated action of the Saxon 21 21 Organising Academia Online Organising Academia Online Fig. 2http://www.hochschulforumdigitalisierung.de/, retrieved on 15 July 2015. Case III: The e-Science Saxony Research Network as a virtual science organisation (since 2011) 4 Clusters and organisational structure in the e-science Saxony research network eScience Network Saxony Cluster I eLearning Cluster III eSystems Cluster II eResearchy State Ministry for Science and Art and the Federal Republic of Germany, the Saxon universities have achieved an excellent level of “computational science”, especially in introducing e-learning support systems (Hener and Buch 2006). Summarised as e- sciences, the current project focusses on e-business, e-learning and e-systems, which are interwoven holistically at universities in the context of teaching and research. Fig. 4 Clusters and organisational structure in the e-science Saxony research network State Ministry for Science and Art and the Federal Republic of Germany, the Saxon universities have achieved an excellent level of “computational science”, especially in introducing e-learning support systems (Hener and Buch 2006). Summarised as e- sciences, the current project focusses on e-business, e-learning and e-systems, which are interwoven holistically at universities in the context of teaching and research. 4.1 Theoretical Considerations About the Functioning of Virtual Organisations in the Academic Sector 4.1 Theoretical Considerations About the Functioning of Virtual Organisations in the Academic Sector Recent digitisation initiatives in academia demonstrate the pressing need of a serious discourse about its fundamental principles and practical meaning for the whole sector. In Germany since its launch in 2014, the Higher Education Forum on Digitisation has created an independent national platform to discuss the multiple facets of digitisation in higher education by consulting in six thematic groups on issues surrounding the digitisation of university teaching.2 Two decades ago, Malone and Davidow (1992) triggered the discussion about new organisation and management concepts in the economic sciences with their path- setting contribution “Virtual Corporation”. Until that moment, organisational change was marked by various headings such as “Computational Organisation”, “Learning T. Köhler et al. 22 T. Köhler et al. Organisation”, “Organisational Communication”, “Society and Internet Develop- ment”, “Trust Leadership and Decision Making” or “Augmented Reality” (cf. Köhler and Schilde 2003). All approaches share a similar basis: organisational units are reduced to their core competencies and have to cooperate in network-like struc- tures. Complex tasks are realised by a number of independent organisational units or enterprises with complementary skills. This calls into question traditional organi- sational concepts, as published in governance research. Direct output and behaviour control, which are feasible in traditionally structured enterprises with divisional and functional organisation patterns, are supplemented or even replaced by concepts of social control. In the 1980s, psychological studies of cooperation and communi- cation in virtual communities depicted computer-mediated communication as typi- cally rather anomic in nature (Sproull and Kiesler 1986), less tolerant (Funkhouser and Shaw 1990) and lacking transferable behaviour (Köhler 2003). Postmes (1997) see this analysis as based on the less medium-socialised population of the “early years”. Therefore, these findings would be difficult to replicate. However, the cases presented here show that today’s changed environment creates completely new ways of medium-socialised collaboration. Once again, the majority are beginners in a new (mediated) organisational culture. Consequently, Lattemann and Köhler (2005) assumed that trust and security of contract would become key factors of cooperation in virtual organisations. This implies that social control becomes a strategic factor in competition among virtual organisations (Barney and Hansen 1994; Krysteck 1997) laying the foundation for new forms of cooperation. 4.1 Theoretical Considerations About the Functioning of Virtual Organisations in the Academic Sector Their analysis based on liter- ature review, and our own empirical studies, lead us to observe that the less output and behaviour can be assigned directly to specific individuals, the more important social control of the community becomes. Our three case studies demonstrate that organisational development towards a networking, virtualised organisational structure can be found in both the academic education and research domains. For both domains, it is obvious that this develop- ment is going beyond existing organisational patterns; however, it is not necessarily sustainable, as the closure of the education portal of Thuringian universities after only ten years shows. Is this development merely the interface of a larger organisational change, or the beginning of a new era? Networking organisations need to move beyond the purely project stage. In all cases, besides new organisational forms we found both close linkage to existing units, including several management instances like steering committees, information offices, and supervisory boards. Neither a classical hierarchy nor a clear linkage to all partners were found in these cases. Structures and opportunities for influencing the processes seem rather soft and depend on functioning communication. In sum, virtual networks with flexibly aligned partners, who deliver different services and competencies, heavily rely on the coordination of and motivation for social control and trust. Appropriate instruments need to be strengthened. Long- established norms cannot be adopted because these are either insufficiently developed or simply not applicable—which led to the central question studied by the authors previously: Which governance concept is most efficient in the diverse forms of a virtualorganisation?Intheirstudy,LattemannandKöhler(2005)examinedtheextent Organising Academia Online 23 to which new governance concepts (i.e. social control) may be applied to forms of e-learning (i.e. virtual collaboration) and could propose a classification system for virtual organisations. Already before and after Köhler et al. (2003, 2010) studied the organisation of online learning. In a next step, the focus was directed on research networks as an organizational artefact, their functionality and technology. What can be concluded on how to steer the development and how to govern that functioning of those structures effectively? 4.2 Forms, Instruments and Mechanisms of Control in Virtual Organisations Organisational theory examines traditional forms of governance (behavioural and output control) in detail, mostly uniformly. However, with the establishment of network-like organisational structures, the concept of social control has only recently been subjected to rigorous debate. Only the following forms of governance are considered here: 1. direct governance—inspection of behaviour (behavioural control), such as on the basis of standards won from experiences (Magretta 1998); 2. indirect governance—determination of output based on given goals (output control) (Thomson 1967; Magretta 1998); 3. social governance (social control)—comparison of conformity to certain moral and cultural rules (Ouchi 1979). 3. social governance (social control)—comparison of conformity to certain moral and cultural rules (Ouchi 1979). As Lattemann and Koehler (2005) argue, instruments of social control can be identified in relation to the level of objective and personnel management (Thomson 1967). Therefore, trust is not related to behavioural and output control mechanisms, as some authors postulate (see, e.g., Manchen and Grote 2000; Bradach and Eccles 1989), but rather supplementary to these (Das and Teng 1998; Ebner et al. 2003). In that sense, traditional control mechanisms and social control describe are different. How can flexible and light organisational structures be designed and imple- mented? Based on the above discussion of the literature and cases, trust can be promoted by appropriate social standards and basic institutional conditions. A number of governance instruments can be applied to exercise social control, such as promoting common cultures among networking partners with homogeneous value creation processes, or reviewing and creating similar moral concepts through rituals or ceremonies. The observed networks apply different means, ranging from a project plan to an inter-institutional agreement. This method is particularly suit- able for networking partners of a similar size, origin and organisational form (Ouchi 1979), that is, with almost no heterogeneity. Other effective means of social control include operational guidelines (Heck 1999), intensive use of modern and uniform ICT (Köhler 2003; Albers et al. 2002), promoters for public relations and conflict management (Hausschild 1997), job rotation or jointly offered training courses. In the three networks observed here, we found both inter-institutional agreements (such T. Köhler et al. T. Köhler et al. 24 as the integrated provision of academic master’s programmes) and other measures (such as joint training) for using the platform. Can the social control model (cf. Fig. 4.2 Forms, Instruments and Mechanisms of Control in Virtual Organisations 5) developed by Lattemann and Köhler (2005) for learning networks be transferred to research organisations with presum- ably less standardised activity? The efficiency of the three governance forms discussed and the possible fields of their application depend upon the nature of the organisational arrangement. The more governance mechanisms are used; the more competencies are required in the process of cooperation. In contrast to traditional enterprises (Type 1 in Fig. 1), where mostly traditional forms of control (behaviour and output control) based on structural gover- nance tools are used to promote coordination (information and communication) and motivation, virtual organisations may adopt concepts of social control with different degrees of intensity. Virtual teams, virtual projects, temporary virtual organisations and meta-networks are characterised as maximally closed networks with unilateral dependency on the Virtual Teams or Projects, Tem- porary Virtual Org., Meta Net- works closed/ fixed open Traditional Enterprises Virtut al Teams or Projo ects, Tem- porary Virtut al Org., Meta Net- works closed/ f open Traditional Enterp r rises Importance of social control high Border of Virtual Organizations Connection between Virtual Organizations Degree of Virtualization low low high Permanent Virtual Org., Cluster Spherical Network (Miles & Snow 86) Borders of Virtual Elements ixed Fig. 5 Social control and organisational virtualisation (figure by authors, cf. Lattemann and Köhler 2005) Border of Virtual Organizations Connection between Virtual Organizations Virtual Teams or Projects, Tem- porary Virtual Org., Meta Net- works closed/ fixed open Traditional Enterprises Virtut al Teams or Projo ects, Tem- porary Virtut al Org., Meta Net- works closed/ f open Traditional Enterp r rises Importance of social control high Organizations Connection between Virtual Organizations Degree of Virtualization low low high Permanent Virtual Org., Cluster Spherical Network (Miles & Snow 86) ixed Fig 5 Social control and organisational virtualisation (figure by authors cf Lattemann and Köhler Spherical Network (Miles & Snow 86) Permanent Virtual Org., Cluster Degree of Virtualization low low Fig. 5 Social control and organisational virtualisation (figure by authors, cf. Lattemann and Köhler 2005) Fig. 5 Social control and organisational virtualisation (figure by authors, cf. Lattemann and Köhler 2005) Organising Academia Online 25 value creation process. The partners provide a wide spectrum of services and prod- ucts. Such networks do not require a high degree of competency for cooperation. This reflects the fact that social governance tools were not applied intensively in these forms of virtual organisations. 4.2 Forms, Instruments and Mechanisms of Control in Virtual Organisations Business relations of this type are shaped by market- oriented or structural management instruments, such as a centralised coordinating body based on contractual arrangements (e.g. services or employment contracts). Virtual organisations like this frequently use ICT to collaborate and communicate. This is because both employees of the enterprise and long-term partners are often closely associated. Thus, ICT structures are implemented and do not need to be built up. Also—which is perhaps far more important—these structures do not need to be mediated between the partners, as they are obligatory in most temporary projects. Moreover, members of permanent virtual organisations and clusters need strong collaborative competencies due to their extremely intertwined mutual relations. A maximum of informal relations is presupposed in spherical networks (Miles and Snow 1986). The roles of individual participants are distributed in a spherical network;resourcesand/orparticipantsareboundlesslyexchangeable.Suchstructures can be assumed in social networks; however, this article refers to profit-making, not non-profit, environments, so spherical networks are not the focus here. Even its proponents state that this structure cannot be observed in reality (Miles and Snow 1986). In practice, the extent to which ICT is used to support coordination processes in virtual organisations varies greatly. However, in all virtual organisations, ICT plays a pivotal role; without it, virtual organisation is impossible. Research which was based on a set of unsystematic findings from case studies (Manchen and Grote 2000; Köhler and Schilde 2003; Köhler et al. 2003), recommended that the minimum required ICT support be identified first. The arrangement of information and commu- nication processes determines the complexity of the ICT infrastructure (e.g. enter- prise resource planning or e-mail). In less complex virtual organisations (e.g. virtual teams or projects), less sophisticated ICT solutions have been used in academic practice for approximately 20 years. However, in these research organisations, ICT- based groupware solutions were still rather exceptional (Köhler and Röther 2002; Köhler and Schilde 2003). More recently, it has been found out that only a small number of scientists are adopting social media technologies like Mahara, Mendeley or ResearchGate. For example, a Germany-wide survey conducted by Pscheida et al. (2015) found that social media applications such as social networks, microblogs and social bookmarking tools are used by a maximum of 8% of scientists in a research context. 4.3 Limitations Given the recent nature of this study, both the available literature and empirical access to the sectoral development were limited. Firstly, the empirical cases represent developments in German academia only. In the next stage, research must include data from other countries, to develop a more general understanding of organisational dynamics in the academic sector and avoid a national-only explanation. Some sources, including website communications, were publicly available docu- ments written by legal professionals or corporate representatives. Therefore, the case study may contain less reliable data than that supplied from exclusively academic sources. Although the authors attempted to adopt a wide range of literature from several sub-disciplines in business, media and education studies, it is difficult to identify whether other researchers intentionally focussed on organisational development or whether this was a by-product of other considerations. Thus, the case made here is largely based on the previous work of the authors. 4.2 Forms, Instruments and Mechanisms of Control in Virtual Organisations Only in 2020 the influence of the Corona pandemic will perhaps lead to a more massive adoption of such collaboration techniques, but not necessarily in a conscious use. All in all, organisational models for academic institutions dealing with both educa- tion and research need to adapt to organisational models of virtual organisations. Universities and other research institutions have to change in both structure and process within their two main areas—education and research. T. Köhler et al. T. 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If material is not included in the chapter’s Creative Commons license 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. B. Mohamed (B) British Lincoln College, Riyadh, Saudi Arabia e-mail: bahaa@bzoor.com T. Köhler Institute for Vocational Education, TU Dresden, Dresden, Germany e-mail: thomas.koehler@tu-dresden.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_3 Keywords Research collaboration · e-science · Web 2.0 technology · Scholarly communication · Doctoral training 1 Introduction Research collaboration is the foundation of research students’ efforts in academia. Independently of disciplinary background, research is based on the social patterns of competition for the best explanation and joint evaluation of the quality of research. Therefore, research collaboration is a form of positive interaction between knowl- edge producers that have taken on management roles by using certain resources and tools to establish and pursue a scientific goal (Ynalvez et al. 2011). We define research collaboration as the current and future regulations, processes, and concepts which support interaction and cooperation between our doctoral candidates. Here, it is important to note that collaboration is not simply students and professors co- authoring a piece of research; instead, it requires establishing connections that might extend to communication which, over time, develops into sustainable collaboration among different researchers with similar interests. Accordingly, we may need to better understand the nature of scientific tasks and the time frame in which they should be completed, as well as how individual beliefs of using ICT and web 2.0 in a research context can help to define how online activities should be organised. In addition, the use of technology can be interpreted in relation to cultural contexts and disciplines. Finally, incentives act as the engine that encourages students to under- take collaborative research, and, in academia, this engine is covered and protected by research ethics. In this paper, we focus on collaboration of all PhD students in their first, second, or third year. This may take into consideration the form of any formal or informal social action and scientific activities that could increase the output and production of scholarly research, improve communication through the text, and encourage resource sharing and collaborative writing. PhD students face new challenges in the age of digital research. In particular, this paper focuses on challenges such as dealing with digital material and resources, learning management systems, personal learning environments, social networks, and collaboration in research networks. Current PhD students, who are largely from the Generation Y demographic group (born between 1982 and 2000), are familiar with technology and are likely to encounter one or more web 2.0 technologies in their everyday life (Zaman 2010). In the academic context, web 2.0 technology shapes how PhD students learn, self-regulate, and communicate. The Fish Model: When Do Researchers Collaborate Online? Bahaaeldin Mohamed and Thomas Köhler Abstract The questions of whether and how doctoral students are motivated for enhanced research collaboration deserve thorough consideration. Even though collaboration in general and its mediated forms, such as computer-supported coop- erative work and collaborative learning (CSCW and CSCL), are prominent research topics, only a little is known about the methods necessary to design various activities to support research collaboration. With the upcoming generation of tools such as Mendeley, Conference Chair, ResearchGate, or Communote, scholars suspect that web 2.0 services play a decisive role in enabling and enhancing research collabora- tion. However, there is almost no data available on the extent to which researchers adopt these technologies, and how they do so. Therefore, the authors first present an overview of the current usage of web 2.0 among doctoral researchers in their daily academic routines, based on a survey (n = 140) conducted in the German Federal State of Saxony. It confirms a wide and often specified usage of web 2.0 services for research collaboration. For theoretical analysis, the authors propose a concep- tual framework that reflects the requirements of scientific participation and scholarly collaboration within an average international doctoral programme adopting current digitaltechnologies.Theaimofthisframeworkistounderstand,support,andenhance research collaboration among doctoral researchers. Our fish model highlights the mutual relationship between the following dichotomous factors: (a) tasks/time factors; (b) beliefs/activities; (c) support/context; and (d) incentives/ethical issues. Our results indicate a significant relationship in terms of research collaboration. This relationship has particularly been identified between two dichotomous factors: beliefs/activities and incentives/ethics. Keywords Research collaboration · e-science · Web 2.0 technology · Scholarly communication · Doctoral training Keywords Research collaboration · e-science · Web 2.0 technology · Scholarly communication · Doctoral training 29 29 © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_3 B. Mohamed and T. Köhler 30 1 Introduction Accordingly, universities have begun to use and provide these facilities of infrastructure to attract and connect students and develop—step by step—a better practice for research collaboration. However, as Zaman (2010) reports, current doctoral programmes struggle to follow up and meet these demands and requirements. Concerning social and scientific inter- action and collaboration among our doctoral students, Mohamed et al. (2013) investi- gated PhD students’ attitudes towards doctoral colloquium, online learning material The Fish Model: When Do Researchers … 31 via Edu-tech,1 and learning management systems via OPAL.2 These scientific activ- ities were used simply to provide an informative website for learning material and scientific events; PhD candidates usually found that the community of practice and the feeling of belonging were lacking. We expect the digital form of research so-called e-research collaboration to comprise the attempt to enhance and develop not only scientific activities such as co-authorship or finding peers and peer reviewers, but what we refer to as “open- kitchen research”. This term refers to sharing research activities not only as a finished product, but also as processes. In fact, during the doctoral candidate education, they attempt to communicate and collaborate only in the context of theoretical curriculum. Theselearningformalcoursesaretraditionallydesignedtoprovidestudentswithonly structured theoretical knowledge but no real practices. In most cases, we observed that part-time PhD students working in third-party projects at our laboratory give priority than ever before to the projects they are working in where there is more community support than working individually with their own dissertation. The relevance of this study can be confirmed by the fact that doctoral educa- tion in Germany is rapidly growing in all academic disciplines, to a recent total number of 200,400 doctoral candidates being supervised at German universities (in the winter semester 2010/2011), while only half of this group (n = 104,000) was officially registered (Forschung & Lehre 2012; Wolters and Schmiedel 2010). How do those registered scholars participate in research activities? Do they follow their academic activities at the same pattern and do they regularly use the same research online tools? We can just guess that the new openness of social media and web 2.0 communication helps to provide similar conditions and borderless collaboration for all scholars depending on their access to the Internet. 1This study focused on the European doctoral network “Education & Technology” (cp. http://edu- tech.eu). 2OPAL, an open-source Learning Management System, used by all universities of the Federal German State of Saxony (cp. https://bildungsportal.sachsen.de/). 1This study focused on the European doctoral network “Education & Technology” (cp. http://edu tech.eu). 2 2OPAL, an open-source Learning Management System, used by all universities of the Federa German State of Saxony (cp. https://bildungsportal.sachsen.de/). 2 The Fish Model: A Conceptual Framework for E-Research Collaboration The authors conceptualised e-research collaboration as follows. Based on a meta- analysis, approximately 200 papers focussing on different aspects and approaches in e-science and e-humanities were recruited, organised, and analysed, in order to formulate a proposed conceptual framework, the fish model, previously published in Mohamed et al. (2013). The framework may be used to deepen our under- standing of the daily scientific tasks, activities, technologies, and incentives that shape everyday academic practices for doctoral scholars, regardless of their disci- plinary heritage. Databases consulted include Science Direct, Pro-quest, EBSCO, Scirus, and Mendeley. Inclusion criteria were limited to full-text papers concerning the use of web 2.0 in research communication and collaboration. Keywords used for collecting scientific articles directly from the mentioned databases included the following: researchers’ digital habits, use of web 2.0 in research, e-research, social media in research, research collaboration, and scholarly communication. The following selection criteria were used for papers: (1) written in English, (2) situated only on the PhD and researcher levels, (3) either empirical or review articles only. In addition, a conceptual definition of collaboration factors from Patel et al. (2011) and the Folk Model of Intentionality (DeAndrea 2012) were used as guides to identify the fish model (Ringle et al. 2005). The first step in analysing the selected papers was to interpret online research behaviours and the academic activities associated with using web 2.0 technologies, in order to predict the future of research collaboration, using the Fish Model (Mohamed et al. 2013). As the model clarifies the factors and concepts behind the best practices associated with research collaboration using web 2.0 technologies, it was proposed to develop an understanding of daily scientific research tasks and activities. As the authors suggested earlier, online research behaviour is controlled by some key factors and indicators, which was first framed in the Model of Collaborative e-Research (Reebs 2011). This model can be used to describe the factors that support online collaboration in e-science. The fish model (Mohamed et al. 2013), however, extends this research by giving evidence that individual factors (beliefs, self-regulation, etc.), in addition to group interaction organised by the institution, and time management, obviously influence the active production of research, communi- cation among researchers, and subsequent collaboration. Using the fish model, the core factors in online research behaviours and the academic activities associated with using web 2.0 technologies all were investigated. 1 Introduction In the German Federal State of Saxony, where the data of this study was collected, the number of PhD degrees has increased more than tenfold, from n = 111 in 1993 to n = 1,206 in 2009 (Saxony State, Statistical Branch 2009). In order to provide an adequate statement about how our novice researchers collab- orate via using web 2.0 services, we explore which factors might shape this collab- oration, particularly the collaborative opportunities offered by web 2.0, we begin by developing a theoretical framework for our investigation, and apply it to the current situation of PhD students in Germany. 32 B. Mohamed and T. Köhler 2 The Fish Model: A Conceptual Framework for E-Research Collaboration It is argued that a doctoral scholar would behave “like a fish living in a specific environment, taking part in a particular community, showing different individual behaviours to respond to an action, led by their own beliefs and framed by a certain culture” (Mohamed et al. 2013, p. 3275). Typical behaviours and activities are managed by incentives related to the qualification addressed and controlled by the scholar’s role in the research ecology. The fish metaphor emerged when framing a body of collaboration patterns for the authors’ previous study (Frewox 2010). 33 The Fish Model: When Do Researchers … “Collaboration in research is managed by a dorsal fin to stabilise research against rolling and protect scientific environment from isolation and weakness. Inhalation through the mouth passes over the gills in fish to obtain fresh oxygen, communi- cation is the oxygen of research project which is necessary for bringing activities and ideas to the project and achieve the tasks related. The backbone of our fish is web 2.0 technologies which connect and facilitate all functions of the whole body, these functions are divided concerning a dichotomous aspect (fish spine) – as we will describe it complementarily in the frame of this paper – in a task/time, activi- ties/beliefs, support/context, and ethics/incentives division” (Tannen 2006, p. 3267 ff.). Research collaboration is usually considered as a planned activity where knowl- edge can be produced and transferred. The authors predicted previously (Mohamed et al. 2013) that collaborative e-research (using web 2.0 technology to improve best research practices) will take place alongside dichotomies. Tannen (Wang 2010), in his book, The Argument Culture (1998), proposes the concept of perceived dichotomies, that is, binarisms between two connected concepts, while not distinguishing between them through the use of vocabulary such as “good” and “bad”. Building on Tannen’s work, the fish model proposes the integration of both factors. Research collaboration in this study can be interpreted as a relationship between eight concepts formed in pars making up the total of four groups: (a) between scientific tasks or candidates’ needs and time available for implementing them; (b) between planned activities and individual research beliefs in dealing with these activities; (c) support from tech- nology and understanding the uses of this technology within a certain context and culture of an institution; and (d) intentions/motivations for collaboration, which are directed by research ethics, as illustrated in Fig. 1. 2 The Fish Model: A Conceptual Framework for E-Research Collaboration CommunicaƟon Ethics IncenƟves Time AcƟviƟes Context web 2.0 Tasks Beliefs Support CollaboraƟon Fig. 1 Fish model: conceptual framework for developing e-research collaboration for PhD students and novice researchers (Mohamed et al. 2013) CollaboraƟon Fig. 1 Fish model: conceptual framework for developing e-research collaboration for PhD students and novice researchers (Mohamed et al. 2013) 34 B. Mohamed and T. Köhler B. Mohamed and T. Köhler H1: p H1-0: An academic task to be done via web 2.0 is driven by a timeframe (when the task should be done/how much time is needed to do it). H1-0: An academic task to be done via web 2.0 is driven by a timeframe (when the task should be done/how much time is needed to do it). H1-1: An appropriate timeframe for a task to be carried out via web 2.0 can lead to academic collaboration H1-1: An appropriate timeframe for a task to be carried out via web 2.0 can lead to academic collaboration 2.1 The Reality of Managing Scientific Tasks in Terms of the Available Time It can be expected that novice researchers are likely to collaborate and work with each other because they are more likely than experienced researchers to break their work down into various tasks, activities, and actions. Such individual behaviour is controlled by time management as short-/long-term academic tasks, primarily related to different actions such as information search, data analysis, reading, or possibly writing (Illeris 2004). Overall, the doctoral education system differs significantly from programmes at masters and bachelor level, as doctoral programmes prepare candidates for high-level careers in industry or provide long practical experience (Zaman 2010). In their previous studies (Mohamed et al. 2013; Mohamed et al. 2013), the authors identified two key tasks that doctoral students undertake in order to carry out their research. The first is marketing, that is, building a scientific competence profile in order to develop a scientific reputation. The second is doing research, that is activities in daily research practice, including mainly reading, writing, investigating, searching, and reviewing. H1: Novice researchers are more likely to collaborate and work with each other when the work task (types, stages, and technologies) and timeframe are specified. 2.2 Online Research Activities Led by Work-Based Beliefs PhD students’ daily research activities include specific online activities, as identified previously (Mohamed et al. 2013): accessing resources, information, and research funds; engagement in scientific discussions and being an active member in one or more academic communities of practice; communication in reviewing, sharing, and exchanging ideas; awareness of recently published scientific papers and events; presenting oneself online in social media and social networking in order to build up a profile and identification (Mohamed 2011; Lahenius 2010; Peggy and Borkowski 2007). Typically, it is expected that PhD research work is completed through three main development phases (Terrell et al. 2009; Zaman 2010; Mohamed et al. 2013): (a) becoming a researcher by training, and reading activities for first-year PhD students; (b) becoming an expert in any required methods and the pressure to start publishing for second-year PhD students; and (c) becoming an author which includes partici- patinginpeer reviewing, co-authoring, andwritingpublications. Eachof thosephases requires a number of planned online activities. Additionally, gradual engagement The Fish Model: When Do Researchers … 35 with the literature of one’s own scientific discipline should be considered, because it leads to particular work beliefs. Three main explanations for scholars’ success were identified (Patel et al. 2011): social culture, the culture of disciplines, and the indi- vidual beliefs (values, motivation, learning style, self-regulation, cognitive compe- tence, confidence, and trust). Usually, beliefs are addressed by psycho-educational research, whereas the role of trust (versus control) as a governance concept has been addressed in earlier research on virtual organisations (Lattemann and Köhler 2005). Only the combination of these accepted beliefs defines a researcher’s individual approach to scientific activities. H2: Novice researchers are more likely to collaborate and work with each other when they believe in the work and participate in academic and research activities (online). H2: Novice researchers are more likely to collaborate and work with each other when they believe in the work and participate in academic and research activities (online). H2-0: Academic activities (online) affect a researcher’s belief in using web 2.0 toward collaboration. H2-0: Academic activities (online) affect a researcher’s belief in using web 2.0 toward collaboration. H2-1: Researchers’ belief in using web 2.0 for research may increase their chances of collaboration 2.4 Incentives Protected by Research Ethics PhD candidates need incentives to be strongly engaged in online collaboration (Pidd 2011); these incentives are intrinsic motivation, satisfaction, and reputation. Purely financial motivation is less important, but the motivation should be protected and controlled by research ethics related to the digital environment (Mutula 2010). The issue of trust should be considered by faculty involved in digital research processes (Jirotka et al. 2006), as it has a special role in steering online networks (Lattemann and Köhler 2005). Young researchers need to develop e-strategies to use research portals to ensure and facilitate authentic human sources for knowledge transfer. While the majority of them have adopted web 2.0 tools already, their willingness to shift from offline to online digital research practices is crucial (Pscheida et al. 2013; 2014) to build trust and protect scientific work in a virtual environment (Lam 2011). H4: Novice researchers are more likely to collaborate and work with each other when they receive incentives (as external motivation) that are protected and combined with their trust and the value of their work (as internal motivation). H4-0: Incentives as an external motivation can influence ethics as an internal motivation for enhancing research collaboration. H4-1: Research ethics as an internal motivation is closely related to research collaboration H4-1: Research ethics as an internal motivation is closely related to research collaboration 2.3 Support for Technology Use in Context Even though web 2.0 is a rather young technology, multiple studies have investigated its benefits for learning, especially in the production and communication of scientific research, or e-science (Pscheida et al. 2013; Kahnwald et al. 2015). A core aspect of ICT infrastructure (web 2.0) is its strong linkage to the sociocultural context and the disciplinary culture. While academic work triggers social interactions among PhD scholars, the cultural context drives and assists their use of web 2.0 technologies in order to interact. ICT and web 2.0 services in learning and research comprise all methods, techniques, online behaviours of scientists, tools used by researchers, knowledge sharing and transfer, acceptance/adoption, and building social networks via e-research identified by literature reviews (Meyer and McNeal 2011). A doctoral candidate’s use of web 2.0 technologies is both supported by and understood through institutional context and discipline culture (Pscheida et al. 2013). Those have a partic- ular need for being involved in one or more academic communities on a national or international level in order to share and develop practice successfully, usually realised through web 2.0 services (Veletsianos and Kimmons 2012; Eyman et al. 2009; Illeris 2004; Gillet et al. 2009; Lam 2011). H3: Researchers are more likely to collaborate when they have received technical support in their academic context. H3-0: web 2.0 technology may enhance research communication, leading to future collaboration. H3-1: Research context has a direct influence on collaboration B. Mohamed and T. Köhler B. Mohamed and T. Köhler 36 3 Method For this paper, data was collected and analysed through the combination of two main methods: (a) description of a quantitative online survey conducted in the German Federal State of Saxony from 22 July 2012 until 22 October 2012, at the Technische Universität Dresden and (b) forming and testing the structured model. The main aim was to investigate novice researchers’ intentionality to collaborate with each other through the use of web 2.0 and digital online technologies in academia. Our survey included two main parts: the first part reveals demographic data and the second part includes a 5-interval Likert scale with points ranging from 1 (strongly disagree) to 7 (strongly agree). The survey addressed doctoral students as novice researchers who are using web 2.0 technology to communicate and collaborate in research daily life. This 45-item measure was created for this study to assess participants’ percep- tions, profiling the nine main factors that shape the final structure of the fish model: task, time, activity, belief, support, context, incentive, ethics, and collaboration. The instrument was then tested by three independent experts in research collaboration before being given to respondents from the target audience. The authors received a total return of n = 140 doctoral students who completed the survey. The data was examined using factor analysis and our fish model was tested with the Partial Least Squares (PLS) technique. SmartPLS, Version 2.0 M3 software was used to test the model (Ringle et al. 2005, p. 1). The Fish Model: When Do Researchers … The Fish Model: When Do Researchers … 37 4 Results The majority of respondents (57.71%) were male, 66.74% were not married and had no children, and 30.45% of respondents were from the School of Science, which includes the 13.41% which were PhD students from the Faculty of Mechanical Engi- neering. This can be considered typical for Saxony’s higher education landscape, as it has a special focus on technical subjects. 4.1 The Measurement Model PLS is “the second-generation structural equation modelling technique that assesses both the measurement and structural model in a single run” and was chosen for two reasons: it works well for smaller sample sizes and eliminates restrictions on data distribution such as normality (Serenko 2008, p. 465). Before analysing this model, its reliability was measured. Cronbach’s alpha exceeded the required threshold of 0.7 for all items, implying high internal consistency of the scales (Serenko 2008). In order to submit an accepted level of eligibility for the questionnaire, half of the items (24 of 45 items) were removed which do not have sufficient weight vis-à-vis their main factor (Table 5, see Appendix). Once these items were removed, the model was re-estimated. Reliability results are given in Table 1. The data shows that the measures are robust in terms of their internal composite reliability. The composite reliability of the different items ranges from 0.8 to 1.0, above the recommended starting value of 0.70 (Serenko 2008). In addition, consistent with the guidelines of Fornell and Larcker (Birnholtz 2005), the average variance extracted (AVE) for every component is above 0.50. Table 2 presents the results of measuring the discriminant validity for variable constructs. The matrix diagonal reports that the square roots of Table 1 Assessment of the measurement model Variable constructs Composite reliability (internal consistency reliability) Average variance extracted/explained (AVE) Time 0.80 0.57 Task 0.80 0.57 Support/tech 0.88 0.66 Incentives 0.83 0.62 Ethics 1.00 1.00 Context 0.82 0.69 Collaboration 0.84 0.58 Beliefs 0.83 0.62 Activities 0.85 0.59 Table 1 Assessment of the measurement model B. Mohamed and T. Köhler 38 Table 2 Discriminant validity (inter-correlations) of variable constructs Latent variables 1 2 3 4 5 6 7 8 9 1. Time 1.00 2. Task 0.67 1.00 3.Support/Tech −0.43 −0.39 1.00 4. Incentives −0.23 −0.20 0.59 1.00 5. Ethics −0.32 −0.30 0.37 0.33 1.00 6. Context −0.027 −0.10 0.30 0.23 0.00 1.00 7. Collaboration −0.31 −0.30 0.50 0.50 0.46 0.06 1.00 8. Beliefs −0.44 −0.36 0.66 0.53 0.49 0.11 0.65 1.00 9. Activities −0.28 −0.22 0.35 0.37 0.34 0.25 0.41 0.54 1.00 the AVEs are greater in all cases than the off-diagonal element in their corresponding row and column, which supports the discriminant validity of the instrument. The instrument was tested additionally through PLS-Graph and for convergent validity. Table 4 (see Appendix) shows the factor loading of all items to their respec- tive latent constructs. 4.1 The Measurement Model All items loaded on their respective construct from a lower pound of 0.70 to the upper pound of 0.85. In addition, the T-test of outer model loading in the PLS-Graph output was highly significant (p < 0.001) for each factor’s loading on its respective construct. The results confirm the convergent validity as demonstrating a distinct latent construct. 4.2 The Structured Model Figure 2 presents the results of the structured model with interaction effect. In order to assess the structured model, a bootstrapping technique was applied. The examination of t-values was based on a 1-tail test with statistically significant levels of p < 0.05 (*), p < 0.01 (**), and p < 0.001 (***). Dotted lines highlight the insignificant paths. Structured components were formulated by multiplying the corresponding indicators of the predictor and moderator construct. For clarity purposes, the outcomes of the structural model in terms of direct effects, bootstrapping, and t-statistics confirmed the majority of the hypotheses, at varioussignificancelevels.However,theresultsshowthatonlytwofactorsinresearch collaboration are associated significantly (Fig. 2). Specifically, “Academic activities” is very significantly associated with “Researchers’ beliefs” (H2-0 at β = −0.67, p < 0.001 level). In this first path, “Researchers’ beliefs” has a significant relation with “Collaboration” (H2-1 at β = 0.41, p < 0.001 level). In the second path, “Incen- tives” and “Ethics” contribute significantly to “Collaboration”. Accordingly, (H4-0) confirms a significant relation between “Incentives” and “Ethics” (H4-0 at β = 0.71, 39 39 The Fish Model: When Do Researchers … Fig. 2 Structure model (PLS bootstrapping “path coefficient”). *significant at 0.05 level (1.96); **significant at .01 level (2.58); ***significant at 0.001 level (3.29) ig. 2 Structure model (PLS bootstrapping “path coefficient”). *significant at 0.05 level (1.96); *significant at .01 level (2.58); ***significant at 0.001 level (3.29) p < 0.001 level) along with the relationship (H4-1) between “Ethics” and shaping “Collaboration” (β = 0.06, p < 0.05). The other two paths of predicting research collaboration are not significant. First, “Technology and support” has a significant relationship with “Context” (H3-0 at β = 0.64, p < 0.05), but, as a second path, the “Context” cannot predict research “Col- laboration” (H3-1 at β = 0.00 not significant). Second, academic “Task” connected strongly with the factor “Time” (H1-0 β = −0.70, p < 0.001). On the other hand, the relationship between “Time” and shaping academic “Collaboration” (H1-1 β = − 0.00, not significant) was unrelated in the context of shaping academic collaboration (Table 3). 5.1 Conclusions Theresultsofthisstudydemonstratethefactorsthatmightinfluenceresearchcollabo- ration among novice researchers in Germany. The study conceptualised and validated thefishmodelforunderstandingresearchcollaborationinthedigitalage,highlighting where the model can be extended. A brief review of the findings raises the question of what drives researchers’ propensity to collaborate using web 2.0 services. B. Mohamed and T. Köhler B. Mohamed and T. Köhler 40 Table 3 Research hypotheses and conclusions Hypothesis β (path-coefficient) t-value p-value Validation H1-0: An academic task to be done via web 2.0 is driven by a timeframe (when the task should be done/how much time is needed to do it) 0.70 12.61 < 0.001 Supported H1-1: An appropriate time frame for a task to be carried out via web 2.0 can lead to academic collaboration −0.00 0.03 n.s. Rejected H1: Novice researchers are more likely to collaborate and work with each other when the work task (types, stages, and technologies) and time frame are specified Rejected H2-0: Academic and research activities (online) affect a researcher’s belief in using web 2.0 for collaboration 0.67 9.71 < 0.001 Supported H2-1: Researchers’ belief in using web 2.0 to support research may increase their chances of collaboration 0.41 5.77 < 0.001 Supported H2: Novice researchers are more likely to collaborate and work with each other when they believe in the work and participate in academic and research activities (online) Supported H3-0: web 2.0 technology may enhance research communication, leading to collaboration 0.64 3.74 < 0.05 Supported H3-1: Research context has a direct influence on collaboration. 0.00 0.00 n.s. Rejected H3: Researchers are more likely to collaborate when they have received technical support in their academic context Rejected H4-0: Incentives as an external motivation can influence ethics as an internal motivation for enhancing research collaboration 00.71 3.79 < 0.001 Supported H4-1: Research ethics as an internal motivation is closely related to research collaboration 0.06 1.74 < 0.05 Supported H4: Novice researchers are more likely to collaborate and work with each other when they receive incentives (as external motivation) that are protected and combined with their trust and the value of their work (as internal motivation) Supported The Fish Model: When Do Researchers … 41 The first collaboration path showed that doing online doctoral research activities might shape beliefs in using web 2.0 technologies for academic purposes and, thus, enhance collaboration. An example is that using social media to connect with like- minded people eventually shapes one’s belief about the importance of web 2.0. 5.1 Conclusions Researchers who believe in using such media are more likely to collaborate and more open to empathy. Overall this study illustrates how the fish model can be applied to an online setting in order to understand how the interaction between academic activities and researchers’ beliefs can influence research collaboration. The results are consistent with the previous mentioned literature as it was discussed by Terrell et al. (2009), being successful can shape a person’s individual beliefs. Engaging in online research activities in order to communicate and collaborate reflects individual beliefs that controltheactionsthatcanenhancefurthercollaborationoffline,ashasbeenobserved in a professional context (Köhler 1997). Researchers’ activities may reveal some of the individual beliefs that back and catalyse collaboration. When researchers engaged in online research activities, their belief in the use of web 2.0 in research increased. Use of web 2.0 services such as social media can also predict productive and conductive research collaboration (Pscheida et al. 2013). The second collaboration path shows that in keeping a balance between internal “ethics” and external “incentives”, motivation can confirm collaboration. An example is that researchers’ trust in sharing their ideas via web 2.0 services only grows when they benefit from using such technology and, accordingly, it may lead to collabo- ration. These findings have important implications for the fish model. Internal and external motivations support future research collaboration. We argue that external and internal motivations are closely related; consequently, in academia both types of motivation help researchers become engaged in collaboration. Higher incentives predict higher levels of trust; researchers are more likely to collaborate when they trust the technologies they use. What motivates researchers to enhance collabora- tion into the web 2.0 sphere depends on the technologies they can trust and use to extend their professional networks. For collaboration among researchers, trust is synonymous with benefit, which is the catalyst for collaboration. 5.2 Limitations In this study, research collaboration was defined as the use of web 2.0 technologies for communication and daily research routines (reading, searching, writing, etc.). The authors addressed a subset of the concept labelled e-science or science 2.0. They empirically observed doctoral scholars. These PhD students came mainly from the Faculty of Mathematics and School of Science at the Technische Universität Dresden in Germany. These aspects may limit the range and meaning of the findings presented. 42 B. Mohamed and T. Köhler Another limiting aspect is that the fish model reported only two significant paths that may predict research collaboration. It would, however, be more informative if measures of the other paths of the fish model (that appeared as non-significant in our study) were measured once again in a different research context with another sample. Appendix See Tables 4, 5, and 6. See Tables 4, 5, and 6. See Tables 4, 5, and 6. The Fish Model: When Do Researchers … 43 Table 4 Factor loadings (bolded) and cross loadings Factor Time Task Support/Tech Incentives Ethics Context Collaboration Beliefs Activities TIM1 0.70 0.46 −0.29 −0.14 −0.19 0.05 −0.08 −0.20 −0.17 TIM2 0.81 0.52 −0.49 −0.25 −0.32 −0.07 −0.33 −0.50 −0.33 TSK1 0.57 0.81 −0.26 −0.20 −0.27 −0.03 −0.29 −0.30 −0.15 TSK2 0.47 0.70 −0.24 −0.11 −0.27 −0.09 −0.17 −0.21 −0.31 SUP1 −0.42 −0.44 0.83 0.44 0.30 0.23 0.44 0.60 0.29 SUP2 −0.35 −0.28 0.82 0.45 0.35 0.27 0.39 0.49 0.29 SUP3 −0.31 −0.24 0.86 0.57 0.29 0.29 0.40 0.58 0.29 INC1 −0.21 −0.11 0.40 0.85 0.32 0.07 0.38 0.45 0.34 INC2 −0.22 −0.26 0.67 0.75 0.21 0.35 0.42 0.50 0.32 INC3 −0.10 −0.14 0.37 0.74 0.23 0.18 0.40 0.31 0.20 ETK −0.32 −0.30 0.37 0.33 1.00 0.00 0.46 0.49 0.34 CON1 0.02 −0.05 0.25 0.24 0.05 0.84 0.08 0.09 0.21 CON2 −0.064 −0.129 0.26 0.14 −0.04 0.83 0.02 0.09 0.21 CLB1 −0.25 −0.29 0.40 0.48 0.25 0.18 0.70 0.50 0.22 CLB2 −0.25 −0.24 0.31 0.32 0.39 0.01 0.76 0.49 0.42 CLB3 −0.19 −0.17 0.38 0.37 0.32 0.05 0.77 0.45 0.30 CLB4 −0.24 −0.22 0.43 0.36 0.41 −0.03 0.81 0.53 0.25 BEL1 −0.22 −0.25 0.48 0.32 0.35 0.04 0.41 0.78 0.50 BEL2 −0.39 −0.29 0.54 0.53 0.50 0.09 0.63 0.84 0.39 ACT1 −0.14 −0.11 0.16 0.26 0.18 0.20 0.22 0.27 0.72 ACT2 −0.34 −0.30 0.39 0.35 0.33 0.15 0.42 0.56 0.84 ACT3 −0.26 −0.16 0.25 0.21 0.28 0.13 0.30 0.44 0.75 (continued) B. Mohamed and T. Appendix Köhler 44 Table 4 (continued) 45 The Fish Model: When Do Researchers … The Fish Model: When Do Researchers … 45 Table 5 Items removed Factor Item TSK3 It is more effective to ask colleagues for a declaration about unclear work tasks by E-Mail or Skype than face-to-face TSK4 The task of reading an online paper is more effective than a printed one TSK5 Task of searching/sorting for literature review by using web 2.0 services more difficult than my traditional way TSK5 When I need to effectively discuss something related to my research with colleagues, web 2.0 services are not the right solution TIM3 It is necessary to invest a lot of time for communicating, researching, and working via web 2.0 services TIM4 Web 2.0 services save time for organising and managing our teamwork and working in a scientific community TIM5 Usage of synchronous web 2.0 services (in real time interaction) such as chat or video conferences is more useful for managing online discussions than asynchronous tools (e.g. Appendix online forum) SUP4 The usage of web 2.0 services in a scientific research is difficult and I can’t understand it SUP5 I use web 2.0 services when others recommend something really interesting for me SUP6 Peers and colleagues warn me to use web 2.0 services in research CON3 My institute/faculty does not formally support using web 2.0 services among doctoral students CON4 The best way to contact my supervisor is through e-mail CON5 Collaboratively reading, writing, and reviewing a paper via web 2.0 services in our project/research group is not familiar yet INC4 Receiving daily information about a recent paper, event, or colleagues’ activity, is a big motivation for me to use web 2.0 services INC5 Editing, commenting, reading, and reviewing dissertation tasks by using desktop word processing software are more familiar to me than using web 2.0 services ETK2 Taking on more responsibility in scientific editing, reviewing, commenting via web 2.0 services among researchers is ambiguous and uncertain ETK3 Web 2.0 services signify for me a place where there is a lower level of data security ETK4 Data security for me is an important issue for participating in any scientific editing, reviewing, commenting, and reading via web 2.0 services ETK5 My data can be stolen easily via web 2.0 services ACT5 Giving online lectures is one of my usual online activities BLF3 I believe that putting my data through cloud services is safe and enhances mobility BLF4 Web 2.0 services may slow down my work load and research progress BLF5 Managing time, procedures, reading, writing, reviewing, and daily events are effectively done without using web 2.0 services CLB5 I intend to communicate only through e-mail in scientific research, due to the fact that research is an individual contribution Table 5 Items removed Factor Item TSK3 It is more effective to ask colleagues for a declaration about unclear work tasks by E-Mail or Skype than face-to-face TSK4 The task of reading an online paper is more effective than a printed one TSK5 Task of searching/sorting for literature review by using web 2.0 services more difficult than my traditional way TSK5 When I need to effectively discuss something related to my research with colleagues, web 2.0 services are not the right solution TIM3 It is necessary to invest a lot of time for communicating, researching, and working via web 2.0 services TIM4 Web 2.0 services save time for organising and managing our teamwork and working in a scientific community TIM5 Usage of synchronous web 2.0 services (in real time interaction) such as chat or video conferences is more useful for managing online discussions than asynchronous tools (e.g. Appendix online forum) SUP4 The usage of web 2.0 services in a scientific research is difficult and I can’t understand it SUP5 I use web 2.0 services when others recommend something really interesting for me SUP6 Peers and colleagues warn me to use web 2.0 services in research CON3 My institute/faculty does not formally support using web 2.0 services among doctoral students CON4 The best way to contact my supervisor is through e-mail CON5 Collaboratively reading, writing, and reviewing a paper via web 2.0 services in our project/research group is not familiar yet INC4 Receiving daily information about a recent paper, event, or colleagues’ activity, is a big motivation for me to use web 2.0 services INC5 Editing, commenting, reading, and reviewing dissertation tasks by using desktop word processing software are more familiar to me than using web 2.0 services ETK2 Taking on more responsibility in scientific editing, reviewing, commenting via web 2.0 services among researchers is ambiguous and uncertain ETK3 Web 2.0 services signify for me a place where there is a lower level of data security ETK4 Data security for me is an important issue for participating in any scientific editing, reviewing, commenting, and reading via web 2.0 services ETK5 My data can be stolen easily via web 2.0 services ACT5 Giving online lectures is one of my usual online activities BLF3 I believe that putting my data through cloud services is safe and enhances mobility BLF4 Web 2.0 services may slow down my work load and research progress BLF5 Managing time, procedures, reading, writing, reviewing, and daily events are effectively done without using web 2.0 services CLB5 I intend to communicate only through e-mail in scientific research, due to the fact that research is an individual contribution B. Mohamed and T. Appendix Köhler 46 Table 6 Final measured items (items used) Factor Item TSK1 Web 2.0 services may hinder my tasks in everyday research activities TSK2 When I need to effectively discuss something related to my research with colleagues, web 2.0 services are not the right solution TIM1 Web 2.0 services are not helpful services in situations when information is needed on the same day TIM2 It is a waste of time to use web 2.0 services to establish communication or collaboration with other colleagues in the context of doing research SUP1 The uses of web 2.0 services are useful for my research SUP2 I enjoy using web 2.0 services in editing, commenting on, and reading a piece of research S3 Using web 2.0 services may help a lot to inform me about important scientific events CON1 My institute provides a proper knowledge management system/web 2.0 services (e.g. Appendix website) for improving communication and collaboration among doctoral students CON2 Officially, Wiki is used as a platform for group activities and collaborative work reports in my research group INC1 Creating a personal profile in web 2.0 services would enhance my reputation INC2 Using web 2.0 services in research helps me to satisfy my interests in my scientific area INC3 Web 2.0 services facilitate the presentation of myself and marketing my research ETK1 I trust sharing my data through web 2.0 services ACT1 I usually engage in one or more online scientific discussions ACT2 Sharing files, links, videos, or photos with colleagues is one of my daily uses of web 2.0 services ACT3 Peer review of scientific work via web 2.0 services is one of my usual online activities ACT4 Commenting and writing in one or more scientific online forums, weblogs, or wikis is also one of my daily/weekly activities BLF1 I believe that using web 2.0 services has become one of my everyday research routines BLF2 I would say, to enhance academic collaboration, you should use web 2.0 services CL1 I intend to engage and involve myself in a community of practice by using web 2.0 services CLB2 I intend to share my reading, writing, review, and resources with other colleagues when it is mediated by web 2.0 services CLB3 I intend to coordinate and work together more when this coordination is facilitated by web 2.0 services CLB4 Willingness to communicate and collaborate in research with other disciplines could be enlarged by using web 2.0 services The Fish Model: When Do Researchers … The Fish Model: When Do Researchers … 47 References Birnholtz, J.P.: When do researchers collaborate? 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Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), 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 license and indicate if changes were made. g The images or other third party material in this chapter are included in the chapter’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the chapter’s Creative Commons license 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. The Use of Digital Tools in Scholarly Activities. Empirical Findings on the State of Digitization of Science in Germany, Focusing on Saxony Steffen Albrecht, Claudia Minet, Sabrina Herbst, Daniela Pscheida, and Thomas Köhler Steffen Albrecht, Claudia Minet, Sabrina Herbst, Daniela Pscheida, and Thomas Köhler Abstract Scholars are only beginning to understand what digitization means for their work, that is, the conduct of science. Taking a broad perspective on e-science, this paper provides empirical insights about two important aspects of the digitization of science, namely the use of digital tools in scholarly activities and scholars’ percep- tions of the change such use entails. The results of a German-wide survey of scholars and supplementary qualitative interviews in the years 2012 and 2013 show that the majority of scholars have adopted digital tools and that scholarly practice is affected profoundly by the use of such tools. This does not apply to web 2.0 tools, which remain a niche medium for some scholars. Small but significant differences exist between disciplines, and decisions about individual tool use are utilitarian. Further research is needed to assess the changes from a longitudinal perspective. Keywords E-science · Digitization · Scholarly practice · Survey results 1 E-Science, Cyberscience, Science 2.0: The Digitization of Science Is on the Move EversinceGalileo’ssuccessfuluseofthetelescope,scientistshavereliedonnewtools in their scholarly practice (Hankins and Silverman 1995). The advent of computer C. Minet Hochschule Mittweida—University of Applied Sciences, Mittweida, Germany e-mail: Minet@hs-mittweida.de S. Herbst · D. Pscheida · T. Köhler Media Center, Technische Universität Dresden, Dresden, Germany e-mail: Sabrina.herbst@mailbox.tu-dresden.de T. Köhler e-mail: Thomas.koehler@tu-dresden.de S. Albrecht (B) Berlin, Germany e-mail: Steffen.albrecht@berlin.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_4 49 C. Minet Hochschule Mittweida—University of Applied Sciences, Mittweida, Germany e-mail: Minet@hs-mittweida.de S. Herbst · D. Pscheida · T. Köhler Media Center, Technische Universität Dresden, Dresden, Germany e-mail: Sabrina.herbst@mailbox.tu-dresden.de T. Köhler e-mail: Thomas.koehler@tu-dresden.de S. Albrecht (B) Berlin, Germany e-mail: Steffen.albrecht@berlin.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_4 49 C. Minet Hochschule Mittweida—University of Applied Sciences, Mittweida, Germany e-mail: Minet@hs-mittweida.de S. Herbst · D. Pscheida · T. Köhler Media Center, Technische Universität Dresden, Dresden, Germany e-mail: Sabrina.herbst@mailbox.tu-dresden.de T. Köhler e-mail: Thomas.koehler@tu-dresden.de S. Albrecht (B) Berlin, Germany e-mail: Steffen.albrecht@berlin.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_4 49 C. Minet Hochschule Mittweida—University of Applied Sciences, Mittweida, Germany e-mail: Minet@hs-mittweida.de 49 49 50 S. Albrecht et al. S. Albrecht et al. technology and digital networks was no exception, impacting not only the commu- nication of research, but also the production of new knowledge. The World Wide Web with its network of hypertexts and its gradual change to web 2.0 with the addi- tional manifestation of online social networks reinforce this impact and generate more potential. Although this cooperative process is not new (Bijker and Law 1992; Mayntz 1993), we are still only beginning to understand the changes that digitiza- tion entails for science. This paper furthers our understanding by providing empirical insights from an online survey of German scholars related to two specific aspects of the digitization of science, namely the use of digital tools in research, teaching and other scholarly activities, and scholars’ perceptions of the change that such use brings. g Several terms have been proposed to apprehend how science is influenced by networked computer technologies. In 1999, the term e-science was introduced by John Taylor, General Director of the Research Council at the Office of Science and Technology of the UK. Taylor realized that new technological infrastructures were needed to foster global cooperation and data-intensive research in science. 1Other notions of the digitization of science, include “digital scholarship” (Weller 2011) and “digital science” (European Commission 2013). 1 E-Science, Cyberscience, Science 2.0: The Digitization of Science Is on the Move In other words, “e-science is not a new scientific discipline; rather, the e-science infrastructure developed […] should allow scientists to do faster, better or different research” (Hey and Trefethen 2005: 818). Jim Gray specified what such “different research” could look like. He identified a “fourth paradigm” of scientific inquiry, “data-intensive science” that is characterized by the use of massive amounts of data to generate new theoretical models (Gray 2009: xix). Michael Nentwich (2003) took a more holistic view of “cyberscience,” including how academic work is organized, how it functions, and what its products are. While emphasizing its novelty compared to “traditional science,” he technically assesses the digitization of science. In a recent update with René König, Nentwich used the term “cyberscience 2.0” to acknowledge the emergence of web 2.0 and its relevance to scholarly communication (Nentwich and König 2012). “science 2.0” is another term that emphasizes the importance of web 2.0 in facilitating openness and collaboration, focusing on online communication tools such as weblogs or wikis that open up science communication to external audiences (Waldrop 2008).1 Despite their nuances, all these terms are more similar than different. A broad notion is best suited to address the diverse issues involved in the digitization of science. Here and in the e-Science Research Network Saxony (www.escience-sachse n.de), we use the term e-science to comprise science, social science, and humanities disciplines, not only in research and collaboration, but also in teaching and science communication. In terms of technology, e-science comprises digital tools used in scholarly work that go beyond the individual computer and represent digital media or online-based, networked software systems. Taking a broad perspective on digitization means normatively assessing this pro- cess without bias. This involves considering not only the changes in technology, but also changes induced by the social environment. Soon before e-science got onto The Use of Digital Tools in Scholarly Activities … 51 the agenda, several authors recognized fundamental changes in how science was generally understood. “In response to the challenges of policy issues of risk and the environment, a new type of science – ‘post normal’ – is emerging,” wrote Silvio Funtowicz and Jerome Ravetz (1993: 739). In a similar vein, Michael Gibbons and colleagues (1994) observed the emergence of what they called “mode 2” science, which was transdisciplinary and involved stakeholders from outside the scientific community. 1 E-Science, Cyberscience, Science 2.0: The Digitization of Science Is on the Move Both diagnoses overlap in noting an increasing external influence on science from politics, the economy, and civil society. The interrelations between technological and social change are not the main focus here, but developments within science such as the role of web 2.0 in opening up the research process might be part of a broader social change, in which technology plays only a moderating role. The aim of this paper is to provide empirical observations of changes in scientific practice in relation to technological change, focusing on media use in science. Our approach is based on two fundamental assumptions. First, we find that considerable attention is devoted to the potential and affordances of digital technologies, but much less notice is taken of what scholars actually do with these technologies in their day- to-day practices, including potential non-adoption and refusal to use them (cf. Barassi and Trer 2012: 1282). Second, while there are a number of empirical case studies of scholars’ use of technology in specific fields, we think a broad view on all aspects of scholarly practice is necessary to identify the changes, before the nature of such change in specific areas can be analyzed. 2 The Empirical Question: Is Digitization Really on the Move? The empirical perspective of this paper goes beyond the rhetoric and euphoric expec- tations of some e-science discourse. We ask three questions. To what extent do scholars use digital media and online tools in their day-to-day academic activities? What kind of new practices emerge from such use? How do such changes in the conduct of science contribute to the bigger structural changes? Technological innovation always takes place in form of co-evolution of engi- neering and social domains (Köhler 1998). Adoption theorists have pointed out that the adoption process is not just a matter of time, but also of individual differences, system characteristics, social influence, and facilitating conditions (Venkatesh and Bala 2008). Against this background, we can assume that the adoption of digital tools is not as straightforward a process as is depicted by some of the theoretical accounts discussed above: it is ongoing and has to be observed empirically to determine its state and direction. Our paper adds to the small, but growing empirical literature about the impact of using digital tools in science. Previous research has shown that investigating scholars’ use of digital tools poses methodological problems. There are a number of different approaches, all with specific merits and pitfalls. We can broadly distinguish a qualitative orientation with 52 S. Albrecht et al. S. Albrecht et al. S. Albrecht et al. a focus on in-depth analysis of a limited number of cases, often based on stakeholder interviews or case studies (see, e.g., Currier 2011; RIN/NESTA 2010; Bullinger et al. 2010), and a quantitative orientation with a focus on assessing the whole field, often based on standardized surveys. As our aim is to provide a holistic and realistic assessment of the state of adoption, we mainly review previous quantitative research. Lattemann et al. (2010), ZBW (2011), Donk (2012), and Pscheida and Köhler (2013) all address a limited target group (principal investigators in funded research projects, economics researchers and students, researchers at one specific university, and scholars at universities in Saxony, respectively). Thus, none of this research is particularlyhelpfulintermsofeithermethodologyorresults.Inanearlystudyof1477 UK re-searchers, Procter et al. (2010) found that 60% used a web 2.0 tool (blogging, commenting, sharing resources, or contributing to wikis) in their scholarly activities, but only 13% did so frequently. The authors consider this figure “rather low” and observe that frequent users are most likely to be computer scientists or mathemati- cians, engineers, or scholars in the arts and humanities. 2 The Empirical Question: Is Digitization Really on the Move? Ponte and Simon (2011) also focus on web 2.0 use, but based on a self-selected sample of 345 persons from across Europe. They report the use of wikis and blogs by about 40% of respondents, academic social networking sites by 35%, and microblogging by 18% of researchers. Results for specific groups are not presented. Bader et al. (2012) analyzed 1053 responses to an online survey of scholars at German universities. They found that communication tools such as e-mail (94%), mailing lists (24%), and Skype (21%) were widely adopted, web 2.0 tools like blogs or research portals were much less used (6% use wikis, 5% use research portals or social networking sites, 4% use academic blogs, and 2% use Twitter). The tools used varied greatly by discipline: wikis were mostly used in science and engineering, whereas mailing lists and blogs were more popular in humanities and social sciences, especially in law, and research portals were favored by social scientists. In general, the authors consider German researchers to be at an “early stage” of adopting digital communication tools. Despitethesmallnumberofstudiesofsufficientscopeandmethodologicalquality, these results raise doubts about the predicted impacts of digital tools on science. In the best case, adoption is too early to have had a significant impact. In the worst case, apart from some small groups, scholars are not tempted to actually use digital tools in their work. The existing research shows that digital tool adoption in scholarly activities is low (apart from very popular tools such as search engines), that web 2.0 tools are much less likely to be used than more conventional ones, and that disciplines seem to play a role in the choice of tool. 3 Hypotheses, Data, and Methods To remedy the obvious lack of comprehensive, quantitative research, our paper seeks to empirically assess the state of adoption of digital tools by scholars and their impacts on the basis of new data from the Science 2.0 Survey 2013 (Pscheida et al. 2014). The Use of Digital Tools in Scholarly Activities … 53 Based on our above analysis of previous research, we assume that to have an impact on scientific activity, digital tools have to be used for scholarly purposes in the first place. This leads us to the following hypotheses and research questions. Based on our above analysis of previous research, we assume that to have an impact on scientific activity, digital tools have to be used for scholarly purposes in the first place. This leads us to the following hypotheses and research questions. Hypotheses. Our first two hypotheses concern the extent to which scholars use digital tools in their activities. H1: The adoption of digital tools in scholarly activities is still in an early phase, with diffusion levels (Rogers 1995) below 50% of the population (“early majority”). H2: Web 2.0 tools like weblogs, wikis or microblogging are used by a minority of scholars for professional activities, with diffusion levels below 16% (“early adoption”). p Our third hypothesis concerns the differences between disciplines and is formu- lated as research question, since previous research is inconclusive. RQ1: Do scholars in different disciplines use digital tools differently? RQ1: Do scholars in different disciplines use digital tools differently? Finally, we are interested in how digital tool use impacts on the conduct of science leading to another research question. Finally, we are interested in how digital tool use impacts on the conduct of science, leading to another research question. Finally, we are interested in how digital tool use impacts on the conduct of science, leading to another research question. RQ2: What changes in the conduct of science as a result of digital tool use do scholars perceive? RQ2: What changes in the conduct of science as a result of digital tool use do scholars perceive? Data. We collected data in two related steps. First, an online survey of 778 scholars at German universities was conducted in autumn 2013, addressing ques- tions such as scholars’ use of 17 different tools and services, their academic and sociodemographic background, their motives for and attitudes to using digital tools (see Pscheida et al. 2The data set of the Science 2.0 Survey 2013 is open access: see www.escience-sachsen.de. 3 Hypotheses, Data, and Methods 2014).2 Although quota sampling of universities was applied in the recruitment procedure, the sample shows some deviations from the popula- tion with regard to gender (women are slightly overrepresented), professional status (professors are overrepresented, research assistants or “WHK” underrepresented), discipline (with medicine strongly underrepresented, humanities, mathematics, and natural sciences slightly overrepresented), location, and type of university. While the latter two could be adjusted by weighting, the other deviations should be kept in mind in interpreting the results. In addition, all scholars at universities in the German federal state of Saxony were invited to participate in the same survey, with 442 ques- tionnaires being submitted. The Saxony sample shows similar patterns of deviations from the population, except that with regard to disciplines, engineers and mathemati- cians/natural scientists are strongly overrepresented, whereas medicine and the fine arts are underrepresented. The quantitative survey was supplemented in the first half of 2013 by 19 interviews with scholars in Saxony, chosen to map the various disciplines and status groups. The semi-structured interviews focused on the scholars’ perception of the use of digital tools and of the changes this entails. Due to the variety of scholarly practices and lack of knowledge about the precise impact of digital tools on them, qualitative interviews were chosen to address our second research question. Methods. The hypotheses and research questions were statistically analyzed, comparing the Saxony and German-wide samples. Adoption was measured by asking scholars “to what extent do you use the following?” followed by a list of 17 different S. Albrecht et al. S. Albrecht et al. S. Albrecht et al. 54 online tools. Answers were categorized by frequency of use. In the analysis, only uses for scholarly work (research, teaching, research administration, and science communication) were taken into account. Based on Schmidt’s (2007) definition, social networking sites, wikis, video/photo community portals, weblogs, microblogs, and social bookmarking services are regarded as “social software” or “web 2.0 tools,” astheyconstitutesocialorhypertextualrelationshipsof(atleastpartially)publicchar- acter (Schmidt 2007: 32). The disciplines were categorized based on the definition of the German Federal Bureau of Statistics (2012) into arts and humanities; (natural) sciences (including mathematics); engineering and social sciences (including law and economics). Finally, the qualitative interviews were transcribed and anonymized, and qualitative content analysis methods were applied to the responses. 4 Results 4.1 General Level of Adoption of Digital Tools in Scholarly Activities 4.1 General Level of Adoption of Digital Tools in Scholarly Activities Scholarly activity at German universities in 2013 was affected considerably by the use of digital tools. Of all 17 tools the survey asked about, ten were used by more than 50% of all respondents in a professional context (with two others by 49%, see Fig. 1). Only general-purpose social networking sites, online editors like Etherpads 0 10 20 30 40 50 60 70 80 90 100 Wikipedia Online Archives Mailing Lists Content Sharing Videoconferencing/VoIP Online Forums Other Wikis Video-/Photo CommuniƟes Reference Management Learning Management Systems Academic Social Networks Chat/IM Social Networks Online Editors Weblogs Microblogs Social Bookmarking Germany Saxony Fig. 1 Level of adoption (in %) of digital tools in scholarly use in Germany and Saxony Fig. 1 Level of adoption (in %) of digital tools in scholarly use in Germany and Saxony The Use of Digital Tools in Scholarly Activities … 55 or Google Docs, weblogs, microblogs like Twitter, and social bookmarking services are used by less than about half of all respondents. Wikipedia is the tool with the broadest diffusion in academia, with 95% of respondents reporting to have used Wikipedia in their scholarly work. Comparably extensive more than three quarters of the respondents use online archives like Arxiv.org and mailing lists. The pattern for scholars in Saxony is quite similar to the national one. Wikipedia, online archives, and mailing lists are the tools with the highest level of adoption in the context of scholarly work. Social networking sites, online editors, weblogs, microblogs, and social bookmarking services are used by less than half of the respon- dents, including professional social networking sites like Xing or Academia.edu. The general level of adoption of digital tools in Saxony is a bit lower than in Germany as a whole. The reverse is true for online forums (64% in Saxony, 56% in Germany) and wikis other than Wikipedia (62% in Saxony, 55% in Germany). Of course, such seems still to be a contradictory observation as many scientists recommend their students not to use digital tools like Wikipedia due to the “non-scientific” nature. So is especially valuable exploring in more detail practices of adoption among scientists. In some cases, digital tools may be used more for general than work-related purposes (see Table 1). 4.1 General Level of Adoption of Digital Tools in Scholarly Activities Content sharing and cloud services, video conferencing and VoIP (“online telephone”) services, online forums, video/photo communities, Table 1 General and work-related use (in %) of digital tools in Germany and Saxony. Note the high level of general use Digital tool Germany Saxony General Work General Work Social networking sites 57.9 32.9 51.1 21.0 Academic networking sites 52.7 48.8 41.0 37.6 VoIP 71.7 58.0 64.3 46.2 Microblogs 15.1 10.5 5.9 1.6 Weblogs 29.2 22.2 28.3 22.6 Wikipedia 98.9 95.2 100 96.2 Other wikis 56.5 55.1 63.6 61.5 Content sharing/cloud server 73.5 67.7 64.3 54.5 Online editors 26.7 24.9 24.4 21.0 Online forums 65.3 56.0 74.0 64.0 Mailing lists 77.4 76.2 74.0 71.5 Chat/IM 69.1 48.7 69.2 44.3 Online archives 79.8 79.3 76.7 76.2 Reference management 52.2 52.2 49.1 48.4 Social bookmarking services 5.9 5.2 4.3 3.8 Video/photo communities 80.4 54.8 78.3 45.7 Learning management systems 52.3 52.2 56.1 55.7 able 1 General and work-related use (in %) of digital tools in Germany and Saxony. Note the igh level of general use S. Albrecht et al. 56 S. Albrecht et al. chat/instant messaging (IM), social networking sites, and microblogs all show a significantly higher level of personal than professional use. Where data for compar- ison exists, the use of digital tools is more widespread among scholars than in the German population in general (cf. data from the ARD/ZDF Online Study 2013, van Eimeren and Frees 2013). With regard to our first hypothesis, we can thus infer that the adoption of digital tools in scholarly activities has left the phase of early adoption and has reached a more mature state with more widespread use. Although a considerable number of scholars do not use certain digital tools, and some tools have not reached broad adoption, the majority of tools our survey asked about are used by more than 50% of respondents. 4.2 Use of Web 2.0 Tools Among Scholars The situation is different for web 2.0 tools such as wikis, blogs, social networking sites, social bookmarking services, and video/photo communities. While about half of respondents use wikis, video/photo communities and academic social networking sites in work-related contexts, only between 5 and 32% of scholars use general- purpose social networking sites, weblogs, and microblogs as well as social book- marking services for work. Considering the broad adoption of digital tools in general and the length of time that web 2.0 tools have been in use, the latter have to be considered a niche product with regard to scholarly use. The figures for Saxony are comparable, but generally lower than for the national level (except for wikis, see above). However, with regard to our second hypothesis, web 2.0 tools have a higher adoption level than the 16% “early adoption” rate, at both the national and the Saxony level, with the exception of microblogs and social bookmarking services. At the same time, only a minority of scholars use web 2.0 tools that have not been designed specifically for academics. Given that these tools have been in use for a long time and are well known among scholars (except for social bookmarking services, which about 50% of respondents said they didn’t know about), we have to conclude that web 2.0 tools have only reached specific groups of scholars (cf. Pscheida et al. 2014: 18). It seems to be difficult for most scholars to find useful applications for these tools. From the results of the survey, we can more generally infer that tools are adopted when a specific use is found for them. Most of the tools with high levels of adoption are specialized for one or more areas of scholarly work. Most respondents said that the digital tools they use are practical or make their work easier and faster (Pscheida et al. 2014: 24f.), indicating the prevalence of utilitarian motivation. This was not equally the case for all tools. General-purpose social networking sites and microblogs show a different pattern of use: both tools are used twice as often in a personal than a professional capacity, that is, utilitarian motivation was less important. 4.2 Use of Web 2.0 Tools Among Scholars The two main reasons for not using general-purpose social networking sites in a scholarly context are disagreement with the terms of use (indicated by 24% of those researchers who The Use of Digital Tools in Scholarly Activities … 57 do not use them for work) and personal use (indicated by 18%). For microblogs, the most salient obstacle is the lack of additional benefit (indicated by 56% of those researchers who don’t use microblogs for work). Besides the prevalence of pragmatic reasons, researchers who use web 2.0 tools (like academic network sites, weblogs, or microblogs) also mentioned an interest in new technologies or that these tools help to boost their reputation. This shows awareness of the social and hedonistic (as one could say) affordances of web 2.0 tools. 4.3 Disciplinary Differences Our third hypothesis was about the differences between disciplines in scholars’ adop- tion of digital tools. The results of the survey indicate a more nuanced picture than previous studies have drawn. Cross-tabulation and computation of Cramer’s V (a bivariate measure of association) for the German study show small but significant differences in professional use of Wikipedia, wikis, online editors, mailing lists, online archives, reference management systems, social bookmarking services, and video/photo communities (see Table 2). In all other cases, no difference between disciplines in the use of digital tools for scholarly purposes is found. Digital tools are most highly adopted in the (natural) sciences and in arts and humanities, whereas engineering and social sciences show lesser degrees of adop- tion. However, engineering scientists use wikis and video/photo communities quite heavily, and social scientists use mailing lists and online archives to a similar degree as the (natural) scientists. For Saxony, significant differences between the disciplines are more frequent and related to other tools than in the German-wide study. Social networking sites, academic networking sites, VoIP, microblogs, weblogs, content sharing services, chat/instant messaging services, reference management systems, and learning management systems all show small but significant differences between disciplines (see Table 3). Social scientists use tools most across all categories, followed by scholars in arts and humanities. The only tools which are used more extensively by natural scientists and engineers are Wikipedia and other wikis, but these findings are not statistically significant. The differences between the Saxony and German-wide results are striking. They might be explained by the special disciplinary structure of universities in Saxony, which have a strong emphasis on natural sciences and engineering. For Germany as a whole, such differences might exist, but are leveled off due to the mix of academic cultures and institutional structures across the various federal states. However, the differences are generally small, with low values of Cramer’s V, so we can conclude with regard to our first research question that there are only small differences between the disciplines, highly dependent on the disciplinary context in which each tool is used. 58 S. Albrecht et al. S. Albrecht et al. 4.3 Disciplinary Differences Table 2 Professional use (in %) of online tools by scholars at German universities in 2013 across the most relevant disciplines: arts and humanities; (natural) sciences; engineering and social sciences Digital tool General n=778 Humanities n=225 Natural sciences n=243 Engineering n=116 Social sciences n=133a Cramer’s Vb Social networking sites 32.9 37.6 32.2 24.1 35.1 − Academic networking sites 48.8 48.7 53.5 44.0 53.8 − VoIP 58.0 57.8 60.7 57.8 56.4 − Microblogs 10.5 12.0 10.7 8.6 11.9 − Weblogs 22.2 25.8 23.0 16.2 23.3 − Wikipedia 95.1 93.8 98.8 94.9 90.2 .112 Other wikis 55.1 52.2 68.7 56.0 44.4 .114 Content sharing/cloud server 67.7 69.9 70.8 59.5 69.9 − Online editors 24.8 28.0 26.7 22.2 21.2 .092 Online forums 56.0 58.0 59.3 65.5 45.1 − Mailing lists 76.2 81.0 76.9 63.8 75.2 .093 Chat/IM 48.7 51.8 54.5 40.5 49.6 − Online archives 79.3 86.3 78.2 67.5 78.9 .110 Reference management 52.2 53.3 63.6 33.3 43.6 .158 Social bookmarking services 5.3 4.4 9.1 2.6 3.8 .100 Video/photo communities 54.8 64.2 48.6 57.8 43.3 .116 Learning management systems 52.2 56.9 44.7 51.3 59.0 − aincluding law and economics bsignificance α<.05 −indicates that no significant correlation is observed aincluding law and economics g bsignificance α<.05 g bsignificance α<.05 −indicates that no significant correlation is observed If discipline does not explain differences in the use of digital tools, how else might we explain them? Some indications can be found in the 19 semi-structured interviews that were conducted to supplement the quantitative investigation. Content analysis methods according to Mayring (2000) were used to analyze these. In a first step, categories of analysis were generated based on the interview guideline. 4.3 Disciplinary Differences These categories were then tested against the empirical material, and continuously The Use of Digital Tools in Scholarly Activities … 59 Table 3 Professional use (in %) of online tools by scholars at universities in Saxony in 2013 across the most relevant disciplines: arts and humanities; (natural) sciences; engineering and social i Table 3 Professional use (in %) of online tools by scholars at universities in Saxony in 2013 across the most relevant disciplines: arts and humanities; (natural) sciences; engineering and social sciences Digital tool General n=442 Humanities n=49 Natural sciences n=124 Engineering n=191 Social sciences n=47a Cramer’s Vb Social networking sites 21.3 28.6 21.8 13.6 34.0 .165 Academic networking sites 37.6 32.7 37.9 31.9 66.0 .165 VoIP 46.8 42.9 53.2 39.3 63.8 .145 Microblogs 5.9 6.1 4.8 1.6 21.3 .197 Weblogs 24.0 30.6 25.0 16.2 38.3 .133 Wikipedia 96.2 91.8 98.4 96.3 93.6 − Other wikis 61.5 59.2 64.5 61.8 61.7 − Content sharing/cloud server 55.0 71.4 50.8 47.1 72.3 .146 Online editors 27.8 20.4 25.8 15.7 31.9 − Online forums 64.0 49.0 67.7 64.9 68.1 − Mailing lists 71.5 77.6 75.8 64.4 85.1 − Chat/IM 45.0 42.9 54.8 36.1 55.3 .140 Online archives 76.2 71.4 77.4 74.9 85.1 − Reference management 48.4 51.0 51.6 40.8 66.0 .138 Social bookmarking services 3.8 4.1 5.6 3.7 2.1 − Video/photo communities 46.4 53.1 45.2 41.9 59.6 − Learning management systems 55.7 77.6 53.2 49.2 80.9 .175 aincluding law and economics b i ifi 05 g −indicates that no significant correlation is observed revised and amended with sub-categories during analysis. In a third step, relations and causalities between categories and sub-categories of analysis were carved out. revised and amended with sub-categories during analysis. In a third step, relations and causalities between categories and sub-categories of analysis were carved out. 60 S. Albrecht et al. S. Albrecht et al. The results do not point to disciplinary differences, but instead to the influence of the tangible working practices in which scholars are involved. These can be collabo- rations, such as in projects with many partners (interview 8), working groups (inter- views 1, 7) or institutions (interview 7), but also institutional contexts, such as when “interdepartmental” wikis are created (interview 8) or the institutional website is used for information sharing, because “those who are concerned and who will look at the information [are] mainly limited to the institute” (interview 19). 4.3 Disciplinary Differences y Another important determinant for the use of a digital tool is its quality and suitability for specific working contexts. Digital tools are expected to make working processes more efficient: “the biggest obstacle and a huge inefficiency is how we communicate data. We copy, we process data again and again” (interview 3). Wikis, for example, are used to facilitate collaborative work: “to manage data, I do not have to send e-mails around where nobody knows what the current state is” (interview 8). Similar motivations underlie the use of cloud services like Dropbox (interview 5) or instant messaging clients and VoIP services such as Skype and ICQ (interview 8). The use of e-mail for collaborative work is considered rather inefficient (interviews 3, 5, 8). Wikis can be used as “encyclopedias,” to provide information in a structured and clearly arranged way, “where you can collect things that you maybe will have to look up in future” (interview 19). Wikis are repositories “where all kinds of information are collected” (interview 19); “just to preserve collected knowledge that you can look up again” (interview 7); “where knowledge for all is provided” (interview 1); “to upload files in the current state, where it can then be downloaded” (interview 8). This also refers to the exchange of administrative information, such as in managing technical infrastructure (interview 9) or as an organizational manual (interviews 9, 15). However, once data protection becomes an issue, web-based tools and services are not used despite their efficiency savings: “I would have proposed Dropbox, but because of data protection requirements we cannot use it” (interview 11). Instead, local network servers are used to exchange data, especially in cases where the cooper- ation is limited to partners in the same institution: “to some extent we have this in our working group internally, using the university file system. There we have our account and there is our stuff, i.e. the programs, and everybody in our working groups who wants can use it” (interview 1). Yet, web-based applications are important “espe- cially if you collaborate with external partners” (interview 8). From a qualitative perspective, too, the conclusion is that the requirements of collaborative work and the affordances of the technology have a stronger influence on scholars’ choice of digital tools than professional affiliations. 4.4 Changing Scholarly Practices The above analysis sheds some light on an important prerequisite for any changes in the conduct of science induced by digitization, namely the actual use of digital The Use of Digital Tools in Scholarly Activities … 61 tools in scholarly activity. But this is just a necessary, not a sufficient, condition for change. The semi-structured interviews indicate what kind of changes scholars in Saxony perceive. Of course, such perceptions might not give an accurate account of the situation, but until better data is available (e.g., from long-term observations of scholarly practices), qualitative interpretation of perceptions from actors within the field with a variety of perspectives gives a good approximation. Our interview partners indicated a number of changes in their work practices which they did not see as related to technology use, but rather to a changing social environment in science. The importance of collaborative work is seen as growing. Short-term research projects can require the use of certain digital tools (interview 8) or new competencies, such as writing research proposals (interview 7). Work biographies are seen as becoming more flexible. Temporary retirement affects the way of working and the adoption of new technologies: “so I did not slowly get used to [web-based tools], I knew work without them and when I was re-entering, I had to use and become acquainted with the different tools” (interview 1). This flexibility also includes geographical mobility and increasing independence from local contexts: the use of Skype “has actually naturalized through stays abroad, only to stay in touch” (interview 14). Interviewees mentioned several changes in their personal way of working that they related to technological conditions. The entire process of scientific enquiry, including literature research, has tremendously accelerated: “you simply find something imme- diately rather than writing letters to ask: ‘what did you do there actually?’” (interview 19). Before using digital archives, “we had to […] ask for interlibrary loan literature and had to wait” (interview 16). Technology is explicitly mentioned as an attractive agent of change: “so I still remember card indexes in libraries and of course when the online catalog was there, then you liked to use it” (interview 14). This also relates to the management of literature: “I think the trigger was that the university offered Refworks and that we got an account for the group” (interview 1). 4.4 Changing Scholarly Practices Communication processes seem to be particularly affected: “if I have a meeting withsomeonetoday, I just searchfor her or himontheInternet beforeandlookupwho it is. If I’m lucky, I have a small CV or at least I see what she or he does” (interview 13). Communication is increasingly shifting into virtual spaces (interview 17): “in times of my diploma one rather met personally, […] so if calling on the telephone did not work, then one rather met personally somehow” (interview 7). What is more, the way information is stored and made available has changed: “I have scarcely printed or written documents, […] all of my documents are digitized. Either as a PDF or HTML page or in another format, like video or other scripts or programs” (interview 2). This in turn influences the access to information: “in the past, I can still remember that I used a usual lexicon from the bookshelf, which I not so long ago just sold because I have not been using it anymore and it stood around useless” (interview 9). Again, the affordances of new technologies are described as attractive: “I notice that I still prefer printed paper, but this changes step by step and in ever more cases, I do not print the reports I read, but rather read them on the screen somewhere and if I have the opportunity also highlight sections as it is possible with various apps on the iPad, 62 S. Albrecht et al. S. Albrecht et al. S. Albrecht et al. S. Albrecht et al. then for me this actually replaces printed and nicely annotated reports because I thus have the same opportunities to work” (interview 18). Advancements in data infrastructure, including the availability of faster and more efficient Internet connections or better computing capacities, primarily affect infor- mation sharing and data analysis, “just because it was somehow difficult to load ten megabytes from the Internet with the first emerging DSL connections” (interview 15), and “if one then changed from modem to ISDN and DSL, then you increasingly used it, it went faster” (interview 14). The ubiquity of computing and network power eases the work process “because you don’t have to rack your brain, should I resize photos in the dataset or not, instead you just send it” (interview 12). 5 Summary and Discussion Our study empirically observes the digitization of science and its effects on schol- arly practices. Starting from the individual use of digital tools by scholars as the most important element in the digitization process, we have measured the adoption of digital tools in scholarly work in Germany, focusing on Saxony. By critically extending previous work, our results show that the majority of scholars adopted such tools and that scholarly practice is affected profoundly by their use. We have also shown that this does not apply to all kinds of tools. Web 2.0 and its affordances for scholars might stimulate much debate, but a minority of scholars only uses tools such as weblogs and social networking sites. Presumably, a neglect of epistemological and technological sociological analyses of scientists’ activities can be identified, which has to be overcome. This goes hand in hand with the need for a review with regard to digital science technologies, which has so far been reflected neither in the curricula for training nor in the self-image of the scientists. Our survey indicates that there are small but significant differences in disciplinary adoption of digital tools. The arts and humanities show higher levels of adoption than engineering and the social sciences. However, the degree of use greatly depends on the tool in question. Similarly, the change which the tools induce varies greatly by scholarly activity. Our analysis of the qualitative interviews has confirmed that tools are chosen based on utilitarian motives, and given rise to new hypothesis about the interrelation between individual, technological, and systemic factors of change in the digitization of science. In comparison with the discourse on e-science, cyberscience, and science 2.0, but also to the results of previous empirical studies, our results show that the digi- tization of science is indeed on the move in Germany. The level of adoption is higher than in previous studies, with many digital tools reaching broad professional diffusion. The full potential of e-science has yet to be exploited. Our interviews indi- cate that institutional cultures and the affordances of the technologies do not fit well enough to let these online applications evolve into widely used professional scholarly tools. Still there is need for further consideration, including individual competency development. Our results certainly do not provide definite answers to the questions raised at the beginning of this paper. 4.4 Changing Scholarly Practices Parts of data analysis are replaced by automated processes: “30 years ago or maybe more, you went with stacks of punch cards to the computing center and tried to compute a t-test or something similar, and now you just have to push the button” (interview 5, cf. interview 19). The availability of portable devices, “that we have just passed on to equip all staff with laptops, [i.e.] no location-bounded work on the computer we sit in front of anymore” (interview 15), supports highly flexible working practices. Finally, the attitude of researchers toward new technologies, their openness and curiosity to try something new also affect their working practices: “then I had a telephone bill of about 80 marks which was very high for a student, just because I intensively explored the Internet” (interview 16). Or, as another interviewee said: “whenever a new technology emerges, I deal with it and watch to see if it makes sense to use it” (interview 3). Last but not least, cost-benefit considerations also play an important role: “If I have the feeling that there is something that helps me on […] then I try it” (interview 19, cf. interview 16). Coming back to our second research question about perceived changes in the conduct of science, the qualitative interviews confirm the result from the survey that in science, digital tools are widely adopted. Scholars are not only using digital tools for work, but also perceive their work as being changed by these tools, partly even dramatically. The change is described as making research more efficient and faster, and this acceleration also affects communication and collaboration. Theprecisenatureofthischangerequiresmorethoroughanalysis.Fromtheresults presented here, it is clear that technology is just one of the driving forces underlying the change, and that the increasing collaboration and mobility of scholars is another important factor interacting with the use of technology. With regard to the motivations for decisions about technology use, both the qualitative and the quantitative analysis underscore the importance of a pragmatic, utilitarian orientation. The affordances of digital technologies and the institutional contexts appear less perceptible, but also relevant factors in determining which technologies are used and to what extent they affect scholarly work. Based on our study, more detailed research into the interplay of these factors can be designed and carried out. 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London, New York (2011). https://www.bloomsburycollections.com/book/the-dig ital-scholar-how-technology-is-transforming-scholarly-practice. Digital Research Infrastructure Maik Stührenberg, Oliver Schonefeld, and Andreas Witt Abstract Digital research infrastructures can be divided into four categories: large equipment, IT infrastructure, social infrastructure, and information infrastructure. Modern research institutions often employ both IT infrastructure and information infrastructure, such as databases or large-scale research data. In addition, information infrastructure depends to some extent on IT infrastructure. In this paper, we discuss the IT, information, and legal infrastructure issues that research institutions face. Keywords Digital research infrastructure · IT infrastructure · Information infrastructure References Accessed 11 Mar 2020 ital-scholar-how-technology-is-transforming-scholarly-practice. Accessed 11 Mar 2020 ZBW: World Wide Wissenschaft – Wie professionell Forschende im Internet arbeiten. Kiel: ZBW Leibniz-Informationszentrum Wirtschaft (2011) ZBW: World Wide Wissenschaft – Wie professionell Forschende im Internet arbeiten. Kiel: ZBW Leibniz-Informationszentrum Wirtschaft (2011) Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), 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 license and indicate if changes were made. g The images or other third party material in this chapter are included in the chapter’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the chapter’s Creative Commons license 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. 1Combinations of more than one category are possible as well. M. Stührenberg (B) Universität Bielefeld, Bielefeld, Germany e-mail: maik.stuehrenberg@uni-bielefeld.de 1 Introduction This paper was originally submitted late 2014 and the final publication was delayed until 2019. The authors are well aware that the view and state of the art for digital research infrastructures have evolved in the last 5 years. A research infrastructure can be defined as a public or private institution that has been established mainly for research, teaching, and the support of young researchers. Research infrastructures can be divided into four main categories (Wissenschaftsrat 2011b, 17f.)1: – large equipment, including research platforms such as scientific research vessels, planes, or satellites; – large equipment, including research platforms such as scientific research vessels, planes, or satellites; 1Combinations of more than one category are possible as well. M. Stührenberg (B) Universität Bielefeld, Bielefeld, Germany e-mail: maik.stuehrenberg@uni-bielefeld.de O. Schonefeld · A. Witt Institut Für Deutsche Sprache, Mannheim, Germany e-mail: schonefeld@ids-mannheim.de A. Witt e-mail: witt@ids-mannheim.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_5 M. Stührenberg (B) Universität Bielefeld, Bielefeld, Germany e-mail: maik.stuehrenberg@uni-bielefeld.de O. Schonefeld · A. Witt Institut Für Deutsche Sprache, Mannheim, Germany e-mail: schonefeld@ids-mannheim.de A. Witt e-mail: witt@ids-mannheim.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_5 M. Stührenberg (B) O. Schonefeld · A. Witt Institut Für Deutsche Sprache, Mannheim, Germany e-mail: schonefeld@ids-mannheim de A. Witt e-mail: witt@ids-mannheim.de 67 © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_5 © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_5 67 M. Stührenberg et al. 68 – IT infrastructure, such as computer hardware and software; – social infrastructure, that is, research institutions that offer scholars a place to exchange ideas and collaborate (Wissenschaftsrat 2011a, 20f.), for example, the Leibniz Center in Dagstuhl Castle, Germany; – information infrastructure, that is, research institutions that collect and curate primary data and make them accessible to a larger group of scholars. – information infrastructure, that is, research institutions that collect and curate primary data and make them accessible to a larger group of scholars. While large technical equipment is only seldom used in digital humanities disci- plines, and social infrastructure is beyond the scope of this paper, combinations of IT infrastructure and information infrastructure are quite common. Therefore, the purpose of this paper is to give insight into various aspects of modern research infrastructures with an emphasis on both the latter categories. 1 Introduction In addition, we have conducted a qualitative analysis by interviewing twelve German research institutions (Fiedler et al. 2012). The institutions were interviewed and asked to participate in a survey. The 74 survey questions were structured into different topic areas, such as organizational aspects, data management, hardware and software, environmental aspects, and legal issues. We will reflect on some of these topics in the respective sections of this article. 2 IT Infrastructure Digital humanities research institutions working with huge amounts of data (e.g., language corpora) have special needs regarding IT infrastructure, such as a growing demand for storage space, computing capacity (for querying and analyzing linked data), and durability (including distributed access over large-scale networks such as the Internet for a huge number of potential users). This results in significant amounts of money spent on hardware and software. In addition, operating costs (divided into maintenance and personnel costs) have to be taken into account, including IT staff, hardware maintenance, software updates, and licensing. Especially energy costs should not be underestimated, as the price of electricity is increasing over time. A green-IT strategy can help an institution to reduce some of these costs. A key way of doing this is buying new equipment and replacing old (less energy-efficient) hardware. However, green IT consists of more aspects, such as efficient cooling (like separation of warm and cold aisles in the data center or using free cooling techniques), institutional policies (e.g., obliging employees to turn their computers off before leaving the workplace), or using supplies made of recycled material (like recycled paper). Implementing a green-IT strategy is generally a project of its own for a research institution and is currently a low priority for the institutions that we analyzed. Therefore,oneoftheissuesmodern-dayresearchinstitutionshavetodealwithisto optimize these costs, usually by undertaking the following steps. Firstly, a transparent accounting system, including every single asset for salaries, maintenance costs, and so forth, has to be established, allowing for a more accurate estimation of current Digital Research Infrastructure 69 and future demands for IT infrastructure. Replacing proprietary software with open- source software may only slightly decrease licensing costs, but may be cheaper in the long run since the latter can be adopted to the institution’s needs and usually has better support of open formats (see Sect. 3.2). However, two points have to be considered regarding this assumption: 1. Additional costs for user training may be necessary if the open-source application differs from the formerly used product; 1. Additional costs for user training may be necessary if the open-source application differs from the formerly used product; 2. In-house IT expertise is necessary to adapt open-source software, which may result in even higher personnel costs. 2. In-house IT expertise is necessary to adapt open-source software, which may result in even higher personnel costs. 2See http://www.clarin.eu for further details. 3See http://www.eprints.org/ for further details. 4See https://www.escidoc.org/ for further details. 3 Information Infrastructure Research data, especially primary data (e.g., recordings, measurements, and curated corpora), are among the most valuable assets for a research institution. Research institutions that can be categorized as information infrastructures (such as libraries, archives, collections, and smaller non-academic research institutions) that collect and curate primary data, scientific and non-scientific knowledge, and databases, and provide access to researchers [34], who may use this data for research projects on their own. To ensure access to the information infrastructure, various technical aspects have to be taken into account. 2 IT Infrastructure For these reasons, it is advisable, especially for smaller research institutions, to collaborate in the field of IT infrastructure to reduce costs. Examples of such coop- eration include a shared Internet connection, server housing, or archival storage. A majority of the interviewed research institutions already collaborate with other external facilities to lower IT costs and to distribute archival and backup storage Since research institutions are nowadays connected to the Internet, storage of and access to the information infrastructure involves special security requirements. Two main issues have to be considered: 1. preventing unauthorized access to systems, processes, or data (including infor- mation infrastructure); 1. preventing unauthorized access to systems, processes, or data (including infor- mation infrastructure); 2. ensuring that hardware and software continue to function. Although there is no such thing as a completely secure network, the first step to prevent unauthorized access is a complete risk analysis for the relevant computer systems, including estimating possible losses and limitations on daily work (e.g., due to vandalism or sabotage). The outcome of this analysis should be a prioritized list of data and systems to be protected. The concrete security measures (the security policy) are defined by the IT security officer and the data protection officer and are mandatory for the whole staff of the research institution (ISO/IEC 27002:2013 2013; BSI 2014). Important points for a security policy are: – prioritization of data according to their value for the research institution; – identification of possible risks (including computer viruses and network infras- tructure attacks); – backup strategy; – data encryption. While a backup strategy for research data is considered crucial (nine out of twelve interviewees have a central backup strategy and the remaining institution plans to implement one), only a third of the institutions surveyed have a central in-house IT security policy. M. Stührenberg et al. 70 5Note that we are talking about the binary .doc, not the XML-based .docx format used by Office 2004 onwards and that is standardized as ISO/IEC 29500-1:2011 (2011). However, even the latter format uses a number of features that cannot easily be interpreted by application programs without further knowledge. 3.1 Repositories and Publication Server Repositories have already been used in large-scale collaborative projects, often inter- national ones, such as CLARIN.2 The CLARIN centers provide repositories storing academic research data (such as curated corpora) accessible via the Internet. Retrieval of a desired information item is highly dependent on metadata. Following on from existing metadata standards such as Dublin Core (ISO 15836:2009 2009; DCMI 2012), IMDI (ISLE Metadata Initiative 2003; Broeder and Wittenburg 2006; ISLE Metadata Initiative 2009), or OLAC (Simons et al. 2008; Bird and Simons 2009), the Component Metadata Structure (CMDI) (Broeder et al. 2011, 2012; Trippel et al. 2012) has been created to facilitate documenting research information and querying it over the distributed repositories. In our survey, five out of the twelve interviewed institutes already run a repository on their own, while four are in the process of building one. Another aspect of information infrastructure is the archiving and accessibility of publications. Establishing and maintaining an in-house publication server can be a way for a research institution to retain both copyright (see Sect. 4.1) and access control over information that has been produced by its academic staff. Open-source implementations, such as ePrints3 or eSciDoc,4 often combine the functionalities of publication servers and primary data repositories. For all these tasks, staff working on IT and information infrastructure need to collaborate closely. In particular, research institutions having their own libraries can benefit from the expertise of IT and information departments regarding archives, metadata, and retrieval. Seven of the interviewees already run a publication server. 71 Digital Research Infrastructure Digital Research Infrastructure 3.2 Data Formats Although the creation of research data is often quite expensive, a large portion of this information gets lost shortly after the end of the project in which it was gathered. Apart from the hardware failures or insufficient metadata discussed above, another possible reason can be a proprietary storage format, for which the corresponding application is not available any more. Data formats usually exist for two reasons: (1) as serialization of a specification, or (2) as the import and export format of an application. A format as such may be open or proprietary, which may be important for processing and archiving the information encoded in it. An example of a proprietary de facto standard format is the ubiquitous.doc format, produced by Microsoft Word.5 Since it is a binary format, it is not possible to extract information with arbitrary text editors; instead, one has to use specific programs, and applications other than MS Word may not be able to successfully render the document as it was intended by the author. For research data which are curated by an information infrastructure, open text- based formats should be preferred. Formats based on the open meta language XML (Bray et al. 2008) are quite common in academic research and can be defined by document grammar formalisms such as XML DTD (part of the aforementioned specification), XML Schema (Gao et al. 2012; Peterson et al. 2012), or RELAX NG (ISO/IEC 19757-2:2008 2008), allowing for on-the-fly validation during the creation of instances. Examples of open XML-based annotation formats in the digital humani- tiesaretheTEIGuidelines(BurnardandBauman2014)orDocBook(Walsh2010)for technical documentation. Information encoded in those formats is not only readable with common text editors, but separates content from formatting, since the rendering is usually controlled by separate XSLT (Kay 2007, 2014) or CSS (Bos et al. 2011) stylesheets. This not only prevents vendor lock-in, but significantly eases the process of archiving. The attitude to open standards and open-source software compared with proprietary in-house development is mixed; however, there is a tendency to use standardized APIs and formats, or at least consider open-source applications. Seven surveyed institutes keep data in proprietary formats, while four aim to use standard formats and one is still determining its strategy. Often, institutes lack the human resources to convert data into standard formats. 6See http://creativecommons.org for further details. 7See http://opensource.org/licenses/bsd-license.php for further details. 8See http://www.gnu.org/licenses/#GPL for further details. 9Especially NC may have undesired side effects, see Klimpel (2012) for a discussion. 10The categories have recently been extended by Kupietz and Lüngen (2014). 11See Görl et al. (2011) for a discussion about the impacts of information infrastructure in universities of North Rhine-Westphalia. 4 Legal Issues Research institutions are confronted with a number of legal issues, the most important of which are: (1) copyright and (2) personal data protection and privacy. M. Stührenberg et al. 72 4.1 Copyright Issues Research data is often based on material contributed by third parties. The primary data of text corpora, for example, often originate from newspaper articles or similar non-academic sources. German copyright law protects literary, artistic, and scientific works (including software) that are the author’s own intellectual creation. Copyright- protected works may only be modified (and, arguably, annotated) with the authoriza- tion of the copyright holder. Copyright expires 70 years after the death of the original author. In Germany (unlike in most other jurisdictions), copyright cannot be trans- ferred and is reserved by the author until his death (and 70 years after it), but it can be licensed. In practice, authors often license their rights out to publishers. Although the German copyright law (UhrG) does not contain the American concept of “fair use”, there are copyright limitations (§§ 44a–63a UrhG) that apply to certain specific uses of copyright-protected works (e.g., citations, personal use, scientific use) (Mönch 2006). However, in order to be covered by a copyright limita- tion of § 52a UrhG, scientific use has to be restricted to “small groups of researchers” (Hoeren 2014, 157). This is especially important if a research institution wants to publishannotatedcorpora-inthatcase,theprimarydatahastobelicensedbeforehand. Research data to which a research institution holds the copyright (e.g., primary data produced in-house) should be made available to others under a liberal license, e.g., an open-access license such as Creative Commons.6 Creative Commons (CC) is a free license (similar to the software license, BSD,7 or the General Public License, GNU8) that was originally developed for creative work and that consists of several building blocks, such as Attribution (BY: minimal requirement), NoDerivatives (ND), NonCommercial (NC),9 and ShareAlike (SA). The current version (4.0) also addresses specific database rights that exist in EU Member States. Apart from human-readable CC license deeds, laundry symbols (similar to those established in the CLARIN research group (Oksanen et al. 2010) for its own specific licenses) provide a quick overview of the license requirements.10 For a detailed discussion about legal implications of institutional repositories see Bargheer et al. (2006). Regarding publications, a research institution’s staff may agree to publish their works on the institution’s publication server under an open-access license (Degkwitz 2007). 12See the text of the declaration at http://openaccess.mpg.de/3515/Berliner_Erklaerung. 13See Stempfhuber (2009, 119) and http://opcit.eprints.org/oacitation-biblio.html for a number of studies about open-access impact factors. 4.1 Copyright Issues Open-access publications have steadily gained ground in countries such as the US, Denmark, or Japan, while there is still an ongoing discussion about them in Germany, especially in the digital humanities disciplines11—although the Berlin 73 Digital Research Infrastructure Declaration on Open Access to Knowledge in the Sciences and Humanities12 has boosted their reputation. While open-access journals are still sometimes seen as less reputable than traditional journals (although both publication types monitor quality throughpeerreview),theyoftenhavehighercitationnumbers.13 Researchinstitutions can play an active role in the process of building the reputation of open access by publishing in this format. It is therefore pleasant to see that an open-access strategy is already present in five of the institutions interviewed, while three of them plan on implementing one. Declaration on Open Access to Knowledge in the Sciences and Humanities12 has boosted their reputation. While open-access journals are still sometimes seen as less reputable than traditional journals (although both publication types monitor quality throughpeerreview),theyoftenhavehighercitationnumbers.13 Researchinstitutions can play an active role in the process of building the reputation of open access by publishing in this format. It is therefore pleasant to see that an open-access strategy is already present in five of the institutions interviewed, while three of them plan on implementing one. 4.2 Personal Data Protection Personal data protection issues may arise when living persons are involved in the process of creating research data, such as voice or video recordings. Publication of personal data is only allowed if the persons recorded have given their (written) consent. For every collection of personal data, a register of processing operations has to be created (according to §4 g, §§18 and 4e of the German data protection law, BDSG. The type of personal information, how it is processed, and the data protection measures, are recorded in this register. Despite the variety of legal issues that may arise for research institutions, most of the interviewees rely either on their own (general) legal department or on cooperation with external law firms. Licensed (IT law) attorneys are seldom employed. 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Universität Münster. https://www.itm.nrw/wp-content/uploads/Skript-Int ernetrecht-April-2014.pdf (2014) ISLE Metadata Initiative: Metadata Elements for Session Descriptions. version 3.0.4. 5 Conclusion Wehavediscussedanumberofinformationinfrastructureissuesthatmodernresearch institutions need to consider. Most of the technical issues can be addressed by imple- menting a sustainable long-term IT strategy that reflects both costs and demands. Additional technical aspects such as security, open storage formats, and metadata can be addressed in such an IT strategy. Legal issues cannot be underrated, espe- cially for service-oriented research institutions. Therefore, a data protection officer should be involved in the early stages of research projects that plan to create personal data. M. Stührenberg et al. 74 Wissenschaftsrat: Übergreifende Empfehlungen zu Informationsinfrastrukturen. 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Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), 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 license and indicate if changes were made. The images or other third party material in this chapter are included in the chapter’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the chapter’s Creative Commons license 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. MOVING: A User-Centric Platform for Online Literacy Training and Learning MOVING: A User-Centric Platform for Online Literacy Training and Learning Keywords MOVING platform · MOVING web application · Recommender system · Adaptive training support Keywords MOVING platform · MOVING web application · Recommender system · Adaptive training support MOVING: A User-Centric Platform for Online Literacy Training and Learning Aitor Apaolaza, Tobias Backes, Sabine Barthold, Irina Bienia, Till Blume, Chrysa Collyda, Angela Fessl, Sebastian Gottfried, Paul Grunewald, Franziska Günther, Thomas Köhler, Robert Lorenz, Matthias Heinz, Sabrina Herbst, Vasileios Mezaris, Chifumi Nishioka, Alexandros Pournaras, Vedran Sabol, Ahmed Saleh, Ansgar Scherp, Ilija Simic, Andrzej M.J. Skulimowski, Iacopo Vagliano, Markel Vigo, Michael Wiese, and Tanja Zdolšek Draksler Abstract In this paper, we present an overview of the MOVING platform, a user- driven approach that enables young researchers, decision makers, and public admin- istrators to use machine learning and data mining tools to search, organize, and manage large-scale information sources on the web such as scientific publications, videos of research talks, and social media. In order to provide a concise overview of the platform, we focus on its front end, which is the MOVING web application. A. Apaolaza · M. Vigo University of Manchester, Manchester, UK e-mail: aitor.apaolaza@manchester.ac.uk M. Vigo e-mail: markel.vigo@manchester.ac.uk T. Backes GESIS, Cologne, Germany e-mail: tobias.backes@gesis.org S. Barthold · P. Grunewald · F. Günther · T. Köhler (B) · R. Lorenz · M. Heinz · S. Herbst Media Centre, TU Dresden, Dresden, Germany e-mail: thomas.koehler@tu-dresden.de S. Barthold e-mail: sabine.barthold@tu-dresden.de P. Grunewald e-mail: paul.grunewald@tu-dresden.de F. Günther e-mail: franziska.guenther1@tu-dresden.de R. Lorenz e-mail: robert.lorenz@tu-dresden.de M. Heinz e-mail: matthias.heinz@tu-dresden.de S. Herbst e-mail: sabrina.herbst@tu-dresden.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_6 A. Apaolaza · M. Vigo University of Manchester, Manchester, UK e-mail: aitor.apaolaza@manchester.ac.uk M. Vigo e-mail: markel.vigo@manchester.ac.uk T. Backes GESIS, Cologne, Germany e-mail: tobias.backes@gesis.org S. Barthold · P. Grunewald · F. Günther · T. Köhler (B) · R. Lorenz · M. Heinz · S. Herbst Media Centre, TU Dresden, Dresden, Germany e-mail: thomas.koehler@tu-dresden.de S. Barthold e-mail: sabine.barthold@tu-dresden.de P. Grunewald e-mail: paul.grunewald@tu-dresden.de F. Günther e-mail: franziska.guenther1@tu-dresden.de R. Lorenz e-mail: robert.lorenz@tu-dresden.de M. Heinz e-mail: matthias.heinz@tu-dresden.de S. Herbst e-mail: sabrina.herbst@tu-dresden.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_6 A. Apaolaza · M. Vigo University of Manchester, Manchester, UK e-mail: aitor.apaolaza@manchester.ac.uk A. Apaolaza · M. Vigo University of Manchester, Manchester, UK e-mail: aitor.apaolaza@manchester.ac.uk M. Vigo e-mail: markel.vigo@manchester.ac.uk T. Backes GESIS, Cologne, Germany e-mail: tobias.backes@gesis.org 77 78 A. Apaolaza et al. A. Apaolaza et al. By presenting the main components of the web application, we illustrate what func- tionalities and capabilities the platform offer its end-users, rather than delving into the data analysis and machine learning technologies that make these functionalities possible. 1 Introduction Scholarsandprofessionalsinvarioussectorsoftheeconomy,includingpublicadmin- istrators, corporate compliance officers, and auditors, deal with an ever-increasing flow of information (new scientific publications, business documents and multimedia files, laws, etc.). They need sophisticated tools to evaluate all this information fast and accurately and to visualize the analysis results. Specifically this means that, on the one hand, they need tools that enable state-of-the-art search and semantic analysis of large digital contents, by providing: (i) access to an extensive source inventory, (ii) MOVING: A User-Centric Platform for Online Literacy Training and Learning 79 advanced search and visualization methods, and (iii) functionalities for generating new knowledge from these digital assets. On the other hand, these tools need to be reasonably easy for their users to understand and support them through: (i) a detailed and scientifically proven help system (tutorials, guidance), individually configurable training programmes (learning modules, videos), and a lively community of people that have similar interests or problems to be solved. To face these challenges, the inter- disciplinary trans-European project called MOVING (“TraininG towards a society of data-saVvy inforMation prOfessionals to enable open leadership INnovation”) (Vagliano et al. 2018) has built an innovative training platform that enables users from various societal sectors to fundamentally improve their information literacy by training in how to choose, use, and evaluate data mining methods in their daily research and business tasks, and to become data-savvy information professionals. 2 Digitized Science Initiatives by the European Union (which has long been pursuing a digital agenda) to support research in the field of digitized science illustrate the need to investigate related change processes (European Commission 2016). Obviously, empirical and theoretical justification is needed to develop the practice of science. The innova- tive approach dealt with here was developed in the MOVING project, which offers an innovative training platform to support scientists and other users from all areas of society to fundamentally improve their information literacy in research-oriented C. Nishioka University of Kyoto, Kyoto, Japan e-mail: nishioka.chifumi.2c@kyoto-u.ac.jp A. Saleh ZBW, Kiel, Germany e-mail: a.saleh@zbw.eu A. Scherp Ulm University, Ulm, Germany e-mail: ansgar.scherp@uni-ulm.de 80 A. Apaolaza et al. A. Apaolaza et al. contexts.1 The project is about training users to select, apply, and evaluate technolo- gies and data mining methods, so that the relevant research staff can develop into ‘data-savvy’ information professionals in their daily research routines (Scherp et al. 2016; Köhler et al. 2016a, b). In terms of content, the research methodological changes in scientific action cannot easily be explained as domain-specific activities. This requires analyses of both current technological developments and the changes in how scientists use these technologies (or methods). The eScience Saxony research network provides state- ments on both perspectives (see, e.g., [Pscheida et al. 2013, 2014]). The network has observed the following: – there is great potential for the use of new digital tools in research; – preferred topics for development are scientist collaboration and the visualization of (often large or new) databases; – transitions between the subject areas of research and teaching can also be observed in technology development; – almost all scientists do most of their work using computer-based technologies and have access to appropriate infrastructures; – scientists sometimes find it difficult to adopt new media technologies in research and teaching (e.g. social media), although there are also subject-specific differ- ences; – there is still uncertainty regarding the requirements, possibilities, and assumed risks of open-access publishing; – research methodology has not been fully systematically discussed and is often inadequately implemented; – there are no clear standards for high-quality research technology and no recog- nizable institutionalization to support open-access trends in science, so these still need to be worked out together; – digital change in science is comparatively rapid from an individual (scientist) perspective, the outcome is not known, especially regarding location-determining infrastructures. 1Platform.moving-project.eu, last accessed 7 May 2020. 2 Digitized Science Indeed the listing matches to a larger proportion with the demands of these cases addressedbytheMOVINGproject.NeverthelessMOVINGdidsetfocusontwomore main characteristics. First there was a serious interest to address research activity not only in academia but as well in public administration and industry. Second, when developing the approach the project consortium decided to include as well a direct focus on the related skill development, i.e. include a serious effort on innovation in the educational dimension (the Online Literacy Training and Learning) that needs to go along with any new technology in every sector. Indeed the listing matches to a larger proportion with the demands of these cases addressedbytheMOVINGproject.NeverthelessMOVINGdidsetfocusontwomore main characteristics. First there was a serious interest to address research activity not only in academia but as well in public administration and industry. Second, when developing the approach the project consortium decided to include as well a direct focus on the related skill development, i.e. include a serious effort on innovation in the educational dimension (the Online Literacy Training and Learning) that needs to go along with any new technology in every sector. MOVING: A User-Centric Platform for Online Literacy Training and Learning 81 3 Overview of the MOVING Platform An overview of the MOVING platform architecture is illustrated in Fig. 1, which shows the most important components and their relationships. The main component Fig 1 MOVING platform architecture Fig. 1 MOVING platform architecture 82 A. Apaolaza et al. A. Apaolaza et al. A. Apaolaza et al. blocks are (i) data acquisition, (ii) data processing, (iii) back-end data storage, user tracking, search and recommendation, and (iv) the MOVING web application that includes the front-end search. In this section, we briefly describe the overall platform. The MOVING web application is the core of the platform and the interface to the user. The main entry points to the web application are the community section, the learning environment, and the search interface. The search interface offers different visual representations of search results. These visualizations allow the user to explore the search results in various ways. For this purpose, four visualizations have been added to the MOVING platform, namely: (i) the Concept Graph, which displays the search results as an interactive network, (ii) uRank, a dynamic document ranking view, (iii) Top Properties, a bar chart visualization that aggregates the results based on their properties, and (iv) a Tag Cloud, showing the most frequently occurring keywords. Moreover, the Adaptive Training Support (ATS) widget supports users learning how to search and provides material suited to their needs (Fessl et al. 2018) and the Recommender System (RS) widget (bridging the front and back ends of the platform) points users to potentially relevant documents by evaluating their last search queries. Thanks to its responsive design, all the views adapt to different screen sizes, automatically changing the layout according to the capabilities of the device. Private user data and public documents are stored in three separate databases: The web application database holds the data for the communities, the learning envi- ronment, and the ATS. The index holds the public documents and generated meta- data information such as topics, authors, and extracted entities. The user-interaction tracking captures user interactions with the web application and stores them securely in a third database. User tracking provides additional data for both the ATS and the RS, which form the basis for user support by these two widgets. The index used by the search interface is populated by various data acquisition components (e.g. web crawlers and a Bibliographic Metadata Injection service), to increase the amount of data accessible through the MOVING platform. 3 Overview of the MOVING Platform To date, it hosts over 22 million documents and metadata records. These records include books, scientific articles, laws and regulations, documents about funding opportuni- ties, videos (e.g. of lectures and tutorials), and social media posts. Data processing components have been incorporated into and applied to these records, to improve the quality of data and make it easier to search. Additional features, the Data Integration Service, Author Name Disambiguation, Deduplication, Named Entity Recognition and Linking, and Video Analysis, all refine and enrich the documents stored in the index. Author name disambiguation addresses the problem that many author names belong to different real-world authors. To deal with this problem, a novel method (Backes 2018a, b) has been developed which applies, for a given author name, agglomerative clustering on features extracted from documents containing the author mention in question, such as affiliation, co-authors, referenced authors, email addresses,keywords,andpublicationyears.Thedisambiguationprocedurecalculates the probability with which author mentions with the same name belong to the same person. Name mentions having a high probability to belong to the same author are MOVING: A User-Centric Platform for Online Literacy Training and Learning 83 Fig. 2 MOVING search and results page Fig. 2 MOVING search and results page assigned a unique internal authorID. By this, authors with the same name are distin- guished if they refer to different real-world persons. As a result, users who click on the name of an author of a document in the result list of a search will only see docu- ments from authors who have the same author ID as the selected author (instead of showing all documents authored by any person with that name). A modified version of this method has been applied for document deduplication. In the following, we present the front end of the MOVING platform in detail, in order to provide a concise summary of what a user can do with it. For details on how individual data processing, data acquisition, and other back-end components work, the interested reader is referred to the relevant publications, such as (Nishioka and Scherp 2016; Galanopoulos and Mezaris 2019; Tzelepis et al. 2018), as well as the documentation available on the MOVING project web site.2 3www.elastic.co, last accessed 7 May 2020. 2www.moving-project.eu, last accessed 7 May 2020. 2www.moving-project.eu, last accessed 7 May 2020. 3www.elastic.co, last accessed 7 May 2020. 4.1 Search Search is a key functionality in the MOVING web application. At the back end, the MOVING search engine is based on Elasticsearch,3 given appropriate parameters, and fine-tuned to efficiently index dozens of millions of documents. At the front end, the user sees a search page (Fig. 2), with various search options and filters on the left, visualizations of the results in the centre of the window, and training functionalities 84 A. Apaolaza et al. Fig. 3 Search history view Fig. 3 Search history view Fig. 3 Search history view such as ATS on the right. The search history of the current user can also be viewed, to support future searches. To enable platform users to view and replicate their previous searches, the search history view is connected with WevQuery (Apaolaza and Vigo 2017). WevQuery serves as an interface to the data generated by UCIVIT (Apaolaza et al. 2013), the tracking tool of which logs user-interaction data. From WevQuery, we get the information about the previous user searches, time when the user performed the searchquery,andthenumberofdocumentsretrieved.Thisinformationisthenutilized to build the search history view, an example of which is shown in Fig. 3. y p g To present the results of a user query effectively, several visualizations have been implemented. Four characteristic ones are: – Concept Graph. For the discovery and exploration of relationships between documents and their properties. – uRank. A tool for the interest-driven exploration of search results. – Top Properties. A bar chart displaying aggregated information about the properties of the retrieved documents. – Tag Cloud. A visualization for the analysis of keyword frequency in the retrieved documents. Concept Graph: an interactive network visualization the Concept Graph (Fig. 4) visualizes direct and indirect connections between retrieved search results. For example, a single, disambiguated author of two different publications is visualized as a node in the graph connecting the corresponding publications. Further extracted and disambiguated entities are visualized in a way that users can grasp, quickly, such as research networks. The initial graph visualization starts with a few collapsed nodes. These nodes can be expanded to visualize initially hidden nodes and to incrementally add more information to the graph. Thus, users are not overwhelmed with too much information when they start their search. These nodes can be expanded to visualize initially hidden nodes and to incrementally add more information to the graph. 4.1 Search Thus, users are not overwhelmed with too much information when they start their search. MOVING: A User-Centric Platform for Online Literacy Training and Learning 85 Fig. 4 Concept Graph with opened filter menu Fig. 4 Concept Graph with opened filter menu uRank: interest-based result set exploration. Based on the search query the top 100 retrieved results are displayed as a ranked list. The keywords extracted from the results are presented in the Tag Cloud in the right sidebar of uRank (Fig. 5, point A). By selecting keywords of interest, the results in the list (Fig. 5, point C) are re-ranked in such a way that the results containing the selected keyword move to the top. The ranking view (Fig. 5, point D) provides visual feedback on the relevance of the result. It is possible to select multiple keywords and even fine-tune their importance by using the slider under the selected words (Fig. 5, point B). Clicking on a result opens a dialogue box, which presents additional information about the retrieved document. The user can export the current view of uRank, with the current search configuration, by clicking on the export button, which initiates the download of a zip file containing an image and a report text file. Top Properties: the Top Properties visualization uses 100 of the most relevant results from the current search query. It shows a bar chart visualization presenting one of the following properties of the available results: Authors, Keywords, Concepts, Sources, and Year of Publication. The results are ordered according to the most frequent values of the selected property, as can be seen in Fig. 6. When the publi- cation year is selected, the sorting order changes so that the years are displayed in chronological order to make it easier to identify year-on-year changes. Clicking on one of the bars shows the results associated with this property in a small dialogue box. The results in this dialogue are sorted in the order provided originally by the A. Apaolaza et al. 86 Fig. 5 uRank and its components—(A) tag cloud, (B) tag box, (C) result list, (D) ranking view Fig. 5 uRank and its components—(A) tag cloud, (B) tag box, (C) result list, (D) ranking view search engine. The Top Properties visualization also supports an export functionality, which exports the current view of the visualization with its search configuration. Tag Cloud: the Tag Cloud visualization (Fig. 7) retrieves the 100 most rele- vant results from the search query and displays them by showing the most frequent keywordsthatoccurinthecorrespondingtitlesandabstracts.Thedisplayedkeywords are initially sorted by their frequency and can be filtered by occurrence, year, or text. Clicking on one of the keywords shows the results associated with this property. The results are sorted in the order provided originally by the search engine. Fig. 6 The Top Properties visualization with the dialogue box showing the result list for a bar of interest Fig. 6 The Top Properties visualization with the dialogue box showing the result list for a bar of interest MOVING: A User-Centric Platform for Online Literacy Training and Learning 87 Fig. 7 Tag Cloud visualization with a dialogue box showing the result list for a keyword 4.2 Recommender System The RS widget, depicted in Fig. 8, is part of the search page. It gives users addi- tional suggestions for resources of which they may not be aware. The RS interacts with the search engine, user-interaction tracking, and dashboard (WevQuery), hence bridging the back and front ends of the MOVING platform. To build user profiles, it obtains the search history from the user data previously logged through UCIVIT and then retrieves the documents to suggest from the index, depending on the user’s profile. The MOVING RS is based on HCF-IDF (Nishioka and Scherp 2016), a novel semantic profiling approach that can exploit a thesaurus or ontology to provide better recommendations. Further information on the MOVING RS is available elsewhere (Vagliano and Nazir 2019). 88 A. Apaolaza et al. Fig. 8 The Recommender System widget suggesting three new items to the user: a video, an article, and a web page (Vagliano and Nazir 2019) Fig. 8 The Recommender System widget suggesting three new items to the user: a video, an article, and a web page (Vagliano and Nazir 2019) 4www.ckeditor.com, last accessed on 7 May 2020. 5www.twitter.com, last accessed on 7 May 2020. 6www.youtube.com, last accessed on 7 May 2020. 4.3 Communities Open collaboration and communication are the foundations of open innovation and open science. MOVING communities offer users a powerful tool to organize group collaboration and communities of practice on the MOVING platform (see Fig. 9). MOVING communities are part of the working environment of the platform and offer a range of social technologies with knowledge and information management, including wikis, forums, blog functions, and group news. MOVING communities are based on the project management tools and technologies of the eScience platform on which the MOVING platform is based. The existing eScience modules, which enabled cooperation in closed teams of researchers, were adapted to the goals of the MOVING platform to provide an open innovation environment and foster open collaboration, communication, and knowledge exchange between its users. Registered users who want to create a new community are offered different options. First, users can create public communities that are visible to everyone in the MOVING platform and can be accessed and edited by anyone interested in the topic. Second, users who want to organize specific project teams or research groups can create private communities that users have to join before they can access and edit content. Private communities are not visible to other users but can be shared with collaborators via email. MOVING: A User-Centric Platform for Online Literacy Training and Learning 89 Fig. 9 MOVING communities Fig. 9 MOVING communities The MOVING CK Editor4 enables the creation of formatted text and the integra- tion of multimedia content in HTML pages that are created by users in the MOVING communities. Videos, pictures, GIFs or documents, and social media content from Twitter5 and YouTube6 can all be easily integrated. Features like the accordion and the option to include expandable items make it easy to structure content in the page. It is a WYSIWYG editor (What You See Is What You Get) so even users that are not familiar with HTML can use it easily to create and edit web-based content within MOVING communities. The wiki module is useful for creating and collaboratively managing large knowledge repositories with a community. The forum module provides space for 90 A. Apaolaza et al. Fig. 10 MOVING MOOC community 90 A. Apaolaza et al. Fig. 10 MOVING MOOC community 90 A. Apaolaza et al. Fig. 10 MOVING MOOC community open communication and information exchange—a precondition for open innova- tion processes. 7moving.mz.tu-dresden.de/mooc, last accessed 7 May 2020. 8www.orcid.org, last accessed on 7 May 2020. 4.3 Communities The forum module contains a user rating functionality that allows the community to publicly rate the content of individual forum entries. Users can vote posts and replies up and down, based on the quality of the contribution. The highest-rated input is highlighted to help users find the best response in a thread, and the summarized score for all received votes is shown on each user profile. The rankingfunctionalityhelpscommunitiesself-organizeandpeerassessuser-generated content. Community administrators can also choose to assign badges to reward users or motivate them to get actively engaged. Badges can be assigned automatically or manually. The ease of user-generated content creation and integration combined with the social features of MOVING communities open up a wide range of possible applica- tions. Users can organize group work in small project teams, or create open commu- nities around scientific or technical topics to discuss research or ask questions to an expert community. MOVING communities can be organized as an open innovation tool but also as a learning management system, as the following example shows. One practical application of MOVING communities is the four-week MOVING MOOC (massive open online course) Science 2.0 and open research methods that was organized on the MOVING platform (see Fig. 10).7 The MOOC is organized on the platform as a private team community, so that participants have to register to gain 91 MOVING: A User-Centric Platform for Online Literacy Training and Learning 91 Fi 11 MOVING MOOC b d access to the learning materials and the forums. For each week of the MOOC, we created a sub-community containing learning materials in different media formats as well as weekly assignments. The forums were used to organize group communication and allow users to share their assignment results. A wiki was created and contained additional information about the course, learning goals, and technical details about using the editor or the MOOC badges that users can earn on the course (Fig. 11). Badges are displayed on the user’s profile, My page, along with their personal and contact details (profile picture, science field, skills, hometown, institution, email, ORCID8). access to the learning materials and the forums. For each week of the MOOC, we created a sub-community containing learning materials in different media formats as well as weekly assignments. The forums were used to organize group communication and allow users to share their assignment results. A wiki was created and contained additional information about the course, learning goals, and technical details about using the editor or the MOOC badges that users can earn on the course (Fig. 11). Badges are displayed on the user’s profile, My page, along with their personal and contact details (profile picture, science field, skills, hometown, institution, email, ORCID8). 92 A. Apaolaza et al Fig. 12 MOVING learning environment 92 A. Apaolaza et al. 92 A. Apaolaza et al. Fig. 12 MOVING learning environment Fig. 12 MOVING learning environment 4.4 Learning Environment MOVING offers a unique combination of working and training features in one plat- form. The heart of the training programme is the MOVING learning environment. Here, all the learning content is organized and directly accessible to the users. The landing page (Fig. 12) gives an overview of the learning materials including the plat- form demo videos and video tutorials, the Learning Tracks for Information Literacy 2.0, and the MOVING MOOC that was discussed in the previous subsection, Science 2.0 and open research methods. The platform demos are videos hosted on videolec- tures.net and are embedded in the learning environment so that users can learn about the different platform features and technologies developed within the MOVING project. Users can improve their data and information literacy as well as digital competences through Learning Tracks for Information Literacy 2.0 (Fig. 13). 4.5 Adaptive Training Support The ATS (Fessl et al. 2018) comprises two widgets for learning how to search and curriculum reflection. The Learning-how-to-search (Fig. 14) widget visualizes information about the use of features provided by the MOVING platform. The widget presents to users how they used the features of the platform in a bar chart to motivate them to explore new features and reflect about their usage behaviour. More information about the widget and its evaluation can be found in (Fessl et al. 2019). The curriculum reflection widget (Fessl et al. 2019) consists of two parts: the curriculum learning and reflection and the overall progress. The first part consists of two main areas. The upper area either contains a learning prompt (suggesting that MOVING: A User-Centric Platform for Online Literacy Training and Learning MOVING: A User-Centric Platform for Online Literacy Training and Learning 93 Fig. 13 Start page of Learning Tracks for Information Literacy 2.0 Fig. 13 Start page of Learning Tracks for Information Literacy 2.0 the user learn more about the next topic in the current sub-module) and a button which opens the respective learning unit in a new tab (Fig. 15 left), or it presents a reflective question that motivates the user to think about the current topic of their learning (Fig. 15 right). The user’s progress in the current sub-module is displayed at the bottom of the widget. The overall progress part of the widget shows the user’s learning progress through the curriculum using a sunburst visualization. Figure 16 shows that the curriculum is divided into three modules. Each module is represented as a section in the inner circle of the visualization and divided into three sub-modules in the outer circle. Every time a user completes a new learning unit, the percentage in the respective section in the sunburst diagram is updated. Progress in each sub-module is encoded by colour. If the user has not completed any learning units in a sub-module (0%), the respective section will be red. Making progress in a sub-module will turn the section yellow (50%) and completing it will turn the section green (100%). This is also explained by the legend below the visualization. Moreover, the sections in the sunburst diagram are ordered to mirror the structure of the curriculum. Starting from the top, the sub-modules are completed clockwise, gradually turning the visualization green. 94 A. Apaolaza et al. Fig. 14 Learning-how-to-search widget: The tracked features are separated into features of the search input interface and search result presentation Fig. 15 Curriculum reflection widget: curriculum learning (left) and reflection (right) Fig. 14 Learning-how-to-search widget: The tracked features are separated into features of the search input interface and search result presentation Fig. 15 Curriculum reflection widget: curriculum learning (left) and reflection (right) Fig. 14 Learning-how-to-search widget: The tracked features are separated into features of the search input interface and search result presentation MOVING: A User-Centric Platform for Online Literacy Training and Learning The Know-Center is funded within the Austrian COMET Programme, Competence Centers for Excellent Technologies, under the auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian Federal Ministry of Economy, Family and Youth and by the State of Styria. COMET is managed by the Austrian Research Promotion Agency FFG. p g ackes, T.: The impact of name-matching and blocking on author disambiguation. In: CIKM ’18: The 27th ACM International Conference on Information and Knowledge Management Torino, Acknowledgements This work was supported by the EU’s Horizon 2020 programme under grant agreement H2020-693092 MOVING. The mentioned eScience Saxony research network has been supported by the Saxon State Ministry for Science and Art. The Know-Center is funded within the Austrian COMET Programme, Competence Centers for Excellent Technologies, under the auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian Federal Ministry of Economy, Family and Youth and by the State of Styria. COMET is managed by the Austrian Research Promotion Agency FFG. 5 Conclusion In this chapter, we presented the MOVING platform, focusing on the MOVING web application with its search interface and novel results visualizations, commu- nity features and learning environment, and components such Adaptive Training Support. These functionalities help users to not only search within and visualize a large multimedia collection using various advanced tools and functionalities, but also to explore the platform more easily, e.g. by showing statistics about their platform use or providing learning guidance. Productive use of the prototype platform in real educational environments, such as the MOVING MOOC, showed how its integrated MOVING: A User-Centric Platform for Online Literacy Training and Learning Apaolaza, A., Harper, S., Jay, C.: Understanding users in the wild. In: Proceedings 10th International Cross-Disciplinary Conference on Web Accessibility (W4A’13), Rio de Janeiro, Brazil (2013) Apaolaza, A., Vigo, M.: WevQuery: testing hypotheses about web interaction patterns. In: Proceedings ACM Human Computer Interaction 1(EICS), 4:1–4:17. (2017) , p g g g The 27th ACM International Conference on Information and Knowledge Management Torino, MOVING: A User-Centric Platform for Online Literacy Training and Learning 95 Fig. 16 Overall progress widget: The first module was completed and the second module is in progress training and working environment contributes to making information professionals data-savvy and improving users’ information literacy skills. Acknowledgements This work was supported by the EU’s Horizon 2020 programme under grant agreement H2020-693092 MOVING. The mentioned eScience Saxony research network has been supported by the Saxon State Ministry for Science and Art. The Know-Center is funded within the Austrian COMET Programme, Competence Centers for Excellent Technologies, under the auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian Federal Ministry of Economy, Family and Youth and by the State of Styria. COMET is managed by the Austrian Research Promotion Agency FFG. Fig. 16 Overall progress widget: The first module was completed and the second module is in progress training and working environment contributes to making information professionals data-savvy and improving users’ information literacy skills. Acknowledgements This work was supported by the EU’s Horizon 2020 programme under grant agreement H2020-693092 MOVING. The mentioned eScience Saxony research network has been supported by the Saxon State Ministry for Science and Art. The Know-Center is funded within the Austrian COMET Programme, Competence Centers for Excellent Technologies, under the auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian training and working environment contributes to making information professionals data-savvy and improving users’ information literacy skills. training and working environment contributes to making information professionals data-savvy and improving users’ information literacy skills. Acknowledgements This work was supported by the EU’s Horizon 2020 programme under grant agreement H2020-693092 MOVING. The mentioned eScience Saxony research network has been supported by the Saxon State Ministry for Science and Art. The Know-Center is funded within the Austrian COMET Programme, Competence Centers for Excellent Technologies, under the auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian Federal Ministry of Economy, Family and Youth and by the State of Styria. COMET is managed by the Austrian Research Promotion Agency FFG. Acknowledgements This work was supported by the EU’s Horizon 2020 programme under grant agreement H2020-693092 MOVING. The mentioned eScience Saxony research network has been supported by the Saxon State Ministry for Science and Art. References Apaolaza, A., Harper, S., Jay, C.: Understanding users in the wild. In: Proceedings 10th International Cross-Disciplinary Conference on Web Accessibility (W4A’13), Rio de Janeiro, Brazil (2013) Apaolaza, A., Vigo, M.: WevQuery: testing hypotheses about web interaction patterns. In: Proceedings ACM Human Computer Interaction 1(EICS), 4:1–4:17. 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The images or other third party material in this chapter are included in the chapter’s Creative Commons license, unless indicated otherwise in a credit line to the material. References If material is not included in the chapter’s Creative Commons license 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. CLARIN-D: An IT-Based Research Infrastructure for the Humanities and Social Sciences Gerhard Heyer and Volker Böhlke Abstract The paper discusses the idea of bridging the gap between computer sciences and the humanities by referring to an e-humanities infrastructure that provides tools and services for well-defined and frequently encountered tasks. The main goal of this infrastructure is to enable researchers in the humanities and social sciences to better exploit their potential by reusing available digital resources, and thus to increase the efficiency of e-humanities projects. CLARIN-D is an example of such a research infrastructure. The paper provides a brief overview of the basic prin- ciples and services of the CLARIN-D infrastructure, such as metadata harvesting, federated content search, and chaining Web services. Keywords Digitalization · Humanities · CLARIN-D Keywords Digitalization · Humanities · CLARIN-D G. Heyer (B) · V. Böhlke Leipzig University, Leipzig, Germany e-mail: heyer@informatik.uni-leipzig.de V. Böhlke e-mail: boehlkev@informatik.uni-leipzig.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_7 1 Introduction To date, computer science and the humanities have taken different approaches to working methodologies, rather than focusing on the potential synergies. However, recent advances in digitizing historical texts, and the search and text-mining tech- nologies for processing these data, indicate an area of overlap that bears great poten- tial. For the humanities, the use of computer-based methods may lead to more effi- cient research (where possible) and raise new questions that could not have been dealt with otherwise. For computer science, turning to the humanities as an area of application may pose new problems that require rethinking the approaches hitherto favored by computer science. As a result, new solutions may develop that help to advance computer science in other areas of media-oriented application. At present, most of these solutions are restricted to individual projects and do not allow the digital humanities community to benefit from other advances in computer science, V. Böhlke e-mail: boehlkev@informatik.uni-leipzig.de 99 99 © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_7 100 G. Heyer and V. Böhlke G. Heyer and V. Böhlke like service engineering. Hence, in this paper we attempt to spell out in detail the idea of an infrastructure for e-humanities. Focusing on the notion of reusability of data and algorithms such as morphological annotation and part-of-speech (POS) tagging, we sketch how a loosely coupled infrastructure based on Web services and a service-oriented architecture (SOA) can help the humanities to better exploit their potential by reusing available digital resources, and thus increase the efficiency of e-humanities projects. As an example, we present a rough overview of Common Language Resources and Technology Infrastructure D (CLARIN-D), a Web-based research infrastructure for the humanities and social sciences. 2 The Impact of Digitization in the Humanities—From Digital Humanities to E-Humanities These methods impact in the following ways: • qualitative improvement of the digital sources (standardization of spelling and spelling correction, unambiguous identification of authors and sources, marking of quotes and references, temporal classification of texts, etc.); • qualitative improvement of the digital sources (standardization of spelling and spelling correction, unambiguous identification of authors and sources, marking of quotes and references, temporal classification of texts, etc.); • the quantity and structure of sources that can be processed (processing of very large amounts of text, structuring by time, place, authors, contents and topics, comments from colleagues and other editions, etc.); CLARIN-D: An IT-Based Research Infrastructure … 101 • the kind and quality of the analysis (broad data-driven studies, strict bottom- up approach using text-mining tools, integration of community networking approaches, etc.). • the kind and quality of the analysis (broad data-driven studies, strict bottom- up approach using text-mining tools, integration of community networking approaches, etc.). At present, most of these solutions are restricted to individual projects and do not allow the scientific community in the e-humanities to benefit from advances in other areas of computer science. We therefore wish to distinguish between two important aspects of e-humanities: 1. creation, dissemination, and use of digital repositories; 2. computer-based analysis of digital repositories using advanced computationa and algorithmic methods. While the first has originally been triggered by the humanities and is commonly known as digital humanities, the second implies a dominance of computational aspects and might thus be called computational humanities. A practical consequence of this distinction in organizational terms would be to set up research groups in both scientific communities, computer science, and the humanities. The degree of mutual understanding of research issues, technical feasi- bility, and scientific relevance of research results will be much higher in the area of overlap between computational and digital humanities than with any intersection between computer science and the humanities. To empower the humanities to enter into a substantial and mutually beneficial dialog with computer science, however, a research infrastructure is needed that enables researchers in the e-humanities to reuse distributed digitized data and tools for their analysis as much as possible. To use such computational methods, an indi- vidual researcher can proceed by employing two strategies, depending on his or her own degree of computer literacy. One strategy is the individual software approach. 2 The Impact of Digitization in the Humanities—From Digital Humanities to E-Humanities To the extent that applications of computer science have always led to a replacement of analog by digital media and processes, digital media and processing models are having an increasing impact on traditional work flows based on analog media in the humanities and social sciences. The interdisciplinary combination of methods from computer science and traditional humanities with large amounts of digital data and advanced tools for processing these is commonly known as e-humanities (cf. McCarty 2005). Although there is no standard definition of terms yet, e-humanities in a broader sense are concerned with the intersection of computing and the humanities in the eScience paradigm, and thus pertain to any digitized data that are subject to investigation in the humanities and the social sciences, such as text, images, and objects (e.g., in archeology). For the humanities, the use of computer-based methods may lead to more effi- cient research (where possible) and raise new questions that could not have been dealt with otherwise. For computer science, turning to the humanities as an area of appli- cation may pose new problems that lead to rethinking approaches hitherto favored by computer science. As a result, new solutions may develop that help to advance computer science in other areas of media-oriented application. By focusing on text as the main data type in the humanities, we can highlight the benefit that can be gained from the combination of digital document collections and new analysis tools from computer science, mainly derived from information retrieval and text mining. In this way, all kinds of sciences that work with historical or present-day texts and documents are enabled to ask completely new questions and deal with text in a new manner. 2 The Impact of Digitization in the Humanities—From Digital Humanities to E-Humanities Given a selection of digital text data, the research question is transferred into a set of issues and methods that can be dealt with by a number of individual programs. This approach allows for highly dynamic and individual development of research issues. It requires, however, a high degree of software engineering know-how. The other approach is to use standard software. For well-defined and frequently encountered tasks, an e-humanities infrastructure will offer solutions that provide the users with data and analysis tools that are well understood, have already delivered convincing results, and can be learned without too much effort (cf. Boehlke et al. 2013). Both approaches are interdependent. Probably good solutions in one domain of text-oriented humanities can be transferred to other domains by just using different kinds of text. A good infrastructure must be capable of making such solutions accessible as best practices. 102 G. Heyer and V. Böhlke 3 CLARIN-D—An Infrastructure for Text-Oriented Humanities Research infrastructures are concerned with the systematic and structured acqui- sition, generation, processing, administration, presentation, reuse, and publication of content. Content services make available the resources and programs needed for that. Public digital text and data resources are linked together and made accessible by common standards. New software architectures integrate digital resources and processing tools to develop new and better access to digital contents. CLARIN-D1 is part of CLARIN Europe, which recently2 became an independent legal entity according to the ERIC3 statutes. CLARIN-D is primarily designed as a distributed, center-based project (cf. Wittenburg et al. 2010). This means that centers are at the heart of an infrastructure that aims at providing consistent data services. Different types of resource centers form the backbone of the infrastructure, provide access to data and metadata, and/or run infrastructure services. Access to data, metadata, and infrastructure services is usually (but not solely) based on Web services and Web applications. The protocols and formats of infrastructure services (like persistent identifiers or metadata systems and standards that are of interest to the CLARIN initiative on the European level) have been agreed upon in the preparatory phase of the project. Additional infrastructure or discipline-specific services are built upon those basic infrastructure services. The usage of general services like registering and resolving persistent identifiers is not limited to CLARIN itself. Other infrastructure initiatives can and do use such services. Important metadata on CLARIN centers—for example, technical access points, standards and contact information—is stored in a centralized centers registry that acts as a starting point for service users and enables the automation of various procedures, such as monitoring and visualizing the state of all infrastructure services. 1http://de.clarin.eu. 2http://ec.europa.eu/research/index.cfm?pg=newsalert&lg=en&year=2012&na=na-290212-1. 3http://ec.europa.eu/research/infrastructures/index_en.cfm?pg=eric. 4https://www.clarin.eu/content/component-metadata. 4 Metadata, Citation, and Search In CLARIN, metadata is usually represented in a component metadata infrastruc- ture (CMDI).4 The underlying technology of CMDI is XML-Schema (components, profiles), XML (instances), and REST (component registry). CMDI addresses the problem of various specialized metadata standards used for specific purposes by different research communities. Instead of introducing yet another standard, CMDI 103 CLARIN-D: An IT-Based Research Infrastructure … Fig. 1 Components, profiles, and component registry Fig. 1 Components, profiles, and component registry aims at describing and reusing, and (when used in combination with ISOcat5) inter- preting and supporting the integration of existing metadata standards. CMDI compo- nents act as basic building blocks that define groups of field definitions. These compo- nents can be combined into profiles that define the syntax and semantics of a certain class of resources and act as blueprints for metadata instances describing items of this class. These components are managed in a component registry, which allows users to archive and share existing components, thus enabling their reuse (see Fig. 1). Through this approach, CMDI supports the free definition and usage of metadata standards dedicated to specific use cases. As long as metadata is stored in XML, CMDI is able to “embrace” other standards. By combining the data itself with semantic informa- tion stored in the ISOcat data-category registry, CMDI forms a solid basis for using sophisticated exploration and search algorithms. Metadata is the backbone of the infrastructure and publicly available in CLARIN from the resource centers (cf. Boehlke et al. 2012) via the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH).6 The openness of metadata is impor- tant to CLARIN since it guarantees high visibility of the provided resources in the research community. OAI-PMH is a well-established standard and is supported by numerous repository systems like DSpace7 and Fedora.8 The OAI-PMH protocol is based on REST and XML and provides the ability to do two things. It offers full access to the metadata provided by the resource centers and allows for selective harvesting of metadata (see Fig. 2) for search portals like the Virtual Language Observatory (VLO). The VLO enables users to perform a faceted search on the metadata that was harvested from the repositories of all CLARIN centers. By using the information stored in the ISOcat data-category registry (cf. Kemps-Snijders et al. 2008) and the CMDI profiles (see Fig. 5http://www.isocat.org/. 6http://www.openarchives.org/pmh/. 7http://www.dspace.org/. 8http://fedora-commons.org/. 9https://www.clarin.eu/content/federated-content-search. 4 Metadata, Citation, and Search 3) associated to the CMDI metadata instances, the VLO map information is stored in these instances onto a predefined set of facets (see Fig. 4). The VLO also supports the extraction and usage of additional, CLARIN/CMDI-specific, metadata 104 G. Heyer and V. Böhlke 104 G. Heyer and V. Böhlke Fig. 2 OAI-PMH harvesting Fig. 3 Metadata records, profiles, and ISOcat. Source https://www.clarin.eu/sites/ default/files/styles/opensc ience_3col/public/cmdi-ove rview.png such as ResourceProxy (e.g., link to download, dedicated search portal) and federated content search (FCS) interfaces. CLARIN also provides support for content-based search. The CLARIN-D FCS9 is based on Search/Retrieval via URL (SRU) and Contextual Query Language (CQL) and allows users to perform a CLARIN-wide search over all repositories that offer a FCS interface by using a simple Web application. This Web application and external applications send a request to an aggregator service This service first queries a Fig. 2 OAI-PMH harvesting Fig. 3 Metadata records, profiles, and ISOcat. Source https://www.clarin.eu/sites/ default/files/styles/opensc ience_3col/public/cmdi-ove rview.png such as ResourceProxy (e.g., link to download, dedicated search portal) and federated content search (FCS) interfaces. CLARIN also provides support for content based search The CLARIN D FCS9 Fig. 3 Metadata records, profiles, and ISOcat. Source https://www.clarin.eu/sites/ default/files/styles/opensc ience_3col/public/cmdi-ove rview.png Fig. 3 Metadata records, profiles, and ISOcat. Source https://www.clarin.eu/sites/ default/files/styles/opensc ience_3col/public/cmdi-ove rview.png such as ResourceProxy (e.g., link to download, dedicated search portal) and federated content search (FCS) interfaces. such as ResourceProxy (e.g., link to download, dedicated search portal) and federated content search (FCS) interfaces. CLARIN also provides support for content-based search. The CLARIN-D FCS9 is based on Search/Retrieval via URL (SRU) and Contextual Query Language (CQL) and allows users to perform a CLARIN-wide search over all repositories that offer a FCS interface by using a simple Web application. This Web application and external applications send a request to an aggregator service. This service first queries a repository registry and searches for compatible interfaces. The initial query is then CLARIN also provides support for content-based search. The CLARIN-D FCS9 is based on Search/Retrieval via URL (SRU) and Contextual Query Language (CQL) and allows users to perform a CLARIN-wide search over all repositories that offer a FCS interface by using a simple Web application. This Web application and external applications send a request to an aggregator service. This service first queries a repository registry and searches for compatible interfaces. 11Stuttgart Tübingen Tagset. See http://www.sfb441.uni-tuebing-en.de/a5/codii/info-stts-en.xhtml 10An organization which maintains a format for digital text representation. See http://www.tei-c. org/index.xml. 11Stuttgart Tübingen Tagset. See http://www.sfb441.uni-tuebing-en.de/a5/codii/info-stts-en.xhtml. 10An organization which maintains a format for digital text representation. See http://www.tei-c org/index.xml. 11 4 Metadata, Citation, and Search The initial query is then CLARIN-D: An IT-Based Research Infrastructure … CLARIN-D: An IT-Based Research Infrastructure … 105 Fig. 4 VLO Fig. 4 VLO sent to all of these interfaces and the individual results are aggregated and sent back to the user or application (see Figs. 5 and 6). Since CLARIN is designed as an open infrastructure, third-party content providers may easily plug their own repository and FCS interface into this process by registering it to the CLARIN repository registry. sent to all of these interfaces and the individual results are aggregated and sent back to the user or application (see Figs. 5 and 6). Since CLARIN is designed as an open infrastructure, third-party content providers may easily plug their own repository and FCS interface into this process by registering it to the CLARIN repository registry. Web services in CLARIN are also described via CMDI (which may very well contain a link to a WSDL file). If more specific metadata is provided (i.e., the infor- mation enforced by a certain CMDI profile is given), these Web services can be used in a workflow system called WebLicht (cf. Hinrichs et al. 2010). WebLicht allows users to build and execute chains of Web services by analyzing the metadata available for each service and ensuring that the format of the data is compatible; that is, that the output of a predecessor service satisfies the specification of a successor service. Web services in CLARIN are also described via CMDI (which may very well contain a link to a WSDL file). If more specific metadata is provided (i.e., the infor- mation enforced by a certain CMDI profile is given), these Web services can be used in a workflow system called WebLicht (cf. Hinrichs et al. 2010). WebLicht allows users to build and execute chains of Web services by analyzing the metadata available for each service and ensuring that the format of the data is compatible; that is, that the output of a predecessor service satisfies the specification of a successor service. Fig. 5 Federated content search. Source http://www.clarin.eu/sites/default/files/FCS_components. png ig. 5 Federated content search. Source http://www.clarin.eu/sites/default/files/FCS_components. ng Fig. 5 Federated content search. Source http://www.clarin.eu/sites/default/files/FCS_components. png 106 G. Heyer and V. Böhlke Fig. 6 CLARIN-D FCS Web application Table 1 Example input specification for a POS tagger Web service Format MyFormat Input text = UTF-8 language = German tokens = present Fig. CLARIN-D: An IT-Based Research Infrastructure … 107 CLARIN-D: An IT-Based Research Infrastructure … Table 2 Example output specification for a POS tagger Web service Format MyFormat Output POS tags = STTS into tokens encoded in an imaginary format. It produces a document of the same format by adding POS tags based on the STTS tagset. The chaining algorithm of WebLicht (cf. Boehlke 2010) is based on the idea that NLP services usually consume a document of a well-defined standard and will also return such a document. The successful invocation of a service for an input document hence depends on which information is available in that document. A POS tagger Web service may only work if sufficient information on sentence and token boundaries is available, while a named entity recognizer (NER) requires appropriate POS tags. Therefore, the standard used for the input document needs to allow for a representation of this kind of information, and, of course, this information needs to be present in the input document itself. This fact is also represented in the interface definition. Thus, for service chaining to work, it must be ensured that this information is available by using a type checker on each step of a chain. This check can be done when building the chain, since all the necessary informa- tion is already available. Based on a formal Web service description according to the proposed structure, a chaining algorithm, which is basically a type checker, can be implemented. A service can be executed if the previous services in the chain meet the following constraints: the format specified in the output is equal to the format specified in the input specification of the service; every parameter-type/standard pair defined in the input specification needs to be one of the pairs in the output specifications of services which have been executed (or scheduled for execution previously in the chain, if we stay on build time). every parameter-type/standard pair defined in the input specification needs to be one of the pairs in the output specifications of services which have been executed (or scheduled for execution previously in the chain, if we stay on build time). These two constraints are of course a simplification. But in many simple cases, an algorithm like this will be sufficient. A short and simplified example of the chaining logic is given in Figs. 4 Metadata, Citation, and Search 6 CLARIN-D FCS Web application Table 1 Example input specification for a POS tagger Web service Format MyFormat Input text = UTF-8 language = German tokens = present When thinking about interchanging neuro-linguistic programming (NLP) data like text, there are several established standards defining how texts can be encoded and how annotations like POS tags may be added. These standardization efforts are supported by WebLicht, hence the following interface definition of a Web service compatible with WebLicht: • the format used is TCF (or TEI10 P5, etc.); • the format used is TCF (or TEI10 P5, etc.); • the document contains German text and is annotated with POS tags; • the POS tags are encoded according to the STTS11 tagset. • the POS tags are encoded according to the STTS11 tagset. A complete interface definition of a WebLicht Web service consists of two iden- tically structured specifications for input and output. Each of these specifications defines the format of a document that is used to represent the data. Additionally, a set of pairs of parameter types is mandatory to invoke the service for the input specification, or is computed and added by the service for the output specification. Each of these parameter types is bound to a standard definition, which binds it to a standardized encoding of the information. Tables 1 and 2 give example input and output specifications of a POS tagger Web service. This service consumes documents that contain German text that was split CLARIN-D: An IT-Based Research Infrastructure … CLARIN-D: An IT-Based Research Infrastructure … 7 and 8, which show part of a chain consisting of Web services A (a tokenizer) and B (a POS tagger). In Fig. 7, Service A can be executed since all constraintsdefinedinitsinputspecificationaremet.Theformatoftheinputdocument is compatible and its content fulfills the requirements because it contains German text encoded in UTF-8. The tokenizer segments the text into sentences and tokens. After its execution, this information is added to the resulting output document. Service B is checked against this updated knowledge about the content of the output document of Service A (see current metadata in Fig. 8). Service B is compatible since all of its input requirements, format and parameters, are available in the output document of Service A. 108 G. Heyer and V. Böhlke 108 G. Heyer and V. Böhlke Fig. 7 Tokenizer service specification Fig. 8 POS tagger service specification 5 Summary and Conclusion Research infrastructures for the humanities can help to share digital resources and content services. In particular, they can help researchers in the digital humanities to save time and effort when developing software to deal with specific research issues, while the development of such infrastructures and their key software compo- nents is a software engineering task that increasingly poses interesting and chal- lenging research problems for computer scientists. In this paper, we have presented Fig. 7 Tokenizer service specification e Fig. 8 POS tagger service specification Fig. 8 POS tagger service specification 5 Summary and Conclusion Research infrastructures for the humanities can help to share digital resources and content services. In particular, they can help researchers in the digital humanities to save time and effort when developing software to deal with specific research issues, while the development of such infrastructures and their key software compo- nents is a software engineering task that increasingly poses interesting and chal- lenging research problems for computer scientists. In this paper, we have presented the European Strategy Forum on Research Infrastructures (ESFRI) project CLARIN and some of its key elements as a research infrastructure for the humanities. In detail, CLARIN-D: An IT-Based Research Infrastructure … 109 we have presented component metadata infrastructure as a means for unifying meta- data descriptions of linguistic resources in the humanities. Based on these metadata, we have also shown how Web services can be built that share data and algorithms in the research infrastructure. Both aspects are closely related: The content-driven use of digitized data and software tools in a specific application scenario in the humanities, and the software and service engineering issues relating to an efficient research infrastructure in the humanities. These two aspects, content and service, clearly need to complement each other in order to establish a culture of best practice in the e-humanities. References Boehlke, V.: A Generic Chaining Algorithm for NLP Webservices. LREC (2010) Boehlke, V., Compart, T., Eckart, T.: Building up a CLARIN resource center—step 1: Providin metadata. In: Workshop on Describing Language Resources with Metadata (2012) Boehlke, V., Heyer, G., Wittenburg, P.: IT-based research infrastructures for the humanities and social sciences—developments, examples, standards, and technology. Inf. Technol. 55(1): 26–33 (2013) Hinrichs, M., Zastrow, T., Hinrichs, E.: WebLicht: web-based LRT services in a distributed eScience infrastructure. 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(eds.), Proceedings of the Seventh conference on International Language Resources and Evaluation (LREC’10), pp 60–63. European Language Resources Association (ELRA) (2010) Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), 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 license and indicate if changes were made. g The images or other third party material in this chapter are included in the chapter’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the chapter’s Creative Commons license 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. Toward Process Variability Management in Online Examination Process in German Universities: A State of the Art Maryam Heidari and Oliver Arnold Abstract In contemporary organizations, multiple variants of the same business process are often considerable. Such business process variability has caused consid- erable challenges, both while modeling processes and in their execution. In order to develop a new approach to managing process variants, or extend an existing one, in this research, we review the state of the art in a particular area: online examina- tion processes. We show to what extent variability should be considered in exam processes, whether this is due to special legal restrictions and regulations, different exam frameworks, or even different technical infrastructure. This could be the foun- dation for developing an approach to managing process variability in the field of e-assessment. Initial findings indicate that examination processes have many simi- larities, but also considerable differentiation. Therefore, there an appropriate model needs to be developed in order to manage variability in e-assessment and the devel- oped approach must then be validated in identifying faculties. This paper constitutes a first step in this direction. Keywords Process variability · Online examination · E-assessment process model · Accreditation M. Heidari TU Bergakademie Freiberg, Freiberg, Germany e-mail: maryam.heidari@bwl.tu-freiberg.de M. Heidari TU Bergakademie Freiberg, Freiberg, Germany e-mail: maryam.heidari@bwl.tu-freiberg.de O. Arnold (B) Westsächsische Hochschule Zwickau, Zwickau, Germany e-mail: oliver.arnold.1@fh-zwickau.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_8 1 Introduction In today’s dynamic world, there are often multiple variations of identical business processes. Rosemann and colleagues noted, for instance, that SAP offers 27 different industry solutions with corresponding business process reference models (Rose- mann and van der Aalst 2007). These models usually include decisions in the work- flow, which could be made before executing process instances. It is impossible for M. Heidari TU Bergakademie Freiberg, Freiberg, Germany e-mail: maryam.heidari@bwl.tu-freiberg.de O. Arnold (B) Westsächsische Hochschule Zwickau, Zwickau, Germany e-mail: oliver.arnold.1@fh-zwickau.de 111 111 © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_8 112 M. Heidari and O. Arnold both variants of such decisions to coexist in a certain domain or process context. However, conventional modeling approaches do not offer the opportunity to differ- entiate between such decisions and regular decisions during the runtime of a process instance. An important element of controlling the variability in business process models is to separate the usual runtime decisions from decisions at configuration time, called variation points. The results of such steps are complex artifacts. The number of artifacts makes the manageability of related workflows more complex. Basedonthereviewedliterature,organizationstakedifferentapproachestomanaging process variability (Ayora Esteras 2012). The existing approaches have limitations in terms of supporting an entire set of elements like control flow, rules, and legal regulations during the construction and execution of business processes. For this paper, we chose an educational field as an example of process variability, in order to observe effects and causes of variability. The goal is to have a compre- hensive overview to address the problem of process variability in online examination processes at German universities and show the necessity of managing it through an appropriate business process model. To achieve this goal, we set out the state of the art in research regarding the process variability of online examinations from different perspectives. This could be the basis for developing a process model to manage existing variability in this field. We evaluate existing approaches and concepts in the context of e-assessment in the literature and clarify current accreditation processes in educational fields. This will help to identify to what extent existing examination procedures reflect variability and demonstrate the necessity of developing a unified e-assessment model to cover all variability in the learning-teaching process. The paper is organized as follows: After illustrating motivation through existing studies in the following section, the research method is explained. 1 Introduction After exploring the literature and data collected in the identified domains, the results are evaluated. Finally, the need for further work is explained in the conclusion. 2 Motivation In this section, we have a close look at process variability and its challenges, iden- tifying the importance of variability management in the organizations. Basically, process models capture an organization’s activities in achieving certain business goals. The aim is to better understand the process, its implementation, and its execu- tion in a workflow (Becker et al. 2013). However, there are a lot of possible variants for one process. Such business process variability creates considerable challenges in process modeling and execution: • the variants may be modeled in a highly redundant way, so there are many identical or similar parts; • the variants may be modeled in a highly redundant way, so there are many identical or similar parts; • there is no strong relation between the variants, so there is no support for automatically combining existing variants; • there is no strong relation between the variants, so there is no support for automatically combining existing variants; Toward Process Variability Management … Toward Process Variability Management … 113 • manual modeling in every single process variant would be time-consuming and error-prone. • manual modeling in every single process variant would be time-consuming and error-prone. • manual modeling in every single process variant would be time-consuming and error-prone. In recent years, the proper management of business process variability has been the subject of numerous scientific studies. A very comprehensive survey article about business process variability can be found in Valenca et al. (2013), which describes more than 80 primary sources. Based on this study, significant numbers of variability approaches exist, where each one addresses different issues in terms of process vari- ability. Valenca and colleagues observed 57 new approaches to different aspects of variability in processes (Valenca et al. 2013). They divided these references into five categories: business process configuration, to capture an instance of the reference model;businessprocesscorrectness,tosemanticallysupportcorrectionoftheprocess model; business process flexibility, to change process models fast and easily; busi- ness process modeling, to visualize variability in process models; business process similarities, to investigate differentiations between business process models. It is argued that only 30% of solutions are practically evaluated through case studies and surveys, especially of industry: The lack of empirical studies in process variability is considerable, with implications for executing process variability (Valenca et al. 2013). 2 Motivation In the public sector, as in business, processes have a lot in common, but signif- icant differences due to the local conditions and legal regulations are considerable. Vogelaar and colleagues analyze and compare the different processes of ten Dutch municipalities which are found to vary in terms of classical standardization processes (Vogelaar et al. 2012). In education, Arnold and Laue studied controllability of variability in examination process models (Arnold and Laue 2014). They investigated six different courses at three different universities in the German Federal State of Saxony, to achieve better comparability. Based on this research, considerable variability in examination processes exists, even in one university between different fields of study. The authors triedtoprovideasolutionbasedonexistingvariabilityapproaches,inordertomanage examination processes. They argued that appropriate process variability modeling requires modeling skills and significant experience in the identified domain (Arnold and Laue 2014). We focus on online examination processes in higher education, presenting the state of the art in three different domains and observing existing process variability in order to gain a comprehensive overview of process variability in this field, highlighting the need for this to be managed. 3 Research Method • We reviewed the state of the art in three identified domains within e-assessment • IT-related approaches; • designing study courses and e-assessment concepts; • accreditation process. In the following, the results of our literature review and data collection in each domain are explained separately. 3 Research Method The purpose is to evaluate the existing variability in higher educational e-assessment processes, as a basis for further research into variability management in this field. The state of the art is identified in five phases (Cooper 1998): The purpose is to evaluate the existing variability in higher educational e-assessment processes, as a basis for further research into variability management in this field. The state of the art is identified in five phases (Cooper 1998): 114 M. Heidari and O. Arnold M. Heidari and O. Arnold 1. Problem formulation: The academic goal and research relevance are defined; 1. Problem formulation: The academic goal and research relevance are defined 2. Literature search and data collection: Literature and data related to the problem formulation are identified; 2. Literature search and data collection: Literature and data related to the problem formulation are identified; 3. Literature evaluation: The acquired literature is assessed for relevance and categorized; 3. Literature evaluation: The acquired literature is assessed for relevance and categorized; 4. Interpretation: The results are analyzed and interpreted; 5. Presentation: The results are presented in a suitable fashion. Assessments are an important part of the educational cycle (Ferrão 2010) and have a great impact on the learning process. They provide valuable information about the effectiveness of a study course in increasing the students’ knowledge (Primiano et al. 2004). An appropriate assessment process is not only important in terms of teaching and learning, but also for accreditation processes and educational standards (Ferrão 2010). Recent developments in e-learning can be seen as an accelerator to developing e-assessment alternatives. It is therefore becoming more important to develop methods for e-assessment and to gain feedback on learning and teaching (Sangi and Malik 2007). Furthermore, Dermo has shown that e-assessment can offer different forms of assessment with immediate feedback to both students and lecturers, so it can be recognized as a complementary tool in the learning framework (Dermo 2009). Exam regulation documents, which are the basis for accreditation processes in higher educational institutions, have a lot in common. But in some points, they differ from one university to another or even from one course to another within the same institution. Therefore, there is variability in assessment processes, which is an obstacle to developing a unified process model for e-assessment. 1Numbers in brackets refer to the references in Appendix 1. 3.1.1 Domain: IT Approaches Data sources: AISel and EBSCO Research period: 2000–2013 Search terms and keywords: e-assessment, education, online examination, e-test, computer-based exam (in abstract and title) Number of related articles: AISel: 51 after reviewing and removing doublets and non-related articles: 14 AISel: 51 after reviewing and removing doublets and non-related articles: 14 Data sources: AISel and EBSCO Research period: 2000–2013 Data sources: AISel and EBSCO Research period: 2000–2013 Search terms and keywords: e-assessment, education, online examination, e-test, computer-based exam (in abstract and title) Number of related articles: Number of related articles: AISel: 51 after reviewing and removing doublets and non-related articles: 14 AISel: 51 after reviewing and removing doublets and non-related articles: 14 AISel: 51 after reviewing and removing doublets and non-related articles: 14 115 Toward Process Variability Management … Toward Process Variability Management … Toward Process Variability Management … 115 Table 1 Pedagogical aspects of e-assessment Pedagogical issues References Evaluation of the impact of e-assessment on learning processes (strengths and weaknesses) Becker et al. (2008, 2013), Braun (1998), Coyle (2009), Dermo (2009), Dittman and Deokar (2008), Ferrão (2010), Gruhn and Laue (2007), Hodgson and Pang (2012), Impagliazzo et al. (2002), Johnson-Glenberg (2010), and Jordan and Mitchell (2009) Formative e-assessment (feedback) Charoen (2009), Davis et al. (2001), El-Ashy (2006), Hall et al. (2010), Hallerbach et al. (2010), Hallerbach et al. (2008), Hodgson and Pang (2012), and Irani et al. (2000) Collaborative e-assessment Ayora Esteras (2012), Boyle (2010), and Davis et al. (2001) Different types of e-assessment and questions Coyle (2009), Gorgone (2006), Gruhn and Laue (2007), and Jordan and Mitchell (2009) Table 2 Technical aspects of e-assessment Technical issues References E-assessment tool evaluation (strengths and weaknesses) Accountants find e-assessment … (2011), Boyle and Hutchison (2009), Braun (1998), Charoen (2009), Cooper (1998), Dascalu and Bodea (2010), Davis et al. (2001), Davis (2007), Dermo (2009), Gorgone (2006), and Impagliazzo and Gorgone (2002) E-assessment implementation (challenges: validity, security, task assessment, adoption, etc.) Attali and Burstein (2006), Braun (1998), Campbell (2008), Daly et al. (2010), Ferrão (2010), Impagliazzo and Gorgone (2002), Irani et al. (2000), Jacob et al. 3.1.1 Domain: IT Approaches (2006), Johannsen and Leist (2012), Johnson-Glenberg (2010), and Jordan and Mitchell (2009) EBSCO: 62 after reviewing and removing doublets and non-related articles: 18 Based on the reviewed articles, a main classification can be recognized in the EBSCO: 62 after reviewing and removing doublets and non-related articles: 18 B d h i d i l i l ifi i b i d i h EBSCO: 62 after reviewing and removing doublets and non-related articles: 18 Based on the reviewed articles, a main classification can be recognized in the context of e-assessment in higher education: EBSCO: 62 after reviewing and removing doublets and non-related articles: 18 Based on the reviewed articles, a main classification can be recognized in the context of e-assessment in higher education: • pedagogical issues (educational view) • pedagogical issues (educational view) • technical issues Different kinds of terms and concepts are used, based on pedagogical and technical approaches: Each one addresses one or more aspects of e-assessment. These issues are summarized in the following Tables 1 and 2.1 Most of these references include multiple issues from the technical and pedagog- ical perspectives. These issues are connected and cannot be separated. 116 M. Heidari and O. Arnold Jacob and colleagues deploy an e-assessment tool, the Black Board Learning System (BBLS), as a comprehensive e-learning software to facilitate continuous assessment and evaluate its effects on learning processes (Jacob et al. 2006). It reveals that the biggest advantage of e-assessment in this system is immediate feedback, which bolsters the formative assessment.2 One weakness of the system is the lack of the automatic evaluation of essay-writing exams. Kehily analyzed the impact of a Web-based e-learning platform that can support effective teaching (a course manage- ment system for lecturers) and formative assessment (a computer-assisted learning tool for students) in a case study (Kehily 2011). Venkatraman developed a four-step student-centered approach to an effective e-learning process and, in a case study of information system (IS) courses, evaluated this approach for different assessment methods including individual, group, peer, and self-assessment (Venkatraman 2007). These four steps are: 1. understanding the students’ learning style and their learning expectations; 2. identifying suitable assessment models; 3. designing a set of assessments; 4. evaluating the impact of the assessment on the learning process. 3.1.1 Domain: IT Approaches Dermo evaluates the possible risks in planning e-assessments such as computer stress, fairness of choosing questions randomly from a bank, accessibility, and the contribution of e-assessment to students’ learning, through six dimensions in a case study (Dermo 2009). These six dimensions are: affective factors, reliability and fairness, validity, security, practical issues, and teaching and learning terms, which are a mixture of pedagogical and technical issues. Daly and colleagues argue that existing e-assessment solutions focus on developing technical and infrastructural issues more than educational aspects (Daly et al. 2010). McCann identifies different factors which affect real implementations of e-assessment systems based on two IS theories: Roger’s theory3 and Eckel and Kezar’s theory4 (McCann 2010). 2Formative assessment encourages deeper engagement with learning and is a motivation and progressive force in learning. The key element of formative assessment is feedback. 3It identifies five variables to demonstrate how and why new ideas are adopted: relative advantage, compatibility, trialability, observability, and complexity (McCann 2010). 4It identifies five core strategies that explain change across institutions: senior administrative support, collaborative leadership, flexible vision, staff development, and visible actions (McCann 2010). 3It identifies five variables to demonstrate how and why new ideas are adopted: relative advantage compatibility, trialability, observability, and complexity (McCann 2010). 2Formative assessment encourages deeper engagement with learning and is a motivation and progressive force in learning. The key element of formative assessment is feedback. 4It identifies five core strategies that explain change across institutions: senior administrativ support, collaborative leadership, flexible vision, staff development, and visible actions (McCann 2010). Toward Process Variability Management … Toward Process Variability Management … In this domain, we began by finding some case studies of e-assessment or online examination at German universities. In order to have an appropriate sample, we selected universities which conducted online examinations or had a project to recog- nize a unified approach or process regarding e-assessment in Germany. Different kindsofprojectsintermsofcomputer-basedexaminationshavebeeninprogressfrom the year 2000 onward. Table 3 summarizes all these projects with their functionality and their relation with exam regulation documents. Of all the universities studied, only the University of Duisburg-Essen proposes a process model for implementing online examination. Proposing such a process model for online exams has the following advantages: • improves the speed of feedback to students; • motivates students and lecturers to increase computer skills through the integra- tion of multimedia elements such as audio and video, and using complex digital systems; • motivates students and lecturers to increase computer skills through the integra- tion of multimedia elements such as audio and video, and using complex digital systems; • significant time saving for lecturers by automatic correcting process. By reviewing the exam regulations and conditions, it becomes obvious that there is no identified exam process model in the administrative processes at different universities. A process model not only supports understanding the complexities of processes properly, but also contributes to advancing and improving defined processes (Irani et al. 2000). Therefore, in order to understand the examination workflows carried in the universities, a process model is required to analyze exam processes comprehensively. 5Association for Information Systems eLibrary. 3.1.2 Domain: Designing Study Courses and E-Assessment Concepts Data sources: German university homepages Research period: 2000–2013 Search terms and keywords: e-assessment, online examination, project, computer- based exam, e-exam, e-test Search terms and keywords: e-assessment, online examination, project, computer- based exam, e-exam, e-test 2Formative assessment encourages deeper engagement with learning and is a motivation and progressive force in learning. The key element of formative assessment is feedback. 117 3.1.3 Domain: Accreditation Process Data sources: Accreditation agencies authorized by AISel5 and EBSCO Research period: 2000–2013 Search terms and keywords: e-assessment, education, online examination, computer-based exam, accreditation process, accreditation criteria (in abstract and title) Data sources: Accreditation agencies authorized by AISel5 and EBSCO Research period: 2000–2013 Data sources: Accreditation agencies authorized by AISel5 and EBSCO Research period: 2000–2013 Search terms and keywords: e-assessment, education, online examination, computer-based exam, accreditation process, accreditation criteria (in abstract and title) Search terms and keywords: e-assessment, education, online examination, computer-based exam, accreditation process, accreditation criteria (in abstract and title) As a definition, accreditation is a criteria-based procedure to assess and evaluate the admissibility of an educational program in terms of quality (Gorgone 2006; Impagliazzo and Gorgone 2002; Reichgelt and Yaverbaum 2007). The main goal of accreditation is to assess the educational quality of an academic program to ensure that it meets certain quality standards, called accreditation criteria (Reichgelt 2007). Based on the European Network for Quality (ENQA), each educational program should fulfill the minimum in the following set of requirements to be accredited: • requirements and objectives; • teaching–learning process; • learning resources; M. Heidari and O. Arnold M. Heidari and O. 3.1.3 Domain: Accreditation Process Arnold 118 Table 3 E-assessment projects in German universities University Description of e-assessment projects Relation to exam regulation documents Free University of Berlin • Since 2005 • Run by the center for digital systems (CeDiS) • Software: LPLUS Test Studio • 407 spaces for e-examinations • Not used for all study courses Not mentioned University of Duisburg-Essen • Since 2007 (in progress) • Software: LPLUS • Faculties: human science, social science, biology and geography, chemistry, engineering, and mathematics • Implementation of e-exams based on a process model e-exams are mentioned in some study courses as one of the exam methods beside other traditional forms Details of the e-exam process are not mentioned in these documents University of Bremen • Since 2004 • Software: LPLUS • 7500 e-exams per semester Since 2010, performing the electronic examinations as one of the examination forms is admissible in the examination rules and regulation documents University of Giessen • Since 2007 • Software: open-source learning platform (ILIAS) • Offers many opportunities such as learning modules for units, online glossary, import of SCORM and HTML tutorials, e-assessment module for online tests, survey module for user surveys, user management in courses and groups • This system is limited due to the lack of appropriate space to increase efficiency of e-examinations Not mentioned University of Mainz • Since 2007 • Software: open-source learning platform (ILIAS) • Exam regulation documents mention that e-exams should be carried out under the same conditions as traditional examinations • The details of the e-exam process are not mentioned in these documents (continued) Table 3 E-assessment projects in German universities • The details of the e-exam process are not mentioned in these documents (continued) 119 Toward Process Variability Management … Table 3 (continued) University Description of e-assessment projects Relation to exam regulation documents University of Koblenz-Landau • Since 2013 • Software: open-source learning platform (ILIAS) • Two years for pilot and evaluation phase • Online exam submission through electronic exam schedule service (eKLAPS) Not mentioned because the project is new and in the pilot phase University of Regensburg • Since 2010 (in progress) • Road map defined which consists of different tasks and stages Legal conditions and e-exam framework during the whole process are stages of the e-assessment road map University of Leipzig • Since 2005 • Software: open-source platform (elateXam) • Around 1000 students per semester • Next step: develop the project as a pilot within the project iAssess.Sax in the universities of Dresden and Zwickau Not mentioned 3.2 Accreditation Processes in Germany In Germany, the federal states are responsible for accreditation processes and at least 11 authorized accreditation agencies in different fields of education (medical, natural science, engineering, economics, etc.) are in operation at present.6 Educational accreditation in Germany is based on two issues: 1. standards of study courses and degrees, which are based on regulations for study and examinations; 2. accreditation in teaching, which is based on quality improvement measures. The requirements in the examination accreditation process are as follows: • examinations are coordinated so that students have sufficient time to prepare themselves; • it must be possible to move directly from the bachelor’s degree to the master’ degree without loss of time; • the form of examination is laid down in the description of each module; • the form of examination is laid down in the description of each mod • examinations should not cause extensions to the period of study; • examinations should not cause extensions to the period of study; • the evaluation criteria are transparent for both lecturers and students; • the degree program ends with a final thesis; • it is checked whether students are capable of oral discussion in their specialis area; • the supervision of the final thesis is subject to precise regulations in the curriculum The archived documents in the accreditation process are test results, drop-ou rates, any quantity results of examinations, as well as feedbacks from the courses. This survey of three domains indicates that multiple perspectives exist, which cause variability in performing and evaluating e-assessment processes. It is therefore essential to develop an appropriate model to account for this variability in online examination processes. • monitoring, analysis, and overview. • monitoring, analysis, and overview. The assessment or examinations are placed in the teaching–learning process, which is the most complex aspect of this model because it includes a mixture of technical, pedagogical, and social competences and, furthermore, there is a great freedom to manage courses in order to achieve identified objectives. According to Reichgelt and colleagues, there are two accreditation types: – institutional accreditation is applied to an academic institution, like an entire university; – institutional accreditation is applied to an academic institution, like an entire university; – specialized accreditation is applied to a subunit in an institution and includes two levels: program accreditation focuses on the content of the program, while admin- istrative accreditation concentrates on the administrative process in a subunit of an institution (Reichgelt and Yaverbaum 2007). The authors explain that there are two main approaches to accreditation processes. The first one is the input-based approach which measures various minimal stan- dards through a checklist based on the learning-input processes such as curriculum, teaching resources, library, laboratory, and other facilities. The second is the outcomes-based approach, which considers the program’s outcomes, such as the institution’s educational objectives and student learning. Reichgelt and colleagues argue that a significant shift from the input-based to the outcomes-based approach 120 M. Heidari and O. Arnold has occurred in recent years and academic institutions attempt to conform themselves with outcome criteria (Reichgelt and Yaverbaum 2007). has occurred in recent years and academic institutions attempt to conform themselves with outcome criteria (Reichgelt and Yaverbaum 2007). 6December 2013. 7All these studies are summarized in a table in Appendix 1. 8These universities are listed in Appendix 2. 4.1 Evaluation of IT Approaches Based on reviewed IT approaches, it can be argued that due to the great advantages of and positive impacts of online exams on learning processes, there is a considerable movement from traditional to electronic assessment in academia today. Furthermore, studies7 show that different issues, from pedagogical to technical and even social matters, cause process variability in higher education examinations. To identify a way of managing this inherent variability and to construct unified e-assessment proce- dures, it seems necessary to have a cross-functional view of e-assessment projects. Someoftheissuesrelatedtoe-assessmentare:theimpactsonstudentlearning;effects on the teaching method; formative and collaborative e-assessment; immediate feed- back and legal issues; evaluating possible risks in planning such as computer stress or fairness impression; developing infrastructural issues, such as security and question banks. 4 Literature and Results This literature review was performed in order to demonstrate existing process vari- ability in e-assessment in different domains of higher education, which occurs for different reasons. The results of each domain and its relations to process variability are analyzed and presented in the following. Toward Process Variability Management … 121 Table 4 Summary of e-assessment projects in German universities Number of studied universities 30 Number of universities which have e-assessment projects (in progress) 18 Number of universities which perform online examination practically in some fields 9 Number of universities which have a paragraph about online examinations in exam regulation documents 3 Number of e-assessment projects in universities in Saxony 2 8These universities are listed in Appendix 2. 4.3 Evaluation of Accreditation The results revealed that accredited educational programs are subject to a variety of quality criteria. These criteria depend on the level and the goals of the courses. Based on the Information Model from the European Network for Quality (ENQA), assess- ment and examination processes are placed within the teaching–learning process, which is one of the complex parts of accreditation. It involves different aspects such as pedagogical, technical, legal, and even social issues. p g g g No framework for examination forms (traditional or computer-based) was identi- fied in this study of the German accreditation process. In exam regulation documents, assessments were only described in the terms listed at the end of Sect. 3.3 above. The form of examinations is not restricted by the accreditation process, but is under the authority of the educational systems and based on the identified objectives of courses. This causes process variability from one educational institution to another. 4.2 Evaluation of Study Courses Thirty German universities from different federal states and different study courses were reviewed.8 The results show that e-assessment or online examination projects are currently in progress in 18 universities, but just nine are performing such assess- ments in practice. It should be noted that although online examinations are in use at some universities, there exists considerable process variability, too, which makes it difficult to extract a unified platform in this area. Furthermore, legal conditions in regulation documents create practical limitations on performing online examinations. In order to make it an acceptable form of assess- ment,electronicexaminationshouldbereferredtoinaparagraphorevenasentencein the corresponding exam regulation document. Based on reviewing examination rules documents in all these universities, Table 4 reveals that only three German universi- ties have a paragraph stating that online examination is an admissible examination form. 122 M. Heidari and O. Arnold 4.4 Summary of the Results For clarity, we summarize the results of the three domains in Table 5. In sum, exam processes show variability for the following reasons: • variability in legal restrictions and regulations in different educational institutions; • variability in exam framework, not only in different universities but also in one university between different courses; • variability in legal restrictions and regulations in different educational institutions; • variability in exam framework, not only in different universities but also in one university between different courses; Table 5 Summary of the results Domain E-assessment limits on PVa Why PV management is necessary IT approach Different perspectives: – teaching–learning issues; – legal issues; – technical issues; – social issues To have a cross-functional and integrated view Course and assessment design Legal conditions are not mentioned in exam regulation documents Different processes are used to perform online examination To develop an appropriate approach to support legal conditions in exam documents Accreditation The form of the exam is not restricted by accreditation criteria, which leads to variability To develop a business process model for clear e-assessment criteria aPV = process variability Toward Process Variability Management … 123 • variability in study course design; • variability in study course design; • variability in technical infrastructure for online examination processes. • variability in technical infrastructure for online examination processes. Based on the obtained results, it can be argued that an appropriate design for variability management has to be aligned with the specified domain of projects and conditions to cover all variability within the identified domain. There is only one process model for performing online examinations in some study courses at Univer- sity of Duisburg-Essen, which could be an appropriate model for conducting online examinations at German universities. We studied existing process variability (effects and causes) in online examination processes from different perspectives. We found that to manage process variability, an appropriate business process model is necessary to cover all examination processes and features of educational institutions. According to the existing literature, one approach to process variability manage- ment is the single model approach, which models all known variants of the process in one common model (Hallerbach et al. 2010; Kumar and Yao 2012). The alternative is to model every variant of a single model, which is called the multi-model approach. The latter models will have a simpler structure (Hallerbach et al. 2010; Kumar and Yao 2012). 4.4 Summary of the Results Some advanced modeling approaches explicitly deal with families of process models, such as configurable event-driven process chains (C-EPCs) (Rose- mann and van der Aalst 2007), PROcess Variants by OPtions (PROVOP) (Hallerbach et al. 2010), ConDec (Pesic and Aalst 2006), and feature modeling, which is normally used in software engineering. Each of these approaches has their own advantages and drawbacks but there is a lack of adaptability between different approaches (Valenca et al. 2013). The next step in this research is to conduct a comprehensive overview of available variability approaches, to identify which of them are more appropriate for online examinations in higher education. Further research is needed to evaluate how existing process variability approaches can be compatible with exam processes, and to what extent existing process variability in this field can be controlled and managed. 5 Conclusion and Further Work The aim of this research is to demonstrate existing variability in examination processes and emphasize the need for variability management. This could be the basis for developing a new approach to business process variability, or extending an existing one. To reach this goal, we concentrated on online examination processes in higher education. As a preliminary stage, we performed a literature review in three different domains: IT approaches; concepts; course design and the accreditation process. This paper demonstrates the important role of business process management in improving and promoting the design of e-assessment processes. 124 M. Heidari and O. Arnold M. Heidari and O. Arnold Combined with this literature review, an analysis of current e-assessment case studies and projects in German universities yielded the following results. Although different kinds of projects under the name of e-assessment or online examination are in progress in German universities, the variability in these processes is recognizable. In other words, similar processes exist, but distinctions and variability are observable as well. Furthermore, the review of the exam regulation documents for various study courses at different universities revealed that these regulations do not yet mention an acceptable framework for performing e-assessments. Process variability exists in e-assessment at German universities. It is necessary to manage this variability through an appropriate business process model to support online examination procedures. This paper describes research in progress which clarifies and identifies the neces- sity of developing an existing approach to manage and control the process variability in university e-assessment. The next step is to study process variability manage- ment to identify an appropriate model in the context of e-assessment. This could be followed by the development of a prototype for the identified approach and finally the validation of the developed method. Appendix 1: Summary of IT Approaches to e-Assessment Appendix 1: Summary of IT Approaches to e-Assessment No. Reference (author, year) Summary 1 F. Braun, 1998 It introduces some web-based tools for online assessment such as Learning space, Web forms, Microtest, and Quizmaker. 2 Charoen, 2007 It indicates the benefits and limitations of implementing an e-learning system in an educational institution in Thailand based on expert interviews. 3 Dittman, 2008 It introduces a structure, the collaborative e-learning template (CET), to improve collaborative activities in the learning process such as collaborative assessments through a course. 4 Papp, 2000 It indicates different critical factors in distance learning. 5 Squires et al., 2004 It is about education policy analysis in Arizona University. 6 Shen et al., 2000 It analyzes the effectiveness of an online collaborative examina-tion process through a questionnaire. 7 D. Hall, 2010 It introduces some tools to assess teachers. (continued) 125 Toward Process Variability Management … (continued) No. Reference (author, year) Summary 8 Jacob et al., 2006 It reveals the importance of assessments in the learning process through different learning approaches. The Black Board Learning System (BBLS) is used as a comprehensive e-learning software platform in the context of continuous assessments. 9 Campbell, 2008 It proposes an application called the Electronic Performance Support System (EPSS) to enhance the performance of assess-ment tasks. 10 Kehily, 2011 It uses a web-based platform, DIT learning teaching and technol-ogy center, as a course management system for lecturers and as a computer-assisted learning tool for students. It is a case study in the Dublin Institute. 11 Attali and Burstein, 2006 It proposes a flexible modeling procedure which can be used to as a basis for expert judgment. 12 Venkatraman, 2007 It is a case study which develops a four-step student-centered approach to increase positive impacts on the learning process. It analyzes the strengths and weaknesses of assessments in IS courses through a survey. 13 Maheswari, 1998 It is an empirical study of technical problems in web-based sys-tems for assisting education. 14 Sybol, 2005 It investigates how use of an online assessment tool, the Com-puter-Assisted Personalized Approach (CAPA), helps achieve teacher and students learning goals. It is a case study of urban courses in Florida University. 15 Webb, 2010 It evaluates how digital technologies such as tablet PCs, wireless technology, and Web 2.0, can facilitate formative and collabora-tive assessment effectively. Appendix 1: Summary of IT Approaches to e-Assessment 16 e-learning age magazine, 2011 It is a case study of The Association of Chartered Certified Ac-countants (ACCA), which wants to deliver all accounting examina-tions electronically through an e-assessment program. 17 Miller, 2011 It is a case study of the positive role of aesthetics design on learner perceptions and task performance in an e-assessment environment. (continued) M. Heidari and O. Arnold M. Heidari and O. Arnold 126 (continued) No. Reference (author, year) Summary 18 Dascalu and Bodea, 2010 It proposes a qualitative analysis of an e-assessment and its role to increase knowledge creation and knowledge management. 19 Sainburg and Benton, 2010 It is a case study of the importance of formative assessment in the learning process in schools. 20 Dermo, 2009 It evaluates the possible risks in planning e-assessment through six identified dimensions in a case study. 21 Jordan and Mitchell, 2009 It explains some methods to facilitate answer and assessment of free-text questions in e-assessment. It examines its model (IAT) in the UK Open University, using information extraction tech-niques and NLP. 22 Ferrao, 2010 It shows that an e-assessment system can be a good alternative to encourage students and has positive effects on the learning process. 23 British Journal of educational studies, 2009 It summarizes different works which all encourage educational institutes to use e-assessment technologies to support the learn-ing process, with emphasis on feedback from e-assessments. 24 Hodgson and Y. C. Pang, 2012 It is a study of statistics students to evaluate the advantage of formative assessment. 25 Glenberg, 2010 It examines the impact of formative quizzes on knowledge con-struction. 26 Daly et al., 2010 It argues that existing assessment solutions focus on developing technical and infrastructure issues more than educational as-pects of assessment through different educational ases. 27 McCann, 2010 It is a case study of a US campus to explore how a new e-assessment system is implemented and to identify factors which affect how it is adopted. 28 Nicol, 2007 It suggests a set of principles for the effective design and evalua-tion of a formative assessment and feedback process through two different case studies. 29 Boyle, 2010 It is about forecasting models like the Bass model, used to evalu-ate how educational systems can adopt themselves to e-assessment methods. (continued) (continued) 127 Toward Process Variability Management … (continued) No. Appendix 1: Summary of IT Approaches to e-Assessment Reference (author, year) Summary 30 Boyle and Hutchison, 2009 It makes the case for the substantial effects of e-assessment on the assessing process and the technical difficulties involved in developing sophisticated assessment tasks. 31 McNeil et al., 2011 It looks at e-assessment from both sides: educational and tech-nical. It develops a model for analyzing the life cycle of institu-tional assessments. 32 Sangi and Malik, 2007 It reviews existing e-assessment models and practices and identi-fies the challenges facing developers in South Asia. Appendix 2: List of German universities reviewed 1. Freie Universität Berlin 2. Universität Bremen 3. Universität Duisburg-Essen 4. Justus-Liebig-Universität Gießen 5. Philipps-Universität Marburg 6. Johannes Gutenberg-Universität Mainz 7. Karlsruher Institut für Technologie 8. Rheinisch-Westfälische Technische Hochschule Aachen 9. Hochschule Koblenz 10. Leibniz Universität Hannover 11. Westfälische Wilhelms-Universität Münster 12. Universität Koblenz-Landau 13. Universität Regensburg 14. Universität Kassel 15. Technische Hochschule Ostwestfalen-Lippe 16. Technische Hochschule Wildau 17. Hochschule Fulda 18. Universität Trier 19. Universität zu Köln 20. Albert-Ludwigs-Universität Freiburg 21. Universität Düsseldorf 22. Hochschule Wismar 23. Universität Ulm 24. Eberhard Karls Universität Tübingen 25. Georg-August-Universität Göttingen 26. Rheinische Friedrich-Wilhelms-Universität Bonn Appendix 2: List of German universities reviewed 1. Freie Universität Berlin 2. Universität Bremen 3. Universität Duisburg-Essen 4. Justus-Liebig-Universität Gießen 5. Philipps-Universität Marburg 6. Johannes Gutenberg-Universität Mainz 7. Karlsruher Institut für Technologie 8. Rheinisch-Westfälische Technische Hochschule Aachen 9. Hochschule Koblenz 10. Leibniz Universität Hannover 11. Westfälische Wilhelms-Universität Münster 12. Universität Koblenz-Landau 13. Universität Regensburg 14. Universität Kassel 15. Technische Hochschule Ostwestfalen-Lippe 16. Technische Hochschule Wildau 17. Hochschule Fulda 18. Universität Trier 19. Universität zu Köln 20. Albert-Ludwigs-Universität Freiburg 21. Universität Düsseldorf 22. Hochschule Wismar 23. Universität Ulm 24. Eberhard Karls Universität Tübingen 25. Georg-August-Universität Göttingen 26. Rheinische Friedrich-Wilhelms-Universität Bonn Appendix 2: List of German universities reviewed 12. Universität Koblenz-Landau 15. Technische Hochschule Ostwestfalen-Lippe 16. Technische Hochschule Wildau 17. Hochschule Fulda 18. Universität Trier 20. Albert-Ludwigs-Universität Freiburg 21. Universität Düsseldorf 22. Hochschule Wismar 23. Universität Ulm 24. Eberhard Karls Universität Tübingen 25. Georg-August-Universität Göttingen 26. Rheinische Friedrich-Wilhelms-Universität Bonn M. Heidari and O. 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References Arnold Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), 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 license and indicate if changes were made. The images or other third party material in this chapter are included in the chapter’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the chapter’s Creative Commons license 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. 1 Background: Theory and Project The results presented in the article are developed in the context of funding measures of the German Ministry of Education and Research (Sustainable Land Manage- ment FKZ 033L004, Agricultural Systems of the Future - ZenKO FKZ 031B736, Urban–Rural Stadt-Land-plus ReGerecht FKZ 033L205) as well as a research and qualification project of TU Dresden. Selected parts of the article base on former work published as Zscheischler et al. (2012) as well as Härtel et al. (2015). Designing External Knowledge Communication in a Research Network The Case of Sustainable Land Management Thomas Köhler, Thomas Weith, Sabrina Herbst, and Nadin Gaasch Abstract Designing knowledge communication with external partners is a core activity of research networks. In science, such communication has been addressed only recently and is still considered as non-academic activity. Successful commu- nication with practitioners, that is knowledge transfer, is a crucial factor for effec- tive research. In the age of online communication, this requires special attention and skills, for example related to social media communication. Based on our own empirical results derived from interviews, the authors identify what factors affect the communication process and how the design of communication content may be influenced. To do so, successful examples of communication with external stakeholders are presented. For the theoretical basis, science communication, knowledge communi- cation, knowledge management, and knowledge transfer were selected and consol- idated. Although the findings stem from a research network specializing in sustain- able land management, they can be transferred to other academic collaborations. Our results indicate that external communication is effective when knowledge has been transferred between academics and practitioners. Keywords Research network · Knowledge management · Open science · Qualitative research · Land management Keywords Research network · Knowledge management · Open science · Qualitative research · Land management T. Köhler Faculty of Education/Institute for Vocational Education, TU Dresden, Dresden, Germany e-mail: thomas.koehler@tu-dresden.de T. Weith Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany e-mail: thomas.weith@zalf.de S. Herbst (B) Media Centre, TU Dresden, Dresden, Germany e-mail: sabrina.herbst@tu-dresden.de N. Gaasch TU Berlin, Office of the First Vice President for Research, Appointment Strategy, Knowledge & Technology Transfer, Berlin, Germany e-mail: nadin.gaasch@tu-berlin.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_9 131 T. Köhler Faculty of Education/Institute for Vocational Education, TU Dresden, Dresden, Germany e-mail: thomas.koehler@tu-dresden.de T. Weith Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany e-mail: thomas.weith@zalf.de S. Herbst (B) Media Centre, TU Dresden, Dresden, Germany e-mail: sabrina.herbst@tu-dresden.de 131 © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_9 © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_9 T. Köhler et al. 132 T. Köhler et al. 1https://www.umweltbundesamt.de/themen/boden-landwirtschaft/flaechensparen-boeden-landsc haften-erhalten#flachenverbrauch-in-deutschland-und-strategien-zum-flachensparen. 1.1 Sustainable Communication in the Sciences Attention-grabbing activi- ties must be taken rather frequently in efforts to change land use, because long- term changes do not have the direct “media marketing value” of disasters like the Fukushima tsunami in 2012. Against all communication efforts, discussion of topics such as soil conservation, land management, or the establishment of regional material cycles remains largely restricted to professional circles. Despite comprehensive knowledge about communication theories and models, and especially about the concept of a sustainability communication, it can be stated that communication processes are not always effectively implemented. Today we may observe a pronounced awareness of sustainability in general and environmental issues in particular; in Germany, 64% of the population consider environmental and climate protection as an important challenge (BMU and UBA 2019) and the German Parliament may state in its 2019 Environmental Report that a “demanding envi- ronmental policy with effective environmental laws and competent environmental administrations is widely accepted by the population” (Deutscher Bundestag 2019, p. 4). Still there is a discrepancy between this awareness and individual behavior in Germany. For example, correlations of affect and cognition with environmental behavior are not particularly strong, but still substantial (r_aff = 0.51 and r_cog = 0.48). This means that people who agree with the affective and cognitive statements generally act more environmentally conscious (BMU 2019, p. 68). In the view of the authors, this is due to the fact that the variety of existing means of communication are not used strategically and thus not exploited to their full potential (Kriese and Schulte 2009; Leipziger 2007). This is especially true in the “bulky” field of sustainability. The Sustainable Land Management (SLM) funding program of the German Federal Ministry of Education and Research (BMBF), described below, is used to critically investigate current practices in research and planning and to identify options for future activity. From 2008 to 2017, the BMBF initiated the SLM program tocreateaknowledgeanddecision-makingbasisforsustainableuseoflandresources. Already in designing the program the funder considered communication efforts as a central requirement for a successful implementation of this objective. This is only possible if all actors are willing to actually apply the new knowledge gained as a result of the program (Hinzen 2009). Targeted communication efforts played a central role in the management of inter- and transdisciplinary research networks of that funding scheme: It was a condition of information exchange, successful collaboration, and collaborative learning. 1.1 Sustainable Communication in the Sciences Information and communication processes and the related content form an impor- tant basis for defining the principles of sustainable spatial development, at least since the 1992 United Nations Conference on Environment and Development in Rio de Janeiro. While forms of information provision and strategic use of communication arefundamental,renewedmediatedinformationandcommunicativeapproacheshave become widespread since the 1990s (Lievrouw et al. 2000). These can be applied fruitfully in different academic disciplines such as education or engineering, or in spatial planning and development processes (Weith et al. 2020). Respective infor- mation and communication technologies are now seen as part of different gover- nance forms and are recommended for tackling various problems. For example, in 2003 the German Council for Sustainable Development initiated a “dialogue area” to strengthen understanding of processes of changing land use. Also the German federal government, whose goal was to reduce land use by settlement and infrastruc- ture by 2020 to 30 hectares per day, began using such new communication instru- ments and triggered activity of further groups (even though the original timeline has meanwhile been extended to 20301). While in a first step tools such as education material, brochures, cartoons, and computer games were produced to sensitize the relevant actors (Bock et al. 2009), in the almost two and a half decades toward the Sustainable Development Goals (SDGs) the focus has changed from information to knowledge management (Weith and Köhler 2019). Specifically knowledge manage- ment is addressed in three of the SDGs (4, 16 and 17) and at the same time linked to education and lifelong learning. Digitization, although relevant for many goals, is explicitly addressed in sub-goal 9c (Industry, Innovation, and Infrastructure): “Sig- nificantly improve access to information and communication technology and ensure universal and affordable access to the Internet in the least developed countries by 2020” (United Nations 2015). Non-governmental organizations (NGOs) such as the Nature Conservation Feder- ation of Germany (Naturschutzbund Deutschland NABU), the Federation for the Environment and Nature Conservation Germany (Bund für Umwelt und Naturschutz Designing External Knowledge Communication … 133 Deutschland BUND), or the international World Wide Fund For Nature WWF now develop targeted campaigns to raise awareness and promote more sustainable use of natural resources. Initiatives such as the International Year of Biodiversity 2010, the International Year of Forests 2011, or the International Year Plant Health 2020 share mainly attempts to do this on an (inter)national level. 1.1 Sustainable Communication in the Sciences Successful communication not only creates awareness of new challenges, but also acceptance for new options, and may initiate behavioral change. It thus contributes significantly to the successful transfer and implementation of scientific findings into practice, in this case regarding the SLM program. But how can communication processes be designed in a targeted and successful way? How can existing knowledge of strategic communication sciences be linked to communicative requirements? How 134 T. Köhler et al. T. Köhler et al. can means of communication be used strategically in such a complex field? What specific challenges have to be considered? And where are the limits of professional communication? This paper presents some initial answers to these questions which were developed by one of the scientific projects accompanying the BMBF-funded SLM network. To achieve better insight, the authors first present the core topics of the network and then explain the role of communication in this context. Subsequently, specific challenges and influencing factors are discussed in order to finally outline a strategic approach. 1.2 Theoretical and Conceptual Considerations for the Design of Communication Processes Human communication is a constant, every day, yet highly complex process that predominantly occurs unconsciously. It is social behavior at a time determined by many factors which accompany the message intendedly sent by a person. These factors include emotions, situational circumstances, and the knowledge and cognition abilities of the communication partners involved and its variety makes the communi- cation process complex. In designing effective communication, it is therefore essen- tial to be aware of the most important factors for the sender and the receiver; the latter include attention, the everyday ecology, and the personal and situational capacity (Kuckartz and Schack 2002). Moreover, communication is expected producing a social exchange of constructions, orientations, ideas, etc., about the world, exclu- sively created in social discourse and checked for their suitability (Frindte and Geschke 2019, p. 107). By social interaction those individual communications form entities of organizational character (Köhler 2014), which lead to an inter-institutional, i.e., external communication and exchange of knowledge, for example in networks. i.e., external communication and exchange of knowledge, for example in networks. Designing knowledge communication with external partners is a core activity of all research, especially of research networks. In science, such communication has been addressed only recently and is still considered as non-academic activity. In the age of online communication, this requires further special attention and skills (Köhler et al. 2019). With Web 2.0, communication technology shifts to a new social form in which content is produced jointly, incorporating all those interested in a certain topic even if they do not have scientific backgrounds. In a society defined by mass media, rivalry for the attention of various target groups is intense, so attracting attention to an issue may need to be the first step. To be perceived is a basic condition for successful communication. But this attention has consequences: Those who create attention must also create content. The term “everyday ecology” takes the real life of the recipient into account. Information may only have an impact if it has a meaning for the recipient, that is, if it can be linked to their real life. Strategic communications utilize this relationship to their advantage by considering the consequences, benefits, and options for the recipient, and presenting them consciously. Basically, a subject should not overwhelm a recipient or a target group. 1.2 Theoretical and Conceptual Considerations for the Design of Communication Processes If they do not have the capacity to process Designing External Knowledge Communication … 135 a topic intellectually or emotionally, they may reject or avoid the information. All of these factors need to be analyzed and adapted to specific audiences. A communication strategy must therefore be adapted to the needs of the intended recipient. Senders have more options, which are determined by variables like authenticity, professionalism, and the available financial resources (ibid.). The authenticity of a source is relevant to its visibility (Köhler 2016). Commu- nication functions less on the level of the actual content than in terms of the type and way it is communicated. Credibility, competence, and empathy are the central determinants here. Increasingly, the communicator needs to be professional in order to compete for the “scarce resource” that is the attention of each target group. This professionalism includes organizational and technical know-how, knowledge about methodology, that is, how to address specific target groups, and practical experience. This can be achieved with further training and the help of external communications consultants or agencies. Experience has shown that too often the only aspect of communication to be considered was the means, and that this was hardly ever strategically communi- cated (Kriese and Schulte 2009; Leipziger 2007). Recent findings focus on the need for human and financial resources as key to planning, designing, and imple- menting communication of innovations successfully (Pscheida et al. 2013). This means scheduling appropriate resources and setting goals for communication activ- ities right from the beginning, at the initial planning stage of a research project. Yet, before the actual communicative tasks and related objectives are formulated, the means are often already fixed, usually without any consideration of whether they meet the purpose. Researchers and communicators need to consider the following questions: Is the chosen means useful in view of the objective? Which channel should be designed to address the target audience? What must be communicated and what must not? What steps need to be taken and in what order to achieve the goal? 1.3 Knowledge Management in the Sustainable Land Management Program as a Challenge for External Communication The Sustainable Land Management program (SLM) had to meet a number of specific challenges toward developing an integrative communication approach. First, the organizational structure of the program was very complex (cf. Fig. 1). In more than two dozen collaborative projects and its 120 subprojects, scientists and practitioners from over 170 organizations were involved. The scientific disciplines involved in SLM brought very different perspectives, methods, and understandings to the overall SLM program. Unsurprisingly, science and practice often have different preferences, and thus communicative goals could be very heterogeneous. It is therefore obligatory to develop a comprehensive communication strategy that is accepted by the parties. 136 T. Köhler et al. Fig. 1 Schematic representation of the network representing the funding program “Sustainable Land Management” (cf. Härtel et al. 2015; translated by authors) Fig. 1 Schematic representation of the network representing the funding program “Sustainable Land Management” (cf. Härtel et al. 2015; translated by authors) Another challenge was to establish communication structures at the beginning of the program. In our case, a new organizational context with new communication channelsneededtobedefinedandthenperpetuatedinthenewSLMresearchnetwork. This was time consuming and required resources, as individual experience from completed projects could not have been reused one to one. But this is a general challenge in science as nowadays, research is often project-based and short-term, that is, the organizational structures are frequently terminated and re-established again. Although bilateral or multilateral research and practice networks remain, the topic-overarching management structure, which includes integrated communication, usually dissolves. This is one reason why it is difficult to implement and perpetuate the results, knowledge, and experiences obtained. In addition, when research starts, the results are not yet available and cannot be presented quickly. But media products to be communicated must be developed first, i.e., cannot be finalized only when advertising needs to begin. At this stage, researchers are still developing models, principles, strategies, and combinations of instruments, which are complex and may be highly abstract. Accordingly, the “new” knowledge is owned only by a small group of experts only but has not been transferred to the target audience yet. g p p y g y Further, SLM is an overarching term, so its actions are not clearly defined. 1.3 Knowledge Management in the Sustainable Land Management Program as a Challenge for External Communication Communications had to clarify what is meant by all three ambiguous and much- debated parts of the term, “sustainability,” “land,” and “management.” This means that all participants of the program had to deal with a high complexity and enormous variety of subjects. In fact SLM combined many issues which embody enormous communicative challenges. The collaborative projects, for example, were dedicated to sustainable water management, regional material and energy cycles, renewable resources, ecosystem services, sustainable urban development, and urban–rural link- ages. The actors, interests, and target groups were also numerous. Thus, from a scien- tific point of view SLM is a highly complex field, which is typical for many research networks, especially for those that link research with its application in practice. 137 Designing External Knowledge Communication … Yet, mass media requires a high level of simplification, which is contrary to the claims of many scientists. They often have difficulty handling active (non-technical) media and do not want their highly complex topics to be reduced to simple, striking stories. This resonates with a common concern about losing their reputation in the scientific community. Scientists feel that they eventually lose control and sovereignty of interpreting their results through publication in the mass media. Black-and- white arguments such as “renewable energy is positive” or “nuclear energy is bad” contradict not only the scientific, but also the communicative self-understanding of science. Due to that fear, scientists begin stepping into public in order to engage for their research, i.e., start acting as lobbyists. Respectively, they become aware to generate findings which may be associated with social consequences—what calls for a renewed consideration of research ethics (Dobrick et al. 2017) and can only be achieved with assessment based on normative values. Roose (2006) therefore speaks of an increasing politicization of science while Weingart (2001) points out the danger of its political exploitation. Altogether, an intelligent communication strategy is required that centers on targeted but achievable action, even though very limited financial resources are avail- able. Indeed communication for a typical research network like SLM cannot follow the rules of classic advertising because of the special funding conditions for such non-commercial topics. Yet, knowledgeof thediscussedkeydeterminants of commu- nication is essential. Therefore, in the following, the methodology for evaluating the most significant factors empirically is briefly introduced. 2.1 Data Collection Social science research objects and their stakeholders, as in the present case of the SLM funding program, are characterized through a complex and procedural context (Witzel 1985, p. 227). Following the research question, it was necessary to identify exemplary information transfer and implementation strategies within SLM funding program represented by the collaborative projects. The problem-centered interview was selected as the survey method to investigate the communication struc- tures of the individual projects (Kaiser et al. 2012). We were interested in both internal and external transfer and implementation strategies. Twelve typical stake- holders concerned were interviewed, in order to collect their experiences and estab- lish a systematic knowledge base. Following a qualitative approach, there was an equivalent consideration of both researchers and practitioners, covering all types of projects. In the course of the investigation, a research guide was developed as a basis for discussion, including aspects related to both content and communica- tion. All researchers of the collaborative projects contributed to the guide, which covered all subject areas of interest regarding transfer and implementation. For the 138 T. Köhler et al. present analysis, the authors focused on the concept of transfer, and especially on communication-related aspects. present analysis, the authors focused on the concept of transfer, and especially on communication-related aspects. 2.2 Evaluation Method To analyze the interviews, the authors applied the qualitative method of content analysis developed by Mayring (2010), which can be used for communication text data. To cope with the length of the text and to serve the purpose of the problem- centered interviews, the authors decided to complete a structured content analysis. Guided by theory-based main categories, we systematically worked through the transcribed material and passages assigned to the categories. By focusing on the transfer and implementation of knowledge in the project network and the resulting questions, main forms of practice can be concluded along the theory in a deductive way, forming main and sub-categories (see Härtel and Hoff- mann 2013). In order to address the criterion of openness of the research process, the authors created an inductive category using the summary content analysis. Overall, the focus was on structured content analysis, in particular on structuring the content: “to filter out certain topics, content, aspects of the material and to summarize it” (Mayring 2010, p. 98). The evaluation was conducted using the software MAXQDA. Specifically devel- oped for structured content analysis, the software allows for the definition and use of codes and sub-codes which reflect the categories in an orderly manner (Kuckartz 2010, p. 114). Methodologically controlled compression of the material was used to work out cross-case statements on regularities in the terms of the research question (ibid., p. 110ff.). 3 Results 3.1 Practitioners and Civil Society as Target Groups of External Knowledge Communication 3.1 Practitioners and Civil Society as Target Groups of External Knowledge Communication In the course of the interview analysis, we identified the target groups of external knowledge communication: These were practitioners in the economy, society, poli- tics, and administration. Addressed economists often represented the agricultural and forestry sector; the former included the food manufacturing, and the latter the wood processing industry. Other practitioners were at the interface between the public and private sectors such as health care (doctors, health insurance), mobility and trans- port (transport networks), the energy sector, and the private education and research sector. Administrative practitioners covered a variety of responsibilities (municipal and state level) and subject matter including conservation, transport infrastructure, Designing External Knowledge Communication … 139 and health. Civil society actors, in a broader sense, included voluntary clubs and NGOs, such as nature conservation associations, support groups, and interest groups such as farmers’ organizations. 3.2 Effects and Interactions of Factors Influencing External Knowledge Communication Various aspects of inter-institutional, i.e., external knowledge communication (which we find in networks as well, going beyond bilateral exchanges) can be derived from the interviews, in terms of both content and process. First, the means of commu- nication are selected with different intentions. Content includes project content and results usually developed for two reasons: to transfer knowledge from science to prac- tice, and to provide feedback from actors during the research process. At the process level, it was observed that region and theme often influenced whether communicated content was picked up. Further, different practitioners often have different expecta- tions onknowledgetransfer. Intheinterviewanalysis, authors identifiedthefollowing dimensions:efficiencyindevelopingsolutionsandeconomyoftheprovidedsolutions (project results, scientific knowledge); practicability of the developed solutions to concrete problems or at least not making such problems worse (positive and negative movement between actors and researched problems); and the meaning of personal attitudes (in form of expectations regarding the research topic). These dimensions influence perception, acceptance of, and willingness for further communication in networks. The success of external knowledge communication is also affected by legal and statutory conditions, such as funding and copyright, the available human and financial resources, and scientists’ capacity for such communication. 3.3 Selecting a Suitable Means of Communication The available financial and human resources often limited the choices regarding meansofcommunicationinthecollaborativeprojects.Forexample,limitedresources hindered knowledge transfer between science and practice: “And then it was evalu- ated how expensive it is (…) and then it was determined that well that would surely exceed the budget” (Interview 1.1). Legal and statutory conditions had a similar effect: Privacy policies impeded access to the target group and restricted the means of communication. External communication needed to be adapted to the concerns of target groups, seasonal or other variations. “[W]e have always started public relations work in May, June, and not before, because […] this is a seasonal theme, and you can’t kindle a fire which keeps [burning] year round” (Interview 1.3). The general attitude of stakeholders, key players, and the audience to the project problem and results (e.g., environmentally sustainable agriculture and renewable energies) could 140 T. Köhler et al. T. Köhler et al. T. Köhler et al. impede or even prevent access to the target group, regardless of the means of commu- nication used: “Of what avail is it, if the owner [of an agricultural land] tells you at the end (…): ‘No, I don’t like it because I have something against renewables anyway.’ (…) There are some, very flat opinions” (Interview 2.9). Obstacles related to the character of the actors have been found to be surmountable using appropriate means of communication. “And it takes a long time for these introverted groups. You can’t hope at this moment. I have just spoken with one of them: ‘Yes, yes, mhm, yes it’s good’. And he didn’t even say goodbye. And then you sit on the phone and think, ‘What just happened?’” (Interview 2.5). It was in particular difficult to access practitioners who demonstrated a lack of trust. Reasons may include negative experiences in the past: “[T]his is certainly the downside we have in East [Germany], that people had pretty big security needs from the political system of the GDR […] And today it is different and therefore people are sometimes overwhelmed and in certain places have been, I’d say, fooled, and that’s why they tend to be careful” (Interview 2.9). 3.3 Selecting a Suitable Means of Communication To reach as many people as possible and to give actors an insight into the status of the project, open-access publications were recommended: “You have to say that very clearly, this is a public [research] project, (…) so that we also see our obligation to make all our results publicly available. (…) [W]e want [the results] to actually be disseminated and accepted and we will then make the best possible information available to the public” (Interview 1.6). Direct face-to-face contact with the target audience could help too to identify representatives who could spread the message: “We went to the event and just talked with people. And at the agricultural fair you get very direct contact with the people. And, in fact, an assumption that I had proved to be correct. Namely, that a well-defined type of farmer […] is the first who we can connect with” (Interview 2.5). 3.4 Selecting and Preparing the Communications Content The content to be communicated has to meet the expectations of the target audience. In the course of the interviews, it came out that certain scientific project content, despite its practical relevance, was too complex and abstract for industry partners to see its relevance. Indeed, the wish was expressed that “the topic is somehow prepared either for the target group or scientifically […] But, do not tell the whole world. Such a claim can only go wrong” (Interview 2.8). For scientists, this means “that science must speak increasingly in the language of the local partner when initiating contacts. So, not the language of science. […] they need to translate for ‘the average Joe’” (Interview 2.9). Content prepared without a target group in mind, such as an exclusive scientific publication of project results, could “not reach all who work in practice” (Inter- view 1.6). For many actors, cost-effectiveness and efficiency are key criteria for the measure which is communicated. This may be a precondition for any dialogue with Designing External Knowledge Communication … 141 actors outside the scientific community. If project content or results are not consid- ered economically or efficiently, it will be very difficult to communicate them to stakeholders. Certain topics in the field of SLM are perceived as “unattractive” or cannot be communicated easily to the wider public per se, such as the issue of short rotation coppice or biodiversity. This is often due to general attitudes of actors in the field of environmental sustainability. If the impact of the project on a target group is expected to be negative, it is necessary to reflect on when and what content can be communicated: “The word ‘re-watering’, that’s what you say after a half-hour conversation. When people know that they will not be inundated. […] You cannot come in with that” (Interview 2.5). Nevertheless, direct involvement can have positive effects, especially in the case of problems that would otherwise enjoy little attention or which create little incentive to generate scientific knowledge. This is true of non-tradable areas in the health sector: “My concern is conducive for health projects […] if they are not able to be commercialized. I’m not talking about pharmaceutical development, where big profits attract attention but where it actually comes to service” (Interview 1.4). This partly precluded the need to prepare the project content, resulting in rather low commitment from scientists. 3.5 Addressing the Attitude of Stakeholders Market conditions and industry policy often influence the attitude of stakeholders to problems, such as climate change adaptation in the food sector. It required special treatment of the content—differences and similarities must have been disclosed and potentials illustrated (see Interview 1.1). Some actors doubt whether the problem exists: “Is the climate really changing? So, are they telling us the right thing? And if they are not telling us the right thing, can I still do what I’ve been doing so far? Yes, they are easy and economic decisions … decisions of habit: I have done it this way before, so why should I do it differently now? And you cannot answer that, you can just say, ‘From OUR perspective if you do it, this and this will happen, and that and that will not happen, and you will have this and that risk’” (Interview 1.5). Another important factor in acceptance of research results and policy implications is vividness: “once it has something presentable. It is precisely what you can show this clientele—the farmers—something that is useful” (Interview 2.5). This may be “something photogenic” (Interview 2.5), but may also include specific transfer measures such as “field days.” Events must specifically be relevant to the practi- tioners who attend, “but this being-on-site feeling and talking about it is what makes something. On that level I can facilitate the transfer easily when I create environments that are unusual” (Interview 2.5). The extent to which communication activities can be institutionalized successfully often depended on the available financial and human resources (Interviews 1.5 and 2.2). The degree of concerns of target audience about the problem addressed in project has partly affected the communication with actors in a positive and negative way. Existing networks could simplify the access to the actors: “facing the transport sector was […] in many respects beneficial that they knew each other and that communica- tion then took place without problems” and “it was always a very good basis to get in contact with these target groups” (Interview 1.2). The means of communication thus became less relevant: “if now by email or […] the better the connection is, the less important the communication means becomes and the more likely the success of communication” (Interview 1.2). Actors in a network make networking work: “if we have three, four who really want it in the county or district, that’s enough. 3.4 Selecting and Preparing the Communications Content “We collect the messages, see what is framed by this and then make a nice communication profile. What was the result? After two reminders came nothing at all. Only after a third, relatively nasty email […], then came the usual suspects […] the ones that had always made them anyways. And then we have with very full, very, very, very petty, very painstaking work somehow collected the messages. But now looking back, they were not really new messages. There were the usual messages” (Interview 2.8). When project outcomes have been prepared properly, focused on the target group by integrating a science journalist, the message reached people who can pass it on, such as journalists (Interview 1.5). Thecontentofexternalknowledgecommunicationmustbetargetedtoitsaudience to ensure successful knowledge transfer. In order for recommendations to be adopted in practice, it is important that “you very strongly address […] the participants and pick them up thematically where they are anchored, that is, when I talk to a farmer who might not necessarily be interested in the depth of the bird world, but who cares more about the agricultural effects” (Interview 1.6). Legal frameworks, such as copyright and intellectual property, can hinder knowl- edge transfer between science and practice, as certain technologies cannot be readily used by the practitioner: “There is a little problem: This is patented. One cannot simply be reconstructed, there are costs. But […] it works, if constructed properly” (Interview 2.4). Another hurdle for knowledge transfer was the profitability and efficiency expec- tations of practitioners. The cost of project results is even described as “the most inhibitory factor” (Interview 2.7) for successful knowledge transfer. This applies not only to economic practitioners but also local governmental ones, such as mayors. The latter could be encouraged to support and potentially pass the message on if they could identify potential for regional development: “because a small community in rural areas has to simply see what options are there to generate added value” (Interview 2.9). T. Köhler et al. 142 T. Köhler et al. 3.5 Addressing the Attitude of Stakeholders We don’t need much more” (Interview 2.5). If it was in the interest of certain groups of actors to process a problem, this could encourage their commitment to successful knowl- edge transfer: “the local players participated because they also partly had a personal interest” (Interview 2.3). At the same time, actors did not give their support when a scientific problem has been considered irrelevant in practice: “without personal involvement, you may encounter limited interest. Because many other things are more important in the view of the people” (Interview 1.4). “Due to the positive development for farmers on the world market and also here in Germany for agricul- tural products, they are not dependent on this new product […]. Everything is going well for him in the field. Why should he tackle these uncertainties?” (Interview 2.4). Designing External Knowledge Communication … 143 In general, different communication tools and channels, and how the content is revised, influence the potential for interacting with external knowledge communica- tion. The analysis shows, the more specific and relevant to practice the content was, the more likely it was to get feedback from the addressed actors, because “people ask only if they know that they can ask. […] You can only communicate that. Or I have a basket full of messages and can precisely position the target and target group” (Interview 2.8). For successful knowledge transfer to a wider public, acceptance and civil society participation was important: “you just involve people that are really objectively confronted with the background information. And people can simply decide what they, as it were, want. And then people can decide” (Interview 2.1). The potential for interaction was increased by extending the interfaces between the project researchers and the target audience, for example by including opinion leaders and key players on external project advisory boards. In general, different communication tools and channels, and how the content is revised, influence the potential for interacting with external knowledge communica- ti Th l i h th ifi d l t t ti th t t Online media could increase the potential for interaction and facilitate target group feedback: “On our website we also get questions, requests for information. And so the messages that are received they have recorded. And […] we hear, for example, that rental charges are a problem at the moment. 3.5 Addressing the Attitude of Stakeholders And we take a look: so, does this really have an economic impact on this calculation, cost calculation, or is this actually a side issue, perhaps with a psychological effect, but has no economic meaning? And we grab the topics and try to then integrate them within our considerations and in our presentations” (Interview 2.4). Mere marketing efforts in external communication were not conducive, but rather direct exchange and regular contact with practitioners and key players: “We just don’t do marketing. Instead we explain to them, we tell the tale. From our experience, from the first research results come conversations with practitioners. And then they share something” (Interview 2.5). 4.1 Background and Communicative Tasks Sustainability communication is about to become a topic in scholarly publications at the intersection to citizen science practices (Weith and Köhler 2019), specifically, the influence of digitization on the genesis of knowledge in the context of a sustainable, fair development as discussed. In the context of land management, there is an overall strong focus on specific branches like tourism (Tiago et al. 2020). In any case that process begins with the collection of information describing the initial communi- cation problem. As it is important to identify the significant data, this includes the consideration of relevant target groups and goals from the very beginning. Initially, only those facts relevant to communication problems are included. This process will identify communicative tasks that derive from the description of the initial situation and the necessity to modify or enhance communication actions. Its interpretation explores the problems to be solved, but does not yet offer solutions. In the specific case addressed here, the task is to identify how land users can most effectively acquire knowledge and develop a decision-making basis for SLM. 4 Conclusions In order to cope with the variety of factors in communication processes and to keep a clear head, theorists from marketing and communication studies recommend a systematic approach with a specified sequence of operations, especially with a clear concept of how social media communication is embedded (cf. Leipziger 2007; Hansen and Schmidt 2010; Kreutzer 2018). Respective steps usually include an anal- ysis of the current situation, the definition of the communicative tasks, the develop- ment of communication goals, the identification of target groups, the development of messages, and the designation of a strategy to implement the selected communi- cation approach. To some extent such an approach matches the generic idea about implementing communication technologies into an organizational configuration in an ideal manner as developed by Munkvold (2003), who divides into four sub-areas of implementing collaboration technologies: Organizational context; Implementation project; 144 T. Köhler et al. Technological context; Implementation phase. Technological context; Implementation phase. Authors did previously explain how such can be transferred easily to the context of information exchange, learning and education (Köhler et al. 2010). 4.4 Formulating Messages Messages are content to be communicated to representatives of a target audience. The larger the target group selected, the simpler the messages should be. Such simple messages should consist only of models for everyday use. Complicated theoretical concepts have no place in the mass media, which presents a major challenge for scientists. It should be clear which effect model shall be implemented and why—if there is a marketing communication or an educational communication addressed. In a complex topic such as SLM with very different target groups and representatives on different levels of influence, it is also advisable to limit the selection of subjects and to focus on key contents. Such contents should contain only the most relevant information and consequences for the selected audience and the respective recipient. If the aim is behavioral change, the messages should present options for action. 4.2 Definition of Communication Objectives After analyzing the current situation and defining the communicative tasks, commu- nication objectives should be formulated in a communication strategy. Objectives describe the desired end state of a process. Those are measurable and thus represent a kind of commitment. However, goals can change over the course of a project and then need to be adjusted. Goal setters must ask whether the objectives can be reached at all. As well certain practices like the sustainability digital communication relationships are especially effective (Tiago et al. 2020). Of course unrealistic goals may not serve as appro- priate, reliable basis for a successful communication concept. For example, including expensive measures within a modest budget will jeopardize the objectives. 145 Designing External Knowledge Communication … 4.3 Definition of Target Groups The more precisely a target group is defined, the better it can be addressed. This definition determines the communication tools and approach to be used. When iden- tifying target groups, it can help to be guided by demographic, lifestyle-related, or functional factors (Hansen and Schmidt 2010). In some cases, target audiences may be divided into subgroups with different patterns of media reception (Fischer 2012). This information is used to decide how to access the target group. It should be noted that people play different roles, at work or at home, with family or friends. A survey of collaborative projects in a workshop of the SLM network revealed that due to the wide range of actors relevant to the topic of land use, a variety of target groups exist. Some target groups could be clearly identified, such as stakeholders from management, agriculture, associations, academia, and research. Other target groups were described only very generally and imprecisely, such as “local people.” This is problematic, in terms of selecting both the communication tools and content to be communicated. 4.6 Activity Planning and Scheduling (“Concerted Activity”) Only when the strategy has been defined does the implementation begin. Now is the time to clarify what measures will be taken when, where, and how often? An appropriate mix of measures is in line with the strategy and aims to attain the objec- tives set. Not every interesting idea is to become an appropriate measure. The results are an action and a schedule that represent all the measures in chronological order, the so-called communication plan. This becomes a management tool, provides an overview of all parties, and allows accurate budgeting. However well thought out a plan may be, its implementation depends on many events which are not clearly predictable. There is the momentum of cross media communication as well as specific preferences of single stakeholders, especially in science, who are eventually not skilled for supporting social media communications (Pscheida et al. 2015; Albrecht et al. 2020). Resulting, delays can occur or journalists may suddenly no longer be interested in the subject because breaking stories take priority. Subsequently, deviations between plan and reality arise and one needs to respond promptly and derive new action consequences. 4.5 Definition of Communication Strategies The next step is to determine how to achieve the designated goals with the resources available. This means looking for the cheapest “lever” with which the target can be achieved most efficiently and effectively. The strategy combines all the resources for a specific parent maxim (Leipziger 2007). More recently, it is suggested that when analyzing sustainability communication a typology of three different communication modeswouldbeappropriate:communicationof,about,andforsustainability(Fischer 146 T. Köhler et al. T. Köhler et al. T. Köhler et al. et al. 2016). Obviously the SLM network applied all three dimensions simultaneously as these have been components of the developmental approach. Well-known and frequently used approaches include the piggyback, testimonial, and provocation strategies (see Hansen and Schmidt 2010; Leipziger 2007). The aim of the piggyback strategy (also known as issue management) is to attach the desired message to a consistent public relations action or to current media issues. The testimonial strategy generates attention through celebrity ambassadors, and the provocation strategy seeks to attract attention by breaking taboos or challenging competitors. So far, our network has favored a piggyback strategy. 4.7 Limitations of the Study The empirical data used for the study is limited to just one research network, in which stakeholders often share a single focus, embedded into a single domain. Even though the configuration of the network is overarching sectors and includes research as well as public administration as well as stakeholders from industry, its outreach is limited. Mainly representativity is hindered by the missing link to the individual citizen as well as the missing direct link to the media sector. Additionally, the role of project advisory boards has not been addressed in detail, that is, political influence may overlap with other effects described. In this case, the direct involvement of the target group also increased the potential for interaction in the communication process. It would also have been possible to assess external knowledge communication needs by questioning the target group directly. Finally, Designing External Knowledge Communication … 147 authorsdidnotexplicitlyaddressthepresumablyhighpotentialforinteractionoffered by the concept of citizen science. authorsdidnotexplicitlyaddressthepresumablyhighpotentialforinteractionoffered by the concept of citizen science. 4.8 Lessons Learned The study demonstrated that sustainable land management is a case which does have specific communicative affordances due to its complex, multi-actor character that brings together different perspectives. Still communication in and for research networks is not consequently addressed, literature both on practice and research is rather limited. Not only with the increasing meaningfulness of digital formats there is an increasing need for a well thought, analytically proven approach in designing communication of and within research networks strategically. 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In: Marsden, C., Tassiulas, L.: Proceedings of the 1st International Conference on Internet Science. References If material is not included in the chapter’s Creative Commons license 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. Researching Scientific Structures via Joint Authorships—The Case of Virtual 3D Modelling in the Humanities Sander Münster Abstract One of the topics addressed by e-science research is the measurement of academic knowledge production based on electronic data and its relevance in defining the academic landscape. The author employs e-science methods to research coop- erative authorships and scientific structures in a specific area of applied e-sciences: virtual 3D modelling in the humanities. Based on the findings, possibilities for cross- disciplinary and international cooperation are discussed. The number of international publications and average number of authors involved in each publication are lower than those found in other scientific fields. Moreover, research indicates that in the humanities, 3D modelling is relatively new and still emergent. Besides such general indications, several key players as people and institutions which interconnect groups of researchers could be identified on a structural level. Keywords Cooperative authorships · 3D modelling · Humanities 1This article reflects the state of my research in 2015. a more recent state was presented in: Münster, S.: Digital cultural heritage as scholarly field—topics, researchers and perspectives from a bibliometric point of view. J. Comput. Cult. Heritage 12, 22–49 (2019). S. Münster (B) Friedrich-Schiller-Universität, Jena, Germany e-mail: sander.muenster@uni-jena.de © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_10 1 Introduction1 A major issue related to the measurement of academic knowledge production is the distinction between disciplines and the mapping of scientific structures. The vast and heterogeneous variety of possible indicators result in a lack of standardisation and homogenisation. Joint standards to measure academic performance—as intended by the German Research Council (Wissenschaftsrat: Empfehlungen zu einem Kern- datensatz Forschung Berlin 2013)—are still being established. Our field of research is a specific area of applied e-sciences: virtual 3D modelling in the humanities. The research started with selecting a sample of publications in order to investigate current trends, scenarios and workflows in this field, and to quantify the scholarly field. The 1This article reflects the state of my research in 2015. a more recent state was presented in: Münster, S.: Digital cultural heritage as scholarly field—topics, researchers and perspectives from a bibliometric point of view. J. Comput. Cult. Heritage 12, 22–49 (2019). 151 151 152 S. Münster initial challenges were to (a) develop a suitable research instrument and to (b) perform an investigation. Due to the limitations of the included information and the magni- tude of the data sample, many potentially interesting research approaches—such as a quantification of current topics, standard references and citation networks—are not applicable. The author examines the scientific community involved in this specific area and their level of cross-disciplinary and international cooperation. Furthermore, we identify the key people and institutions, which interconnect groups of researchers. 1.1 Defining Disciplines To start, a definition: disciplines are characterised by common methods and theories and have similar “reference systems, disciplinary ways of thinking, quality criteria, publication habits and bodies” (Schophaus et al. 2003) as well as similar institutional- isation. Likewise, Knorr-Cetina thought that each discipline has its own “epistemic culture” in the sense of different “architectures of empirical approaches, specific constructions of the referent, particular ontologies of instruments, and different social machines” (Knorr-Cetina 1999). Although disciplines and their boundaries are results of social construction processes (Weingart 1987), a number of phenotypic fields can be identified (Knorr-Cetina 2002). One basic classification scheme is the distinction between humanities and sciences. In a more elaborate classification, the OECD distinguishes between six scientific fields containing about 40 disciplines (OECD 2002, 2007). Furthermore, especially library classification delivers highly sophisticated distinction categorisation schemes (Semenova and Stricker 2007). 2Originally published in: Münster, S., Köhler, T., Hoppe, S.: 3D modeling technologies as tools for the reconstruction and visualization of historic items in humanities. A literature-based survey. In: Traviglia, A. (ed.) Across Space and Time. Papers from the 41st Conference on Computer Applications and Quantitative Methods in Archaeology, Perth, 25–28 March 2013, pp. 430–441. Amsterdam University Press, Amsterdam (2015). 2 The Case of Virtual 3D Modelling in the Humanities 2.1 Field of Research 1.2 Defining Cross-Disciplinarity Cross-disciplinarity refers to a “confrontation of several disciplines with a [joint] topic or issue” (Schophaus et al. 2003). In regard to this, Schelsky speaks of a “partial scientific development unit at the empirical object” (Schelsky 1966). Cross- disciplinary collaboration is characterised by developing a multidisciplinary termi- nology and a joint methodology (Gibbons 1994; Münster et al. 2014). The degree of institutionalisation of cross-disciplinary fields ranges from temporary collaborations to the creation of new “hybrid” research disciplines (Klein 2000) such as the digital humanities, in which computing is applied to foster humanities research. 153 Researching Scientific Structures … 2.1 Field of Research 3D models and visualisation have always been an important medium for teaching, illustratingandresearchinghistorical facts anditems. Whilehistorical picturesources usually provide elusive and fragmentary impressions, digital three-dimensional models of historical objects and their depictions offer the chance to convey holistic and easily accessible impressions. Until 2000, virtual 3D modelling technologies and computer-generated images of cultural heritage objects were used merely as a digital substitute of physical models (Novitski 1998). Nowadays, 3D models are widely used to present historic items and structures to the public (Greengrass and Hughes 2008) as well as in research (Favro 2004) and education (El Darwich 2005). In addition, 3D technologies can obviously serve cultural heritage management and conservation tasks, and even their advertising. An important distinction needs to be drawn between still extant, no longer extant, and never realised objects. 3D modelling technologies make it possible not only to digitise historic objects which are still extant, but even to virtually reconstruct objects that are no longer extant physically and only known from descriptions.2 Research design This investigation of scientific structures related to the usage of 3D modelling techniques for both extant and no longer extant types of historical objects is based on an analysis of published project reports and presentations. An upstream problem was the identification of relevant publications. Unlike, for example, in medicine, there are no comprehensive publication databases extant for cultural studies and humanities. Prior to creating the database, three experts—chairholders in the fields of archaeology, art history and geomatics—were queried to identify relevant journals and conferences. This yielded the following findings: • On the one hand, in the field of cultural and history studies, no multidisciplinary, periodically held international conferences are known that deal specifically with 3D modelling. However, there are a number of local or non-periodic conferences and workshops that deal with specific questions or topics. • On the other hand, there are four major conferences on the topic in the fields of archaeology and cultural heritage: The International Workshop for 3D Virtual Reconstruction and Visualization of Complex Architectures (3DARCH); the Computer Applications and Quantitative Methods in Archaeology Confer- ence (CAA); the International Symposium on Virtual Reality, Archaeology and Cultural Heritage (VAST); and the Visualisation in Archaeology workshop (VIA). 154 S. Münster S. Münster • The Journal for Digital Heritage represents an overarching publication organ for digital content on all humanities. • The Journal for Digital Heritage represents an overarching publication organ for digital content on all humanities. 2.2 Data Sample These findings formed the basis for collecting the data sample presented in Table 1. As a scope for conference proceedings, entire volumes were included and relevant journal articles were identified via keyword search. A sample of 452 journal articles and conference proceedings was included during the first stage of the analysis. The articles selected were written in English and, for practical reasons, had to be available electronically. Especially the latter selection criterion meant that no publications of the VIA conference and only single volumes of CAA and VAST could be included. In addition to these conference papers, relevant articles from the Journal for Digital Heritage and other periodicals were included using a keyword-based search. One major obstacle to building a research database was the fact that most of the included conferences and journals were not listed in citation repositories or in publi- cation databases such as ISI Web of Science, Scopus, or Google Scholar in 2012 when the database was compiled. This made it necessary to retrieve metadata by crawling data from each single contribution. For each article, the following information was obtained: • names and affiliations of contributing authors • names and addresses of affiliated institutions • source data (conference and publication name, year, type of document) • title of publication. • names and affiliations of contributing authors mes and addresses of affiliated institutions Moreover, conference contributions were classified based on their content. As pointed out in (Münster et al. 2013), one-third (37%) of these articles deal with neither 3D modelling nor historical objects. Nearly the same number of articles report about single projects. This means that they describe workflows for rebuilding certain historicitemsas3Dmodels.Anothergroupofcontributionsdealswithcertainaspects Table 1 Sample (n = 452) Publication Volume No. 3DArch Conf. 2005–2009 112 CAA Conf. 2007, 2009 130 VAST Conf. 2003–2007, 2010 105 J. Digital Heritage From 2000a 52 Various project reports and publications dealing with no longer extant objects 1999–2011 79 aImportant articles were selected via a keyword-based search Table 1 Sample (n = 452) Publication Volume No. 3DArch Conf. 2005–2009 112 CAA Conf. 2007, 2009 130 VAST Conf. 2003–2007, 2010 105 J. 2.2 Data Sample Digital Heritage From 2000a 52 Various project reports and publications dealing with no longer extant objects 1999–2011 79 aImportant articles were selected via a keyword-based search Researching Scientific Structures … 155 of 3D modelling for historical purposes, such as presentation and modelling strate- gies, data acquisition methods, or handling and classification of 3D data. Focussing on project reports only, a further investigation takes into consideration whether an original object is still extant. To quantify, more than 2/3 of project reports deal with extant objects or their fragments, while another 1/3 focus on non-extant objects. While digitisation of extant objects is mostly based on acquired data and uses widely automated algorithms, reconstruction of no longer extant or never realised objects usually involves manual model creation using CAD or VR software tools. For each type of object, the model creation processes are very different. For this reason, one aim here is to investigate whether both topics might attract different contributors and build slightly different sub-communities. 2.3 Scientific Approach: Analysis of Scientific Authorship Relations One approach is to calculate key numbers in various ways, such as an average count of authors per publication or a rate of publications authored by single individuals. As one example, the cutting-edge analyses of De Solla Price (1963) in the early 1960s employed key numbers to investigate the transformation processes of scien- tificproduction.Asecondapproachistoclusterauthors,forexamplebynationality,to study preferences for international joint authorships (Glänzel 2001). Both research approaches are employed in our study to investigate cooperative authorship. A third approach uses author data to measure disciplinary characteristics such as disci- plinary productivity, used in this article by employing the Lotka Coefficient (Egghe 2009; Lotka 1926). Furthermore, Schubert and Glänzel studied preference patterns of cross-national authorships (Schubert and Glänzel 2006) and stated that there was a “major influence [of] historical, cultural and linguistic proximities” (p. 426). Such an approach is not applicable to this investigation due to the small number of samples. Several investigational approaches focus on topics described in researched arti- cles. As one example, a topic graph structure classifies current research topics in a certain scientific area (Glenisson et al. 2005; Schoepflin and Glänzel 2001). More- over, approaches like epidemiology of ideas (Goffman and Newill 1964) or scien- tograms focus on predicting emergent trends based on an evolution of the importance of topics. Over the last few years, citations have become a very popular object of research into scientific performance. This includes measuring individual impact factors via indexes, most popularly the h-index invented by Hirsch (2005), or the total impact of certain journals via the Garfield index (Vinkler 2012). Furthermore, co-citation analysis provides clues about the evolution of a scientific area over time and its standard works (Bellis 2009). Neither citations nor topics are covered by the available data, so these objects of study are not included in our investigation. Scientific communities as a “group of scientists […] agreed on accepting one paradigm” (Jacobs 2006) are another research object of bibliometrics. One partic- ular approach, the study of co-authorship networks, focusses on detecting structures of scientific cooperation employing graph analysis methods (Vargas-Quesada and Moya-Anegón 2007). Although such research approaches are limited to a structure representation (Hardeman 2013) and include a number of potential sources of error and limitations, computer-based analysis and evaluation of co-authorships fosters several new insights related to scientific cooperation (De Stefano et al. 2011; Lu and Feng 2009). 2.3 Scientific Approach: Analysis of Scientific Authorship Relations From a disciplinary point of view, an investigation of “laws governing the production, flow and application of information in science” (Vinkler 1996) by a numerical anal- ysis of publications is part of bibliometrics. This discipline contains a wide spectre of measures and methods to investigate scientific structures and output. Based on former categorisation and formalisation attempts (Vinkler 2001; Egghe 2009; Gauf- friau et al. 2007), several bibliometric approaches are distinguishable, according to their objects of study (Table 2). Not all research approaches are applicable to the described data sample. The limiting factors are the low number of samples and the types of information collected. The metadata of publications are a major object of study. Related approaches include classification of various attributes, like publication type, journal, disciplinary Table 2 Brief overview of bibliometric approaches Object of study Approach (example) Publications Classification (i.e. De Solla Price 1963) Scaling laws (i.e. Bettencourt et al. 2008) Authors Key numbers (i.e. De Solla Price 1963) Clustering of authors (i.e. Glänzel 2001) Disciplinary productivity (i.e. Lotka 1926) Topics Topic graphs (i.e. Schoepflin and Glänzel 2001) Scientograms (i.e. Vargas-Quesada and Moya-Anegón 2007) Epidemiology of ideas (i.e. Garfield 1980) Citations Impact (i.e. Hirsch 2005; Smith 2012) Co-citation analysis (i.e. Bellis 2009) Communities Structures (i.e. Newman 2001a; Glänzel and de Lange 2002) Protagonists (i.e. Otte and Rousseau 2002; Newman and Girvan 2004; Kretschmer and Aguillo 2004) Table 2 Brief overview of bibliometric approaches Object of study Approach (example) Publications Classification (i.e. De Solla Price 1963) Scaling laws (i.e. Bettencourt et al. 2008) Authors Key numbers (i.e. De Solla Price 1963) Clustering of authors (i.e. Glänzel 2001) Disciplinary productivity (i.e. Lotka 1926) Topics Topic graphs (i.e. Schoepflin and Glänzel 2001) Scientograms (i.e. Vargas-Quesada and Moya-Anegón 2007) Epidemiology of ideas (i.e. Garfield 1980) Citations Impact (i.e. Hirsch 2005; Smith 2012) Co-citation analysis (i.e. Bellis 2009) Communities Structures (i.e. Newman 2001a; Glänzel and de Lange 2002) Protagonists (i.e. Otte and Rousseau 2002; Newman and Girvan 2004; Kretschmer and Aguillo 2004) 156 S. Münster S. Münster backgrounds or dates. These classes allow for comparison and evaluation of distri- bution functions, as well as monitoring of trends and prediction of emergent fields of research based on time rows (Bettencourt et al. 2008). While the latter approach in particular relies on plenty of lossless data, it does not seem applicable to our research. Another important object of study is related to authors of publications. 2.3 Scientific Approach: Analysis of Scientific Authorship Relations For example, a comprehensive investigation of publications in the fields of medicine, science and computing (Newman 2001a, b, c) reveals that the “small-world phenomenon” (Milgram 1967) (i.e. any two authors are connected in a chain of on average five to six parties) could be identified for these scientific commu- nities. A number of smaller studies also deal with co-authorship within individual disciplines (Aleixandre-Benavent et al. 2012), or for individual countries or regions 157 Researching Scientific Structures … (Abramo et al. 2010; Morelli 1997; Gaillard 1992). Besides describing scientific networks, another issue is to identify important players as protagonists of scientific communities (Kretschmer and Aguillo 2004; Hou et al. 2007). This latter aspect is of interest regarding the community dealing with 3D modelling in the humanities. 3.1 Indication 1: Cooperative Authorship One of the essential characteristics of modern research is the large number of authors involved in a single publication. In 1962, De Solla Price pointed out that in 1900, more than 80% of publications had a single author (De Solla Price 1963). In 2000, a study of scientific articles listed in the Science Citation Index (Glänzel et al. 2004) revealed an average contribution of 4.2 authors per article, wherein the proportion of articles written by individual authors was only 11%. Within our research sample, an average of 3.4 authors was involved in each publication. From the perspective of cross-disciplinary and international cooperation, the disciplinary affiliation of the author collectives seems especially interesting. As shown in Fig. 1, the majority of the studied publications were written by authors or author collectives belonging to the same area of research and only a limited number of publications were cross- disciplinary. The author’s disciplinary affiliation was identified from the correspon- dence addresses noted in publications. However, such data only provides informa- tion about the disciplinary focus of an employing institution and not on the author himself. To overcome this potential flaw, an alternative method which takes personal disciplinary backgrounds into account—self-sorting by authors via questionnaire— is intended for the next stage of the research, but not yet realised for this set of data. In this data, for 21% of authors the respective disciplines at affiliated institutions could not be identified or distinguished precisely. Fig. 1 Number of participating disciplines Fig. 1 Number of participating disciplines 158 S. Münster S. Münster With regard to the distinction between types of modelling, the number of cross- disciplinary publications describing the digitisation of extant objects is significantly higher than for reconstruction projects. With regard to the distinction between types of modelling, the number of cross- disciplinary publications describing the digitisation of extant objects is significantly higher than for reconstruction projects. Another interesting aspect is the disciplinary background of the authors’ employing institutions depending on the type of object modelled. In the table shown in Fig. 2, cross-disciplinary collaborations were included proportionately and each cross-disciplinary publication has been counted with 1, while for publications including two disciplines, each of them has been counted with 0.5. 3.1 Indication 1: Cooperative Authorship It seems remark- able that a large number of articles describing reconstruction projects of unrealised or non-extant objects were written by authors affiliated with institutions in the field of architecture, while publications for digitisation projects were often written by authors with a background in engineering and geosciences. A plausible explanation is provided by the competence profiles of these departments. For example, automated data acquisition via remote sensing techniques is a focus of the geosciences, while architectural studies incorporate extensive know-how about both architectural history and CAD modelling. Figure 3 shows cross-disciplinary authorships in the researched publications. Each node stands for a single publication and each edge represents the disciplinary assignment of the participating authors. The graph shows that authors from institutions in the digital humanities are especially frequently involved in cross- disciplinary cooperative authorships. Preferred partners are authors from institu- tions in the field of computer science, while joint publication with authors from the humanities tends to occur rarely. As shown in Fig. 4, a significant number of publications were written by authors whose employing institutions are in the same nation. Compared to findings related to other scientific domains, which estimate an overall rate of international publications at 35% (Acosta et al. 2010), the number of international publications in the sample is Fig. 2 Disciplinary affiliation of publication authors Fig. 2 Disciplinary affiliation of publication authors 159 Researching Scientific Structures … Fig. 3 Cross-disciplinary authorship Fig. 3 Cross-disciplinary authorship significantlylower.Analogoustothefindingsrelatedtointerdisciplinarycooperation, the number of international publications describing digitisation projects is above average, while only 8% of the publications describing reconstruction projects were written by international teams. significantlylower.Analogoustothefindingsrelatedtointerdisciplinarycooperation, the number of international publications describing digitisation projects is above average, while only 8% of the publications describing reconstruction projects were written by international teams. The findings of a below average rate of international and cross-disciplinary author- ships in combination with a large variety of involved disciplines indicate the fuzzy 160 S. Münster S. Münster demarcation of the field. This assumption is supported by the finding that only 30% of authorsareemployedininstitutionswhichprioritisehumanitiesordigitalhumanities. 3Originally published in: Münster, S., Köhler, T., Hoppe, S.: 3D modeling technologies as tools for the reconstruction and visualization of historic items in humanities. a literature-based survey. In: Traviglia, A. (ed.) Across Space and Time. Papers from the 41st Conference on Computer Applications and Quantitative Methods in Archaeology, Perth, 25–28 March 2013, 430–441. Amsterdam University Press, Amsterdam (2015). 3.2 Indication 2: Lotka Coefficient One of the most common indicators is the number of publications per author. Relat- edly, Lotka (1926) developed a distribution function for the publication frequency of individual authors which covers a wide range of disciplines and their publications. The distribution curve shows that a large number of authors with only one publication are contrasted by a very small number of authors with multiple publications. y y p p Related to the investigated publication data, a classical Lotka distribution already revealed an extensive congruence (Fig. 5). This follows the formula Y = C/Xn Fig. 4 Cross-national publications Fig. 5 Frequency distribution curves for publications Y = C/Xn Fig. 4 Cross-national publications Y = C/Xn Fig. 4 Cross-national publications Y = C/Xn Fig. 4 Cross-national publications Fig. 5 Frequency distribution curves for publications Fig. 5 Frequency distribution curves for publications Fig. 5 Frequency distribution curves for publications Researching Scientific Structures … 161 where C is the total number of authors included (n = 1120) and X indicates the number of publications of each cohort (authors with 1, 2 or more publications). The exponent n is a constant. From his studies, Lotka postulated an average exponent of n = 2, which varies significantly depending on the investigated discipline (Egghe and Rousseau1990; Egghe 2000), while recent studies assumed an average value of 2.3 to 2.5 (Chung and Kolbe 1992; Pulgarín 2012). In the empirical findings, the distribution function of the investigated publications coincides with n = 2.8 … 2.9. Any further interpretation of these values must be estimated in the context of the relatively small and potentially flawed sample. Compared to the lower mean values of the exponent mostly cited in literature, the above-average exponent found here indicates low publication productivity with a disproportionate number of authors who are only occasionally involved. There are several studies on scientific communities and inherent social interaction, i.e. Stützer, C.: Knowledge transfer in web-based collaborative learning systems (PhD-Thesis), Dresden 2013. 3.3 Indication 3: Key Players3 Another hypothesis is that collaborative publications establish knowledge commu- nication between authors. The basic idea is that, in most cases, common author- ship would be related to a personal connection and interaction between all included authors. Depending on sociological role theory, such a connection between people— regardless of its strength (Granovetter 1973)—could foster sharing and exchange of ideas and information. Regarding structure, connections between people across disci- plinary and national borders play a key role in disseminating information in social communities.4 Nevertheless, information transfer in the context of joint publications is just assumed and intensity or even information transfer between authors cannot be reconstructed based on empirical data. The sample publications were authored by 1500 individuals who were connected by over 3000 links (Fig. 6). Most of the publications were written by authors belonging to institutions of the same discipline and nationality. All the individuals at each institution were incorporated into Fig. 7. Key players were highlighted in the graphs: these were the people and institutions that were in the top ten in the cate- gories of (a) number of connections to other authors (degree), (b) the relevance as a connecting factor between author groups (betweenness centrality) or (c) the number of publications. (Wasserman and Faust 1994) But there are also several interna- tional or cross-disciplinary networks visible whose members have written more than just one joint publication. It was possible to identify some important key players 162 S. Münster Fig. 6 Author—co-author relations—individuals (key players highlighted) Fig. 6 Author—co-author relations—individuals (key players highlighted) who connect groups of researchers. From an institutional perspective, the coopera- tion between the University of Leuven and the technical universities of Vienna and Zürich has produced a particularly large number of cross-disciplinary and interna- tional publications. A further, if smaller, cluster includes mostly French and Italian institutions, but also encompasses authors from Japan and Germany. Generally, there is a high level of networking and number of publications from people and institutions workingondata-basedvisualisation.Finally,thekeyplayersaremostconnected,both internationally and cross-disciplinarily. To validate this, the results were discussed with experts. Generally, these key players are not only active publishers, but often Researching Scientific Structures … 163 Fig. 7 Author—co-author relations—institutions (key institutions highlighted) 163 Researching Scientific Structures … Fig. 7 Author—co-author relations—institutions (key institutions highlighted) also play key roles in the community in other ways, too, whether as members of scientific committees, conference chairs, and initiators or leaders of projects. 3.3 Indication 3: Key Players3 We also investigated the connection between theory and practice in the field of 3D modelling in the humanities. We compared, for each institution, the number of participating digitisation and reconstruction projects described in articles and the number of publications. The results show that institutions with a high publication output are usually also involved in an exceptionally large number of projects. A significant difference between ranks of publication activity and project participation was identified in just a few institutions, such as the TU Wien or the Istituto di Scienza e Tecnologie dell’Informazione (Table 3). This leads to the assumption that a scientific community is primarily a community of practice (Lave and Wenger 1991), with a close link between practical project work and theory, while specific think tanks as theory building institutions are currently not visible for this field of research. 164 S. Münster Table 3 Ranks of project and publication participation by institution Table 3 Ranks of project and publication participation by institution Institution Projects (Rank) Publications (Rank) Politecnico di Milano 10 (1) 14 (1) ETH Zürich 8 (2) 12 (4) National Research Council Canada 7 (3) 11 (5) University of Florence 7 (4) 12 (3) Istituto di Scienza e Tecnologie dell’Informazione 6 (5) 13 (2) Centre for Scientific and Technological Research 6 (6) 7 (7) University of Virginia 5 (7) 6 (14) Tokyo Denki University 4 (8) 6 (12) CNR Institute of Technology Applied to Cult. Heritage 4 (9) 6 (15) TU Wien 4 (10) 11 (6) 4 Conclusion With regard to the aim of identifying scientific structures via co-authorships, it was found that the field of 3D modelling in the humanities at an international level is widely dominated by research interests and approaches from archaeology and cultural heritage research. However, the authors involved come from a large variety of disciplinary backgrounds. Another finding is that the number of publications written by international teams and average number of authors involved in each publication are lower than in other scientific fields. It seems remarkable that publications about digitisation projects which deal with extant objects are significantly more often written by cross- disciplinary and international teams than publications describing a reconstruction of no longer extant or never realised objects. This may be caused by the slightly different disciplinary constitutions and uses of publications in digitisation and reconstruction projects. Taking the relatively small and potentially flawed sample into account, further investigations and additional data are required for a valid evaluation. 3D modelling in the humanities is relatively new and emergent field of research. This is indicated by the above-average coefficient for a Lotka distribution describing the frequency of publications per author. Nevertheless, contributors from various disciplines were involved in the researched publications, which may indicate a currently blurry demarcation of the scientific field. Even if these findings are endorsed by other studies (Albrecht 2013), both indications provide only a hint that the field is becoming established. Whataretheimplicationsforresearchone-sciences?Thisarticledescribedseveral strategies for investigating scientific structures in the field of 3D modelling in the humanities, based on electronic data and using software tools for graph analysis and QDA software for qualitative content analysis. Information was retrieved about struc- tures and publication practices in the field. It was found that the investigated publi- cations were mostly about archaeology and cultural heritage, while other research Researching Scientific Structures … 165 interestslikeaspectsofculturalorarthistoryweretreatedmostlyvianationalcommu- nities and published in offline media. 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Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), 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 license and indicate if changes were made. The images or other third party material in this chapter are included in the chapter’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the chapter’s Creative Commons license 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. A. M. J. Skulimowski (B) Department of Automatic Control and Robotics, AGH University of Science and Technology, Kraków 30-059, Poland e-mail: ams@agh.edu.pl International Centre for Decision Sciences and Forecasting, Progress & Business Foundation, Kraków 30-048, Poland A. M. J. Skulimowski (B) Department of Automatic Control and Robotics, AGH University of Science and Technology, Kraków 30-059, Poland e-mail: ams@agh.edu.pl International Centre for Decision Sciences and Forecasting, Progress & Business Foundation, Kraków 30-048, Poland © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_11 16 A. M. J. Skulimowski (B) Department of Automatic Control and Robotics, AGH University of Science and Technology, Kraków 30-059, Poland e-mail: ams@agh.edu.pl International Centre for Decision Sciences and Forecasting, Progress & Business Foundation, Kraków 30-048, Poland 1 Introduction Based on the results of the foresight project, SCETIST (Skulimowski 2013), and a Delphi study on future development trends of knowledge platforms performed within the recent Horizon 2020 project MOVING (Köhler and Skulimowski 2019), this paper aims to provide an insight into the future of e-science. The focus is on three specific aspects of this perspective: the emergence of new research tools related to global expert systems (GESs), researcher communication with computers through brain–computer interfaces (BCIs), and the role of researchers in shaping holistic knowledge development systems that will emerge over the next few decades. The aims of the aforementioned foresight projects include making recommenda- tions to R&D and ICT policymakers, while pointing out prospective ICT develop- ment and research trends relevant to individual researchers and research teams. The time horizon of foresight was 2025, with an impact analysis of selected anticipated technological breakthroughs up to 2030. Some of the project results related to e- science are presented in Skulimowski (2016b); the results on the emergence of GESs are published in Skulimowski (2013), while the relation to artificial autonomous decision systems (AADSs) is discussed in Skulimowski (2014b, 2016b). A diverse spectrum of methods was applied to elaborate on technological and social scenarios and forecasts. Those used predominantly included bibliometric anal- yses, extrapolation Delphi surveys (Skulimowski 2019), group building of a hierar- chical state-space model of information society evolution (Skulimowski et al. 2013) and anticipatory networks (Skulimowski 2014a). For the purposes of e-science foresight, the computer-assisted multi-round expert Delphi questionnaire retrieval (cf. e.g. Skulimowski et al. 2013, 2019), combined with expert panel meetings and outcomes of bibliometric and patentometric research proved most useful within the overall project. The analysis of expert responses was combined with an information retrieval strategy from the open Web and from major bibliographic databases. Different procedures were elaborated for fusing quantitative and qualitative knowledge and providing recommendations to the ICT industry and policymakers. A trust and competence factor system was used to compensate for the impact of diverse expert biases and competences. Each survey respondent was assigned a vector with trustworthiness coefficients of this expert in the particular subject areas of the Delphi exercise. A weighted combination of individual responses with coordinates of the trustworthiness vector was applied, wherever appropriate, to take account of the difference in respondents’ credibility. Section 2 outlines certain basic ICT/AI development trends that may influence future research tools. Visions of a Future Research Workplace Arising from Recent Foresight Exercises Andrzej M. J. Skulimowski Abstract The results of recent foresight projects reveal the impact of future ICT tools on the practice of scientific research. This paper presents several aspects of the process of building scenarios and trends of selected advanced ICT technologies. We point out the implications of emerging global expert systems (GESs) and AI- based learning platforms (AILPs). GESs will be capable of using and processing global knowledge from all available sources, such as databases, repositories, video streams, interactions with other researchers and knowledge processing units. In many scientific disciplines, the high volume, density and increasing level of interconnection of data have already exhausted the capacities of any individual researcher. Three trends may dominate the development of scientific methodology. Collective research is one possible coping strategy: Group intellectual capacity makes it possible to tackle complex problems. Recent data flow forecasts indicate that even in the few areas, which still resist ICT domination, research based on data gathered in non-ICT supported collections will soon reach its performance limits due to the ever-growing amountofknowledgetobeacquired,verified,exchangedandcommunicatedbetween researchers. Growing automation of research is the second option: Automated expert systems will be capable of selecting and processing knowledge to the level of a professionally edited scientific paper, with only minor human involvement. The third trend is intensive development and deployment of brain–computer interfaces (BCIs) toquicklyaccessandprocessdata.Specifically,GESsandAILPscanbeusedtogether with BCIs. The above approaches may eventually merge, forming a few AI-related technological scenarios, as discussed to conclude the paper. Keywords ICT foresight · E-science · Technological development trends · Global expert systems · Brain–computer interfaces · Artificial intelligence (AI) scenarios © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_11 169 © The Author(s) 2021 C. Koschtial et al. (eds.), e-Science, Progress in IS, https://doi.org/10.1007/978-3-030-66262-2_11 A. M. J. Skulimowski A. M. J. Skulimowski 170 1 Introduction The roles played by AI-based learning platforms (AILPs) and GESs will gain importance when fusing ever-growing information flows, culmi- nating in deeper automatic data refinery before presenting them to researchers. GESs will be capable of processing “big data” to “big knowledge”. New knowledge fusion methods will be developed, such as hybrid and scenario-based anticipatory networks (Skulimowski 2014a), e-science foresight (Skulimowski 2016b), including combinations of forecasts (Elliott and Timmermann 2004) or recommendations 171 Visions of a Future Research Workplace … (Skulimowski 2017a). Finally, Sect. 3 presents the results of the Delphi surveys on information systems prospects, which were conducted for SCETIST and MOVING projects (Skulimowski et al. 2013; Köhler and Skulimowski 2019). We show that different technological trends will have a synergetic impact on e-science. Artificial intelligence-based (AI) tools and approaches will play a major role. New tools will make the research conducted by humans more efficient by reaching predefined goals faster and more accurately. Recommendations that may be useful to R&D policymakers, artificial intelligence researchers, and innovative companies will be presented in Sect. 4. We will also explore the relationship between BCIs and the future methodology of storing and processing scientific information in GESs and AILPs. Moreover, Sect. 4 discusses the opportunities, challenges, and threats posed by the development of AI tools and how BCIs could be used to quickly overcome the problem of accessing big data streams and knowledge repositories. 1https://www.statista.com/statistics/267202/global-data-volume-of-consumer-ip-traffic/ [access Jan 10, 2020]. 2An estimate after http://en.wikipedia.org/wiki/Exabyte [access Jan 10, 2020]. 3https://www.millforbusiness.com/how-many-websites-are-there/ [access Jan 10, 2020]. 4https://www.verisign.com/en_US/domain-names/dnib/index.xhtml [access Jan 10, 2020]. 2 Integration of Future Research Tools in Global Expert Systems GESs were originally intended as a generalization of large-scale expert surveys and intelligent digital libraries (Leidig and Fox 2014), capable of merging heterogeneous information. They were defined in Skulimowski (2013, p. 582) as “all knowledge sources, sensors, databases, repositories, and processing units, regardless of whether they are human, artificial, animal, or hybrid, provided that they are all mutually connected and endowed with … the usual expert system functionalities.” Nodes of a GES are marked as “users” and each GES has a specific user hierarchy. Moreover, a GES must offer each user an efficient information management system providing “knowledge transfer on immediate demand” (ibid.). The growing coverage of scientific information by search engines, with an increasing share of open access resources, further enhances the capabilities of autonomous information retrieval, which is the base of the GES paradigm. In the e-science context, the rationale justifying the introduction of GESs is to determine rules and principles for the design of knowledge-based systems capable of gathering and processing big scientific data, information and knowledge at different stages of verification and refinery. The access of autonomous webcrawlers and other GES tools to paid or sensitive information sources may be ensured with automatic subscription passwords or automatic micropayments and may be facilitated by distributed ledger technologies such as Linux Foundation’s Hyperledger Fabric blockchain (Thakkar et al. 2018). It is also assumed that the researchers will pursue the trend to upload the results of their work to public open access repositories such as researchgate.net, zenodo.org, or academia.edu. The development of GES and the simultaneous emergence of AILPs will ensure similar progress in learning approaches (Skulimowski 2019). It has also been 172 A. M. J. Skulimowski argued (Skulimowski 2013) that GESs may play an important role in solving the human–computer convergence problem, which touches upon the AILPs as well. The following Internet development trends that support the above claims were identified in Skulimowski (2013, 2014b): • growing integration of heterogeneous information sources (ISs); • increasing interconnection of knowledge units, online and offline; • increasing sophistication of information processing within each knowledge unit; • growing availability of sensor and other scientific measurement data, including information from Internet of things (IoT); • growing need to apply big data technologies in scientific information processing driven by the overall growth of the amount of information available online; • the emergence of common standards for scientific information management (Jeffery et al. 2014). 2 Integration of Future Research Tools in Global Expert Systems Google and Bing rose to 6.27 × 1012 in January 2020.5 When the tools offered by search engines become sufficiently sophisticated, this system of interconnected Web sites may become a real GES with strong analytic capacities. Another salient trend shaping the future of e-science is the emergence of a new form of collaborative learning (Köhler and Skulimowski 2019) that is facilitated and made more efficient with AILPs. This trend supports collaborative research, the overall growth of collective intelligence of research teams (Mohamed et al. 2013) and their fusion in GESs. Although in the mid-term future, the intellec- tual capacity of scientists can be outperformed by autonomous “global brain” type analytic engines (Heylighen 2017), using GESs and AILPs as the composite tools for learning and research will keep them aligned to the recent progress of autonomously performed research. In addition, the “explainable AI” paradigm (Xu et al. 2019), when commonly applied, can use combined GESs and AIPLs as tools to make avail- able the results of any kind of autonomous research in a comprehensible form for any GES/AILP user. Internet-based information supply chains of constantly growing size and complexity necessitate new approaches to designing search-and-survey procedures and to delegating more of this design work to autonomous agents. In a creative deci- sion process (Skulimowski 2011), the user defines an initial subset of ISs according to some criteria, assigns them trust or credibility coefficients (Gligor and Wing 2011) and activates the procedure that transforms selected IS to autonomous agents with capabilities similar to those of the user. The procedure runs recursively from the initial IS, so that second-stage ISs are selected and activated. This allows the agents to pursue the search autonomously and simultaneously, until a prescribed stack level or thedesiredretrieval goal is achieved. Acreativity-stimulatingcontent-basedsearch and recommendation has been investigated within the recent Horizon 2020 project (Skulimowski 2017a). The design of GES knowledge provision procedures must ensure that the reply to each query is given at a specified level of trust. When trust coefficients ϕi, 0 ≤ϕi ≤1, are assigned to each source of information available to this GES, the resulting trust τ(q) in the information retrieved in reply to a query q can be higher than any of its individual sources. Autonomous management of complex queries processed by a GES is a multicri- teria combinatorial optimization problem (Skulimowski 1994). 2 Integration of Future Research Tools in Global Expert Systems • the emergence of common standards for scientific information management (Jeffery et al. 2014). The above trends are amplified by qualitative and quantitative refinement of the information stored and processed online as well as by the growing availability of the learning content. The latter is fed to AILPs and boosts their development. The usability of online information for scientific purposes depends upon how well it is structured and accessible via search engines. For instance, the percentage of all data stored on the open Web and indexed by the search engine Google rose from 1% in January 2007 to 6% in January 2010 and exceeded 10% in January 2012. This estimated ratio has been preserved until at least 2019. At the same time, the estimated amount of information available online rose to 800 exabytes (1018 B) in 2009 and 1.3 zettabytes (1021 B) in 2013. According to the Delphi survey in Skulimowski et al. (2013), question [I.8], it is expected to rise to 1.6 zettabytes in 2020 and to reach the value of 3.5 zettabytes in 2025 and about 7 zettabytes in 2030. The recent Internet metrics data1 yield the value of 2 zettabytes of information contained in indexed Web sites as of 2019, which does not deviate much from the Delphi forecasts from 2012 to 2013 (Skulimowski et al. 2013). The same survey provided replies to the question of whether the information available online is really useful to scientists. The results are presented in Sect. 3. The number of Web sites exceeded 1700 million in 2016,2 then slightly declined and rose again to 1730 million in 2019 (Mill provides the value of 1.27 × 109 as of December 2019). Only 15% of all Web sites are active.3 They are hosted in about 360 million top-level domains.4 Forecasts of a further increase until 2025 and beyond diverge considerably depending on whether exclusively machine-operated and used (M2M) sites in the Internet of things are considered or not. Estimations vary between 3 and 50 billion sites in 2025. The number of Web pages indexed by Visions of a Future Research Workplace … 173 Google and Bing rose to 6.27 × 1012 in January 2020.5 When the tools offered by search engines become sufficiently sophisticated, this system of interconnected Web sites may become a real GES with strong analytic capacities. 5https://www.worldwidewebsize.com/ [access Jan 10, 2020]. 2 Integration of Future Research Tools in Global Expert Systems All activated units are deactivated after the information requested in qij is gathered. As previously mentioned, the above procedure is a special case of a multicriteria search strategy optimization problem, where the resulting strategy maximizes the amount of information, which is to be gathered in the least amount of time, at a minimum effort of all activated units, and at minimum cost for the initial unit. Such a search strategy may be endowed with a certain level of free will and may be designed to fulfill the definition of a creative decision process (cf. Skulimowski 2011). The natural question of whether science is capable of accommodating any kind of future AI technology for research purposes and how it can be achieved appears when projecting the GES future. From a purely economic standpoint, the role of AADSs in e-science will grow, encompassing new areas of intellectual activity and the replacement of human researchers. Performing a complex Web search strategy by an intelligent autonomous web crawler is a real-life example of such empowerment. The development of GESs will challenge users with a growing complexity of queries, a growing amount of gathered information, and with a need to comprehend the search workflow. Rejecting useful information due to the lack of an appropriate explanation of its provenance (Malaverri et al. 2013) may cause the recipients to lose the reply, but they may prefer to proceed so as to avoid infringing cybersecurity rules. 2 Integration of Future Research Tools in Global Expert Systems The order of queries from different users and the sequence of information sources to be contacted can be assessed from the point of view of precision, recall, and other information retrieval measures, such as timeliness. The GES functioning proposed in Skulimowski (2013) is based on a snowball principle: The node that generated a query activates other units until the desired information is found. The following principles of query processing in a GES have been defined in Skulimowski (2013). (a) Each knowledge unit K activated by another one, Ki with a query qij returns the information specified by qij to Ki or passes to (b). (a) Each knowledge unit K activated by another one, Ki with a query qij returns the information specified by qij to Ki or passes to (b). j (b) If the query qij can be only partly responded by Kj, the latter unit modifies it to qjk to ask for the missing information. Thus Kj activates further knowledge j (b) If the query qij can be only partly responded by Kj, the latter unit modifies it to qjk to ask for the missing information. Thus Kj activates further knowledge 174 A. M. J. Skulimowski A. M. J. Skulimowski units Kk1, …, Kkn(k) with the query qjk in the order specified as a solution of the search optimization problem as proposed in Skulimowski (1994). The resulting information search strategy minimizes the number of repeated activations of the same knowledge unit. units Kk1, …, Kkn(k) with the query qjk in the order specified as a solution of the search optimization problem as proposed in Skulimowski (1994). The resulting information search strategy minimizes the number of repeated activations of the same knowledge unit. units Kk1, …, Kkn(k) with the query qjk in the order specified as a solution of the search optimization problem as proposed in Skulimowski (1994). The resulting information search strategy minimizes the number of repeated activations of the same knowledge unit. (c) (c) The procedure (b) activates recursively further units. Each unit Kj activated by Ki fuses the information received from units activated by itself and returns them to Ki. All activated units are deactivated after the information requested in qij is gathered. (c) The procedure (b) activates recursively further units. Each unit Kj activated by Ki fuses the information received from units activated by itself and returns them to Ki. 3 Results of the Delphi Survey on e-Science Tools and Factors This section highlights a sample of the Delphi survey results (Skulimowski et al. 2013). This survey based on the novel “Extrapolation Delphi” principle was performed twice, the first time within the above-cited project and once during its durability period. Specifically, we present the results concerning the future devel- opment of advanced expert systems, heading toward advanced GESs, which were the subject of questions contained in survey Section 11 titled “Future prospects of knowledge base, expert systems, information streams and decision support systems integration” (Skulimowski et al. 2013). The replies to five questions most relevant to this article’s topics are presented out of 36 questions in the above mentioned survey section. Visions of a Future Research Workplace … 175 Table 1 Estimated share ϕ1 [in %] of researchers considering the online information widely available through browsers and search engines as fully representative in their areas of scientific research. Analysis of the replies to question No. 11.1a in (Skulimowski et al. 2013) weighted with combined trust/competence coefficients of respondents Specification of results Estimates for 2015 Forecasts for 2020 Forecasts for 2025 Forecasts for 2030 No. of replies 47 47 47 47 Shapiro–Wilk test negative negative positive negative Unimodality test positive positive positive positive Mean weighted value 25,519 28,73 40,146 47,337 Weighted standard deviation 18,006 16,737 21,449 22,66 Weighted left semideviation 15,27 16,906 18,867 22,7 Weighted right semideviation 22,93 17,18 25,806 23,373 Weighted median value: 20 25 35 45 1st weighted quintile 5 10 15 20 2nd weighted quintile 10 20 30 40 3rd weighted quintile 20 30 35 50 4th weighted quintile 50 50 50 60 Interquintile range IQVR 45 40 35 40 Interquartile range IQR 30 30 30 25 No. of reply clusters 1 1 1 1 Table 1 Estimated share ϕ1 [in %] of researchers considering the online information widely available through browsers and search engines as fully representative in their areas of scientific research. Analysis of the replies to question No. 11.1a in (Skulimowski et al. 2013) weighted with bi d t t/ t ffii t f d t 3.1 Delphi Survey Background and Scope The survey results are presented in tables, which provide the basic statistical char- acteristics of replies, together with Delphi-specific consensus measures of experts and a cluster analysis (von der Gracht 2012). The latter is then used to construct the development scenarios of investigated information systems. The survey respon- dents were requested to define certain numerical development indicators for four time horizons: 2015 (as forecast in 2013 and an estimate in 2016), 2020, 2025, and 2030 (forecasts). The following indicators have been calculated for all replies and for all time horizons: A. M. J. Skulimowski 176 – the average value, standard deviation, left and right semideviations, – the median, 1st and 3rd quartile and four quintiles, – the median, 1st and 3rd quartile and four quintiles, – the interquartile range (IQR), defined as the difference between the third and first quartile, – the interquartile range (IQR), defined as the difference between the third and first quartile, – the interquintile range (IQVR), defined as the difference between the fourth and first quintile, – the interquintile range (IQVR), defined as the difference between the fourth and first quintile, q – Hartigans’ dip test of unimodality (Hartigan and Hartigan 1985); if negative, it was followed by a clustering of replies and the number of clusters of replies was determined, – Hartigans’ dip test of unimodality (Hartigan and Hartigan 1985); if negative, it was followed by a clustering of replies and the number of clusters of replies was determined, – the Shapiro–Wilk (log) normality test, applied to replies either directly or to their logarithms when the question touched upon growth ratios. The consensus indicators IQR and IQVR should be normalized, for example by dividing them by the maximum data range R: = rmax −rmin after eliminating the outliers. Then, the consensus is defined by one or both inequalities IQR/R ≤η1, IQVR/R ≤η2, where ηk, k = 1, 2, are certain threshold values and η1 ≤η2. We can clearly see that given the same threshold value, the IQVR provides a stronger consensus test. A positive result of the Shapiro–Wilk normality test indicates a potentially unimodal distribution of replies and rejects the hypothesis that there is more than one cluster of replies. 6The current version of the system is available at www.forgnosis.eu. 3.2 The Future Use of Information Systems for e-Science—The Results of the Delphi Survey 3.2 The Future Use of Information Systems for e-Science—The Results of the Delphi Survey The first of the above-mentioned survey outcomes presented in this paper is a basic statistical analysis of question 11.1a pointing out the forecasted shares of scientists that consider online information to be accurately representative of their research. It is shown in Table 1. The above question did not distinguish between the research areas, so the replies only provide a rough estimate by merging humanities, engineering, etc. However, it shows the average value of online researchers’ share almost doubling between 2015 and 2030, while the mean square ex-ante forecast error rose only by about 20%, and the relative error decreased considerably. All but one (2025) reply sets for the estimation (2015) or forecasting (2020, 2025, 2030) horizons were considerably irregular and did not pass the weighted Shapiro–Wilk normality test. However, all value distributions were unimodal and concentrated in one cluster. Let us note that all quantiles (quartiles, quintiles, median) and consequently, the consensus measures, are integers because the respondents select their replies from the standard integer pick list [0:100]. The same list was used for all questions in Section 11 of the survey where the replies were to be provided in %. Table 2 shows the breakdown of the verified and raw quantitative information available on the Web for the same estimation/forecasting. The respondents estimated the amount of trustworthy information (i.e., knowl- edge) to comprise about one-fifth of all quantitative information available. This cannot be seen as an optimistic estimate. The forecast for 2030—about 40% of refined information—presumes the emergence of a new data refinery mechanism. This share is almost double in comparison with the estimate for the present state of the Internet. Nevertheless, the share of unverified Web information will still be close to the larger part of the golden proportion, which is an indication of the power of disinformation and fake data. The question in the first two rounds just touched upon the knowledge, irrespective of whether it was quantifiable or not. Based upon the respondents’ postulates, the question for the follow-up round was formulated more precisely, but without a statistically essential impact on outcomes. 3.1 Delphi Survey Background and Scope The statistical analysis was first performed under the hypothesis that the replies be weighted according to a self-assessment of certainty by the respondents’ survey, in combination with a self-assessed credibility coefficient of individual replies, and an automatically assigned individual expert competence score. This score was computed by the Delphi support system6 (Skulimowski 2017), based on previous survey partic- ipation, the record of publications, research projects, and other achievements in the question-related area. It has been observed (Skulimowski 2016a) that for most survey questions, there was no significant difference between the statistical indica- tors for weighted and non-weighted responses. This observation also touches upon the consensus measures and indicates that the expert group’s ability to estimate the future evolution of indicator values was homogeneous. Therefore, in this section we concluded that the resultant analysis variant yields a smaller statistical error (in terms of the standard deviation) for a majority of forecasting horizons. The sum of errors was a decisive factor, for an equal number of dominating values at different hori- zons. Out of five questions selected for this section, only the replies to question 11.8 (Table 4) exhibited smaller errors when analyzed without weighting coefficients. The survey in the project SCETIST (Skulimowski 2013) consisted of two rounds and was conducted in 2012 and 2013. There was also a post-project update round with the same participants, questions and Delphi support software. The respondents could select the questions to answer, according to their competences. Therefore, from over Visions of a Future Research Workplace … 177 100 respondents, the number of those replying to questions in Section 11.1 varied between 43 and 48 in the first and second rounds. 100 respondents, the number of those replying to questions in Section 11.1 varied between 43 and 48 in the first and second rounds. 7http://www.wolframalpha.com. 3.2 The Future Use of Information Systems for e-Science—The Results of the Delphi Survey A characteristic feature of the above replies is smaller than the usual difference between the IQR and IQVR consensus measures, which indicates a relatively large number of equal replies between the 1st quartile and 1st quintile as well as between the 3rd quartile and 4th quintile. The next question (11.3) assumed the emergence of a next generation of Wolfram’s Alpha7—an expert system capable of providing informed replies to virtually any 178 A. M. J. Skulimowski Table 2 Amount of processed and verified quantitative knowledge available online (in % of all quantitative information available). Replies to question no. 11.2 weighted with combined trust/competence coefficients Table 2 Amount of processed and verified quantitative knowledge available online (in % of all quantitative information available). Replies to question no. 11.2 weighted with combined trust/competence coefficients Specification of results Estimates for 2015 Forecasts for 2020 Forecasts for 2025 Forecasts for 2030 No. of replies 47 47 47 47 Shapiro–Wilk test negative negative negative positive Unimodality test positive positive positive positive Mean weighted value 17,186 22,732 27,664 38,079 Weighted standard deviation 11,66 12,865 16,657 24,339 Weighted left semideviation 9,363 12,572 18,072 21,447 Weighted right semideviation 15,135 13,633 16,008 28,604 Weighted median value: 15 20 30 35 1st weighted quintile 5 10 10 15 2nd weighted quintile 10 15 20 25 3rd weighted quintile 15 25 30 40 4th weighted quintile 25 30 40 50 Interquintile range IQVR 20 20 30 35 Interquartile range IQR 15 20 30 32 No. of reply clusters 1 1 1 1 query. This question touched upon a quantitative characteristic of a future GES capabilitytoreachtheexistinginformation,namely,itsmaximumrecallvaluerelative to the query provided by the system user. Replies equal to “0” were representative of the disbelief of this particular survey respondent that such software will be created (Table 3). query. This question touched upon a quantitative characteristic of a future GES capabilitytoreachtheexistinginformation,namely,itsmaximumrecallvaluerelative to the query provided by the system user. Replies equal to “0” were representative of the disbelief of this particular survey respondent that such software will be created (Table 3). Unlike in the case of the two previous questions, the replies to question 11.3 above indicate a sharp rise in the GES search range, from an initial estimate of about 2– 27% in 2030, with a high yet relatively decreasing uncertainty, expressed by standard deviation and semideviations. 3.2 The Future Use of Information Systems for e-Science—The Results of the Delphi Survey A symmetrical problem to that shown above was considered in question 11.8 (Skulimowski 2013); namely, we investigated the Internet users’ attitudes to Visions of a Future Research Workplace … 179 Table 3 The share of information available on the Web that can be processed by advanced expert software (GES) capable of analyzing heterogeneous data (quantitative economic information, multimedia, publications, video streaming) and providing GES users with informed replies to any given question (in % of available information used for this purpose) expert software (GES) capable of analyzing heterogeneous data (quantitative economic information, multimedia, publications, video streaming) and providing GES users with informed replies to any given question (in % of available information used for this purpose) Specification of results Estimates for 2015 Forecasts for 2020 Forecasts for 2025 Forecasts for 2030 No. of replies 48 47 47 47 Shapiro–Wilk test positive positive positive negative Unimodality test positive positive positive positive Mean weighted value 2,156 5,525 14,536 26,926 Weighted standard deviation 4,928 6,877 14,319 20,797 Weighted left semideviation 2,091 4,477 10,295 15,467 Weighted right semideviation 11,713 10,861 18,675 30,245 Weighted median value: 0 2 10 20 1st weighted quintile 0 0 2 10 2nd weighted quintile 0 0 5 15 3rd weighted quintile 0 3 15 25 4th weighted quintile 1 10 20 50 Interquintile range IVQR 1 10 18 40 Interquartile range IQR 0 10 10 40 No. of reply clusters 1 1 1 1 searching for solutions to their problems on the Web. The analysis of replies is given in Table 4. A predominance of solving problems through access to online information is not a surprise. Actually, the above characteristics may be burdened by a relatively high share of elderly people who have Internet access via their mobile phones, but use it sparingly. The most recent research performed within the project (Skulimowski 2019) yields considerably higher estimates for 2025 and 2030, reaching more than 90% of all queries. The last set of results presented in this section touches upon the emergence of qualitatively new capabilities and phenomena in GESs, manifesting itself through A. M. J. 3.2 The Future Use of Information Systems for e-Science—The Results of the Delphi Survey Skulimowski 180 Table 4 Answers to problems, questions, and queries of all kinds (translations, spelling, defini- tions, geographical information, graphical object finding, legislation, etc.) that will be sought online: in% of all queries from user with Internet access (mobile or landline); unweighted Specification of results Estimates for 2015 Forecasts for 2020 Forecasts for 2025 Forecasts for 2030 No. of replies 46 45 45 45 Shapiro–Wilk test negative negative negative negative Unimodality test positive positive positive positive Mean value 38,553 49,189 60,676 71,919 Standard deviation 19,134 18,428 18,64 19,836 Median value: 40 55 65 75 1st quintile 15 25 30 40 2nd quintile 25 40 55 70 3rd quintile 40 55 65 75 4th quintile 50 60 70 85 Interquintile range 35 35 40 45 Interquartile range 32,5 28,75 27,5 20 No. of reply clusters 1 1 1 1 solving previously intractable problems or answering unresolved questions. Namely, the integration of knowledge on the Internet will allow for a new level of quality in resolving problems presented by GES users, specifically those intractable prob- lems, and providing replies to queries, which are unavailable through contemporary information processing methods (Table 5). solving previously intractable problems or answering unresolved questions. Namely, the integration of knowledge on the Internet will allow for a new level of quality in resolving problems presented by GES users, specifically those intractable prob- lems, and providing replies to queries, which are unavailable through contemporary information processing methods (Table 5). Both the uncertainty expressed by the standard deviation and semi-deviations, as well as the consensus indicators IQR and IQVR for question 11.9, are relatively lower than in case of the two previous forecasts. Fitting the above replies with the logistic curve (Skulimowski 2017b), we can calculate the expected time when the majority of problems and queries can be better solved by GESs, namely the year 2037. This year can thus be regarded as a kind of a singularity (Skulimowski 2014b); however, in a limited sense. To conclude this section, let us note that reaching a consensus need not be the ultimate goal of a Delphi survey. Usually, if the unimodality test is negative, a lack of consensus indicates the existence of several clusters of replies. 3.2 The Future Use of Information Systems for e-Science—The Results of the Delphi Survey If this is not the case and the IQR or IQVR values are rather high, while growing more slowly than the trend investigated by the survey, it means that there is a common expectation of a certain trend or event among the survey respondents, with a high uncertainty regarding its time of occurrence, however. Visions of a Future Research Workplace … 181 Visions of a Future Research Workplace … Table 5 The share in % of problems and queries that will be more adequately solved by GES, compared to the solutions and replies provided by human experts (question 11.9) Specification of results Estimates for 2015 Forecasts for 2020 Forecasts for 2025 Forecasts for 2030 No. of replies 46 45 45 45 Shapiro–Wilk test negative negative positive positive Unimodality test positive positive positive positive Mean weighted value 14,477 23,12 31,653 45,813 Weighted standard deviation 9,439 9,786 11,459 18,268 Weighted left semideviation 7 7,436 8,881 16,184 Weighted right semideviation 12,231 12,634 15,542 21,121 Weighted median value: 10 20 30 40 1st weighted quintile 5 15 20 25 2nd weighted quintile 10 15 30 35 3rd weighted quintile 10 20 30 40 4th weighted quintile 20 30 40 60 Interquintile range IQVR 15 15 20 35 Interquartile range IQR 15 10 20 25 No. of reply clusters 1 1 1 1 Table 5 The share in % of problems and queries that will be more adequately solved by GES compared to the solutions and replies provided by human experts (question 11.9) 4 Discussion and Conclusions The results of the Delphi survey presented in Sect. 3 provide clues, arising from expert judgments, regarding the amount of information available online and its use for e-science purposes until 2030. It is expected that by 2030, the corresponding information retrieval tools will reach sufficient enough levels to provide virtually all necessary scholarly information to researchers. Furthermore, within a similar time frame, GESs are expected to outperform human experts in solving complex knowledge processing tasks. Another AI trend that may have a relevant impact on e-science is the development of brain–computer interfaces (BCIs) and their deployment in enhancing research, their joint use with GESs and AILPs, as well as in intelligent decision support 182 A. M. J. Skulimowski systems.TheresultsofaDelphisurveyonBCIsarepresentedinSkulimowski(2014b, 2016b). Here, we briefly discuss a summary of these findings. By definition, in a BCI, outward information is retrieved by recognizing the brain’s electromagnetic neural activity, while for the inward transfer direction, a BCI triggers the neural circuits directly (Brunner et al. 2011; Jiang et al. 2019). The best transmission rates and qualities were obtained with invasive BCIs, based on intracranial implants, but the greatest hope in enhancing human capabilities is placed on non-invasive BCIs, such as wearable devices that are used to retrieve EEG or fMRI signals. They are expected to facilitate efficient bidirectional communication with GES (Zhang et al. 2013) as well as direct communication between human brains, called hyperinteraction (Grau et al. 2014; Jiang et al. 2019). The ability of a BCI to directly connect researchers’ brains with powerful expert systems will speed up progress in global data integra- tion provided by GESs. It will also increase the efficiency of scientific collaboration (Leidig and Fox 2014; Shi et al. 2017) and the use of AILPs. The positive effect of BCIs on researchers who obtain efficient and instant access to big research data may partly compensate for the negative impact of data explosion. However, the ques- tion of whether e-science can fully exploit the capabilities of emerging advanced AI tools and technologies such as AILPs, GESs, and BCIs to increase the quality and efficiency of scientific research remains to be seen. The analysis of the full set of SCETIST Delphi survey replies resulted in deriving three human–AI interaction scenarios (cf. Skulimowski 2014b, 2016a, b). Here, we adjust them slightly to provide conditional responses to the above question. 4 Discussion and Conclusions The full and beneficial use of AI defines the optimistic scenario of human–AADS interaction, while the negative response is associated with the pessimistic scenario, often referred to as the AI threat problem. The foresight results presented in Skulimowski (2014b) suggest that the main condition triggered between the positive and negative scenarios is the capability of future BCIs to provide a direct interface to GESs and facilitate the creative process of GES users. In the optimistic scenario, the growing empowerment of AADSs will be compen- sated for by the ability of human supervisors and authorized users to control them directly with BCIs. This scenario is backed by results of the Delphi survey presented in Sect. 3, which suggest that GESs and AILPs supported by high-performance BCIs and enhanced reality will ensure control over advanced AI technologies. Further results of the Delphi survey on the development of artificial creativity and creativity support systems performed in SCETIST (Skulimowski 2016a) highlight the impor- tance of coupling human users with GESs and AILPs via BCIs to stimulate their creative abilities. The pessimistic scenario presumes that a growing share of human creative activity, specifically in research, will be replaced by AADSs due to the ever- growing complexity of research and decision problems to be solved along with increasingly large data volumes. In this scenario, AADSs will specify goals, criteria and constraints, target quality and the scope of applicability of solutions. Human researchers will only perform auxiliary and assistive roles. In the third, neutral scenario, technological development is generally slowed down in the face of various setbacks. In this case, the AADS/human competition problem Visions of a Future Research Workplace … 183 will be deferred to a more distant future, beyond horizon 2030 of the foresight studies presented here. will be deferred to a more distant future, beyond horizon 2030 of the foresight studies presented here. In conclusion, the results of recent foresight studies highlight the relevance of development trends in selected advanced AI technologies for future e-science, e-learning, and e-research. According to the outcomes of the research projects (Skulimowski et al. 4 Discussion and Conclusions 2013; Köhler and Skulimowski 2019), the areas of inten- sive ICT/AI development efforts that can be of utmost relevance for e-science are GESs driven by autonomous web crawlers and dedicated decision support systems, creativity support systems capable of stimulating or at least preserving human creative abilities, and bidirectional non-invasive BCIs providing direct links to GESs and other researchers to efficiently tackle large amounts of scientific data. Acknowledgements The author is grateful for the support of the research project “Scenarios and Development Trends of Selected Information Society Technologies until 2025” (acronym “SCETIST”), financed from the ERDF funds within the Innovative Economy Operational Programme, contract No. WND-POIG.01.01.01-00-021/09. 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Natural Language Processing and Chinese Computing. NLPCC 2019. Lecture Notes in Computer Science 11839, pp. 563–574. Springer, Cham (2019). https://doi.org/10.1007/978-3- 030-32236-6_51 Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), 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 license and indicate if changes were made. g The images or other third party material in this chapter are included in the chapter’s Creative Commons license, unless indicated otherwise in a credit line to the material. 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Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products
Ciência rural
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Maniçoba para ovinos e caprinos: produção de forragem, estratégias de conservação, desempenho do animal e qualidade dos produtos RESUMO: Nas regiões secas mundiais, fornecer alimentos para ruminantes tem sido um grande desafio, havendo necessidade de utilizar plantas que contribuam para a resiliência dos sistemas de produção. A maniçoba é vista como um potencial recurso forrageiro no semiárido brasileiro, sendo utilizada como feno ou silagem para alimentação de ruminantes. O objetivo desta revisão foi sumarizar os resultados quanto à produção de forragem da maniçoba, além do consumo de matéria seca (MS), desempenho produtivo e qualidade dos produtos de origem animal obtidos com dietas à base de maniçoba, quando comparados com dietas compostas por outros volumosos para caprinos e ovinos. Considerando os estudos avaliados, a produtividade média da maniçoba variou de 367 a 1.592 kg de MS ha-1, com aumento da produção de forragem pela maior fertilização da planta e densidade de plantio. As dietas à base de maniçoba promoveram resultados semelhantes ou superiores para ingestão de matéria seca e desempenho produtivo de caprinos e ovinos, quando comparadas às dietas compostas por outros recursos forrageiros. A qualidade dos produtos de origem animal também foi semelhante às proporcionadas por dietas à base de volumosos tradicionais, como feno Tifton 85 ou palma-forrageira. Portanto, a maniçoba apresenta produção de forragem que pode contribuir com os sistemas de produção de ruminantes em ambiente semiárido, e promover desempenho produtivo e qualidade dos produtos de origem animal compatíveis com as proporcionadas pelas forrageiras tradicionais. p p p p f g Palavras-chave: alternativa forrageira, recurso forrageiro, mandioca silvestre, Manihot, planta cianogênica. Ci Received 12.19.20 Approved 06.03.21 Returned by the author 07.30.21 CR-2020-1096.R2 Editors: Rudi Weiblen Henrique Mendonça Nunes Ribeiro Fiho Maria Letícia Rodrigues Gomes1 Fabiana Castro Alves1 José Renaldo Vilar da Silva Filho1* Clesio Morgado de Souza2 Maria Naiara Pereira da Silva1 Roberto Araújo Santana Junior1 Luara Coelho de Souza3 Tadeu Vinhas Voltolini4 Maria Letícia Rodrigues Gomes1 Fabiana Castro Alves1 José Renaldo Vilar da Silva Filho1* Clesio Morgado de Souza2 Maria Naiara Pereira da Silva1 Roberto Araújo Santana Junior1 Luara Coelho de Souza3 Tadeu Vinhas Voltolini4 1Centro de Ciências Agrárias, Universidade Federal do Vale do São Francisco (UNIVASF), 56304-917, Petrolina, PE, Brasil. E-mail: renaldovilar.zootecnia@gmail.com. *Corresponding author. 2Instituto Federal de Educação, Ciência e Tecnologia do Sertão Pernambucano (IFSertãoPE), Santa Maria da Boa Vista, 3Universidade de Pernambuco (UPE), Petrolina, PE, Brasil. ( ), , , esa Brasileira de Pesquisa Agropecuária (Embrapa Semiárido), Petrolina, PE, Brasil. ( ) 4Empresa Brasileira de Pesquisa Agropecuária (Embrapa Semiárido), Petrolina, PE, Brasil. ABSTRACT: In dry regions worldwide, providing feed for ruminants has been a great challenge, with a need to use plants which contribute to the resilience of production systems. Maniçoba is seen as a potential forage resource in the Brazilian semiarid, being used as hay or silage to feed ruminants. This review summarized results regarding forage production of maniçoba, in addition to dry matter (DM) intake, productive performance, and quality of animal products obtained providing maniçoba based diets, when compared to diets composed by other roughages for goats and sheep. Considering the evaluated studies, the average yield of maniçoba varied from 367 to 1,592 kg DM ha-1, enhancing the forage yield by increasing plant fertilization and planting density. Diets based on maniçoba promoted similar or higher intake of DM and productive performance for goats and sheep, when compared to diets comprising other forage resources. The quality of animal products was also similar to the ones obtained with diets based on traditional roughages, such as Tifton 85 hay or spineless cactus. Therefore, maniçoba allows a forage production that may contribute to ruminant production systems in semiarid environment and promote productive performance and animal product quality compatible to the ones provided by traditional forage plants. Key words: forage alternative forage resource wild cassava Manihot cyanogenic plant Key words: forage alternative, forage resource, wild cassava, Manihot, cyanogenic plant. Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products Maria Letícia Rodrigues Gomes1 Fabiana Castro Alves1 José Renaldo Vilar da Silva Filho1* Clesio Morgado de Souza2 Maria Naiara Pereira da Silva1 Roberto Araújo Santana Junior1 Luara Coelho de Souza3 Tadeu Vinhas Voltolini4 Maniçoba for sheep and goats - forage yield, conserva Ciência Rural, Santa Maria, v.52:3, e20201096, 2022 Maniçoba for sheep and goats - forage yield, conserva Ciência Rural, Santa Maria, v.52:3, e20201096, 2022 ormance and quality of products. 1 ISSNe 1678-4596 http://doi.org/10.1590/0103-8478cr20201096 animal production INTRODUCTION forage plants that are inserted in the socioeconomic context of the population and contribute to new strategies for supplying nutrients for ruminants, reducing production losses and increasing animal yield and farm income. Food security for herds has been an important challenge for livestock production in arid and semiarid regions (MLAMBO & MAPIYE, 2015) and there is great concern about food production to meet the demands of the world’s growing population, with drylands playing a relevant role in this scenario (TARRASÓN et al., 2016). In this sense livestock systems need to improve land use by using adapted Maniçoba comprises plants (wild species) of the genus Manihot, including Manihot glaziovii Müll. Arg., Manihot catingae Ule and Manihot carthaginensis (Jacq.) Müll. Arg, all native to the Brazilian semiarid, showing genetic and Gomes et al. 2 morphoagronomic diversity (CAMPOS et al., 2020). The plants are perennial, tolerant to cuttings and long periods of drought, with morphological adaptation related to water retention (NASSAR et al., 2010), and physiological mechanisms via control of stomatal aperture to maintain a positive carbon balance even in drought conditions (MORGANTE et al., 2020). In ruminant feeding, maniçoba is used exclusively as hay or silage to reduce the toxicity of hydrocyanic acid, thus allowing a safe feeding for animals (MATOS et al., 2005; SOARES, 2000; SOUZA et al., 2006). morphoagronomic diversity (CAMPOS et al., 2020). The plants are perennial, tolerant to cuttings and long periods of drought, with morphological adaptation related to water retention (NASSAR et al., 2010), and physiological mechanisms via control of stomatal aperture to maintain a positive carbon balance even in drought conditions (MORGANTE et al., 2020). In ruminant feeding, maniçoba is used exclusively as hay or silage to reduce the toxicity of hydrocyanic acid, thus allowing a safe feeding for animals (MATOS et al., 2005; SOARES, 2000; SOUZA et al., 2006). Soil management using ridges and the cutting heights of the plants (MOREIRA FILHO et al., 2008), the water depths and the nitrogen (N) fertilization (ARAÚJO FILHO et al., 2013) are also factors that affect the plant growth and increase the forage yield. Presumably, the ridges increase the accumulation and availability of nutrients in the soil, favoring the development of the plant root system. The increase in productivity with N fertilization suggested that maniçoba has efficient metabolic responses to the use of this nutrient. INTRODUCTION Productive and qualitative characteristics of the plant must be considered, along with its potential to constitute diets that provide a proper productive performance to the animal. In this sense the evaluation of yield and quality of maniçoba forage, as well as the assessment of dry matter (DM) intake, productive performance of goats and sheep, and its influence on animal product quality, are important aspects to understand the potential of this plant as an alternative for livestock production systems in semiarid environments. Beyond the forage yield, BELTRÃO et al. (2008) pointed out the proportion of leaves on the plant, reporting that approximately 50% of the produced forage (kg DM-1 ha-1) corresponds to this component, which may still be incremented by management practices, as for instance organic fertilization. These results denoted that maniçoba allows forage yield compatible with the semiarid environment. Therefore, it contributed to the forage input for ruminant production systems, while management factors may increase the productive efficiency of the crop. The present review summarized the results of forage yield of maniçoba in the semiarid region of Brazil, the DM intake and productive performance of goats and sheep fed maniçoba-based diets, and the quality of animal products. It is important that there should be a greater number of studies evaluating this forage resource, especially including diverse locations in the semiarid region, thus enlarging the database on crop yield, above all regarding long-term studies. Forage quality 3 Table 1 – Mean and maximum forage yield (kg DM ha-1) of maniçoba, cutting intervals (days), municipality, and rainfall (mm/period) from studies carried out in Brazilian semiarid in rainfed condition. Table 1 – Mean and maximum forage yield (kg DM ha-1) of maniçoba, cutting intervals (days), municipality, and rainfall (mm/period) from studies carried out in Brazilian semiarid in rainfed condition. from studies carried out in Brazilian semiarid in rainfed condition. Mean productivity ---Maximum productivity--- ----Cutting interval---- ---------Municipality-------- --------Rainfall-------- 4561 626 240 Areia-PB 893.5* 4712 1,800 1,095 Cubatí-PB 321 3673 462 152 Campina Grande-PB 765 1,1784 1,746 120-240 Areia-PB 893.5-1,163 1,5925 3,733 365-456 Petrolina-PE 937** 1BELTRÃO et al. (2008) *accumulated rainfall of years 2002 and 2003 in Areia-PB from AESA (2020), 2MOREIRA FILHO et al. (2008), 3VASCONCELOS et al. (2010), 4ARAÚJO FILHO et al. (2011), 5SOARES (1989). **accumulated rainfall of years 1987 and 1988 in Petrolina-PE (Meteorological Station of Embrapa Semiárido). 1BELTRÃO et al. (2008) *accumulated rainfall of years 2002 and 2003 in Areia-PB from AESA (2020), 2MOREIRA FILHO et al. (2008), 3VASCONCELOS et al. (2010), 4ARAÚJO FILHO et al. (2011), 5SOARES (1989). **accumulated rainfall of years 1987 and 1988 in Petrolina-PE (Meteorological Station of Embrapa Semiárido). compatible with or higher than the ones presented by other forage resources used to feed ruminants in the Brazilian semiarid. High CP and low NDF are positive aspects in roughage for feeding ruminants. SANTOS et al. (2017) evaluated different forages in natura and observed 208.0 g kg-1 CP and 434.0 g kg-1 NDF plant (MOREIRA FILHO et al., 2009), indicating the conservation process of maniçoba as an important tool to maintain the nutrients. compatible with or higher than the ones presented by other forage resources used to feed ruminants in the Brazilian semiarid. High CP and low NDF are positive aspects in roughage for feeding ruminants. SANTOS et al. (2017) evaluated different forages in natura and observed 208.0 g kg-1 CP and 434.0 g kg-1 NDF Maniçoba exhibited high lignin levels, which may reduce the forage digestibility. Conversely, this forage also showed high CP and low NDF, able 2 – Crude protein (CP), ash, ether extract (EE), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose (HE cellulose (CELL) and lignin (LIG) of maniçoba (in natura, hay and silage). Ciência Rural, v.52, n.3, 2022. Forage quality The results of five experimental trials (n = 50 treatments) in the Brazilian semiarid evaluated the forage production of maniçoba, considering single-crop and rainfed conditions. These studies were carried out in the states of Pernambuco and Paraíba, with cutting intervals varying from 152 to 1,095 days and accumulated rainfall in the period varying from 321 to 1,163 mm. The average forage yield reported for maniçoba ranged from 367 to 1,592 kg DM-1 ha-1 (Table 1), considering different cutting intervals of the plant, reaching 3,733 kg DM-1 ha-1 regarding the sum of the production of two consecutive harvests, performed after up to fifteen months (SOARES, 1989).l The dry matter content of fresh maniçoba varied from 204.4 to 289.2 g kg-1 (ARAÚJO FILHO et al., 2011; SILVA et al., 2011). The chemical composition of the plant, based on data from 21 articles, reported by authors as hay, silage or fresh (in natura) maniçoba, consisted on average of crude protein (CP), ash, ether extract (EE), neutral and acid detergent fiber (NDF and ADF), hemicellulose (HEM), cellulose (CELL) and lignin, at 156.5; 79.4; 43.9; 473.4; 354.9; 125.3; 231.5 and 109.2 g kg-1, respectively (Table 2). Crude protein levels ranged from 90.8 to 227.5 g kg-1, and NDF varied from 355.0 to 586.0 g kg-1 (Table 2). The offered forms of maniçoba (fresh, hay or silage) did not result in great differences on main parameters of chemical composition. On average, fresh maniçoba showed 173.8 g kg-1 for CP, while as hay and silage CP levels were 141.1 and 154.7 g kg-1. Additionally, NDF for fresh maniçoba was 449.8 g kg-1, while as hay and silage it was 475.5 and 494.8 g kg-1, respectively (Table 2). The authors attributed changes in chemical composition mainly to the proportion of leaf/stem (FRANÇA et al., 2010), as well as genotype and development stage of the Several factors influence the production of maniçoba forage. ARAÚJO FILHO et al. (2011) verified that organic fertilization increased the yield by up to 80%, in comparison to non-fertilized maniçoba, due to the nutrient supply to the crop. The increase in plant density also increased the forage yield, with plant densities reaching 6,667 (ARAÚJO FILHO et al., 2011) or 10,000 plants ha-1 (SOARES, 1989), indicating that maniçoba can respond favorably to intensive crop management. Ciência Rural, v.52, n.3, 2022. Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products. Source: 1BELTRÃO et al. (2015); 2FRANÇA et al. (2010); 3DANTAS et al. (2008); 4CAMPOS et al. (2020); 5SOUZA et al. (2006); 6BACKES et al. (2014); 7SILVA et al. (2011); 8VASCONCELOS et al. (2010); 9MATOS et al. (2005); 10SANTOS et al. (2017); 11CARVALHO et al. (2018); 12BARROS et al. (1990); 13MOURA et al. (2020); 14CASTRO et al. (2007); 15MENEZES et al. (2012); 16SANTOS et al. (2021); 17COSTA et al. (2008); 18MACIEL et al. (2019); 19MATIAS et al. (2020); 20SOARES II et al. (2017); 21LOIOLA FILHO et al. (2012). Ciência Rural, v.52, n.3, 2022. Forage quality In addition, N and K contents differed according to the municipality of origin of the maniçoba sample, associated with soil and climatic characteristics. for maniçoba, while Cunhã (Clitorea ternatea L.), Sabiá (Mimosa caesalpiniifolia Benth.), Gliricídia (Gliricidia sepium (Jacq.) Steud.) and Mororó (Bauhinia cheilanta (Bong.) Steud.) presented 148.0; 124.0; 175.0; and 115.0 g kg-1 CP and 604.0, 679.0, 510.0 and 683.0 g kg-1 NDF, respectively. for maniçoba, while Cunhã (Clitorea ternatea L.), Sabiá (Mimosa caesalpiniifolia Benth.), Gliricídia (Gliricidia sepium (Jacq.) Steud.) and Mororó (Bauhinia cheilanta (Bong.) Steud.) presented 148.0; 124.0; 175.0; and 115.0 g kg-1 CP and 604.0, 679.0, 510.0 and 683.0 g kg-1 NDF, respectively. The nutritional value of maniçoba is influenced by divers factors, such as chemical fertilization, soil types and management, plant cutting height and stage of development of the plant (ANDRADE et al., 2014; MOREIRA FILHO et al., 2009). In a study carried out by PARENTE et al. (2007), maniçoba in natura showed 13.91% CP when supplied with 100 kg N ha-1, while without nitrogen fertilization the CP content was 8.58%, Sodium, iron, zinc, and manganese were the main microminerals presented by maniçoba (Table 4). Mineral elements exert an important role in the plant, including structural functions and metabolic process, and they are also essential for animals. The insufficiency of even one element may negatively affect animal growth, as well as health and reproductive functions. In the Brazilian semiarid the main source of minerals for ruminants is forage, and the supply of minerals through maniçoba forage contributes to meeting the requirements for these elements. According to MENEZES et al. (2012), the potential DM degradability of maniçoba hay was 70%, while the effective degradability (5%/h) was 57.4%. The potential degradability of CP was 92.5% and the effective one (5%/h) was 80%. SOUZA et al. (2006) reported a potential degradability of NDF varying from 52.12 to 54.45%, with an effective degradability (5%/h) varying from 32.41 to 32.55%. Furthermore, the knowledge of mineral contents in maniçoba enables the comprehension of extraction and exportation of nutrients by the plant, and determines the mineral reposition, according to the forage yield. FRANÇA et al. (2010) observed that the DM degradability is related to a great participation of leaves in the produced biomass, presenting tissues with less thickened walls and lower lignification, promoting higher degradability than the stem part. Forage quality p ( ), , ( ), g ( ), g ( ), ( ), cellulose (CELL) and lignin (LIG) of maniçoba (in natura, hay and silage). ---------------------------------------------------------------------Contents (g kg of DM)---------------------------------------------------------------------------- Fractions ---------------in natura------------- ---------------Hay---------------- -------------Silage------------- ----Overall average---- Mean Min. – Max. Mean Min. – Max. Mean Min. – Max. CP 173.8 141.1 154.7 156.5 110.9 – 227.51,2,3,4,5,6,7,8,9,10,11 90.8 – 196.02,12,13,14,15,16,17 125.0 – 188.05,6,18,19,20,21 Ash 76.4 76.9 85.0 79.4 61.0 – 142.8,2,3,4,5,6,8,10,11 61.7 – 99.52,12,13,15,16,17 71.5 - 97.85,6,18,19,20,21 EE 42.1 50.3 39.3 43.9 20.6 – 102.01,2,3,4,5,6,7,9,10,11 22.0 – 99.62,12,13,14,15,17 29.8 – 62.05,6,18,19,20,21 NDF 449.8 475.5 494.8 473.4 359.0 - 557.11,2,3,4,5,6,7,8,9,11 355.0 - 586.02,12,13,14,17 400.2 – 584.5,6,20,21 ADF 337.3 351.8 375.7 354.9 264.5 – 466.51,3,4,5,6,7,8,9,10,11 279.0 – 462.72,12,13,14,15,16,17 264.6 – 473.05,6,20,21 HEM 129.0 113.0 133.9 125.3 95.0 – 189.81,4,8,10 113.0 – 113.012 57.0 – 210.86,19 CELL 197.1 258.7 238.6 231.5 116.2 – 242.01,4,10 230.3 - 287.012,14 191.2 - 286.06,19 LIG 106.6 113.1 108.0 109.2 65.1 – 141.4,2,3,4,6,7 93.0 - 171.02,12,14,15,16,17 78.5 – 182.06,19,20,21 Source: 1BELTRÃO et al. (2015); 2FRANÇA et al. (2010); 3DANTAS et al. (2008); 4CAMPOS et al. (2020); 5SOUZA et al. (2006); 6BACKES et al. (2014); 7SILVA et al. (2011); 8VASCONCELOS et al. (2010); 9MATOS et al. (2005); 10SANTOS et al. (2017); 11CARVALHO et al. (2018); 12BARROS et al. (1990); 13MOURA et al. (2020); 14CASTRO et al. (2007); 15MENEZES et al. (2012); 16SANTOS et al. (2021); 17COSTA et al. (2008); 18MACIEL et al. (2019); 19MATIAS et al. (2020); 20SOARES II et al. (2017); 21LOIOLA FILHO et al. (2012). Source: 1BELTRÃO et al. (2015); 2FRANÇA et al. (2010); 3DANTAS et al. (2008); 4CAMPOS et al. (2020); 5SOUZA et al. (2006); 6BACKES et al. (2014); 7SILVA et al. (2011); 8VASCONCELOS et al. (2010); 9MATOS et al. (2005); 10SANTOS et al. (2017); 11CARVALHO et al. (2018); 12BARROS et al. (1990); 13MOURA et al. (2020); 14CASTRO et al. (2007); 15MENEZES et al. (2012); 16SANTOS et al. (2021); 17COSTA et al. (2008); 18MACIEL et al. (2019); 19MATIAS et al. (2020); 20SOARES II et al. (2017); 21LOIOLA FILHO et al. (2012). Ciência Rural, v.52, n.3, 2022. Ciência Rural, v.52, n.3, 2022. Gomes et al. 4 leaf development and the plant location. They observed N and K differences in the leaves at the beginning of the senescence process compared with expanding or completely expanded leaves, attributed to the nutrient translocation, especially N from old to new leaves. Ciência Rural, v.52, n.3, 2022. Forage quality These authors also reported that the main factor promoting low degradability of NDF was the thickening and lignification of cell walls, especially in stem tissues. As secondary compounds, da SILVA (2016) reported the presence of steroids, saponins, tannins and flavonoids in maniçoba leaves, with differences in concentration among evaluated accessions and leaf maturation stages. In addition, BELTRÃO et al. (2015) reported total tannins varying from 0.2 to 5.3% DM and HCN ranging from 97.2 to 291.6 mg kg-1 DM in maniçoba, while FRANÇA et al. (2010) observed tannin levels of 1.58 and 1.87% DM, respectively for maniçoba in natura or hay, and reported an important anti- nutritional action when they exceeded 5% DM in Macromineral levels in maniçoba are shown in table 3. Nitrogen and potassium presented the greatest contents, followed by calcium and magnesium. According to ANDRADE et al. (2014), N and K levels of maniçoba are influenced by the stage of Table 3 – Content of macrominerals in maniçoba in natura, subject to fertilization, pruning and different planting spacings. Mineral ------------------------------------------------Contents (g kg-1 DM)---------------------------------------------------- ----------------Mean--------------- --------------Minimum------------ --------------Maximum--------------- Nitrogen1,2 30.74 17.26 40.30 Phosphorus4 2.54 1.46 4.28 Potassium 4 13.75 4.10 20.48 Calcium3 4.65 3.54 13.50 Magnesium3 4.45 3.60 5.45 Sulfur2 1.85 1.80 1.90 Sources: 1,4ANDRADE et al. (2014); 1,2,3,4ARAÚJO FILHO et al. (2011); 3,4FERREIRA et al. (2009); 3,4PARENTE et al. (2007) . f macrominerals in maniçoba in natura, subject to fertilization, pruning and different planting spacings. Table 3 – Content of macrominerals in maniçoba in natura, subject to fertilization, pruning and different planting spacings. Sources: 1,4ANDRADE et al. (2014); 1,2,3,4ARAÚJO FILHO et al. (2011); 3,4FERREIRA et al. (2009); 3,4PARENTE et al. (2007) . Ciência Rural, v.52, n.3, 2022. Ciência Rural, v.52, n.3, 2022. Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products. 5 Table 4 - Micromineral contents in maniçoba genotypes, in natura, cut at intervals of six months of regrowth. Micromineral -----------------------------------------------Contents (mg kg-1 DM)---------------------------------------------- ----------------Mean--------------- --------------Minimum------------- ---------------Maximum-------------- Boron 14.40 9.46 18.6 Copper 20.40 17.72 22.04 Iron 239.13 125.19 644.10 Manganese 111.00 91.48 146.97 Zinc 129.61 106.15 228.75 Sodium 2,548.33 1,970.00 3,280.00 Source: LIMA (2019). Table 4 - Micromineral contents in maniçoba genotypes, in natura, cut at intervals of six months of regrowt icromineral contents in maniçoba genotypes, in natura, cut at intervals of six months of regrowth. Forage quality diets, indicating there is no negative effect of tannin levels presented by maniçoba on DM digestibility. are also important to reduce HCN levels in the forage, providing safe feed. The chemical composition of maniçoba offers opportunities to perform studies aiming the evaluation and selection of genotypes with lower concentrations of hydrocyanic acid and lignin, and greater degradability of fiber, as well as the evaluation of crop management practices that increase the degradability of the fibrous fraction. The high presence of cyanogenic glycosides in maniçoba, when hydrolyzed, release hydrocyanic acid (HCN) through the action of enzymes such as ß-glucosidase (linamarinase), which may be poisonous to animals, depending on the ingested quantity. Ingestion greater than 2.4 mg of HCN/kg of body weight may cause several disorders (SOARES, 2000). i SOUZA et al. (2006) verified 972 mg kg-1 of HCN in maniçoba in natura (% DM) and 162 mg kg-1 in silage (% DM), while SOARES (2000) reported a reduction in HCN by over 65% in maniçoba silage after the first 29 days of ensilage, reaching a reduction of up to 78% after 174 days. According to MATOS et al. (2005) the enzyme linamarinase is inactivated by heat and the ensiling process also contributes to the fermentation of glycosides by anaerobic micro- organisms, reducing HCN concentration. Ciência Rural, v.52, n.3, 2022. Dry matter intake and productive performance of goats and sheep (2008) 1,168.5 1,060.11** Sheep MACIEL et al. (2019) 1,066.92 1,060.11 Sheep MACIEL et al. (2019) 1Tifton 85 grass; 2Maniçoba silage; 3Leucaena; 4Gliricidia. 30% DM of maniçoba in diets (MACIEL et al., 2019; MOREIRA et al., 2008), 40% DM of maniçoba in diets (LIMA JÚNIOR et al., 2014, 2015a), *maniçoba hay had greater DMI compared to gliricidia hay. **maniçoba hay had greater DMI than tifton 85 hay. Gomes et al. 6 Table 5 – Dry matter intake (DMI) of goats and sheep fed diets based on maniçoba in comparison to diets based on the other roughages. DMI (g animal-1 day-1) --------Animal specie------- -------------------------Reference------------------------- Maniçoba ----Others roughages---- ----------------------------------------------------------------------------Hay-------------------------------------------------------------------------------------- 839.8 799.041 Sheep LIMA JÚNIOR et al. (2014) 544.2 415.91 Goat LIMA JÚNIOR et al. (2015a) 545 5793 Goat MOREIRA et al. (2008) 545 1784* Goat MOREIRA et al. (2008) 1,168.5 1,060.11** Sheep MACIEL et al. (2019) 1,066.92 1,060.11 Sheep MACIEL et al. (2019) 1Tifton 85 grass; 2Maniçoba silage; 3Leucaena; 4Gliricidia. 30% DM of maniçoba in diets (MACIEL et al., 2019; MOREIRA et al., 2008), 40% DM of maniçoba in diets (LIMA JÚNIOR et al., 2014, 2015a), *maniçoba hay had greater DMI compared to gliricidia hay. **maniçoba hay had greater DMI than tifton 85 hay. 1Tifton 85 grass; 2Maniçoba silage; 3Leucaena; 4Gliricidia. 30% DM of maniçoba in diets (MACIEL et al., 2019; MOREIRA et al., 2008), 40% DM of maniçoba in diets (LIMA JÚNIOR et al., 2014, 2015a), *maniçoba hay had greater DMI compared to gliricidia hay. **maniçoba hay had greater DMI than tifton 85 hay. 1Tifton 85 grass; 2Maniçoba silage; 3Leucaena; 4Gliricidia. 30% DM of maniçoba in diets (MACIEL et al., 2019; MOREIRA et al., 2008), 40% DM of maniçoba in diets (LIMA JÚNIOR et al., 2014, 2015a), *maniçoba hay had greater DMI compared to gliricidia hay. **maniçoba hay had greater DMI than tifton 85 hay. to 5.40% BW (ARAÚJO et al., 2004; CASTRO et al., 2007; SILVA et al., 2007; MENDONÇA JÚNIOR et al., 2008; ARAÚJO et al., 2009a; MOURA et al., 2020). performance, seeing that DMI determines the supply of nutrients. Diets composed of maniçoba provided up to 290 g day-1 of weight gain for feedlot sheep, including 20 to 40% DM (CASTRO et al., 2007) or 30% DM of this roughage (CARTAXO et al., 2008). In addition, one study evaluated milk yield of goats fed increasing levels of maniçoba in diets (30 to 60% DM) (ARAÚJO et al., 2009b). Dry matter intake and productive performance of goats and sheep Increasing maniçoba (% DM) in diets promoted greater DMI (ARAÚJO et al., 2004) or did not alter the DMI of sheep and goats (Table 6), indicating this roughage can be included in considerable proportion in diets, without harming the DMI. The results for productive performance of sheep and goats fed maniçoba diets demonstrate weight gain compatible to the one promoted by diets comprising traditional roughages, and enable the inclusion of considerable levels of this plant in animal diets. In addition, other research fronts are important to be pursued, providing a better understanding of the maniçoba based diets for ruminants, regarding the methane emission and the interactions of nutrition and immunological or reproductive responses. Five studies evaluated the average weight gain (ADG) (CASTRO et al., 2007; LIMA JÚNIOR et al., 2014; MACIEL et al., 2019; MOREIRA et al., 2008) of sheep or goats, comparing maniçoba based diets to rations comprising other roughages, or assessing increasing levels of maniçoba in diets (Table 7). In one of those studies, comparing maniçoba hay with Tifton 85 in diets for Moxotó goats, LIMA JÚNIOR et al. (2015a) reported that animals fed with this roughage had -9 g day-1 of body weight variation, while the Tifton 85 based diet (control diet) promoted 10 g day-1 of weight gain (Table 7), without statistical difference for diets. The authors attributed the low ADG promoted by both diets to a lack of adaptation of the animals to the feedlot management, because they had come from an extensive production system, in addition to the advanced age of the animals, and the low DMI presented by goats. Dry matter intake and productive performance of goats and sheep Dry matter intake (DMI) data for goats and sheep fed on maniçoba based diets (hay or silage) were obtained from 13 studies (n = 46 treatments). In four of them maniçoba was compared to other roughages (Table 5), while in nine increasing levels of this forage in diets were evaluated, replacing roughages (MENDONÇA JÚNIOR et al., 2008; MOURA et al., 2020) or concentrates (CASTRO et al., 2007; ARAÚJO et al., 2009a) (Table 6). Maniçoba silage can be made without using additives promoting a proper fermentation process to the ensiling mass, showing aerobic stability for up to 14 days after silo opening (SOUZA et al., 2006); although, the use of additives, such as corn meal, can contribute to the quality of the silage (BACKES et al., 2014). Maniçoba diets promoted similar DMI compared to diets composed by others roughages offered to goats and sheep, and even higher DMI when compared to feed based on hay from feijão-bravo (Capparis flexuosa L.) and gliricidia (Table 5), which might be associated to the presence of anti-nutritional factors, such as tannins and coumarins, respectively, impairing the acceptance of the feed by the animals (LIMA JÚNIOR et al., 2014; MOREIRA et al., 2008). In addition, MACIEL et al. (2019) reported greater DMI by sheep fed maniçoba hay based diets compared to a Tifton 85 based diet (Table 5). Similarly, FRANÇA et al. (2010) reported HCN values of 512.83 and 86.34 mg kg-1 DM for maniçoba in natura or hay, respectively. During the haying process, the plant is chopped and dehydrated promoting the HCN volatilization by the action of sunlight and wind (ARAÚJO et al., 2004). The use of maniçoba silage or hay did not affect the DMI and the average daily gain of sheep (MACIEL et al., 2019). Therefore, both conservation strategies (hay or silage) can be offered to ruminants, seeing that they On average, DMI promoted by maniçoba diets was 4.30% body weight (BW), ranging from 2.85 Ciência Rural, v.52, n.3, 2022. 6 Gomes et al. Table 5 – Dry matter intake (DMI) of goats and sheep fed diets based on maniçoba in comparison to diets based on the other roughages. DMI (g animal-1 day-1) --------Animal specie------- -------------------------Reference------------------------- Maniçoba ----Others roughages---- ----------------------------------------------------------------------------Hay-------------------------------------------------------------------------------------- 839.8 799.041 Sheep LIMA JÚNIOR et al. (2014) 544.2 415.91 Goat LIMA JÚNIOR et al. (2015a) 545 5793 Goat MOREIRA et al. (2008) 545 1784* Goat MOREIRA et al. Ciência Rural, v.52, n.3, 2022. Quality of animal products Using maniçoba for sheep did not result in changes in carcass traits (LIMA JÚNIOR et al., 2014; MACIEL et al., 2015) and non-carcass components yield (MACIEL et al., 2015) when compared to Tifton 85 hay based diets, neither were there changes in the yield of “buchada” and “panelada” (typical dishes using organs and viscera) (LIMA JÚNIOR et al., 2015a). The productive performance of animals receiving maniçoba diets was similar when compared to the other roughages or increasing levels of this roughage in diets in all studies, except MOREIRA et al. (2008), who observed greater ADG for goats fed on a diet based on maniçoba hay compared to a gliricidia based diet, due to the greater DMI (Table 7). The food consumption of animals fed maniçoba diets is an important factor influencing the productive Increasing maniçoba in diets (35 - 70%) for Moxotó and Canindé goats did not alter the centesimal composition, final pH and color of the meat (LISBOA et al., 2010), evincing proper digestive and metabolic responses. The replacement of spineless cactus by maniçoba in sheep diets did not change the physical- chemical composition of the meat, its color or the weight loss in cooking (MOURA et al., 2020). Ciência Rural, v.52, n.3, 2022. Ciência Rural, v.52, n.3, 2022. Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products. 7 Table 6 – Intake of dry matter for sheep or goats receiving diets composed by maniçoba in different levels of inclusion (% DM – Dry matter). Table 6 – Intake of dry matter for sheep or goats receiving diets composed by maniçoba in different levels of inclusion (% DM – Dry matter). Levels (% DM) -----Dry Matter Intake (g day-1)---- -------Animal specie------- ------------------Reference------------------ ---------------------------------------------------------------------Maniçoba hay------------------------------------------------------------------ 30 591.0 Sheep ARAÚJO et al. (2004)1* 40 604.0 50 633.0 60 683.0 70 710.0 20 1240.0 Sheep SILVA et al. (2007)1 40 1240.0 60 1200.0 80 1300.0 20 1160.0 Sheep CASTRO et al. (2007)1 40 1280.0 60 1220.0 80 1190.0 30 1940.0 Goat ARAÚJO et al. (2009a)1 40 2060.0 50 1910.0 60 1910.0 0 845.8 Sheep MENDONÇA JÚNIOR et al. (2008)2 50 912.8 100 960.6 0 1290.0 Sheep SANTOS et al. (2021)1 10 1270.0 20 1240.0 30 1430.0 0 1022.8 Sheep MOURA et al. (2020)1 20 1146.0 40 1183.4 60 1134.8 --------------------------------------------------------------------Maniçoba silage--------------------------------------------------------------- 60 470.0 Goats LOIOLA FILHO et al. Quality of animal products (2012)1 70 500.0 80 470.0 90 430.0 25 957.0 Goats MATIAS et al. (2020)2* 50 1113.0 75 1127.0 100 1220.0 *Indicates crescent linear DMI with inclusion of maniçoba; 1Levels of maniçoba in diets; 2Levels of maniçoba replacing the roughage portion in diets. *Diet exclusively composed by roughages. Intake of dry matter for sheep or goats receiving diets composed by maniçoba in different levels of inclusion (% DM – Dry matter) *Indicates crescent linear DMI with inclusion of maniçoba; 1Levels of maniçoba in diets; 2Levels of maniçoba replacing the roughage portion in diets. *Diet exclusively composed by roughages. *Indicates crescent linear DMI with inclusion of maniçoba; 1Levels of maniçoba in diets; 2Levels of maniçoba replacing the roughage portion in diets. *Diet exclusively composed by roughages. MOURA et al. (2020), based on sensory evaluation of lamb meat, reported greater purchase intention for meat of lambs fed on diets with greater inclusion of maniçoba in comparison to the spineless cactus based diets, evincing greater consumer preference, indicating the meat of lambs fed maniçoba hay diets has adequate equilibrium in sensory parameters as color, aroma, tenderness, juiciness, and flavor. Additionally, MADRUGA et al. (2006) reported adequate polyunsaturated fatty acid levels and polyunsaturated / saturated fatty acids for sheep fed maniçoba diets. An inclusion of maniçoba of up to 60% DM in diets for lactating goats did not modify the physical-chemical composition (proteins, fat, Ciência Rural, v.52, n.3, 2022. Ciência Rural, v.52, n.3, 2022. Ciência Rural, v.52, n.3, 2022. Gomes et al. 8 Table 7 – Productive performance (weight gain or milk yield) of sheep and goats fed on diets comprising maniçoba compared to others roughages or increasing maniçoba levels in diets. Table 7 – Productive performance (weight gain or milk yield) of sheep and goats fed on diets comprising maniçoba compared to others roughages or increasing maniçoba levels in diets. Table 7 – Productive performance (weight gain or milk yield) of sheep and goats fed on diets comprising maniçoba compared to others roughages or increasing maniçoba levels in diets. ------------------------------------------------------------------Average weight gain (g day-1)---------------------------------------------------------------- Animal specie -----Maniçoba----- -------Others roughages------ -Inclusion level (% DM)- --------------Reference--------------- Sheep 122.05 139.01,5 40 LIMA JÚNIOR et al. (2015b) Sheep 146.18 153.31 30 Sheep 135.3 153.31 30 MACIEL et al. (2019) Goat 181a 187a2 30 MOREIRA et al. (2008) 181a 60b3 30 181a 50b4 30 Goat -9.07 10.01 40 LIMA JÚNIOR et al. ACKNOWLEDGEMENTS lactose, dry extract, density and acidity) of the milk (ARAÚJO et al., 2009b; COSTA et al., 2008), nor the fatty acid contents (saturated, monounsaturated and polyunsaturated) (MESQUITA et al., 2008), or the sensorial parameters (odor, taste and overall appearance) (COSTA et al., 2008). We thank FACEPE for the scholarship of the first author IBPG-1424-5.04/18. This study was also financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brasil– Finance code 001. Therefore, the use of maniçoba for goats and sheep has not promoted changes in qualitative parameters of animal products, especially meat and milk, compared to traditional roughages. Further studies are important to increase the database for this forage plant on quality of animal origin products. CONCLUSION The author M L R Gomes was responsible for structuring the manuscript. The authors M L R Gomes and L C Souza wrote topic 2 (Productivity and factors that affect the yield). The authors F C Alves, C M Souza and M N P Silva wrote the topics 3 (Forage quality) and 4 (Dry matter intake and productive performance of goats and sheep). The authors J R V Silva Filho and R A Santana Júnior wrote topic 5 (Quality of animal products). The author T V Voltolini was responsible for correcting all topics and structuring the manuscript. Maniçoba presents forage productivity that may contribute to livestock production systems in the Brazilian semiarid, besides providing forage with adequate nutritional value. Its use in diets for sheep and goats has allowed dry matter intake, productive performance, and quality animal products similar to the ones provided by traditional forage resources, such as Tifton 85 or spineless cactus, reinforcing the possibility of its use in the sheep and goat production systems. Quality of animal products (2015a) Sheep 290.84 - 20 CASTRO et al. (2007)* 293.62 - 40 253.35 - 60 208.48 - 80 --------------------------------------------------------------------Milk yield, kg day-1-------------------------------------------------------------------------- Goat 1.40 - 30 ARAÚJO et al. (2009b) 1.45 - 40 1.33 - 50 1.36 - 60 1Tifton 85 grass; 2Leucaena; 3Caatinga (native vegetation); 4Gliricidia. In line, means followed by different lowercase letters differs by Tukey test (P < 0.05). *indicates a linear decreasing on daily gain with greater inclusion of maniçoba. 5Calculated as follow (weight at slaughter – initial body weight) / number of days. 1Tifton 85 grass; 2Leucaena; 3Caatinga (native vegetation); 4Gliricidia. In line, means followed by different lowercase letters differs by Tukey test (P < 0.05). *indicates a linear decreasing on daily gain with greater inclusion of maniçoba. 5Calculated as follow (weight at slaughter – initial body weight) / number of days. 1Tifton 85 grass; 2Leucaena; 3Caatinga (native vegetation); 4Gliricidia. In line, means followed by different lowercase letters differs by Tukey test (P < 0.05). *indicates a linear decreasing on daily gain with greater inclusion of maniçoba. 5Calculated as follow (weight at slaughter – initial body weight) / number of days. 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Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products. Chemical characterization of different sorts of maniçoba (Manihot Pseudglaziovii Pax and Hoffm) of interest forage. Engenharia Ambiental, v. 12, n. 2, p. 135–142, 2015. Available from: <http://ferramentas.unipinhal.edu.br/ engenhariaambiental/viewarticle.php?id=1247. Accessed: Dec. 2, 2020. MACIEL, M. DO V. et al. Maniçoba hay or silage replaces Tifton 85 hay in spineless cactus diets for sheep. Acta Scientiarum - Animal Sciences, v. 41, n. 1, p. 1–6, 2019. Available from: <http://doi. org/10.4025/actascianimsci.v41i1.42553>. Accessed: Mar. 27, 2020. CAMPOS, F. S. et al. Morpho-agronomic parameters, chemical composition and genetic divergence among Manihot sp. access. Research, Society and Development, v. 9, n. 7, p. 1–21, 2020. MACIEL, M. DO V. et al. Carcass and non-carcass characteristics of sheep fed on cassava (Manihot pseudoglaziovii Pax & K. MACIEL, M. DO V. et al. Carcass and non-carcass characteristics of sheep fed on cassava (Manihot pseudoglaziovii Pax & K. Ciência Rural, v.52, n.3, 2022. Gomes et al. 10 meatsci.2019.107975>. Acessed: Jul. 8, 2020. doi: 10.1016/j. meatsci.2019.107975. meatsci.2019.107975>. Acessed: Jul. 8, 2020. doi: 10.1016/j. meatsci.2019.107975. Hoffm.). Chilean Journal of Agricultural Research, v. 75, n. 3, p. 307–312, 2015. Available from: <http://dx.doi.org/10.4067/ S0718-58392015000400006>. Accessed: Mar. 27, 2020. NASSAR, R. et al. Modeling global atmospheric CO2 with improved emission inventories and CO2 production from the oxidation of other carbon species. Geoscientific Model Development, v. 3, n. 2, p. 689–716, 2010. Available from: <https://doi.org/10.5194/gmd-3-689-2010>. Accessed: Jun. 5, 2020. doi: 10.5194/gmd-3-689-2010. MADRUGA, M. S. et al. Effect of genotype and sex on chemical composition and fatty acid profile of sheep meat. Revista Brasileira de Zootecnia, v. 35, n. 4 suppl, p. 1838–1844, 2006. Available from: <http://dx.doi.org/10.1590/S1516-35982006000600035>. Accessed: Apr. 30, 2020. PARENTE, H. N. et al. Effect of the mineral fertilization on the initial growth and chemical and mineral composition of maniçoba (Manihot sp.). Revista Científica de Produção Animal, v. 9, n. 2, p. 102–110, 2007. Available from: <https://agris.fao.org/agris-search/ search.do?recordID=BR2008008796>. Accessed: May. 12, 2020. MATOS, D. S. DE et al. Chemical composition and nutritional value of the maniçoba silage (Manihot Epruinosa). Archivos de Zootecnia, v. 54, n. 208, p. 619–629, 2005. Available from: < http://www.redalyc. org/articulo.oa?id=49520804>. Accessed: Apr. 12, 2021. MENDONÇA JÚNIOR, A. F. et al. Evaluation of the chemical composition, Intake and in vivo digestibilidade of the diets with different levels of maniçoba hay (Manihot glaziovii Muell. Arg.), SANTOS, K. C. et al. Nutritional potential of forage species found in Brazilian Semiarid region. Livestock Science, v. 195, n. November 2016, p. 118–124, 2017. Maniçoba for sheep and goats - forage yield, conservation strategies, animal performance and quality of products. Quality of wilted manioc (Manihot Epruinosa) silages. Archivos De Zootecnia, v. 55, n. 212, p. 351–360, 2006. Available from: <http://www.redalyc.org/articulo. oa?id=49521203>. Accessed: Jan. 9, 2020. TARRASÓN, D. et al. Land degradation assessment through an ecosystem services lens: Integrating knowledge and methods in pastoral semi-arid systems. Journal of Arid Environments, v. 124, p. 205–213, 2016. Available: <https://doi.org/10.1016/j. jaridenv.2015.08.002>. Acessed: Nov. 18, 2020. MOREIRA, J. N. et al. Roughages alternatives for growing goats. Revista Brasileira de Saúde e Produção Animal, v. 9, n. 3, p. 1398–1398, 2008. Available from: <https://www.cabdirect.org/ cabdirect/abstract/20093272543>. Accessed: Nov. 14, 2020. MORGANTE, C. V. et al. Genetic and physiological analysis of early drought response in Manihot esculenta and its wild relative. Acta Physiologiae Plantarum, v. 42, n. 2, p. 1–11, 2020. Available from: <https://doi.org/10.1007/s11738-019-3005-8>. Accessed: Jul. 7, 2020. VASCONCELOS, W. et al. Morphometry, production and chemical composition of Maniçoba and Pornunça as function of different fertilizer source. Revista Trópica: Ciências Agrárias e Biológicas, v. 4, n. 2, p. 36–44, 2010. Available from: <https:// scholar.google.com.br/scholar?start=40&q=morfometria+ca racterização+caprinos+nativos&hl=pt-BR&as_sdt=0,5&as_ ylo=2010&as_yhi=2015#6>. Acessed: Jul. 15, 2020. MOURA, M. DE S. C. et al. The inclusion of spineless cactus in the diet of lambs increases fattening of the carcass. Meat Science, v. 160, p. 107975, 2020. Available from: <https://doi.org/10.1016/j. Ciência Rural, v.52, n.3, 2022. Ciência Rural, v.52, n.3, 2022.
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Los discursos masculinos como dispositivos de control y tensión en la configuración del liderazgo y empoderamiento femenino
Revista Estudos Feministas
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cc-by
9,023
Paulina Irene Salinas Meruane Escuela de Periodismo de la Universidad Católica del Norte, Chile Los discursos masculinos como dispositivos de control y tensión en la configuración del liderazgo y empoderamiento femenino Resumen esumen: En el presente artículo se exponen algunos de los antecedentes centrales del proyecto de investigación “Los Discursos de la Masculinidad”: El Empoderamiento Femenino desde el Análisis Critico del Discurso.1 Utilizando un enfoque cualitativo, se desarrollaron entrevistas abiertas con el objetivo de comprender el significado que le asignan los hombres al liderazgo femenino. Los discursos fueron analizados en base a la Teoría Fundamentada de Anselm Strauss y Juliet Corbin (2003).2 Los resultados muestran que los varones coinciden en términos generales respecto a los cambios que ha habido en los roles de género, en que las mujeres tienen y deben tener más oportunidades, en que hay una mayor incorporación de éstas en el mercado laboral y en la necesidad de tener relaciones más equitativas al interior de la familia. Así mismo, emergen tensiones que configuran el malestar de la masculinidad, traspasando la esfera íntima y cuestionando las relaciones de intergénero actuales. También hay discursos más progresistas en los varones, que se aventuran hacia un reconocimiento de las capacidades y roles que han ido asumiendo las mujeres en el espacio público, aunque se trata de un reconocimiento vigilante, ambivalente, mediatizado por una percepción de confianza/desconfianza, eficiencia/ incompetencia, hacia lo que ellas son capaces de lograr. Palabras claves claves: empoderamiento; transformaciones; genero Copyright ¤ 2007 by Revista Estudos Feministas. 1 Investigación realizada entre el 2005 y 2006 y que contó con el financiamiento de la Dirección General de Investigación y Postgrado de la Universidad Católica del Norte, Antofagasta. 2 STRAUSS y CORBIN, 2003. 2 STRAUSS y CORBIN, 2003. Introducción En el presente artículo se exponen algunos hallazgos obtenidos en el proyecto de investigación: Los Discursos de la Masculinidad: El Empoderamiento Femenino desde el Análisis Crítico del Discurso, realizado el 2006. Este trabajo se enmarca en una línea investigativa que se desarrolla desde el 2003, periodo en el que se abordó la comprensión del liderazgo de las mujeres en organizaciones de la I y II región de Chile. Dicho trabajo permitió describir el liderazgo femenino e identificar fortalezas y debilidades en el ejercicio Estudos Feministas, Florianópolis, 15(3): 336, setembro-dezembro/2007 541 PAULINA IRENE SALINAS MERUANE 3 Norman FAIRCLOUGH y Ruth WODAK, 2000. del mismo. Luego nos plateamos avanzar en la comprensión de este fenómeno, teniendo en cuenta dos premisas centrales: la primera, que las preguntas acerca de las mujeres implica comprender la perspectiva de los varones, ya que el género es un sistema de interacciones sociales y no un sistema de compartimientos estancos, es decir, lo que afecta a unas implica a otros. Y la segunda, referida a concebir el lenguaje y el habla como una forma de práctica social, es decir se trata de desentrañar la relación dialéctica entre un suceso discursivo particular y las situaciones, instituciones y las estructuras sociales que lo enmarcan.3 En consecuencia, analizar la práctica discursiva de los hombres sobre el liderazgo y empoderamiento femenino es un factor significativo en la comprensión subjetiva de este fenómeno y ayuda a develar el lenguaje como productor y reproductor de las relaciones de poder desiguales. Dicho esto, el artículo se centra en analizar los significados que le asignan los hombres al empoderamiento femenino, las tensiones, ambigüedades y mecanismos de control que tienen respecto a las transformaciones en el ejercicio del poder femenino. Nos interesó profundizar desde la perspectiva masculina, ¿cómo perciben los varones el poder personal que han alcanzado las mujeres?, ¿hay transgresiones y/o reivindicaciones en el empoderamiento femenino?, ¿qué obstáculos reconocen ellos en este proceso? La perspectiva de análisis desde los discursos masculinos se centra en la búsqueda de una comprensión holística del fenómeno del liderazgo y participación femenina, entendiendo la perspectiva de género como una categoría relacional de todos los procesos y fenómenos sociales, y no sólo como un tema que se constriñe a la configuración de las identidades y roles. Este estudio presenta algunos adelantos en este sentido, ya que se plantea la comprensión de los aspectos subjetivos relacionados a la conformación del liderazgo, teniendo presente que se han producido transformaciones significativas, vinculadas con el cuestionamiento que elaboran los varones acerca de las demandas que se les hace como hombres, lo que representa una expresión de malestar o una cierta perplejidad que se extienden más allá de la esfera íntima y que los interpela en el ejercicio de roles en tanto hombres, padres, parejas, amigos. El contexto discursivo La producción y comprensión del discurso implica tomar en cuenta el contexto, y particularmente en lo que respecta al empoderamiento de las mujeres en América 542 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN... Ximena MACHICAO Barbery, 2006. 4 5 PNUD, 2004; INE, 2002; OIT, 2000. 6 José OLAVARRÍA, 2001b, p. 31. latina debe hacerse referencia al elemento sincrónico del proceso, ya que efectivamente se han producido transformaciones importantes desde la segunda mitad del siglo XX en adelante. Tanto en América Latina como el Caribe se observa una apertura política que se traduce en una mayor incorporación de las mujeres a los espacios de poder, en cargos de ministras en Chile, Argentina, Brasil, Bolivia y Uruguay; en el área legislativa, judicial, en los gobiernos municipales o proyectándose como candidatas a la presidencia o vicepresidencia, como fue el caso de México y Costa Rica, lo que junto a la larga historia que tienen luchando por una mayor participación y representación política, dan cuenta de que se han producido transformaciones en favor de una ruptura de la hegemonía masculina en el ejercicio del poder político.4 En esta dirección, en marzo 2006 se marca un hito en la historia política del país: por primera vez una mujer logra ser elegida presidenta de la república, siendo este hecho en si mismo un avance sin precedentes para las mujeres, y que sólo el análisis posterior de la historia podrá dimensionar en toda su magnitud. Sin embargo, instalado el gobierno de Michelle Bachelet, es oportuno analizar la conflictiva relación de las mujeres y el poder y las reivindicaciones y transgresiones que esta analogía provoca. En este sentido, si presentan algunos antecedentes preliminares para comprender la dimensión de este fenómeno, y si apuntan a una transformación de los códigos culturales del país y a una democratización real de la sociedad, o estamos presenciando algunos cambios para que todo permanezca igual. Diversos estudios coinciden favorablemente en que en Chile se ha producido un aumento gradual tanto de la participación como del liderazgo femenino en las distintas áreas del quehacer nacional. Por ejemplo en el ámbito laboral, la incorporación de las mujeres experimentó, durante la década de los mil novecientos noventa, un incremento sustantivo desde un 28,06% en 1992 a un 35,5% en el año 2002, lo cual marca un incremento superior a 7 puntos porcentuales.5 También en la política un enclave eminentemente masculino ha sido levemente modificado, con la inclusión de la paridad como principio articulador del poder ejecutivo – léase ministerios, intendencias, gobernaciones. En cambio, se constatan resistencias en sectores como las organizaciones sindicales, las que siguen controladas por los varones que son quienes articulan los espacios y redes de homo sociabilidad y, en general, lo mismo se observa en los puestos de mayor jerarquía pública.6 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 543 PAULINA IRENE SALINAS MERUANE 7 Teresa VALDÉS y Mariza WEINSTEIN, 1993; Olga RUIZ, Sandra SOLANO y Claudia Zapata, 1998; SERNAM, 2000; GIM, 2002; VALDÉS, 2001; Paulina SALINAS, 2002; PNUD, 2004. 8 PNUD, 2004, p. 87. 9 PNUD, 2004, p. 17. 10 Mala HTUN, 2003. Otros estudios profundizan las complejidades que han experimentado las mujeres en su lucha por alcanzar un mayor protagonismo y reconocimiento en la sociedad.7 Estas investigaciones develan las tensiones que han existido entre las mujeres y su acceso a los espacios de poder. Algunos de los argumentos que se arguyen para explicar este fenómeno se relacionan con pesados lastres y grandes brechas que caracterizan la distribución de recursos y derechos existentes en la sociedad chilena. El quinto Informe sobre Desarrollo Humano identifica dos elementos que frenan un mayor y mejor aprovechamiento de las oportunidades que el país ofrece, y que se relacionan con la insuficiente disposición de poder social y una desigual distribución del poder de acción personal, ambas afectando la capacidad de los ciudadanos para aprovechar las oportunidades y levantando barreras a la asociatividad.8 Otras amenazas más imperceptibles se vinculan a la permanencia del statu quo de parte de quienes no quieren ceder poder: el temor a entregar poder a otras personas, especialmente a las mujeres, y a las organizaciones. Hay desconfianza en las capacidades de estos actores para tomar decisiones.9 Otras resistencias son hacia lo que implica promover la participación ciudadana, sean estas en iniciativas colectivas o individuales; hay temor al “desborde”, a los pliegos de peticiones, al aumento de expectativas, entre otras. Por lo tanto, analizar los avances y retrocesos en el proceso de empoderamiento y construcción ciudadana de las mujeres como sujetos políticos con relevancia social, facilita la comprensión de los cambios en su verdadera dimensión como una manera de visualizar los desafíos que tiene la sociedad chilena en su conjunto, entendiendo que los avances en la consolidación de la democracia están entramados al desarrollo sostenible y a un crecimiento económico equitativo. Sin embargo, la mayor libertad política y la promoción de mercados más liberalizados no han desencadenado directamente avances sustantivos en cuanto a los derechos ciudadanos, ni respecto al bienestar económico de la población en su conjunto. De hecho plantea Mala Htun que en la medida que las brechas salariales se incrementan, muchas mujeres en Latinoamérica carecen de las capacidades básicas y permanecerán excluidas de los sectores elegibles para ocupar cargos de mando.10 Por ejemplo, no es menor que, no sólo en el país, sino que en el resto del mundo las mujeres, aunque representan más de la mitad del electorado, apenas 544 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN... 11 MACHICAO, 2006, p. 20. 12 PNUD, 2004, p. 21. 13 OLAVARRÍA, 2001b, p. 24. 14 Robert W. CONNEL, 1998, p. 77. alcanzan al 12,7% del total de bancadas parlamentarias en el mundo, y que en América Latina no logran el 10%. Si bien en algunos países como Argentina y Costa Rica muestran logros importantes, en otras naciones los progresos han sido relativos o nulos, a pesar de las medidas de discriminación positiva, que de hecho no tienen un carácter vinculante a la Constitución Políticas de los Estados. Por lo tanto, su aplicación se encuentra supeditada a la voluntad de los gobiernos de turno. 11 En este contexto, cabe preguntarse para el caso chileno, en qué medida la pariedad introducida por el gobierno de Bachelet por ejemplo, ¿es una iniciativa que perdurará en el tiempo?, ¿será que la presencia de las mujeres en el poder ejecutivo marcará la agenda pública?, ¿cuáles son los obstáculos que enfrentan en los puestos de poder?, ¿la mayor presencia de las mujeres en cargos de representación conlleva modificaciones en los mandatos de género?, es decir son múltiples los cuestionamientos plausibles de hacerse y las sospechas que se generan sobre el tipo de política que se está construyendo en el país. Además, las alianzas políticas femeninas no siempre han logrado resistir con éxito las exigencias partidarias con la inclusión de temas que favorezcan los derechos de las mujeres. Estas interrogantes permiten abrir la discusión hacia esferas que hoy día son gravitantes para el desarrollo y la consolidación del sistema democrático. Chile ha tenido logros importantes en materia de indicadores sociales, ha alcanzado un destacado posicionamiento en cuanto al Desarrollo Humano en el contexto latinoamericano,12 a lo que se suma un mejoramiento en la búsqueda de un mayor equilibrio en las relaciones entre hombres y mujeres, producto de la evolución económica, social y cultural de la sociedad chilena y del mundo en general.13 Tanto la globalización como los cambios de la economía han potenciado demandas de modernización en el espacio íntimo, cuestionándose las bases de la masculinidad autoritaria y la familia nuclear patriarcal, por perpetuar esta última la inequidad, limitar la autonomía, la diversidad y las relaciones democráticas al interior de la familia. Asimismo, los debates respecto a las relaciones de género se están produciendo globalmente. Las relaciones de género forman parte de la estructura de la sociedad mundial y es necesario reconsiderar muchos temas a la luz de este hecho.14 Junto a lo anterior, la sociedad chilena también presenta irrefutables fracturas, una inequitativa distribución de los ingresos, insuficiente política de igualdad de oportunidades, entre otras. En consecuencias, hoy día es una condición sine qua non del desarrollo humano Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 545 PAULINA IRENE SALINAS MERUANE fortalecer la participación ciudadana, entregando más poder a cada uno y a la sociedad en su conjunto. Estrategia metodológica y corpus 15 WODAK, 2003, p. 19. 16 Ron SCOLLON, 2003. 17 Teun A. VAN DIJK, 1997, p. 15. 18 Angelika HENNECKE, 2004, p. 107. 19 FAIRCLOUGH y WODAK, 2000. 20 Lupicinio IÑIGUEZ Rueda, 2003, p. 94. Como mencionamos anteriormente, la propuesta investigativa se inscribe dentro del Análisis Critico de Discurso (en adelante ACD), concebido éste como un enfoque que se ocupa de develar las relaciones de dominación, discriminación, poder y control, tal como se manifiesta a través del lenguaje. En otras palabras plantea Wodak,15 el ACD se propone investigar de forma crítica la desigualdad social tal como viene señalada, expresada, constituida, legitimada por los usos del lenguaje. El lenguaje acompaña frecuentemente a nuestras acciones, y las acciones acompañan gran parte de lo que decimos. 16 Así entonces, el ACD propone analizar críticamente el discurso como una forma de abordar los problemas sociales que se van concadenando en los discursos. Vale decir nos interesó analizar qué y cómo hablan los hombres respecto a las transformaciones en el empoderamiento de las mujeres, cómo discursean sobre los cambios que se han experimentado ellas en la sociedad, qué tensiones se generan, y cómo viven esta experiencia tanto en el ámbito público como privado. El ACD es la denominación genérica que se aplica a un planteamiento especial dedicado a estudiar los textos y el habla y que emergen de la crítica lingüística, semiótica, y, en general, del modo sociopolítico consciente y oposicionista en que se estudia el lenguaje, el discurso y la comunicación.17 La ampliación de la lingüística del texto pragmático – comunicativa por el Análisis Crítico del Discurso – consiste en que ésta le permite visualizar la relevancia social y política de los textos, faculta mostrar una dimensión de significado que sobrepasa el encasillamiento a un marco situacional, concreto y actual.18 Es una forma de intervenir en la práctica social y en las relaciones sociales.19 Es considerado una práctica tridimensional, en el sentido que la práctica analítica opera en tres dimensiones: a) el discurso en tanto texto, b) el discurso como práctica discursiva enmarcado en una situación social concreta, y el c) el discurso como un ejemplo de práctica social, que no sólo expresa o refleja identidades, prácticas, relaciones, sino que la constituye y conforma.20 A la luz de esta propuesta analítica se desarrolló un estudio descriptivo con fines interpretativos, es decir, una propuesta investigativa eminentemente cualitativa, en la que se concibe la realidad social como subjetiva, múltiple y cambiante, como resultado de una construcción de los 546 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN... José Ignacio RUIZ, 1999; Miguel S. VALLES, 2000; María Paz SADÍN Esteban, 2003. 21 22 STRAUSS y CORBIN, 2002. 23 RUIZ, 1999, p. 64. 24 STRAUSS y CORBIN, 2002. sujetos participantes que se encuentran en interacción con otros miembros de la sociedad.21 El corpus del estudio estuvo conformado por los discursos de 59 hombres. En la primera fase investigativa se aplicaron 20 entrevistas individuales en profundidad, durante el 2005. Esta etapa se desarrolló en forma secuencial (comparación constante),22 de tal manera que una vez que la primera entrevista fue realizada, se procedió a su trascripción y análisis preliminar; de este modo la segunda entrevista incorporó los aportes de la primera y así sucesivamente. Luego en una segunda fase, durante el 2006, se entrevistaron 39 hombres en cuatro entrevistas grupales, de tal manera de triangular la información obtenida en la modalidad individual y así acceder al discurso social de los varones. Para seleccionar a los entrevistados se utilizó un muestreo cualitativo intencional,23 buscando distintos representantes del universo masculino en la región. Se entrevistó en la modalidad individual a varones, con distintos niveles socioeducacionales, nueve profesionales universitarios, cinco con formación técnica, tres estudiantes universitarios y tres con cuarto año medio rendido. Las edades fluctuaron entre los 19 y los 63, con edad promedio de 40 años. En la primera entrevista grupal participaron 10 varones, cuyas edades fluctúan entre 21 y 46, con un promedio de 30 años, todos tienen cuarto año medio rendido y se desempeñan como operarios en la empresa C.S.M, Tecnología Ltda. de Antofagasta. En la segunda, participaron 14 varones, cuyas edades fluctúan entre 39 y 56 años, y 46 años de edad promedio, el nivel de escolaridad de los participantes es de enseñanza básica (5), enseñanza media (6) y algunos tiene formación técnica (3). En la tercera, participaron 7 varones, cuyas edades fluctúan entre los 32 y 49 años, y 38 años de edad promedio. Se desempeñan como auxiliares de servicio en el Liceo Experimental Artístico de Antofagasta. El nivel de escolaridad de los entrevistados es enseñanza básica completa (3), enseñanza media incompleta (3) y completa (1). Y en la cuarta entrevista participaron 8 varones que se desempeñan como personal en la Cárcel de Hombres de la ciudad de Antofagasta (gendarmes y vigilantes), cuyas edades fluctúan entre 19 y 43 años, con 29 años de edad promedio. Todos poseen cuarto año medio rendido. El análisis de los datos complementó dos propuestas: la primera corresponde a la utilización de una teoría base de análisis cualitativo como la Teoría Fundamentada, de Barney Glaser y Anselm Strauss,24 identificando de esta manera las prácticas sociales de los sujetos; luego para comprender las prácticas discursivas y textual se hizo una Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 547 PAULINA IRENE SALINAS MERUANE 25 JÄGER, 2003. 26 Luis Enríque ALONSO, 2003, p. 204. CONNELL, 1998; OLAVARRÍA, 2001a, 2001b, 2005; María José MORENO Ruiz, 2001. 27 28 OLAVARRÍA, 2005. aproximación de acuerdo a la propuesta de ACD de Siegfried Jäger.25 Esta aproximación implicó rescatar los elementos más significativos y pertinentes para el estudio. Por lo tanto, nos centramos en identificar el hilo discursivo, su caracterización y la combinación de un análisis global y fino de la textualidad de los discursos de los hombres. Estas propuestas de análisis fueron apropiadas para la investigación, ya que generaron resultados que describen el fenómeno y permiten establecer relaciones teóricas. Se trató de situar los discursos no sólo en consideración al marco situacional, sino que también a los propios sujetos y sus subjetividades.26 Resultados y análisis: hilando los discursos Casi dos décadas después de los avances experimentados en las sociedades industrializadas, se inician los estudios sobre la masculinidad en Chile, sobre todo los referidos a la construcción de la identidad de género de los hombres. Sirviéndose de los adelantos ya alcanzados en otros contextos, ha comenzado un interés creciente en distintas universidades y centros de estudios del país por abordar interrogantes sobre sí la masculinidad se encuentra en crisis, cómo se construye hoy la masculinidad. ¿Hay una nueva masculinidad? Más que responder estos cuestionamientos exhaustivamente abordados por diferentes autores 27 concluyen sobre las transformaciones que se han experimentado en las identidades de género y que están estrechamente vinculadas a procesos estructurales como la globalización, la sociedad de la información y el modelo neoliberal. Asimismo, los estudios realizados en Chile expresan que, aunque los hombres se muestran proclives a las demandas de las mujeres, en la vida cotidiana no se advierten cambios significativos, ya que ellas siguen siendo las principales responsables de lo doméstico y de la crianza de los hijos. Igualmente se confirma una cierta fragilidad en los discursos que hablan de una nueva masculinidad, ya que no tienen un correlato empírico que los sustente. Más aún, aspectos como la intensidad del lazo amoroso tendría un papel preponderante en la relación de pareja, de manera que facilitaría negociar de mejor manera la participación del varón en la unidad doméstica.28 A partir de estos hallazgos, nos centramos, en aquellas transformaciones de la masculinidad que han provocado una ruptura en la exclusividad de los espacios de poder que históricamente eran asignados a los hombres, tanto en el ámbito público como en el privado, configurándose nuevas formas de relacionarse en el interior 548 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN... Kathia ARAUJO y Francisca ROGERS, 2000, p. 60. 29 de la familia, en el ámbito laboral y en las distintas esferas de sociabilidad. Estos procesos de fracturas socioculturales han modificado los equilibrios previos, surgiendo nuevos órdenes de género en los que se cuestionan algunos valores como la masculinidad hegemónica, el autoritarismo, la violencia intrafamiliar, entre otros. Estas variaciones han sido referidas por algunos autores como una ruptura de ciertos sustentos estructurales que se acompañan por la pérdida de los significados de la masculinidad, develando distintas formas de ser hombre, ampliando las identidades y las formas de construir lo masculino.29 Desde aquí se propuso en este estudio hacer un giro respecto a la tendencia que se ha dado en las investigaciones de género, en el sentido de abordar estas temáticas generalmente en forma dicotómica, ya sea lo femenino o lo masculino. En este sentido buscamos destacar el carácter relacional de los cambios, ya que han desencadenado modificaciones en la construcción de identidades de hombres y mujeres marcadas por las transgresiones, rupturas resistencias de género, que están lejos de lograr un acomodo social, por lo tanto, avanzar en su análisis posibilita su abordaje y comprensión. Dicho esto, a continuación presentaremos una síntesis sobre algunos resultados del estudio que se aproximan a delinear las tensiones en los espacios de poder y liderazgo femenino, desde la textualidad masculina. Los caminos zigzagueantes de las mujeres al poder: entre el control y la tensión Irene VASILASCHIS DE GIALDINO, 2003. 30 En los discursos analizados, tienen como elemento transversal la dificultad de los hombres para hablar desde el yo; la tendencia es que ellos se explayan en un lenguaje general que no los interpela en sus experiencias individuales. El hilo discursivo que cruza el habla masculina está marcado por una serie de oposiciones30 personal/impersonal, particular/general afirmativo/negativo, gusto/disgusto, aceptación /rechazo. Esto queda de manifiesto en formulaciones ambivalentes respecto a las percepciones que tienen sobre el poder alcanzado por las mujeres en los ámbitos laborales, políticos y familiares. Los hombres elaboran un discurso proactivo, favorable al cambio de roles que se ha experimentado en la sociedad chilena, que ha impulsado la incorporación de las mujeres al mercado laboral, pensando en las transformaciones como un proceso normal de evolución hacia un mayor protagonismo de las mismas. Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 549 PAULINA IRENE SALINAS MERUANE 31 Entrevista individual, hombre 62 años. 32 María Asunción GONZÁLEZ DE CHÁVEZ Fernández, 1998, p. 16. 33 Entrevista individual, hombre 60 años. 34 Entrevista individual, hombre 55 años. Paulina SALINAS y Susana ARANCIBIA, 2006. 35 Las mujeres estaban relegadas a la casa y no podían votar, no tenían ninguna participación ciudadana, no tenia ningún tipo de decisión cívica, era difícil que ellas llegaran a acceder al poder, pasan los años y la mujer se comienza a incorporar a la fuerza laboral, más aún de manera más formal, accede más a la educación, antes era muy difícil.31 Los conflictos de las mujeres de hoy están vinculados con las restricciones impuestas al modelo de mujer/ feminidad vigente, con las dificultades que presentan ellas para descubrir/aceptar/expresar sus deseos al margen de dicho modelo, y con la vigencia de una organización social y una identidad masculina, compartida por las mujeres, que no permite el cuestionamiento real del statu quo, al no integrar como responsabilidad y (dis) valores “femenino”, estigmatizados y/o hiperdemandado a las mujeres que luchan por un nuevo modelo social y de género.32 Como ejercen el poder hoy día las mujeres… yo creo que siempre, sin perder su rol femenino y yo creo que eso les ayuda mucho, yo te diría esa coquetería innata que tiene la mujer, no puede perderla; aunque pudiera mandar, porque ya me veo una niña buenamoza te fijas, y es la jefa más encima.33 Ahora hay mujeres que han alcanzando, cargos que antiguamente ni siquiera se habían soñado. Pienso que las mujeres son muy capaces en los puestos son más metódicas, son, “menos corruptas” que los hombres, desde mi punto de vista personal, yo creo que están entrando en una esfera donde ya no deberían haber muchos distingos de sexo.34 Junto a esta visión proactiva al cambio de roles de las mujeres en la sociedad se devela en los discursos también la vigencia de mandatos socioculturales que las constriñen en un imaginario social masculino de: mujer/ madre/feminidad, configurándose, entonces, un proceso dinámico, transformador, con elementos de control y tensión, ruptura y continuidad en las relaciones entre los géneros. En otras palabras, en los discursos se constata la vigencia de la perspectiva esencialista en los hombres, y que circunscribe a estas últimas a una identidad de mujer, pasiva sensible, femenina, correspondiente con una identidad homogénea construida desde la estructura patriarcal y que retrotrae a las mujeres al espacio privado como principales responsables de las tareas domésticas y reproductivas, y con una marcada distribución sexual de los roles.35 Mi esposa hace poco se puso a trabajar, hace poco, yo creo que hace un año más o menos. La percepción 550 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN... 36 37 38 39 Entrevista grupal Nº 2. que tengo de este asunto, personalmente, hemos tenido algunos problemas por el asunto, por el problema de que ahora que ella… aparte del dinero que yo le entrego, ella ahora recibe su dinero cierto, pero ahora por ejemplo a veces tenemos conversaciones, y ella como que se pone muy altanera, o sea como que ahora como que dispara más de lo que se disparaba antes. Yo creo que como se puede decir vulgarmente, como que se creen el cuento.36 Entrevista grupal Nº 2. Tiene su pro y su contra que la mujer trabaje. Yo ahora estoy teniendo problemas por ese asunto, porque yo siempre llevé el dinero a la casa, cierto yo, o sea, no es que ella me pase a llevar, sino como que ella tiene otra percepción de este asunto; digamos ahora, según, como que se pone más altanera, así ya, me levanta más la voz, y uno que es..., yo me considero un hombre machista, para mi es molesto.37 Entrevista grupal Nº 3. Por mi parte, no me gustaría que la mujer trabajara o sea, yo no soy machista, pero yo creo que el hombre es el que, que las lleva en la casa, uno le da alimento a ella, porque la mujer cría los hijos.38 SALINAS y ARANCIBIA, 2006. GONZÁLEZ DE CHÁVEZ, 1998, p. 15. 40 Estas resistencias, como decíamos, se traslapan con discursos más progresistas en los varones que se aventuran hacia un reconocimiento de las capacidades y nuevos roles que han ido asumiendo las mujeres en el espacio público, aunque se trata de un reconocimiento vigilante, ambivalente, ya que está mediatizado por una percepción de confianza/desconfianza, eficiencia/incompetencia, hacia lo que ellas son capaces de lograr, lo que, muchas veces, también es autoreferido por las propias mujeres.39 De ello se infiere la actualidad que tiene en la identidad femenina una construcción en la que preexiste una naturaleza o una esencia femenina o masculina, subsidiaria de un orden simbólico dado, también construido, y, por tanto, no único posible e inmodificable. Tales identidades van enraizadas a un sistema de representaciones y a elaboraciones culturales que sirven de base y las cimentan.40 Estas representaciones ambiguas tienen altos costos afectivos y emocionales para las mujeres y que redundan en insatisfactorias relaciones inter género y que por su naturaleza son de difícil contención. En el ámbito privado ellas se articulan, ya sea cediendo, traspasando o negando sus propias aspiraciones. Y en el ámbito público, espacio de desarrollo en el que se juegan aspiraciones como el reconocimiento de los otros, el respeto, la valoración, son logros que alcanzan a costa habitualmente de otros aspectos de su vida, la familia, la relación con los hijos, con la pareja, ya que estos últimos y las propias mujeres Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 551 PAULINA IRENE SALINAS MERUANE 41 42 43 GONZÁLEZ DE CHÁVEZ, 1998. responden al imaginario social de la mujer como sujeto capaz de cubrir todas demandas y con alta capacidad, para estar simultáneamente cubriendo “exitosamente” las distintas demandas del espacio público y privado. A pesar de la mayor apertura del campo laboral para las mujeres, ellas se encuentran en dificultades para compatibilizar el papel tradicional que de ellas se espera en el hogar con la inclusión en un medio cultural androcéntrico. Ya que este ámbito altamente competitivo ha sido organizado por el hombre para cumplir con el nivel de exigencia acorde con las circunstancias, contando con el contingente provisto por la mujer para cubrir las necesidades vitales y emocionales de él y de los hijos. En consecuencia, la tensión que experimentan las mujeres en la configuración de su identidad y en el proceso de empoderamiento como mujeres y como madres, es donde se plasma con mayor énfasis el conflicto y las resistencias, llenando de sentimientos de culpabilidad e inadecuación a aquéllas que se desmarcan de él o comparten duramente diversas tareas intra y extrafamiliares. Por otra parte, muchas madres, gratificadas a menudo en detentar el lugar – la fantasía – de la omnipotencia, han tenido y tienen dificultades internas y sociales para escaparse al papel y la imagen en que han sido encerradas.41 Entrevista grupal Nº 2. Por ejemplo, el cambio también lo que yo me he dado cuenta también que por ejemplo mis niños cierto y a veces yo me he levantado y los niños tienen puesta la mesa digamos, las tacitas todo, la tetera y todo el asunto, o sea como que ellos también se están acostumbrando a ese sistema pero también les ha afectado, por ejemplo la niña no hace tareas hasta cuando llegue la mamá, el más chiquito también, tiene que hacer algún trabajo y todo, lo hace, pero está esperando a su mamá.42 Entrevista grupal Nº 2. Yo creo que hay dos cosas, que trabaje la mujer es bueno, porque también tiene derecho igual que el hombre a estudiar, a desarrollarse profesionalmente todo el asunto, pero a la vez también es un atentado contra la familia porque alguien tiene que estar más, como cerca con los hijos. Son dos cosas, una que la mujer se pueda desarrollar profesionalmente y otra ¿pero qué pasa con la familia? ¿qué pasa con los hijos?, y todos estos problemas que se han suscitado ahora.43 El modelo de mujer-madre conserva toda su vigencia ética, en los discursos masculinos, llenando de sentimientos contradictorios las existencias femeninas. Hay un deseo de la maternidad arraigado a la socialización primaria de las mujeres, y que encuentra un cimiento idealizador en los 552 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN... hombres. Por lo tanto para aquéllas que desean distanciarse de esta construcción resulta culpabilizador, complejo cargado de dificultades internas y sociales, ya que implica negar un imaginario social que ha sostenido la familia nuclear patriarcal. 44 45 Entrevista grupal Nº 4. Aparte que de todo esto del cambio, también la mujer es… una… parte súper importante, es protagonista, porque en estos tiempos igual, hay mujeres que dicen, por ejemplo tú dices ya, voy a lavar, voy a cocinar, voy a hacer esto otro y la mujer te dice no, yo hago eso, no, yo plancho, entonces como que la mujer también se siente amenazada porque tú estay ocupando el rol que ocupa ella. Entonces ahí la mujer cumple una función principal y si realmente queremos lograr un equilibrio y una igualdad la mujer también va a tener que cambiar la mentalidad .44 Entrevista grupal Nº 4. Hay bastantes mujeres que aunque trabajen y todo, tienen una mentalidad machista, o sea al hombre no lo dejan hacer sus cosas y lo terminan haciendo ellas dándole en el gusto en todo.45 En los discursos los varones hablan de los nuevos roles que las mujeres desempeñan en la sociedad actual, sobre todo en el ámbito laboral y la compatibilidad de ellos, pues aprueban que las mujeres trabajen y aporten al sustento de la familia, pero ojalá esto no modifique el orden familiar y por ende, aunque ellos ya no sean los único proveedores, sus expectativas se aferran a los mandatos de género de la familia tradicional, respecto a la crianza y cuidado de los hijos. Entrevista individual, técnico, 20 años. 46 Es que antes eran distintos los cambios, la sociedad era distinta, o sea, con la mujer tenía muchos más hijos que ahora, y era por la circunstancia, ante se podía tener más hijos, ahora ya no se puede tener tantos hijos como antes, entonces la mujer debe tomar otros roles también más protagónicos en la parte laboral, para poder mantener un equilibrio económico, porque ya no alcanza a lo mejor con un sueldo, o simplemente que la mujer sea dueña de casa, ya no basta con por la política económica que actualmente estamos viviendo.46 La participación social igual ha ido en menoscabo un poco de la participación que las mujeres tenían en la crianza de los hijos antiguamente. Hoy en día, la mujer pasa mucho tiempo fuera del hogar como que ha mermado, en cierta forma las relaciones familiares, pero igual es positivo que esté trabajando, esté ocupando cargos, porque igual posee capacidades…que son bien positivas también, en todas las cosas existen ventajas y desventajas. Y la desventaja es esa, la crianza Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 553 PAULINA IRENE SALINAS MERUANE 47 48 Entrevista grupal Nº 4. María Elena VALENZUELA, 2000. Rosalía TODARO, Amália MAURO y Sonia YAÑEZ, 2000, p. 94. 49 de los hijos ya se le está delegando a la escuela, a los profesores, a las academias, no sé, a los gimnasios, a los clubes deportivos… ya no es tanto la casa, la familia, como el núcleo de la formación de una persona.47 En las últimas décadas han surgido nuevos modelos productivos que han afectado significativamente el sistema de relaciones laborales y la calidad de los empleos. Estos modelos tienen como centro la flexibilidad del empleo y de la organización de las empresas, y han brotado en medio de una masiva incorporación .de las mujeres a la fuerza de trabajo. En el Cono Sur, Chile registró el mayor incremento en los últimos 30 años, aun cuando el nivel de participación laboral de las mujeres se sitúa bajo el promedio regional.48 Sin embargo, la incorporación masiva de las mujeres al empleo ha sido acompañada de una notable precarización del mismo. Aspectos de la calidad del empleo de las mujeres, tales como la regularidad y estabilidad laboral, los ingresos, las horas de trabajo y su intensidad, los peligros ocupacionales para la salud, el ambiente de trabajo, la protección laboral y social, los contenidos de los empleos y las oportunidades que ofrecen para el desarrollo personal y las trayectorias laborales, como el estatus social que proporciona, están siendo fuertemente permeados por el fenómeno de la segregación de género.49 Aunque la identidad masculina tradicional sigue vigente, se aprecian transformaciones en su forma y en su fondo, ya no se trata del hombre que exige abiertamente que la mujer permanezca en el espacio doméstico y que realice las tareas que históricamente se le han asignado al sexo femenino, vale decir, socialmente se reconoce que las mujeres deben cumplir un rol más activo en la sociedad, tener un trabajo y realizarse como persona. Sin embargo, el histórico machismo se ha camuflado y hoy se basa más en el control y en la coerción psicológica que en la discriminación o en las restricciones físicas. Es el dominio que se ejerce en la clandestinidad, el denominado neomachismo. Sabe una cosa yo pienso que cuando, que las mujeres se ahogan mucho de que cuando se habla mucho de que se ha incorporado al ámbito laboral. Es cierto si hay mujeres de que se han superado y han… han digamos ehh… al hombre lo han superado digamos, en muchas, en muchas carreras, muchas etapas, pero si es cierto entra a una empresa y empiezan a discriminarla, me entiende, a aislarla, o sea siempre el hombre va por naturaleza, va a tirarla pal lao…Porque es así, yo lo veo de esa manera, no porque soy machista ni nada de eso, por naturaleza se da así, se da así, la 554 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN... 50 51 Entrevista grupal Nº 2. mujer…llega una jefa y el jefe de al lado y… le hace la guerra y ella no tiene nada que ver con los empleados es una guerra de jefatura digamos.50 Entrevista grupal Nº 2. Me ha afectado bastante esta situación de que la mujer trabaje, porque como tú siempre dices que tú vas a aportar siempre y ahora que te sientes con un poco menos derechos de repente, que tienes que llegar como de otra manera.51 Si bien la participación de los hombres en el espacio doméstico ha aumentado, presenta algunas restricciones: primero los hombres conciben su participación como un apoyo generoso a la mujer, es decir, está condicionada por el lazo afectivo que estos tengan con la pareja y el éxito que logren las mujeres en las negociaciones cotidianas, vale decir no es el resultado de una convicción cabal de éstos por hacerse cargo de las tareas domésticas por el solo hecho que son parte de un grupo familiar. Segundo, este apoyo también se limita a algunas tareas dentro de la estructura familiar, de hecho los hombres se toman la opción de elegir qué hacen y qué no, en cambio para las mujeres esta opción no existe. Los hilos discursivos Al analizar lo discursos en forma longitudinal y transversal se pueden distinguir tópicos centrales y que se presentan en oposición respecto al poder alcanzado por las mujeres, y los obstáculos que visualizan ellos en el proceso de empoderamiento. · Observan una transformación social, un cambio de mentalidad respecto a los roles que desempeñan actualmente las mujeres en la sociedad. · La globalización implica el poder tener acceso a otras culturas distintas donde hay más tolerancia, y así alejarse del pensamiento religioso y tener más apertura. · Con la llegada de la democracia se han abierto más espacios para la mujer, que está adquiriendo cada vez más poder. · Los hombres aprueban el discurso oficial respecto a la igualdad de derechos que tienen hombres y mujeres en la sociedad. · El hombre ejerce el poder por el poder, las mujeres ejercen el poder y le agregan las relaciones humanas y el trato. · Las mujeres son las que manejan las relaciones personales en todos los ámbitos. · Las mujeres son más capaces, más metódicas, menos corruptas, más delicadas y meticulosas. Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 555 PAULINA IRENE SALINAS MERUANE · Son relevantes los ingresos económicos que generan actualmente las mujeres para el bienestar de la familia. · Valoran positivamente que las mujeres sean un par con la cual se puede conversar y que no deben responder a las expectativas de lo que se considera “un macho proveedor”. · En la familia la mujer ejerce el poder. · Hay resistencia de parte de las mujeres para ceder el poder al interior de la familia. · Las actividades propias del hogar deberían ser compartidas, no puede seguirse cargando la mano a una sola persona (mujer). · Las mujeres se están incorporando en diferentes áreas y no se sabe si el mercado logrará absorber toda esa mano de obra. · La mujer está preparada para hacer lo que quiera, pero incomoda. · En los puestos de ministros hay paridad, sin embargo no se sabe si serán capaces como los hombres en puestos tan altos. · Para los hombres que aspiran al poder, consideran a la mujer como una persona que se le cruza en el camino. · Las mujeres no deben perder sus características innatas, ni su rol femenino. · Las mujeres tienen que demostrar más que los hombres para poder ejercer liderazgo, tienen que tener más cuidado, los hombres pueden hacer más cosas, que a las mujeres no se les perdonaría. · Los hombres están siendo igual que las mujeres y por eso surgen problemas en las relaciones de pareja. · En el norte del país el poder masculino ha sido emblemático, por ser descendientes de la cultura pampina, donde la virilidad masculina se medía con el poder absoluto. · La asunción de Michelle Bachelet a la presidencia de la república significo una perdida importante para los hombres. · Las mujeres se desenvuelven bien en los centros de madres, en las juntas de vecinos, son cargos que debieran llevar ellas por naturaleza, porque es un centro social que tiene la facultad de ocuparse de la comunidad y de los niños. · A las mujeres les cuesta más llegar al poder, no tienen plataforma, eso hace mucho en el tema del liderazgo. 556 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN... A modo de conclusión 52 FAIRCLOUGH y WODAK, 2000. 53 Jorge LARRAÍN, 2001. En base a tres de los principios teóricosmetodológicos del ACD 52 analizaremos, a modo de conclusión, cómo se relaciona cada uno de ellos con el análisis crítico realizado sobre los discursos masculinos. · Las relaciones de poder como elementos discursivos, el ACD subraya el carácter discursivo de las relaciones sociales de poder en la sociedad contemporánea, carácter que proviene en parte de cómo se ejerce y negocian las relaciones de poder en el interior del discurso. Al respecto, el habla de los hombres devela el malestar e incomodidad que le produce la incorporación de la mujeres a los espacios de poder que históricamente han sido ocupados por ellos, sean estos en el mercado laboral o en los espacios de decisión, ministerios, presidencia de la república, entre otros. Los hombres refuerzan en sus discursos la vigencia de las características esencialistas de las mujeres, la femineidad, la responsabilidad que se le asigna en la manutención de las relaciones de pareja y su preocupación por las actividades de la comunidad y de los niños. · El discurso modela la sociedad y la cultura, y esto implica que el lenguaje hace su propia contribución a la reproducción y/o transformación de la sociedad y la cultura, incluidas las relaciones de poder. En los hilos discursivos identificados en las entrevistas se observan con intensidad elementos de continuidad y de cambio en los discursos masculinos, es decir, el proceso argumentativo en la producción del texto evidencia una serie de oposiciones capacidad/incapacidad, más participación/menos liderazgo, menos corruptas/sin plataforma política, etc. Hay ambigüedad y un cierto continuum en las representaciones que hacen los hombres sobre las mujeres, donde se da una dialéctica entre características tradicionales y modernas, estas últimas reconocidas como eminentemente masculinas. · El discurso es histórico, y esto implica que se produce en un contexto, hay convenciones y reglas subyacentes que es necesario reconocer como asimismo los elementos del pasado que nos remite el discurso. En este sentido podemos señalar que la ambigüedad y tensión discursiva analizada es concomitante con el proceso identitario de la sociedad chilena actual, que se caracteriza por la existencia de profundas transformaciones que conjugan aspectos tradicionales con otros más modernizadores, es decir, en el proceso identitario de la sociedad chilena hay una coexistencia de diversas dimensiones que van conformando un proceso dinámico y en construcción.53 Lo anterior Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 557 PAULINA IRENE SALINAS MERUANE se manifiesta, por ejemplo, en que se mantiene una tradición de autoritarismo en las relaciones junto con una valoración de relaciones más democráticas; hay una mayor apertura producto de la globalización y el mayor contacto con el resto del mundo, pero también existe un racismo más bien oculto, sobre todo con los países vecinos. El machismo tiene plena vigencia en algunos segmentos de la sociedad, mientras que en otros se encuentra más camuflado. Cada una de estas dimensiones nos permite visualizar la ambigüedad y sincretismo presentes en el proceso modernizador que experimenta la sociedad chilena. Finalmente, las trayectorias de las mujeres hacia la autonomía y el posicionamiento en el ámbito público son zigzagueantes en el sentido que están plasmadas por tensiones entre las resistencias que provocan en el espacio intra y extra familia, como por las oportunidades que han sido capaces de ir generando en la sociedad. Esta oposición marca el desempeño y posicionamiento de las mujeres en los distintos planos del quehacer nacional. En los discursos analizados queda en evidencia las tensiones que están vivenciando los hombres respecto al empoderamiento femenino. Hay reconocimiento y temor, hay seguridad frente al desempeño y capacidades de las mujeres, pero al mismo tiempo incomodidad y el deseo a que las mujeres mantengan sus características “naturales”, de femineidad, sensibilidad, etc. Los obstáculos que refieren los hombres respecto al empoderamiento de las mujeres se relacionan con que las limitantes que se les pueda generar a ellos en aquellos espacios donde han tenido control, el trabajo o la actividad política. Analizar los discursos y el habla, en este caso masculina ha posibilitado, desmontar las estructuras esencialistas presentes en el lenguaje que producen y reproducen prácticas sociales discriminatorias, y que se van reforzando en el imaginario social de los sujetos. Referencias bibliográficas ALONSO, Luis Enríque. La mirada cualitativa en sociología. Una aproximación interpretativa. Madrid: Editorial Fundamentos Colección Ciencia, 2003. ARAUJO, Kathia; ROGERS, Francisca. “El Hombre: ¿Existe?” En: OLAVARIA, José; PARRINI, Rodrigo (Eds.). Masculinidad/es. Identidad, sexualidad y familia. Primer Encuentro de Estudios de Masculinidad. Santiago de Chile: FLACSO-Chile/Universidad Academia de Humanismo Cristiano/Red de Masculinidades, 2000. p. 59-66. 558 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN... CONNELL, Robert W. “El imperialismo y el cuerpo de los hombres”. En: VALDÉS, Teresa; OLAVARRÍA, José (Eds.). Masculinidades y equidad de género en América Latina. Santiago de Chile: FLACSO, 1998. p. 76-89. FAIRCLOUGH, Norma; WODAK, Ruth. “Análisis critico del discurso”. En: VAN DIJK, Teun A. (Comp.). El discurso como interacción social. Estudios sobre el discurso II. Una introducción multidisciplinaria. Barcelona: Editorial Gedisa, 2000. p. 367-404. GIM – Grupo Iniciativa Mujeres. El Nuevo Contrato Social Dirigido a las Mujeres. Balance de una década de democracia en Chile. Santiago de Chile: Gim, Cedem, Cem, La Morada, Corsap, Domos, Flacso, Fundación Instituto de la Mujer, Isis Internacional, Mench, Prosam, 2002. GONZÁLEZ DE CHÁVEZ Fernández, María Asunción. Feminidad y masculinidad. Subjetividad y orden simbólico. Madrid: Biblioteca Nueva, 1998. HENNECKE, Angelika. El discurso como flujo de conocimientos a través del tiempo. Córdoba, Argentina: Comunicarte Editorial., 2004. HTUN, Mala. Mujeres y poder político en Latinoamérica. International Institute for Democracy and Electoral Asístanse, 2003. Documento de la Web: www.idea.int/ publications/wip/upload/chapter_01-2.pdf . INE – Instituto Nacional de Estadísticas de Chile. Censo 2002. Documento de la Web: www.ine.cl/cd2002/ sintesiscensal.pdf. IÑIGUEZ Rueda, Lupicinio. “El análisis del discurso en las ciencias sociales: variedades, tradiciones y práctica”. En: IÑIGUEZ Rueda, Lupicinio (ed.). Análisis del discurso. Manual para las ciencias sociales. Barcelona: Editorial UOC, 2003. p. 83-123. JÄGER, Siegfried. “Discurso y conocimientos aspectos teóricos y metodológicos de la crítica del discurso y del análisis de dispositivos”. En: WODAK, Ruth; MEYER, Micael (Coords.). Métodos de análisis crítico del discurso. Barcelona: Editorial Gedisa, 2003. p. 61-99. LARRAÍN, Jorge. Identidad chilena. Santiago de Chile: Lom Ediciones, 2001. MACHICAO Barbery, Ximena. “Algunas reflexiones sobre el contexto, paridad y desafíos para los movimientos feministas”. Revista Con-spirando. Revista Latinoamericana de Ecofeminismo, Espiritualidad y Teología, Santiago de Chile,. n. 52, p. 20-27, abril 2006. MORENO Ruiz, María José: “Masculinidades en la cultura de la globalización”. En: OLAVARRIA A., José (Ed.). Hombres: identidades y violencia. 2º Encuentro de Estudios de Masculinidades: Identidades, Cuerpos, Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 559 PAULINA IRENE SALINAS MERUANE Violencia y Políticas Públicas. Santiago de Chile: FLACSOChile/Universidad Academia de Humanismo Cristiano/ Red de Masculinidades, 2001. p. 37-54. OIT – Organización Internacional del Trabajo. ¿Más y mejores empleos para las mujeres?. La experiencia de los países del MERCOSUR y Chile. Editores: María Elena Valenzuela y Gerhard Reinecke. Santiago de Chile: OIT, 2000. OLAVARRÍA, José. “De la identidad a la política: masculinidades y política públicas: auge y ocaso de la familia nuclear patriarcales en el siglo XX”. En: OLAVARRÍA, José (Ed.). Hombres: identidad/es y violencia. Encuentro de Estudios de Masculinidades: Identidades, Cuerpos, Violencia y Políticas Públicas. Santiago de Chile: FLACSO-Chile/Universidad Academia de Humanismo Cristiano/Red de Masculinidades, 2000. p. 11-28. OLAVARRÍA, José. “Los varones heterosexuales: sexualidad, deseo y placer”. En: OLAVARRÍA, José. ¿Hombres a la deriva? Poder, trabajo y sexo. Santiago de Chile: FLACSO, 2001a. p 39-88. OLAVARRIA A., José (Ed.). “Hombres: identidades y violencia”. En: 2º Encuentro de Estudios de Masculinidades: Identidades, Cuerpos, Violencia y Políticas Públicas. Santiago de Chile: FLACSO, 2001b. OLAVARRÍA, José. “¿Dónde está el nuevo padre? Trabajo doméstico: de la retórica a la práctica”. En: Seminario “Familia y Vida Privada ¿Transformaciones, Tensiones, Resistencias y Nuevos Sentidos?” Santiago de Chile: FLACSO-Chile, CEDEM, UNFPRA, 2005. p. 215-250. PNUD – Programa para las Naciones Unidas para el Desarrollo. Desarrollo Humano en Chile. El Poder: ¿Para qué y para quién? Santiago de Chile: PNUD, 2004. RUIZ, Olga; SOLANO, Sandra; ZAPATA, Claudia. “Redes de mujeres pobladoras de la comuna de San Joaquín. Participación y ciudadanía emergente”. Revista Proposiciones, Sociedad Civil, Participación y Ciudadanía Emergente, Santiago de Chile: SUR Ediciones, n. 28, p. 213-230, 1998. RUIZ, José Ignacio. Metodología de la investigación cualitativa. Bibao, España: Universidad de Deusto, 1999. SADÍN Esteban, María Paz. Investigación cualitativa en educación. Fundamentos y tradiciones. Madrid: Mc Graw Hill, 2003. SALINAS, Paulina. “Ciudadanía y género. Mujeres y liderazgo en las Provincias de Antofagasta, El Loa y Tocopilla”. Revista Electrónica de Trabajo Social. Publicación anual editada por el Departamento de Servicio Social, Facultad de Ciencias Sociales, Universidad de Concepción, Chile, p.1-4, 2002. 560 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 LOS DISCURSOS MASCULINOS COMO DISPOSITIVOS DE CONTROL Y TENSIÓN... SALINAS, Paulina. “Asociatividad y género: construcción del liderazgo femenino en la región de Tarapacá y Antofagasta”. Revista Salares, Universidad de Antofagasta, año 7, n. 5, p. 79-98, 2005. SALINAS, Paulina; ARANCIBIA, Susana. “Discursos masculinos sobre el poder de las mujeres en Chile. Sujetos y subjetividades”. Revista Ultima Década, Valparaíso, Chile: Centro de Estudios Sociales CIDPA, año 14, n. 25, p. 65-90 . 2006. SCOLLON, Ron. “Acción y texto: para una comprensión conjunta del lugar del texto en la (inter) acción social, el análisis mediato del discurso y el problema de la acción social”. En: WODAK, Ruth; MEYER, Micael (Coords.). Métodos de análisis critico del discurso. Barcelona: Editorial Gedisa, 2003. p. 205-266. SERNAM – Servicio Nacional de la Mujer. Plan Regional de Igualdad de Oportunidades entre Mujeres y Hombres 2000-2010, Región de Antofagasta. Antofagasta, Chile: SERNAM, 2000. SERNAM – Servicio Nacional de la Mujer. Detección y análisis de la prevalencia de la violencia intrafamiliar. Santiago de Chile: SERNAM/Universidad de Chile. Centro de Análisis de Políticas Públicas, 2001. STRAUSS, Anselm; CORBIN, Juliet. Bases de la investigación cualitativa. Técnicas y procedimientos para desarrollar la teoría fundamentada. Medellín, Colombia: Contus/ Editorial Universidad de Antioquia, Facultad de Enfermería de la Universidad de Antioquia, 2002. TODARO, Rosalía; MAURO, Amalia; YAÑEZ, Sonia. “Chile: la calidad del empleo. Un análisis de género”. En: VALENZUELA, María Elena; REINECKE, Gerhard (Eds.). ¿Más y mejores empleos para las mujeres?. La experiencia experiencia de los países del MERCOSUR y Chile. Santiago de Chile: OIT, 2000. p. 193-265. VALDÉS, Teresa; WEINSTEIN, Mariza. Mujeres que sueñan: las organizaciones de pobladoras 1973-1989. Santiago de Chile: FLACSO, 1993. VALDÉS, Teresa (Coord.). El Indice de Compromiso Cumplido -ICC. Una estrategia para el control ciudadano de equidad de género. Santiago de Chile: FLACSO-Chile, 2001. VALENZUELA, María Elena. “La situación laboral y el acceso al empleo de las mujeres en el Cono Sur”. En: OIT – Organización Internacional del Trabajo. ¿Más y mejores empleos para las mujeres?. La experiencia de los países del MERCOSUR y Chile. Santiago de Chile: OIT, 2000. p. 9-27. Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007 561 PAULINA IRENE SALINAS MERUANE VASILACHIS DE GIALDINO, Irene. Pobres, pobreza, identidad y representaciones sociales. Barcelona: Editorial Gedisa, 2003. VALLES, Miguel S. Técnicas cualitativas de investigación social. Reflexiones metodológicas y práctica profesional. Madrid: Editorial Síntesis, 2000. VAN DIJK, Teun A. Racismo y análisis crítico de los medios. Paidós: Barcelona, 1997. WODAK, Ruth. “De que se trata el análisis crítico del discurso (ACD). Resumen de su historia, sus conceptos fundamentales y sus desarrollos”. En: WODAK, Ruth; MEYER, Micael (Coords.). Métodos de análisis crítico del discurso. Barcelona: Editorial Gedisa, 2003. p. 17-59. [Recebido em novembro de 2006 e aceito para publicação em fevereiro de 2007] Masculine Discourses as Control and TTension ension Devices in W omen ’s LLeadership eadership and Empowering Women omen’s Configuration Abstract Abstract: The present contribution deals with the meaning of the feminine leadership from a masculine perspective. By using a qualitative approach, open interviews were developed to understand the meaning that men assign to the feminine leadership. The speeches were analyzed on the basis of the Strauss/Corbin-theory (2003). The results show that men agree with the changes experienced by the gender roles. In a specific way, men agree that women need to have more societal-economic opportunities, which are necessary for more equitable relationship inside the family. However, within this positive framework emerging tensions configure a dissatisfaction of the masculinity that, in turn, impact the intimate sphere questioning the present day inter-gender relationship. Finally, there is a men’s group with more progressive speeches which venture towards a positive evaluation of the women’s capacities and their assumed public space-roles. However this positive evaluation is vigilant, ambivalent, and influenced by a perception of confidence/ uncertainty, efficiency/inefficiency of the effective societal contribution that women are able to reach. Key W ords Words ords: Power; Societal Changes; Gender. 562 Estudos Feministas, Florianópolis, 15(3): 541-562, setembro-dezembro/2007
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New GDP Series and Earlier Estimates for the Pre-national Accounts Era
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© The Author(s) 2017 L. Prados de la Escosura, Spanish Economic Growth, 1850–2015, Palgrave Studies in Economic History, DOI 10.1007/978-3-319-58042-5_8 New GDP Series and Earlier Estimates for the Pre-national Accounts Era How do the new GDP series compare to earlier estimates?1 Let us examine them first. Unlike contemporaries who were interested in assessing national income levels, early Spanish research has been con- cerned with trends and fluctuations in real output and expenditure.2 All available GDP estimates are output indices constructed with a fixed, single benchmark level whose economic significance tends to decline as one moves away from the base year.3 Moreover, trends in real gross value added are proxied by production indices, which imply the unlikely assumption that total output and input consumption evolve in the same direction and with the same intensity.4 Three types of yearly GDP estimates can be distinguished: official estimates by the Consejo de Economía Nacional, its revisions and extensions, and independent estimates. 153 © The Author(s) 2017 L. Prados de la Escosura, Spanish Economic Growth, 1850–2015, Palgrave Studies in Economic History, DOI 10.1007/978-3-319-58042-5_8 L. Prados de la Escosura 154 8 New GDP Series and Earlier Estimates … An index of total production was obtained by combining agricultural and industrial indices with fixed weights (0.6 and 0.4, respectively, over 1906–1929, and 0.5 each, thereafter). In addition, to allow for short-term fluctuations over the period 1906–1935, a de-trended nuptiality index was combined with the total production index. Nuptiality was excluded after the Civil War (1936–1939) as unsuitable for post-war cycles. In a second stage, the total production index was linked to an estimate of national income for 1923 in order to derive national income at constant prices.7 A further step was to obtain national income figures at current prices by reflating real income with a wholesale price index. Finally, for the years 1957–1964, CEN computed national income directly. 8.2 Revisions and Extensions of CEN Estimates Modern national accounts constructed according to OECD rules are available in Spain since 1954. Attempts to extend them backwards led to revisions of CEN figures that, occasionally, were expanded to cover the expenditure side. Three estimates are worth mentioning. 8.1 Consejo de Economía Nacional Estimates In 1944, the Consejo de Economía Nacional or National Economic Council (CEN, thereafter) was asked to estimate a set of national accounts for Spain (CEN 1945, 1965). Three were the main targets: to provide income figures for the years prior to the Civil War (1936–1939), to evaluate 1940 GDP on the available, fragile statistical basis, and to design a direct method to estimate national income for the years to come (Schwartz 1977: 460). Dearth of data forced CEN to split output indices into two segments with 1929 as the link year. In each case, independent production indices for agriculture and industry were obtained, from which an aggregate index was derived to approximate national income. No regard was paid to services and was implicitly assumed that output in services evolved as a weighted average of agricultural and industrial production. For the earlier period, 1906–1929, an agricultural output index was built up on the basis of eleven products, mostly dry farming crops (while no livestock output was included), representing half the value of total output. The index of industrial production included eighteen products, rendering a good coverage for mining, but insufficient for manufacturing and construction. Output indices were obtained for agriculture and industry by weighting each single product with its average price over 1913–1928, and the aggregate results were expressed by taking the average for 1906–1930 as 100. The composition of agricultural and industrial indices changed from 1929 onwards. Thirteen new crops were added to the agricultural index, distributed into eight main groups of products, that reached up to 80% of total production, while the industrial index’s coverage rose to 38 products distributed into ten different groups.5 To derive output indices for agriculture and industry, quantities were weighted by 1929 farm-gate prices and unit value added, respectively.6 Improvements in data cov- erage took place in the 1950s, but the method remained practically unaltered until 1956. 155 8 New GDP Series and Earlier Estimates … 8.2.1 Comisaría del Plan de Desarrollo A first attempt to revise CEN’s estimates was carried out by Comisaría del Plan de Desarrollo, the Development Planning Authority (CPD, thereafter), and covered the period 1942–1954 (CPD 1972).8 CPD economists were concerned with the high volatility shown by CEN figures that they attributed to its high dependence on agricultural output and to the exclusion of services. The alternative proposed by CPD was to construct a new index of aggregate performance in which services were added to CEN’s indices of agricultural and industrial output. Services output was obtained by combining series on transport and communi- cations and banking.9 A real product index was calculated by weighting each sectoral index with the shares of agriculture, industry and services in L. Prados de la Escosura 156 1954 GDP at factor cost, as established in official national accounts (CNE58).10 GDP at constant prices for 1942–1953 was, then, derived through backward extrapolation of the 1954 GDP level with the real product index. GDP at current prices was computed, in turn, by reflating real output with a composite index of wholesale prices (0.3) and the cost-of-living index (0.7).11 g GDP was completed with a breakdown of its expenditure components that included direct estimates of investment, public consumption and net exports of goods and services. To approximate private non-residential fixed capital formation, a physical index of private investment was built up by combining, with 1954 weights (CNE58), steel and cement output, machinery imports, electric power and registered transport vehicles. An index of residential investment was proxied by the number of completed dwellings. Public investment, in turn, resulted from adding up invest- ment in agriculture and public works and provincial and local public investment, deflated by a wholesale price index. Levels of each type of investment for 1954 were taken from the national accounts and pro- jected backwards with each investment index to derive real capital for- mation series and, then, reflated with price indices for production goods and construction materials. Total expenditure of public administration (central, provincial and local governments) re-scaled to match national accounts was used for public consumption and, then, deflated with a wholesale price index. Net exports of goods (at current and constant prices) were used as a proxy for net exports of goods and services, except in the case of tourism, in which the number of tourists (and the cost of living index as deflator) was accepted. 8.2.1 Comisaría del Plan de Desarrollo Private consumption was obtained as a residual from GDP at market prices (derived by adding indirect taxes net of subsidies to GDP at factor cost, obtained through the production approach) and the directly estimated components of expenditure. 8.2.3 Naredo An apparent inconsistency in the CEN series that would have led to underestimating national income for the post-Civil War years motivated José Manuel Naredo’s revision of CEN’s national accounts (Naredo 1991). The rationale for the under-registration of economic activity in official national accounts lies in the response of economic agents to systematic regulation and intervention of markets under Francoist autarchy.15 He also noticed that CEN’s implicit income-elasticity of demand for imports in the 1940s was too low. Naredo proposed, then, an alternative real GDP series for 1920–1950 based upon the revision of official national account estimates by hypothesizing higher income- elasticity of the demand for imports in the 1940s and by assuming a 10% fall in GDP resulting from the Spanish Civil War (1936–1939). 8 New GDP Series and Earlier Estimates … 157 1976).12 For the period 1901–1935, Alcaide derived an index of domestic production by combining, with 1906 fixed weights, CEN indices for agricultural and industrial output, and total employment in services, as a proxy for its output.13 GDP at current prices was obtained by reflating real output with a wholesale price index.14 8.2.2 Alcaide A revision of CEN series was also attempted by Julio Alcaide, a pioneer of Spanish national accounts, who, concerned for its volatility and cyclical behaviour, attempted to smoothing CEN’s real output (Alcaide 8 New GDP Series and Earlier Estimates … 8.3.1 Información Comercial Española The contribution by the research unit of the Ministry of Commerce and published in its journal, Información Comercial Española (ICE, there- after), represented a major improvement over earlier indices of Spanish aggregate performance (ICE 1962).16 The ‘general index of total pro- duction’, as its authors named it, covered 1951–1960 and represented a Laspeyres volume index in which three major sectors, agriculture and fishing, mining, manufacturing and construction, and trade and services, were combined with 1958 gross value added as weights. For each sector, a Laspeyres volume index with 1958 weights was constructed, in which L. Prados de la Escosura 158 L. Prados de la Escosura four branches were included for agriculture, sixteen for industry, and six for services, the latter appearing for the first time in pre-national accounts GDP estimates.17 Real product series was complemented with a quantity index for investment based on construction and public works, afforestation and the consumption (production plus imports) of machinery and equipment. 8.3.2 Schwartz A major attempt at overcoming CEN’s estimates for the period 1940– 1960 was carried out by Pedro Schwartz, at the Bank of Spain’s research unit, where he assembled new empirical evidence and used transparent methods in which indirect methods and regression analysis were com- bined (Schwartz 1976). In the new series, gross value added for every major sector in the economy was obtained by regressing their value-added levels (derived from official national accounts) on a set of indicators over 1954–1960, and the resulting structural relationship was applied to the set of variables or indicators to compute sectoral value added for the earlier pre-national accounts period 1940–1953. Gross domestic product (nominal and real) was derived by aggregation.18 8 New GDP Series and Earlier Estimates … 159 clothing) are those of lower income-elasticity of demand.22 In addition, the use of end-year (1958) fixed weights could underestimate GDP growth since relative prices for capital goods, the fastest growing com- ponent of expenditure, declined over time rendering, hence, a lower weight for investment than would have been the case if relative prices of any previous year were used.23 8.3.3 Carreras The most ambitious attempt to derive historical series of real GDP was produced by Albert Carreras (1985) who built up an index from the demand side, covering a longer time span, 1849–1958.19 Weights for the main aggregates (private and public consumption, investment, net exports) were derived from the 1958 benchmark from the national accounts, while the 1958 input–output table allowed the breakdown of each series into its main components.20 However, a few shortcomings can be observed in an otherwise major piece of research. For example, the consumption series only cover food, beverages and tobacco, and clothing while services are neglected.21 Actually, it could be argued that consumption growth may be possibly biased downwards since the goods included in the series (food and 8 New GDP Series and Earlier Estimates … 8.4 Comparing the New and Earlier GDP Estimates How does the new GDP series compare to the earlier estimates? There is a significant agreement about performance over the long run between Carreras estimates and my new series, although significant discrepancies emerge in the short term. During the first half of the twentieth century, the new GDP series present slower growth than those by Alcaide and CEN (Fig. 8.1). When the focus is placed on specific periods, the variance across different estimates emerges. World War I years seem to have been of fast Fig. 8.1 Alternative real GDP estimates, 1850–1958 (1958 = 100) (logs) L. Prados de la Escosura 160 growth (CEN, Alcaide and Carreras), in which the economy would have taken advantage of Spain’s neutrality to cater for the needs of belligerent nations while domestic industry expanded on the basis of import sub- stitution. This conventional depiction is challenged by the new GDP series. Then, the post-war years and especially the 1920s exhibit accel- erated growth in CEN and Alcaide’s. estimates while Carreras’ suggest deceleration. The new GDP series provide an even more optimistic picture than Alcaide’s. The impact of Great Depression in Spain (1929–1933) varies dra- matically according to different authors. Spain’s economy decelerated but continued growing in Alcaide’s view, stagnated in Naredo’s, mildly contracted in Carreras’ computations and definitely shrank in CEN’s estimates. The new series side along CEN’s but with a less intense decline. Earlier estimates are discontinued between 1936 and 1939, so com- paring output levels in 1935 and 1940 is the only way to assessing the impact of the Civil War (Fig. 8.2). A consensus exists about a substantial contraction in economic activity during the war years, around 6% per annum, but for Naredo’s mild −2.1%. In my new estimates, the Civil War represented a milder but still deeper shrinkage than Naredo’s.24 The impact of Great Depression in Spain (1929–1933) varies dra- matically according to different authors. Spain’s economy decelerated but continued growing in Alcaide’s view, stagnated in Naredo’s, mildly contracted in Carreras’ computations and definitely shrank in CEN’s estimates. The new series side along CEN’s but with a less intense decline. Earlier estimates are discontinued between 1936 and 1939, so com- paring output levels in 1935 and 1940 is the only way to assessing the impact of the Civil War (Fig. 8.2). 8.4 Comparing the New and Earlier GDP Estimates A consensus exists about a substantial contraction in economic activity during the war years, around 6% per annum, but for Naredo’s mild −2.1%. In my new estimates, the Civil War represented a milder but still deeper shrinkage than Naredo’s.24 Fig. 8.2 Alternative real GDP estimates, 1900–1958 (1958 = 100) (logs) Fig. 8.2 Alternative real GDP estimates, 1900–1958 (1958 = 100) (logs) 8 New GDP Series and Earlier Estimates … 8 New GDP Series and Earlier Estimates … 161 Table 8.1 Real GDP growth in the pre-national accounts era: alternative estimates, 1850–1958 (%) CEN CPD Alcaide Naredo ICE Schwartz Carreras New series 1850–1958 1.7 1.7 1901–1958 2.6 2.8 1.6 1.8 1850–1883 2.2 1.7 1883–1913 0.6 1.1 1901–1913 1.6 2.3 0.1 1.2 1913–1918 1.4 1.9 2.2 0.3 1918–1929 2.5 2.6 1.6 1.5 3.9 1929–1933 −2.1 1.0 −2.1 −0.6 −1.5 1933–1935 4.3 1.5 4.3 −1.1 3.0 1935–1940 −6.7 −6.0 −2.1 −5.9 −3.5 1940–1944 3.6 0.7 2.6 4.8 2.6 6.5 4.0 1944–1950 0.8 2.8 2.5 2.9 0.6 −1.5 0.2 1950–1958 7.2 6.2 5.8 5.8 5.1 6.0 5.0 5.8 Note ‘New Series’ are GDP estimates at market prices. Sources New Series, see the text. CEN (1945, 1965), ICE (1962), CPD (1972), Alcaide (1976), Naredo (1991), Schwartz (1976), and Carrerras (1985) 8.1 Real GDP growth in the pre-national accounts era: alternative tes, 1850–1958 (%) Note ‘New Series’ are GDP estimates at market prices. Sources New Series, see the text. CEN (1945, 1965), ICE (1962), CPD (1972), Alcaide (1976), Naredo (1991), Schwartz (1976), and Carrerras (1985) The post-war recovery was mild (but for Carreras and Naredo esti- mates) and short-lived (CEN, Carreras and Schwartz), and only resumed at a fast pace in the 1950s (except for Alcaide) (Table 8.1). The new GDP estimates concur with the view of a post-Civil War mild and long recovery, which makes Spanish post-war experience different from western Europe’s fast return to pre-war output levels (Maddison 2010). 1. Attempts to provide historical GDP at benchmark years have been carried out by economic historians. Bairoch (1976) and Crafts (1983, 1984) included Spain in their estimates for the nineteenth century computed along Beckerman and Bacon (1966) indirect approach. Following Deane (1957), Prados de la Escosura (1982) reconstructed Mulhall (1880, 1884, 1885, 1896) figures in a consistent way and derived a set of benchmark estimates for Spanish national income for 1832–1894. In addition, GDP estimates for seven benchmarks over the period 1800–1930 from the industry of origin approach are provided in Prados de la Escosura (1988). L. Prados de la Escosura 162 2. It is worth mentioning Mulhall (1880, 1884, 1885, 1896) estimates of national income for a large number of countries, including Spain, in the late nineteenth century. The main contemporary attempts to derive levels of Spain’s national income have been collected in Schwartz (1977). The literature on Italy, where detailed benchmark estimates have been con- structed, provides a counterpoint (Rey 1991, 1992, 2000, 2002). 2. It is worth mentioning Mulhall (1880, 1884, 1885, 1896) estimates of national income for a large number of countries, including Spain, in the late nineteenth century. The main contemporary attempts to derive levels of Spain’s national income have been collected in Schwartz (1977). The literature on Italy, where detailed benchmark estimates have been con- structed, provides a counterpoint (Rey 1991, 1992, 2000, 2002). p p y 3. Unfortunately, the 1958 GDP benchmark is the earliest available in Spain. New, direct GDP estimates for benchmark years prior to 1958, e.g. 1910 or 1930, years for which population censuses are available, would be required to provide a rigorous check on GDP figures derived by projecting benchmarks backwards with quantity and price indices. p p y 3. Unfortunately, the 1958 GDP benchmark is the earliest available in Spain. New, direct GDP estimates for benchmark years prior to 1958, e.g. 1910 or 1930, years for which population censuses are available, would be required to provide a rigorous check on GDP figures derived by projecting benchmarks backwards with quantity and price indices. 4. The reader should be aware that my own estimates suffered from this bias (see Section III). Actually, only a double deflation procedure for inputs and output would provide a correct alternative. By double deflation is meant independent deflation, with their own price indices, of final production and intermediate inputs, so real value added is obtained as a residual. Cf. Cassing (1996). 4. The reader should be aware that my own estimates suffered from this bias (see Section III). Actually, only a double deflation procedure for inputs and output would provide a correct alternative. By double deflation is meant independent deflation, with their own price indices, of final production and intermediate inputs, so real value added is obtained as a residual. Cf. Cassing (1996). 5. In order to reduce the downward bias for manufacturing, CEN (1945, 1965) overweighted electricity output. 5. In order to reduce the downward bias for manufacturing, CEN (1945, 1965) overweighted electricity output. 6. Notes 1. Attempts to provide historical GDP at benchmark years have been carried out by economic historians. Bairoch (1976) and Crafts (1983, 1984) included Spain in their estimates for the nineteenth century computed along Beckerman and Bacon (1966) indirect approach. Following Deane (1957), Prados de la Escosura (1982) reconstructed Mulhall (1880, 1884, 1885, 1896) figures in a consistent way and derived a set of benchmark estimates for Spanish national income for 1832–1894. In addition, GDP estimates for seven benchmarks over the period 1800–1930 from the industry of origin approach are provided in Prados de la Escosura (1988). 1. Attempts to provide historical GDP at benchmark years have been carried out by economic historians. Bairoch (1976) and Crafts (1983, 1984) included Spain in their estimates for the nineteenth century computed along Beckerman and Bacon (1966) indirect approach. Following Deane (1957), Prados de la Escosura (1982) reconstructed Mulhall (1880, 1884, 1885, 1896) figures in a consistent way and derived a set of benchmark estimates for Spanish national income for 1832–1894. In addition, GDP estimates for seven benchmarks over the period 1800–1930 from the industry of origin approach are provided in Prados de la Escosura (1988). L. Prados de la Escosura L. Prados de la Escosura Mining was allocated 22.68% of total industrial output; utilities (rep- resented by electric energy), 20.96%; and manufacturing only 56.36%. If the size of the industrial sample (2077 million pesetas) is compared to Banco Urquijo ‘s estimate of industrial output circa 1924, its coverage represents 25% of total industrial value added. 6. Mining was allocated 22.68% of total industrial output; utilities (rep- resented by electric energy), 20.96%; and manufacturing only 56.36%. If the size of the industrial sample (2077 million pesetas) is compared to Banco Urquijo ‘s estimate of industrial output circa 1924, its coverage represents 25% of total industrial value added. 7. CEN (1945) used an arithmetic average of Banco Urquijo (1924) and Vandellòs (1925) estimates assuming that were independent from each other. Assessments of CEN (1945) income figures are provided by Guerreiro (1946), Hemberg (1955) and Fuentes Quintana (1958), all reprinted in Schwartz (1977). Hemberg (1955) pioneering computation of income using a production approach showed that there were enough statistical data to carry out a direct estimate of GDP from the supply side. 8. The purpose of CPD estimates was to provide statistical background for the econometric model used in simulations during the third ‘plan de desarrollo’, an instrument of planification indicatif in the early 1970s. 9. Fixed value-added weights from 1954 National Accounts were accepte 10. National accounts are named after the benchmark year used for its construction. Thus, CNE58 is Contabilidad Nacional de España with 1958 as the base year. 163 8 New GDP Series and Earlier Estimates … 8 New GDP Series and Earlier Estimates … 11. The weights tried to reflect the relative importance of private con- sumption (70%) and the rest of the demand components of GDP (30%). 11. The weights tried to reflect the relative importance of private con- sumption (70%) and the rest of the demand components of GDP (30%). 12. Alcaide carried out another revision of the historical accounts for the period 1901–1985 that did not challenge, however, his earlier findings for real product in the pre-national accounts period (Banco de Bilbao 1986). Nevertheless, nominal levels were revised upwards as the his- torical series were linked to more recent figures from Banco de Bilbao’s own GDP estimates. Alcaide (2000) revised his estimates for the early twentieth century, starting in 1898, and spliced them with Fundación BBV’s GDP estimates for 1955–1998 (also Alcaide’s own work). Unfortunately, Alcaide neither discusses his methods nor substantiates his arguments with empirical evidence, while no sources are provided. 13. Weights were 0.4 for agriculture, 0.25 for industry and 0.35 for services. Since historical active population figures are only available at census years, either Alcaide interpolated census data or applied participation rates, derived at census intervals, to available yearly figures for total population. Alcaide claimed to having adjusted employment in services ‘to accute changes in total production’ (Alcaide 1976: 1129). As stressed by Tortella (1987), using employment as a proxy for output implies the assumption of stagnant labour productivity in services. 14. Alcaide’s revision of CEN figures for 1940–1954 is also far from clear. He relies on a revision of CEN’s real output carried out by Tamames without providing the reference. Moreover, while in the case of GDP only the wholesale price index seems to have been used, it appears that Alcaide reflated real national income with the cost of living and wholesale price indices weighted by the shares of consumption and investment in 1954 national accounts, respectively. 15. Naredo (1991) illustrated his argument by referring to the 26% increase in agricultural output in a single year (1951), following the abolishment of food rationing, which partially liberalized the domestic market. 16. The first independent attempt to derive national income estimates on an yearly basis was carried out by José Castañeda (1945) who provided an estimate of national expenditure from a sample of indirect taxes and government’s monopoly revenues, deflated by a wholesale price index, for the period 1901–1934. p 17. 8 New GDP Series and Earlier Estimates … Each of the 26 groups of goods and services, defined according to the 1958 input–output table’s (TIOE58) classification of economic 17. Each of the 26 groups of goods and services, defined according to the 1958 input–output table’s (TIOE58) classification of economic 17. Each of the 26 groups of goods and services, defined according to the 1958 input–output table’s (TIOE58) classification of economic 164 L. Prados de la Escosura activities, was constructed as a Laspeyres volume index with 1958 weighting. In ICE estimates, the coverage of output was far superior to CEN’s, with 227 and 45 basic series for industry and services. For agricultural output (excluding livestock, forestry and fishing, for which 21 basic new series were used), CEN revised index was adopted. Weights applied to agriculture, industry and services to derive the “general index of total production” were 0.2693, 0.3200 and 0.4107, respectively. 18. An indicator is, according to Balke and Gordon (1989), a time-series variable that is correlated with real product in the time period when real GDP is known, i.e. the post-1954 years. 19. The only precedent of Carreras‘ demand approach is CPD (1972), but it did not represent an independent estimate. 20. Some objections can be raised to the use of a 1958 benchmark as it comes from an autarchic period in which prices were intervened by government regulation and protection. This is a similar case to those of Italy’s 1938 (Bardini et al. 1995:123) and Germany’s 1937 (Broadberry, 1997) benchmarks. It can be argued, however, that the 1958 input– output table is not only the first one available but also the most detailed Spanish one (207 sectors) to date. 21. Food and clothing represent 70% of total consumption in the bench- mark year 1958 (CNE58). However, the sample of consumption goods used in the construction of the annual index only reaches a coverage of 20% up to 1928, and 41% thereafter, as measured for the 1958 benchmark (Carreras 1985: 38–39, 45). Naredo (1991: 144) claimed that Carreras reliance on García Barbancho’s (1960) food consumption data led him to use out-dated, downward biased agricultural output statistics. 22. Income elasticity of demand for housing, durables, personal care, transport, recreation, etc. was significantly higher than for food and clothing in 1958 Spain (Lluch, 1969: 68, 78). 22. Income elasticity of demand for housing, durables, personal care, transport, recreation, etc. 8 New GDP Series and Earlier Estimates … 165 official values for exports and imports that exaggerate commodity trade deficit for most of the period up to 1913 (see Sect. 7.3). official values for exports and imports that exaggerate commodity trade deficit for most of the period up to 1913 (see Sect. 7.3). official values for exports and imports that exaggerate commodity trade deficit for most of the period up to 1913 (see Sect. 7.3). p p 24. Actually, my yearly estimates indicate a sharper decline between 1935 and 1938, at −11% per year, followed by a recovery up to 1944. 8 New GDP Series and Earlier Estimates … was significantly higher than for food and clothing in 1958 Spain (Lluch, 1969: 68, 78). 22. Income elasticity of demand for housing, durables, personal care, transport, recreation, etc. was significantly higher than for food and clothing in 1958 Spain (Lluch, 1969: 68, 78). 23. Two other objections could also be raised to Carreras’ pathbreaking contribution. Government consumption was deflated by a wholesale price index, and not by a consumer price index, a better suited deflator, as wages and salaries constituted its main component, since no com- prehensive CPI was available at the time the paper was written. In addition, the trade balance only covers commodities. Carreras used 8 New GDP Series and Earlier Estimates … Castañeda, J. 1945. El consumo de tabaco en España y sus factores. Revista de Economía Política, I, 1: 195–292. Partially reprinted in P. Schwartz, ed. References Alcaide Inchausti, J. 1976. Una revisión urgente de la serie de renta nacional en el siglo XX. In Datos básicos para la historia financiera de España, 2 vols., 1126–1150. Madrid: Instituto de Estudios Fiscales. Alcaide Inchausti, J. 1986. Series históricas de las principales macromagnitudes en España. Banco de Bilbao. Informe Económico Anual. Madrid: Banco de Bilbao. Alcaide Inchausti, J. 2000. La renta nacional de españa y su distribución. Serie años 1898 a 1998. In 1900–2000 Historia de un esfuerzo colectivo, ed. J. Velarde Fuertes, 2 vols., 375–449. Madrid: Planeta. Bairoch, P. 1976. Europe’s Gross National Product: 1800–1975. Journal of European Economic History V 2: 273–340. Balke, N.S., and R.J. Gordon. 1989. The Estimation of Prewar Gross National Product: Methodology and New Evidence”. Journal of Political Economy 97: 38–92. Bardini, C., A. Carreras, and P. Lains. 1995. The National Accounts for Italy, Spain and Portugal. Scandinavian Economic History Review XLIII 1: 115–146. Beckerman, W., and R. Bacon. 1966. International Comparisons of In Beckerman, W., and R. Bacon. 1966. International Comparisons of Income Levels: A Suggested New Measure. Economic Journal LXXVI: 516–536. Broadberry, S.N. 1997. Anglo-German Productivity Differences 1870–1990: A gg J Broadberry, S.N. 1997. Anglo-German Productivity Differences 1870–1990: A Sectoral Analysis. European Review of Economic History 1 (2): 247–267. gg berry, S.N. 1997. Anglo-German Productivity Differences 1870–1990: A Sectoral Analysis. European Review of Economic History 1 (2): 247–26 Carreras, A. 1985. Gasto nacional bruto y formación de capital en España, 1849–1958: primer ensayo de estimación. In La Nueva Historia Económica en España, ed. P. Martín Aceña, and L. Prados de la Escosura, 17–51. Madrid: Tecnos. Cassing, S. 1996. Correctly Measuring Real Value Added. Review of Income and Wealth 42 (2): 195–206. Castañeda, J. 1945. El consumo de tabaco en España y sus factores. Revista de Economía Política, I, 1: 195–292. Partially reprinted in P. Schwartz, ed. L. Prados de la Escosura 166 1977. El Producto Nacional de España en el siglo XX, 209–215. Madrid: Instituto de Estudios Fiscales. 1977. El Producto Nacional de España en el siglo XX, 209–215. Madrid: Instituto de Estudios Fiscales. Comisaria del Plan de Desarrollo Economico y Social. 1972. Series cronológicas del modelo econométrico, vol. II. Madrid: Presidencia del Gobierno. Comisaria del Plan de Desarrollo Economico y Social. 1972. Series cronológicas del modelo econométrico, vol. II. Madrid: Presidencia del Gobierno. Consejo de Economia Nacional. 1945. La Renta Nacional de España, 2 vols. Madrid: C.E.N. References Consejo de Economia Nacional. 1965. La Renta Nacional de España, 1906–1965. Madrid: C.E.N. Crafts, N.F.R. 1983. Gross National Product in Europe, 1870-1910: Some New Estimates. Explorations in Economic History 20 (4): 387–401. Crafts, N.F.R. 1983. Gross National Product in Europe, 1870-1910: Some New Estimates. Explorations in Economic History 20 (4): 387–401. Crafts, N.F.R. 1984. Patterns of Development in Nineteenth Century Europe. Oxford Economic Papers XXXVI 4: 438 458 Crafts, N.F.R. 1983. Gross National Product in Europe, 1870 1910: Some New Estimates. Explorations in Economic History 20 (4): 387–401. Crafts, N.F.R. 1984. Patterns of Development in Nineteenth Century Europe. Oxford Economic Papers, XXXVI 4: 438–458. f p Deane, P. 1957. Contemporary Estimates of National Income in the Second Half of the Nineteenth Century. Economic History Review IX: 451–461. Fuentes Quintana, E. 1958. Las estimaciones de la renta nacional de España. In La contabilidad nacional de España (Cuentas y cuadros de 1954), ed. M. De Torres, 13–48. Madrid: Instituto Sancho de Moncada. Reprinted in P. Schwartz (ed.). 1977. El. Producto Nacional de España en el siglo XXInstituto de Estudios Fiscales Madrid 369–422. Garcia Barbancho, A. 1960. Análisis de la alimentación española. Anales de Economía 66: 72–119 and 67: 271–367. Guerreiro, A. 1946. A propósito de ‘La Renta Nacional en España’. Moneda y Crédito 17: 3–18. Reprinted in P. Schwartz,1977 El Producto Nacional de España en el siglo XX Instituto de Estudios Fiscales Madrid 233–263. Hemberg, P. 1955. Informe preliminar sobre la renta interior de España. Revista de Economía Política VI (2): 114–171. Reprinted in P. Schwartz, ed. (1977), El Producto Nacional de España en el siglo XX, 265–341. Madrid: Instituto de Estudios Fiscales. Informacion Comercial Española. 1962. Datos y reflexiones sobre el desarrollo de la economía española. Información Comercial Española 341: 39–97. Informacion Comercial Española. 1962. Datos y reflexiones sobre el desarrollo de la economía española. Información Comercial Española 341: 39–97. Lluch, C. 1969. Elasticidades de Engel y de precios para las grandes categorías de bienes de consumo en España. Moneda y Crédito 108: 47–94. Maddison, A. 2010. Statistics on world population, GDP and per capita GDP, 1-2008 AD, Horizontal file. http://www.ggdc.net/maddison/. Mulhall, M.G. 1880. The Progress of the World in Arts, Agriculture, Commerce, Manufactures, Instruction, Railways, and Public Wealth since the Beginning of h Ni h C L d Ed d S f d Lluch, C. 1969. References Elasticidades de Engel y de precios para las grandes categorías de bienes de consumo en España. Moneda y Crédito 108: 47–94. Maddison, A. 2010. Statistics on world population, GDP and per capita GDP, 1-2008 AD, Horizontal file. http://www.ggdc.net/maddison/. Mulhall, M.G. 1880. The Progress of the World in Arts, Agriculture, Commerce, Manufactures, Instruction, Railways, and Public Wealth since the Beginning of the Nineteenth Century. London: Edward Stanford. 8 New GDP Series and Earlier Estimates … 8 New GDP Series and Earlier Estimates … 167 Mulhall, M.G. 1884, 1886, 1892, 1899. Dictionary of Statistics. London: Routledge and Sons. g Mulhall, M.G. 1885. History of Prices since the Year 1850. London: Longmans, Green, and Co. Mulhall, M.G. 1896. Industries and Wealth of Nations. London: Longmans, Green, and Co. Naredo, J.M. 1991. Crítica y revisión de las series históricas de renta nacional de la postguerra. Información Comercial Español 698: 132–152. 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Madrid: Instituto de Estudios Fiscales. Schwartz, ed. 1977. El Producto Nacional de España en el siglo XX, 443–592. Madrid: Instituto de Estudios Fiscales. Tortella, G. 1987. El sector terciario en España antes de 1936: una nota de escepticismo sobre las estimaciones al uso. Revista de Historia Económica V 2: 587–597. Vandellós, J.A. 1925. La richesse et le revenu de la Péninsule Ibérique. Metron V 4: 151–186. Urquijo, Banco. 1924. El progreso y la riqueza de España. Madrid: Imprenta de Samarán y Compañía. 168 L. Prados de la Escosura Open Access This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/ 4.0/), 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 license and indicate if changes were made. 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The ARRIVE Guidelines Checklist Animal Research: Reporting In Vivo Experiments Carol Kilkenny1, William J Browne2, Innes C Cuthill3, Michael Emerson4 and Douglas G Altman5 1The National Centre for the Replacement, Refinement and Reduction of Animals in Research, London, UK, 2School of Veterinary Science, University of Bristol, Bristol, UK, 3School of Biological Sciences, University of Bristol, Bristol, UK, 4National Heart and Lung Institute, Imperial College London, UK, 5Centre for Statistics in Medicine, University of Oxford, Oxford, UK. ITEM RECOMMENDATION Section/ Paragraph Title Abstract INTRODUCTION introducion introducion METHODS Methods, paragraph 1 Results, paragraph 1, 2 Methods, paragraph 1,5,6 Methods, paragraph 1,5,6 Results, paragraph 1, 2 The ARRIVE guidelines. Originally published in PLoS Biology, June 2010 1 The ARRIVE guidelines. Originally published in PLoS Biology, June 2010 1 Methods, paragraph 1 Results, paragraph 1, 2 Results, paragraph 1, 2 Results, paragraph 1, 2 Methods, paragraph 8 RESULTS Methods, paragraph 1,5,6 Results, paragraph 1, 2 Results, paragraph 1, 2 DISCUSSION Discussion paragraph Discussion paragraph Acknowled gements
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Age-Related Patterns in Human Myeloid Dendritic Cell Populations in People Exposed to Schistosoma haematobium Infection Norman Nausch1*, Delphine Louis2,3, Olivier Lantz2,3,4, Isabelle Peguillet2,3, Franc¸ois Trottein5, Isobel Y. D. Chen1, Laura J. Appleby1, Claire D. Bourke1¤a, Nicholas Midzi6¤b, Takafira Mduluza7, Francisca Mutapi1 Norman Nausch1*, Delphine Louis2,3, Olivier Lantz2,3,4, Isabelle Peguillet2,3, Franc¸ois Trottein5, Isobel Y. D. Chen1, Laura J. Appleby1, Claire D. Bourke1¤a, Nicholas Midzi6¤b, Takafira Mduluza7, Francisca Mutapi1 1 Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom, 2 Institut Curie, De´partement de Biologie des Tumeurs, Paris, France, 3 Centre d’Investigation Clinique IGR-Curie, CIC-BT-507 Paris, France, 4 Unite´ Inserm 932, Institut Curie, Paris, France, 5 Center for Infection and Immunity of Lille, Inserm U 1019, CNRS UMR 8204, Universite´ Lille Nord de France Institut Pasteur de Lille, Lille, France, 6 National Institute of Health Research, Causeway, Harare, Zimbabwe, 7 Department of Biochemistry, University of Zimbabwe, Mount Pleasant, Harare, Zimbabwe Abstract 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 by the World Health Organisation (grant no. RPC264), the Wellcome Trust (grant no. WT082028MA; www.wellcome.co.uk) and by Thrasher Research Funds (www.thrasherresearch.org). 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 exis * E-mail: nnausch@staffmail.ed.ac.uk ¤a Current address: Biology Department, University of York, York, United Kingdom ¤b Current address: Research Council of Zimbabwe, Harare, Zimbabwe ¤a Current address: Biology Department, University of York, York, United Kingdom ¤b Current address: Research Council of Zimbabwe, Harare, Zimbabwe infection levels increasing to peak in early to late childhood, typically around 9–15 years and then declining in adulthood [2– 4]. This profile is believed to be largely reflective of the gradual development of protective acquired immunity reducing re- infection levels [2,5,6]. The consequence of this age profile is that individuals with comparable infection levels who have resided in a schistosome endemic area since birth (e.g. egg negative children Abstract Background: Urogenital schistosomiasis is caused by the helminth parasite Schistosoma haematobium. In high transmission areas, children acquire schistosome infection early in life with infection levels peaking in early childhood and subsequently declining in late childhood. This age-related infection profile is thought to result from the gradual development of protective acquired immunity. Age-related differences in schistosome-specific humoral and cellular responses have been reported from several field studies. However there has not yet been a systematic study of the age-related changes in human dendritic cells, the drivers of T cell polarisation. Methods: Peripheral blood mononuclear cells were obtained from a cohort of 61 Zimbabwean aged 5–45 years with a S. haematobium prevalence of 47.5%. Two subsets of dendritic cells, myeloid and plasmacytoid dentritic cells (mDCs and pDCs), were analyzed by flow cytometry. Findings: In this population, schistosome infection levels peaked in the youngest age group (5–9 years), and declined in late childhood and adulthood (10+ years). The proportions of both mDCs and pDCs varied with age. However, for mDCs the age profile depended on host infection status. In the youngest age group infected people had enhanced proportions of mDCs as well as lower levels of HLA-DR on mDCs than un-infected people. In the older age groups (10–13 and 14–45 years) infected people had lower proportions of mDCs compared to un-infected individuals, but no infection status-related differences were observed in their levels of HLA-DR. Moreover mDC proportions correlated with levels of schistosome- specific IgG, which can be associated with protective immunity. In contrast proportions of pDCs varied with host age, but not with infection status. Conclusions: Our results show that dendritic cell proportions and activation in a human population living in schistosome- endemic areas vary with host age reflecting differences in cumulative history of exposure to schistosome infection. Citation: Nausch N, Louis D, Lantz O, Peguillet I, Trottein F, et al. (2012) Age-Related Patterns in Human Myeloid Dendritic Cell Popula Schistosoma haematobium Infection. PLoS Negl Trop Dis 6(9): e1824. doi:10.1371/journal.pntd.0001824 s D, Lantz O, Peguillet I, Trottein F, et al. (2012) Age-Related Patterns in Human Myeloid Dendritic Cell Populations in People Exposed to m Infection. PLoS Negl Trop Dis 6(9): e1824. doi:10.1371/journal.pntd.0001824 Editor: Rodrigo Correa-Oliveira, Rene´ Rachou Research Center, Brazil Received October 13, 2011; Accepted August 6, 2012; Published September 27, 2012 Received October 13, 2011; Accepted August 6, 2012; Published September 27, 2012 Copyright:  2012 Nausch et al. Author Summary Since in most schistosome endemic areas people are exposed to infection from as young as 6 months old [41], and may already be carrying heavy infections within the first decade of life [8], these early infection events may have a profound effect on the proportions of the DCs present in the host. Characterising the role of these cells during natural immune responses to helminth infection in the different age groups is vital for vaccine development, since people targeted by anti-schistosome vaccines in endemic areas will have been previously exposed to infection and their cellular immune responses will already be primed by repeated exposure to parasite antigens. In this context variations in antigen presenting cell populations, including DCs, might directly affect the efficacy of vaccination in different age groups. Lessons from the discontinued human hookworm vaccine trials, illustrate the importance of characterising existing natural immune responses in endemic populations and designing vaccine to avoid undesirable patholog- ical outcomes of vaccination [42]. Therefore, the aim of this study was to characterise the relationship between age and DCs during natural schistosome infections and determine if these patterns are affected by host infection status across different age groups reflecting different dynamics in the acquisition and loss of schistosome infection. versus egg negative adults) can differ significantly in their immune response against the parasite and thus their levels or resistance to re-infection. Several studies characterizing human immune responses to schistosome infections have shown age related differences in antibody levels [7–9], plasma cytokines [10], parasite-specific cytokines [11] and regulatory T cell proportions [12]. This concept is supported by theoretical modelling of the development of acquired immunity, which predicts that correla- tions between immunological responses and infection is positive in younger age groups and subsequently decreasing and potentially turning in a negative correlation [13]. Moreover this pattern is not restricted to schistosome infections, but is a characteristic of immune responses associated with protection from a variety of helminth species in endemically-exposed populations [14,15]. As investigations of the nature and development of protective acquired immunity progress, there has been a move to decipher the mechanisms and pathways behind these observed age-related patterns. Human field studies show that the immune response against schistosomes is characterized by a very complex interaction of TH1, TH2 and regulatory responses [10–12,16–18] with differences between natural human infections and experimental mouse models [19,20]. Author Summary A characteristic feature of most helminth infections is the convex age infection profile, where infection levels rise to peak in early childhood and decline in adulthood, a pattern thought to result from the development of protective acquired immunity. Thus, several investigations characterizing protective responses to inform vaccine research have focused on responses present in older people, who despite continued exposure to infection carry little or no infection. To date, such studies have identified key responses which are correlates of resistance. However, there is a paucity of information on cell types that are mediators rather than effectors of the immune responses. One such group where there are limited studies in human schistosome infections is dendritic cells which are impor- tant for the polarizations of CD4+ T cell responses. Therefore, we characterized the age profile of dendritic cells in Zimbabweans exposed to Schistosoma haemato- bium infection. We found an age-related pattern in the proportions of myeloid dendritic cells (a subset of dendritic cells) in this population. Furthermore, in the case myeloid dendritic cells, the age profile differed between schistosome infected and un-infected people. Thus our study suggests that activation and migration of myeloid dendritic cells also develop in an age-related pattern consistent with the cumulative history of exposure to schistosome parasites. In particular, studies analysing DCs directly from humans exposed to schistosomes are limited. The first study addressing this question, published by Everts and colleagues in 2010, elegantly showed changes in DCs during chronic schistosomiasis (S. haematobium) [32] suggesting that chronic schistosomiasis can suppress DCs, which might play a role in immune modulation by schistosomes. y Peripheral blood DCs can be divided in two major subsets [33,34], myeloid dendritic cells (mDC; or conventional DC) and plasmacytoid (pDC). Myeloid DCs express CD11c, but low levels of CD123 and have a more pronounced role in antigen processing and initiation of T cell response [35]. Plasmacytoid DCs express CD303 (BDCA-2), ILT7, high levels of CD123 (IL-3Ra), but are negative for the classical marker CD11c [33,36–38]. These pDCs play a critical role in anti-viral immunity as well as in immune tolerance [39,40]. Everts et al’s [32] study focusing on people aged 17–39 years showed that the frequencies of mDCs and pDCs are reduced in infected people compared to un-infected and that mDCs are functionally impaired in response to toll-like receptor ligands and in driving T cell responses ex vivo. Introduction Schistosoma haematobium helminth parasites cause urogenital schistosomiasis which affects about 112 million people mainly in rural areas of subtropical countries [1]. Infections with S. haematobium are most common in school-age children. Populations in endemic areas show a characteristic age-infection profile with September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org PLOS Neglected Tropical Diseases | www.plosntds.org 1 Myeloid Dendritic Cells and S.haemtobium Infection and early TH2-promoing activities can be diminished by TLR-3 [30]. Overall studies are rare addressing the role of the innate immune cells in the immune response against schistosomes [31]. Author Summary Nevertheless, the induction of a TH2 response is important in the immune response against schistosomes [21] and in particular for the development of protection [22]. As a major antigen-presenting cell population dendritic cells (DCs) are responsible for acquiring, processing and presenting parasite antigens to T cells and the latter interaction leads to activation and polarisation of the acquired immune response. The impor- tance of DCs in the induction of the TH2 immune responses in the context of schistosome infections has been recently highlighted in an experimental mouse model [23]. This study indicates that DCs are required for the induction and development of TH2 responses during schistosome infections supporting other studies showing the importance of DCs in the context of TH2 induction [24–27]. PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 Study population and parasitology This study was performed in Chipinda village which is located in the Mashonaland East Province in Zimbabwe (31u949E; 17u679S). The village was selected because health surveys regularly conducted in the region showed little or no infection with soil- transmitted helminths (STH) and a low S. mansoni prevalence (,2%), which elicit immune responses that cross-react with those against S. haematobium [43,44,45]. The low STH and S. mansoni prevalence is consistent with earlier surveys in this area of Zimbabwe [46–48]. Villagers are subsistence farmers who have frequent contact with water sources posing a risk of infection (as assessed by questionnaires) due to insufficient safe water provision and low coverage of sanitation facilities as is typical in rural Zimbabwe. Drinking water is collected from open wells while bathing and washing is conducted in perennial rivers surrounding the village. This area has not been included in any Schistosome It has been shown that schistosome derived compounds can activate dendritic cells by toll-like receptors (TLR)-2 and 3 [28,29] PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 September 2012 | Volume 6 | Issue 9 | e1824 2 Myeloid Dendritic Cells and S.haemtobium Infection Myeloid Dendritic Cells and S.haemtobium Infection Control Programmes and therefore participants had not received any anti-helminthic treatment for schistosomiasis or other helminth infections prior to this study. Thus their natural immune responses could be assessed in the absence of drug-altered schistosome-specific responses [49,50]. Urine and stool samples were collected on three consecutive days and examined micro- scopically for S. haematobium (urine filtration, Mott method [51]) or S. mansoni and intestinal helminths (Kato-Katz method [52]) respectively using standard procedures. Participants were screened for malaria by microscopic examination of Giemsa stained blood smears and HIV status was determined by immunochromato- graphy (DoubleCheckGoldTM HIV 1&2, Orgenics) with HIV positive samples subsequently re-tested by a second rapid assay (Determine HIV 1/2 Ag/Ab Combo, InvernessMedical) to confirm HIV status [53]. Study participants had to meet the following criteria: (1) be life-long residents in this area (assessed by questionnaires) so that age would be a proxy for duration of exposure to S. haematobium infection, (2) should not have received anti-helminthic treatment prior to this study, (3) should have provided at least two urine and two stool samples on consecutive days for parasitological diagnosis, (4) should have tested negative for intestinal helminths including S. Blood collection and isolation of PBMC Depending on age of the participants up to 25 ml of venous blood was collected in heparinized tubes of which approximately 5 ml was used for serological assays as well as microscopic detection of malaria parasites. The remaining blood was used for the isolation of peripheral blood mononuclear cells (PBMC) through density gradient centrifugation using Lymphoprep (Axis- Shield, Cambridgeshire, UK). These PBMC were subsequently enumerated, cryo-preserved in 10% DMSO, 90% fetal calf serum and stored in liquid nitrogen in Zimbabwe prior to shipping to Edinburgh in dry shippers for assaying. Ethical statement Permission to conduct the study in the region was obtained from the Provincial Medical Director and institutional and ethical approval was received from the University of Zimbabwe’s Institute Review Board and the Medical Research Council of Zimbabwe respectively. Only compliant participants were recruited and they were free to drop out at any point during the study. At the beginning of the study, participants and their parents/guardians (in case of children) had the aims and procedures of the project explained fully in the local language, Shona, and written consent was obtained from participants and parents/guardian before parasitology and blood samples were obtained. After collection of all samples, all participants were offered anti-helminthic treatment with the recommended dose of praziquantel (40 mg/kg of body weight). DC phenotyping Thawing of cryo-preserved PBMC was performed by rotating cryovials in a 37uC water bath until a small crystal was remaining in the cell suspension. Cells were then slowly re-suspended in RPMI 1640 supplemented with 10% FCS, 2 mM L-glutamine and 100 U Penicillin/Streptomycin (all Lonza, Verviers, Belgium). Cells were washed twice with media, counted and viability assessed using trypan blue (Sigma-Aldrich, Dorsert, UK). The median viability of the PBMCs was 71.4% which is within the range of published values [54]. In addition it was confirmed that including a viability marker did not change analysis of subsets. Afterwards, cells were washed with Dulbecco’s-PBS (Lonza) and surface stained with the following antibodies: Qdot-605-conjugated anti- CD14 (clone TUK4, Invitrogen), FITC-conjugated anti-CD11c (clone Bu15, Invitrogen), APC-H7-conjugated anti-HLA-DR (clone L243, BD Biosciences), PE-Cy5. anti-CD123 (clone 9F5, BD Biosciences) and V450 BD Horizon-conjugated anti-CD86 (clone 2331, BD Biosciences), PE-conjugated anti-BDCA-2 (clone AC144, Miltenyi Biotec) and APC-conjugated anti-BDCA-4 (clone AD5-17F6, Miltenyi Biotec). Stained cells were acquired on a FACSCantoII (BD Biosciences) and analyzed using FlowJo software software (TreeStar, USA). Study population and parasitology mansoni to focus on single infections with S. haematobium, (5) should be negative for HIV and malaria (Prevalence of both HIV and malaria were too small for inclusion in the statistical analysis (HIV prevalence in Chipinda village was 8% and no-one was positive for malaria infection at the time of sampling) and (6) have provided a sufficient volume of blood to isolate peripheral blood mononuclear cells (PBMC). The selected cohort comprised 61 individuals and details to the cohort are provided in Table 1. Epidemiology of study population p gy y p p This study was designed to focus on the immune modulation in a population exposed to S. haematobium. The northeast part of Zimbabwe is endemic for S. haematobium with many regions having a moderate to high prevalence of S. haematobium, but low prevalence of S. mansoni and soil-transmitted helminths [47,48]. The overall prevalence in Chipinda was (39%). This is defined by the World Health Organisation (WHO) as a moderate transmis- sion area [58]. The overall prevalence of S. haematobium in the selected study population (N = 61) was 47.5% which is higher but not significantly different from (x2 = 1.688, df = 1, p = 0.097) the village prevalence of 39% and still within the WHO definition of moderate transmission. The difference in infection prevalence between the youngest age group (35.3%) compared to more than 50% in the older age groups was not significant (x2 = 0.806, df = 1, p = 0.185; details in Table 1). However, youngest individuals (5–9 years) who were infected carried high infection levels (Figure 1 and Table 1). Individuals aged 10–13 years still showed high infection levels, but with a higher prevalence than the first age group. In contrast, in the oldest age group (14–45 years), the prevalence remained high, but most individuals show lower infection intensities (Figure 1). The consequence of the infection profile is that individuals who are life long residents in the area and have never received treatment with anti-helminthic drugs (see selection criteria in Methods) differ in their cumulative histories of exposure despite carrying comparable infection intensities. This was supported by an analysis of the serum levels of adult worm specific (whole worm homogenate – WWH) antibody levels. As shown in Figure 2A and B levels of WWH-specific IgE and IgG, which are associated with history of infection and resistance to infection [59–61], increase significantly with age. In contrast IgM against WWH as marker of current infection starts to decrease in the oldest age group (Figure 2C). Statistical analysis y The proportions of DC cell subsets were square root arcsine transformed whereas expression levels of HLA-DR and CD86 were square root transformed to allow the use of parametric tests in subsequent analyses [56]. To analyse which factors influence the proportion of DC subsets, a univariate analysis of variance using sex (male/female), host age groups (group 1: 5–9 years; group 2: 10–13 years; group 3: 14+ years) and infection status (un- infected = 0 mean egg count per 10 ml and infected .0 mean egg count per 10 ml; all variables categorical) as independent variables was performed. The three different age groups were selected to reflect epidemiological groupings (i.e. where infections are acquired, peak and decline) by age and infection intensity and to obtain comparable sample sizes between the groups. Post hoc tests between infected and un-infected individuals were conducted in each age group. In addition post hoc analysis was performed to determine differences in pDCs between the three age groups. To determine if the mDC populations showed an age profile consistent with those for protective immune responses as predicted by quantitative studies [13], correlation analyses between infection intensity (log10 (mean egg count+1) transformed) and proportions of mDCs was conducted after allowing for the effect of sex. The correlation coefficients were then tested for homogeneity using the Fisher’s r-to-z transformation [57]. Correlation analyses between WWH-specific IgG and DC cell subsets were performed after allowing for the effects of sex, age and infection intensity. All statistical tests were conducted using the software package SPSS v14 and p values were taken to be significant at p,0.05. Figure 1. Age – infection profile of the study population. The study population was divided into three age groups: 5–9 years (N = 17), 10–13 years (N = 23) and 14+ years (N = 21). Mean infection intensities from at least two urine samples for each individual are given. The mean for each group is indicated. doi:10.1371/journal.pntd.0001824.g001 Characterization of mDCs and pDCs in total study population To analyze mDCs and pDCs, PBMC were gated on CD14negHLA- DR+ cells (Figure 3A, B). Gated cells were stained with CD123 and CD11c to distinguish mDCs (CD11c+CD123neg/low) from pDCs (CD123hiCD11cneg; Figure 3C). To further verify specificity of pDC gated CD123hiCD11cneg were analysed for the expression of BDAC- 2/CD303 and BDCA-4/CD304 [62] and granularity of gated cells was analysed in an FSC/SSC plot (Figure 3D). Therefore other cell types such as basophiles or B cell potentially able to express CD123 are excluded from the analysis. mDC did not express either BDCA-2 or BDCA-4 (Figure 3E). Subsets were expressed as percentages of PBMC or as percentage of CD14negHLA-DR+ cells. Both subsets were subsequently analysed for the expression of CD86 (Figure 3D, E) and levels of HLA-DR within the two different DC populations as indicators of DC activation status and their ability to present antigen and co-stimulatory signals to T cells. When the study population was portioned by infection status (un- infected versus infected), neither mDCs (Figure 4A) nor pDCs (Figure 4B) showed a significant difference between both popula- tions. Comparable results were obtained if DC subsets were expressed as percentage of CD14negHLA-DR+ (data not shown). Myeloid DCs showed a significant association with sex (Table 2), in which female had slightly higher proportions than males. This was then statistically accounted for in all subsequent analyses. Antibody ELISAs y Serum antibody levels were measured by enzyme-linked immunosorbent assays (ELISA) following established protocols [8,55]. Whole worm homogenate (WWH) was obtained from the Theodor Bilharz Research Institute (Giza, Egypt). In short, microtiter plates were coated overnight at 4uC at 10 mg/ml. Serum samples were diluted at 1:20 for WWH-IgE and 1:100 for WWH-IgG and IgM and incubated for 2 hours at 37uC. Horse- radish peroxide conjugated antibodies were diluted 1:1000 for IgG, IgE and IgM and incubated for 1 hour at 37uC. ELISAs were developed using ABTS (Southern Biotech) and stopped after 15 minutes for IgG and IgM, and 30 minutes for IgE. Absorbance was read at 405 nm. Serum was available from 45 out of 61 individuals. Table 1. Study population. Table 1. Study population. S. haematobium Age group N mean age in years (range) Male/female Prevalence in % (95% CI) Mean egg count ± SEM (range) Total 61 14.1 (5–45) 27/34 47.5 (35.6–59.9) 51.6619.3 (0–859) Group 1 17 7.6 (5–9) 8/9 35.3 (15.9–54.8) 78.1651.4 (0–859) Group 2 23 11.1 (10–13) 8/15 52.2 (36.0–68.5) 47.7625.9 (0–571) Group 3 21 22.6 (14–45) 11/10 52.4 (35.0–69.9) 34.5626.0 (0–550) SEM – Standard error of mean, CI – Confidence interval. doi:10.1371/journal.pntd.0001824.t001 PLOS Neglected Tropical Diseases | www.plosntds.org 3 September 2012 | Volume 6 | Issue 9 | e1824 September 2012 | Volume 6 | Issue 9 | e1824 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org Myeloid Dendritic Cells and S.haemtobium Infection Figure 1. Age – infection profile of the study population. The study population was divided into three age groups: 5–9 years (N = 17), 10–13 years (N = 23) and 14+ years (N = 21). Mean infection intensities from at least two urine samples for each individual are given. The mean for each group is indicated. doi:10.1371/journal.pntd.0001824.g001 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org Expression of CD86 and HLA-DR on mDCs and pDCs Expression of CD86 and HLA-DR on mDCs and pDCs Up-regulation of CD86 is hallmark of maturation and activation of DCs and their ability to provide co-stimulatory signals to T cells. HLA-DR expression can be used as an indicator both of DC activation status and their potential to activate antigen-specific T cells. Neither infection status nor the interaction between infection status and age group influenced expression of CD86 on mDC as Age dependent pattern of mDCs and pDCs Age dependent pattern of mDCs and pDCs The age in the total population ranged from 5–45 years. Age group significantly affected the proportions of pDCs (Table 2), September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 4 Myeloid Dendritic Cells and S.haemtobium Infection Figure 2. Schistosome-specific antibody profiles. Serum levels of WWH-specific IgE (A), IgG (B) and IgM (C) were analysed by ELISA. Obtained data are presented after diving into the three indicated age groups. Correlation coefficient b and significant values are indicated. The effect of sex has been statistically allowed for. doi:10.1371/journal.pntd.0001824.g002 Figure 2. Schistosome-specific antibody profiles. Serum levels of WWH-specific IgE (A), IgG (B) and IgM (C) were analysed by ELISA. Obtained data are presented after diving into the three indicated age groups. Correlation coefficient b and significant values are indicated. The effect of sex has been statistically allowed for. doi:10.1371/journal.pntd.0001824.g002 with a significant increase between 5–9 year olds (age group 1) and 14+ year olds (age group 3; p = 0.033). In contrast for mDCs the relationship with age varied depending on infection status (significant interaction between age group and infection status; Table 2). Based on these results post hoc analysis of mDC proportions by infection status was performed after partitioning the study population into the three different age groups (details in Table 1). In the youngest age group (Figure 5A) infected people had significantly higher mDC percentages than un-infected people. Results were comparable if expressed as percentage of CD14negHLA-DR+ (Figure S1A). This pattern differed in the second age group, where infected individuals showed fewer mDCs than un-infected individuals (Figure 5B) a difference which was even more pronounced in the oldest age groups (Figure 5C). A comparable analysis could be made by correlating infection intensity (rather than infection status) to percentages of mDCs in the three different age groups. In the youngest age group both parameters were positively correlated (b = 0.707, p = 0.001), whereas in the second age group the correlation was instead negative (b = 20.441, p = 0.018). This negative correlation was more pronounced in the third group (b = 20.540, p = 0.007; Figure 6). Age dependent pattern of mDCs and pDCs A test for the homogeneity of the correlations coefficients showed a significant difference between age group one and two (z = 3.89, p = 0.0001) and between the first and the third age group (z = 4.17, p,0.0001). Interaction between mDCs and WWH-IgE Interaction between mDCs and WWH IgE Adult worm specific IgG can be used as a marker development of resistance against infection [59–61]. WWH-specific IgG increases with age and in our population especially between the first and second age group (Figure 2B) and to the same time changes in mDC proportions between un-infected and infected individuals occurred. Therefore the interaction between mDC and WWH-specific IgG was analysed. As indicated in Table S1, WWH-specific IgG is influenced by sex, age and infection intensity, but addition also by proportions of mDC. mDC are directly correlated to WWH-specific IgG after allowing for the effects of sex, age and infection (Figure 9A). Although showing the same tendency pDCs and WWH-specific IgG were not signifi- cantly correlated (Figure 9B). This correlation was most obvious in the oldest age group (Table S2) and overall more significant in un- infected (protected) individuals. Correlation between mDC pro- portions and WWH-specific IgE and IgM were not significant. In contrast, to the clear picture in the case of mDCs, there was no significant difference in the proportion of pDCs (expressed either relative to live PBMC or CD14negHLA-DR+) between un- infected and infected people in any of the three age groups as shown in Figure 7, Figure S1B and Table 2. Age dependent pattern of mDCs and pDCs A test for the homogeneity of the correlations coefficients showed a significant difference between age group one and two (z = 3.89, p = 0.0001) and between the first and the third age group (z = 4.17, p,0.0001). determined by ANOVA (Table 2), which was confirmed by post hoc tests comparing CD86 expression between un-infected and infected people after partitioning into age group (Figure 8A). However HLA-DR expression was significantly influenced by an interaction of age group and infection status (Table 2). Post hoc test showed that HLA-DR expression differed between un-infected and infected individuals, in the youngest age group. In this age group HLA-DR was significantly lower on mDCs from infected people compared to un-infected (Figure 8B). In contrast no difference was observed in HLA-DR expression in people 10–13 years of age or in the oldest age group. Neither CD86 nor HLA- DR expression on pDCs were dependent on age group, infection status or the interaction of these variables (Table 2). with a significant increase between 5–9 year olds (age group 1) and 14+ year olds (age group 3; p = 0.033). In contrast for mDCs the relationship with age varied depending on infection status (significant interaction between age group and infection status; Table 2). Based on these results post hoc analysis of mDC proportions by infection status was performed after partitioning the study population into the three different age groups (details in Table 1). In the youngest age group (Figure 5A) infected people had significantly higher mDC percentages than un-infected people. Results were comparable if expressed as percentage of CD14negHLA-DR+ (Figure S1A). This pattern differed in the second age group, where infected individuals showed fewer mDCs than un-infected individuals (Figure 5B) a difference which was even more pronounced in the oldest age groups (Figure 5C). A comparable analysis could be made by correlating infection intensity (rather than infection status) to percentages of mDCs in the three different age groups. In the youngest age group both parameters were positively correlated (b = 0.707, p = 0.001), whereas in the second age group the correlation was instead negative (b = 20.441, p = 0.018). This negative correlation was more pronounced in the third group (b = 20.540, p = 0.007; Figure 6). PLOS Neglected Tropical Diseases | www.plosntds.org Discussion Urogenital schistosomiasis caused by S. haematobium shows a characteristic age-infection profile with increasing infections intensities during early childhood, peaking usually between the age of 9–15 years and than slowly declining towards adulthood [2– September 2012 | Volume 6 | Issue 9 | e1824 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org 5 Myeloid Dendritic Cells and S.haemtobium Infection Figure 3. Phenotyping DCs. Live PBMCs (A) are gated on CD14negHLA-DR+ cells (B) which subsequently are analysed for the expression of CD11c and CD123 (C). CD123+CD11cneg (D) and CD123neg/lowCD11c+ (E) were subsequently analysed for the expression levels of BDCA-2/CD303 and BDCA- 4/CD304, CD86 and HLA-DR. Presented plots are an example and derived from a 5 year old female individual. doi:10.1371/journal.pntd.0001824.g003 Figure 3. Phenotyping DCs. Live PBMCs (A) are gated on CD14negHLA-DR+ cells (B) which subsequently are analysed for the expression of CD11c and CD123 (C). CD123+CD11cneg (D) and CD123neg/lowCD11c+ (E) were subsequently analysed for the expression levels of BDCA-2/CD303 and BDCA- 4/CD304, CD86 and HLA-DR. Presented plots are an example and derived from a 5 year old female individual. doi:10.1371/journal.pntd.0001824.g003 Figure 3. Phenotyping DCs. Live PBMCs (A) are gated on CD14negHLA-DR+ cells (B) which subsequently are analysed for the expression of CD11c and CD123 (C). CD123+CD11cneg (D) and CD123neg/lowCD11c+ (E) were subsequently analysed for the expression levels of BDCA-2/CD303 and BDCA- 4/CD304, CD86 and HLA-DR. Presented plots are an example and derived from a 5 year old female individual. doi:10 1371/journal pntd 0001824 g003 4]. This study investigated whether the age-related changes in schistosome infection pattern impacted on the proportions and phenotype of DCs. 4]. This study investigated whether the age-related changes in schistosome infection pattern impacted on the proportions and phenotype of DCs. specific IgG are correlated with proportions of mDCs. This effect was more significant in the oldest age group, in which protective immunity becomes effective. We provide evidence that indeed there is an age-related pattern in the proportions of mDCs, if infected and un-infected people were compared. The proportion of mDCs were found to be present in significantly higher proportions in infected individuals compared to un-infected individuals in the youngest age group carrying heaviest infection levels. This subsequently changes in older age groups, were older infected individuals had lower relative numbers of mDCs compared to un-infected people. September 2012 | Volume 6 | Issue 9 | e1824 Discussion PBMC (N = 61) were analysed for proportions of (A) CD123neg/lowCD11c+ mDCs or (B) CD123hiCD11cneg pDCs (expressed as % of PBMC). Data of the total population were divided in un-infected (N = 32, white box) and infected individuals (N = 29, gray box). Data are presented as Whiskers boxplot (10–90 percentiles). Differences were analysed by univariate analysis after accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g004 Plasmodium or HIV, that in Gabon had co-infections with microfilaria observed in 48% of the schistosome infected individuals which could affect the pDCs proportions. clearly shown for schistosome-specific IgG, IgE and IgM. The importance of DC in TH2 induction has been recently shown [23]. By altering cytokine responses DC could finally be involved in isotype switching and development of protective immunity. This is supported by our finding of the correlation between schisotosome- specific IgG and mDCs. Both our study and that of Everts et al [32] clearly indicate the difference in mDC populations between infected and un-infected adults. However, since infections in moderate to high transmission areas occur at relatively young age, we were interested in the dynamics of the DCs over time, which was not possible in Evert’s study. We wanted to determine when if at all the difference between infected and un-infected people was established. There- fore, we analysed DC cell populations in younger age groups. Our study demonstrates that a lower frequency of mDCs in infected people can be already observed in 10–13 year olds. This is accordance with changes in other immunological parameters as Changes with age have been also observed for serum cytokines in other study populations with moderate/high schistosome transmission [10,11,64]. For instance, high levels of parasite- specific or serum levels of IL-10 have been reported already at this age in different populations [11,65] and might contribute to such changes. For example, DCs treated with the regulatory cytokine IL-10 inhibit T cell activation [66–69]. Earlier studies showed that T cell hypo-responsiveness can be already observed at early ages Table 2. Effects of sex, age group and infection status on mDC and pDC proportions and levels of HLA-DR, CD86 expression on both subsets. e group and infection status on mDC and pDC proportions and levels of HLA-DR, CD86 expression on Table 2. Effects of sex, age group and infection status on mDC and pDC proportions and levels of HLA both subsets. Table 2. Discussion The gradual change between the three age groups became more apparent when the correlation between infection intensity (rather than infection status) and mDCs proportions were considered. In this case both parameters were positively correlated in the youngest age group and became a negative correlation with increasing age. This pattern is consistent with that predicted by quantitative studies for protective immune responses and has already been demonstrated for antibody responses associated with protection to re/infection in human hookworm [63] and schistosome infections [64]. Importantly levels of adult worm Our data confirm some of the major findings of a previous study of DC populations in human schistosomiasis conducted by Everts et al [32]. Proportions of mDCs were lower in an age group 14–45 years (mean 22.6 years) which is comparable to the population studied by Everts et al (17–39 years). Since cellular immune responses might depend on many different parameters such as transmission dynamics or genetic background of the investigated study population the consistency in DC proportions in schisto- some-exposed human between our study and that by Everts et al, by itself is an important finding. A major difference between the two studies is that we did not observe differences in pDC percentages in regards to infection status, although we had high variation in pDC levels in the oldest age group. In deed a slight tendency of lower pDC proportions (expressed as percentage of PBMC) was observed in this age group. Differences in co- infections may also account for the differences between our observations and those of Everts et al [32] in Gabon. While the population in Zimbabwe had no co-infection with other helminths, September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 6 Myeloid Dendritic Cells and S.haemtobium Infection Figure 4. Proportions of DCs in the study population. PBMC (N = 61) were analysed for proportions of (A) CD123neg/lowCD11c+ mDCs or (B) CD123hiCD11cneg pDCs (expressed as % of PBMC). Data of the total population were divided in un-infected (N = 32, white box) and infected individuals (N = 29, gray box). Data are presented as Whiskers boxplot (10–90 percentiles). Differences were analysed by univariate analysis after accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g004 Figure 4. Proportions of DCs in the study population. Results from univariate analyses of variance determining the effect of host sex, age group and infection status. Variables with significant influence are highlighted in bold. df –degree of freedom. For mDCs and pDCs proportions of PBMC were analysed, whereas the MFI was used for HLA-DR and CD86 expression. doi:10 1371/journal pntd 0001824 t002 PLOS Neglected Tropical Diseases | www.plosntds.org 7 September 2012 | Volume 6 | Issue 9 | e1824 Discussion Effects of sex, age group and infection status on mDC and pDC proportions and levels of HLA-DR, CD86 expression on both subsets. Dependent variable Proportions of DCs HLA-DR expression CD86 expression DC population Explanatory variable df F – value p – value df F – value p – value df F – value p – value mDC sex 1, 60 4.659 0.35 1, 60 2.049 0.158 1, 60 0.297 0.588 age group 2, 60 0.646 0.528 2, 60 0.068 0.934 2, 60 0.064 0.938 infection status 1, 60 3.392 0.071 1, 60 0.372 0.544 1, 60 0.424 0.518 Age group * infection status 2, 60 11.963 ,0.001 2, 60 3.865 0.027 2, 60 0.763 0.471 pDC sex 1, 60 2.509 0.119 1, 60 2.240 0.140 1, 60 0.015 0.902 age group 2, 60 3.544 0.036 2, 60 0.075 0.928 2, 60 0.092 0.912 infection status 1, 60 1.237 0.271 1, 60 0.842 0.363 1, 60 1.184 0.281 Age group * infection status 2, 60 0.074 0.929 2, 60 1.246 0.296 2, 60 1.267 0.290 Results from univariate analyses of variance determining the effect of host sex, age group and infection status. Variables with significant influence are highlighted in bold. df –degree of freedom. For mDCs and pDCs proportions of PBMC were analysed, whereas the MFI was used for HLA-DR and CD86 expression. doi:10.1371/journal.pntd.0001824.t002 Results from univariate analyses of variance determining the effect of host sex, age group and infection status. Variables with significant influence are highlighted in bold. df –degree of freedom. For mDCs and pDCs proportions of PBMC were analysed, whereas the MFI was used for HLA-DR and CD86 expression. doi:10.1371/journal.pntd.0001824.t002 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 7 Myeloid Dendritic Cells and S.haemtobium Infection Figure 5. Proportions of mDCs in different age groups. The study population was divided into three age groups: 5–9 years (A), 10–13 years (B) and 14+ years (C). Proportions of mDCs were compared between un-infected (white box) and infected (gray box) individuals and expressed as % percentage of PBMC. Differences between un-infected and infected groups in the different age groups were analysed by univariate analysis after accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g005 Figure 5. Proportions of mDCs in different age groups. Discussion The study population was divided into three age groups: 5–9 years (A), 10–13 years (B) and 14+ years (C). Proportions of mDCs were compared between un-infected (white box) and infected (gray box) individuals and expressed as % percentage of PBMC. Differences between un-infected and infected groups in the different age groups were analysed by univariate analysis after accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g005 [70,71]. The role of mDCs in induction of this impairment remains to be further investigated. cytokines as well as IL-10 in older individuals (17–39 years). The mechanisms involved are still unclear since despite this impair- ment of DC function, older individuals carrying schistosome infection can show enhanced immunopathology [74,75] indicating an effective immune response. Other reasons for reduced relative numbers of mDCs in infected individuals in older age groups remain to be determined, e.g. enhanced apoptosis, reduced bone marrow output or increased migration to inflamed tissues or lymphoid organs were proposed by Everts et al [32]. Indeed enhanced migration in the context of TH2 priming DCs has been reported [25,72]. This was induced by eosinophil-derived neurotoxin; a molecule elevated in serum of S. haematobium infected people [73]. Everts et al reported a more general impairment of DCs affecting both TH1 and TH2 In contrast, our data show that in the younger individuals (5–9 years) mDCs proportions were higher in peripheral blood of infected individuals in comparison to un-infected. Potential reasons for this include enhanced bone marrow output or reduced migration of DCs in the context of blood-born antigens [76]. Infection levels were highest in the youngest age group of our Figure 6. Correlation between infection intensity and mDCs. The study population was divided into three age groups: 5–9 years (left panel), 10–13 years (middle panel) and 14+ years (right panel). Proportions of mDCs expressed as % of PBMC are plotted against infection intensity (log10 (mean egg count+1) transformed). Correlation coefficient b and significant values of a correlation analysis after allowing for the effect of sex are indicated. doi:10.1371/journal.pntd.0001824.g006 Figure 6. Correlation between infection intensity and mDCs. The study population was divided into three age groups: 5–9 years (left panel), 10–13 years (middle panel) and 14+ years (right panel). Proportions of mDCs expressed as % of PBMC are plotted against infection intensity (log10 (mean egg count+1) transformed). Correlation coefficient b and significant values of a correlation analysis after allowing for the effect of sex are indicated. Discussion doi:10.1371/journal.pntd.0001824.g006 September 2012 | Volume 6 | Issue 9 | e1824 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org 8 Myeloid Dendritic Cells and S.haemtobium Infection Figure 7. Proportions of pDCs in different age groups. The study population was divided into three age groups: 5–9 years (A), 10–13 years (B) and 14+ years (C). Proportions of mDCs were compared between un-infected (white box) and infected (gray box) individuals and expressed as percentage of PBMC (B). Differences between un-infected and infected groups in the different age groups were analysed by univariate analysis after accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g007 Figure 7. Proportions of pDCs in different age groups. The study population was divided into three age groups: 5–9 years (A), 10–13 years (B) and 14+ years (C). Proportions of mDCs were compared between un-infected (white box) and infected (gray box) individuals and expressed as percentage of PBMC (B). Differences between un-infected and infected groups in the different age groups were analysed by univariate analysis after accounting for the effect of sex. doi:10.1371/journal.pntd.0001824.g007 study population and young people might have more blood migrating schistosome stages affecting proportions of circulating mDCs. In contrast enhanced immune response including enhanced migration of mDCs might lead to increased killing of infiltrating schistosomula in older age groups. we observed no changes in expression of CD86 in infected people. However HLA-DR levels differed. In the youngest age group (5–9 years), where we found higher percentages of mDCs, expression levels of HLA-DR were lower in infected people. Reduced HLA-DR expression might be an indication of less matured and possibly fewer migrating cells, which subsequently could result in a less pronounced induction of T cell response in an early phase of exposure to schistosomes we observed no changes in expression of CD86 in infected people. However HLA-DR levels differed. In the youngest age group (5–9 years), where we found higher percentages of mDCs, expression levels of HLA-DR were lower in infected people. Reduced HLA-DR expression might be an indication of less matured and possibly fewer migrating cells, which subsequently could result in a less pronounced induction of T cell response in an early phase of exposure to schistosomes Dendritic cell activation/maturation is characterised by up- regulation of cell-surface markers such as CD86 and MHC class II molecules. As previously reported by Everts et al [32], Figure 8. PLOS Neglected Tropical Diseases | www.plosntds.org Discussion Expression levels of CD86 and HLA-DR on mDCs. PBMC were gated on mDCs as indicated in Figure 2 and analysed for the expression of CD86 (A) and HLA-DR (B). Data partitioned into three age groups as indicated and compared between un-infected (white columns) and infected individuals (gray columns). doi:10.1371/journal.pntd.0001824.g008 Supporting Information accompanied by a more regulatory environment due to Tregs and parasite-specific IL-10 [11,12,65]. Analysis of Tregs from another study cohort from the same population revealed a comparable pattern as recently published by our group [12]. In addition a direct comparison of mDCs and Tregs would need a larger sample size, since statistical power is lost by comparing the two parameters in the presence of other potentially confounding variables such as host age. Figure S1 Proportions of mDCs and pDCs expressed as percentage of CD14neg-HLA-DR+ cells. The study popula- tion was divided into three age groups: 5–9 years (A), 10–13 years (B) and 14+ years (C). Proportions of mDCs (A) or pDC (B) were compared between un-infected (white box) and infected (gray box) individuals and expressed as % percentage of CD14neg-HLA- DR+. Differences between un-infected and infected groups in the different age groups were analysed by univariate analysis after accounting for the effect of sex. (TIF) In contrast to the study by Everts et al, we did not observe a significant difference of HLA-DR levels in the older age groups. Again more significant changes of HLA-DR in these age groups might be due to cumulative effect of co-infections, not present in our study population. Acknowledgments In summary this study clearly shows there is an age-related pattern in the proportions mDCs in people exposed to S. haematobium infection as is typical for many already investigated humoral and cellular responses. Furthermore, in the case of mDCs, this pattern differs between schistosome infected and un- infected people and also follows the age profile with infection of protective responses, which is supported by the correlation between schistosome-specific IgG and proportions of mDCs. We would like to thank the residents and children of Chipinda village as well as the teachers from Chipinda primary and secondary school for their participation and generous and kind support of this study. We are also very grateful for the co-operation of the Ministry of Health and Child Welfare in Zimbabwe. We like to thank the Provincial Medical Director of Mashonaland East, the Environmental Health Workers, nursing staff at Chitate Clinics and Murehwa Hospital. We are grateful to the members of the National Institutes of Health in Harare and the Biochemistry Department at University of Zimbabwe for technical and logistical support. The mechanism and consequences (such as alterations in the potential to induce different T cell phenotypes) behind the association between mDCs and infection remain to be determined. Understanding the nature and dynamics of immunological parameters in natural helminth infections and, in particular, changes of DCs involved in polarising the immune responses has an important impact on the development of vaccines against schistosomes. Table S1 Interaction between WWH-IgE and mDC or pDC. Inhibition of up-regulation of activation markers such as CD86 has been suggested to be involved in induction of tolerogenic DCs [66]. However we did not see changes in the activation marker CD86. There is need to analyse other markers, such as B7-H1, B7-H2, lg-like transcripts 3 and 4 which might play a role in the function of tolerogenic DCs [77–81], particularly in younger age groups. Figure 8. Expression levels of CD86 and HLA-DR on mDCs. PBMC were gated on mDCs as indicated in Figure 2 and analysed for the expression of CD86 (A) and HLA-DR (B). Data partitioned into three age groups as indicated and compared between un-infected (white columns) and infected individuals (gray columns). doi:10.1371/journal.pntd.0001824.g008 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org 9 Myeloid Dendritic Cells and S.haemtobium Infection Figure 9. Correlation between WWH-IgG and proportions of mDCs and pDCs. Serum levels of WWH-specific IgG were measured by ELISA. The effects of sex, age and infection intensity was statistically allowed for and residuals of this analysis were plotted against proportions of mDCs (A) or pDCs (B) in percentage of PBMC. b-coefficient and p- values of a linear correlation are indicated. doi:10.1371/journal.pntd.0001824.g009 Figure 9. Correlation between WWH-IgG and proportions of mDCs and pDCs. Serum levels of WWH-specific IgG were measured by ELISA. The effects of sex, age and infection intensity was statistically allowed for and residuals of this analysis were plotted against proportions of mDCs (A) or pDCs (B) in percentage of PBMC. b-coefficient and p- values of a linear correlation are indicated. doi:10.1371/journal.pntd.0001824.g009 Table S2 Correlation between WWH-IgE and mDC or pDC. p (TIF) Functional studies, will be very informative and will clarify some of these areas, but were beyond the scope of this study. 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Geiger SM (2008) Immuno-epidemiology of Schistosoma mansoni infections in endemic populations co-infected with soil-transmitted helminths: present knowledge, challenges, and the need for further studies. Acta Trop 108: 118– 123. 18. Watanabe K, Mwinzi PN, Black CL, Muok EM, Karanja DM, et al. (2007) T regulatory cell levels decrease in people infected with Schistosoma mansoni on effective treatment. Am J Trop Med Hyg 77: 676–682. 46. Chandiwana SK (1989) The problem and control of gastrointestinal helminthi- ases in Zimbabwe. Eur J Epidemiol 5: 507–515. 19. Capron A, Dombrowicz D, Capron M (1999) Regulation of the immune response in experimental and human schistosomiasis: the limits of an attractive paradigm. Microbes Infect 1: 485–490. 47. Ndhlovu P, Chimbari M, Ndamba J, Chandiwana SK (1992) 1992 National Schistosomiasis Survey. Blair Research Laboratory, Harare, Zimbabwe. 20. Dunne D, Mountford AP (2001) Resistance to infection in human and animal models. Schistosomiasis; Mahmoud AAF, editor. London: Imperial College Press. 48. Author Contributions Conceived and designed the experiments: NN OL NM TM FT FM. Performed the experiments: NN DL IP IYDC. Analyzed the data: NN DL OL. Wrote the paper: NN FM LJA CDB. Contributed to field work: LJA CDB. Contributed to final version of the manuscript: LJA CDB OL FT. September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org 10 Myeloid Dendritic Cells and S.haemtobium Infection Myeloid Dendritic Cells and S.haemtobium Infection Myeloid Dendritic Cells and S.haemtobium Infection Myeloid Dendritic Cells and S.haemtobium Infection 56. Mutapi F, Roddam A (2002) p-values for pathogens: statistical inference from infectious-disease data. Lancet Infectious Disease 2: 219–230. pressive cytokines induce antigen-specific anergy and regulatory properties in memory CD4+ T cells. J Immunol 184: 1765–1775. pressive cytokines induce antigen-specific anergy and regulatory properties in memory CD4+ T cells. J Immunol 184: 1765–1775. 57. Zar JH (1998) Biostatistical Analysis: Prentice Hall. 70. King CL, Medhat A, Malhotra I, Nafeh M, Helmy A, et al. (1996) Cytokine control of parasite-specific anergy in human urinary schistosomiasis. IL-10 modulates lymphocyte reactivity. J Immunol 156: 4715–4721. 58. World Health Organization (2002) Prevention and control of schistosomiasis and soil-transmisted helminthiasis. Geneva: World Health Organisation. Available: http://www.who.int/wormcontrol/documents/joint_statements/en/ppc_ unicef_finalreport.pdf Accessed 2011 Oct. p. y p y y 71. Grogan JL, Kremsner PG, Deelder AM, Yazdanbakhsh M (1998) Antigen- specific proliferation and interferon-gamma and interleukin-5 production are down-regulated during Schistosoma haematobium infection. J Infect Dis 177: 1433– 1437. 59. Hagan P, Blumenthal UJ, Dunne D, Simpson AJG, Wilkins AH (1991) Human IgE, IgG4 and resistance to reinfection with Schistosoma haematobium. Nature 349: 234–245. 72. Yang D, Rosenberg HF, Chen Q, Dyer KD, Kurosaka K, et al. (2003) Eosinophil-derived neurotoxin (EDN), an antimicrobial protein with chemotac- tic activities for dendritic cells. Blood 102: 3396–3403. 60. Mutapi F, Hagan P, Ndhlovu P, Woolhouse MEJ (1997) Comparison of humoral responses to Schistosoma haematobium in areas with high and low levels of infection. Parasite Immunology 19: 255–263. 73. Tischendorf FW, Brattig NW, Burchard GD, Kubica T, Kreuzpaintner G, et al. (1999) Eosinophils, eosinophil cationic protein and eosinophil-derived neuro- toxin in serum and urine of patients with onchocerciasis coinfected with intestinal nematodes and in urinary schistosomiasis. Acta Trop 72: 157–173. 61. Satti MZ, Lind P, J VB, Sulaiman SM, Daffalla AA, et al. (1996) Specific immunoglobulin measurements related to exposure and resistance to Schistosoma mansoni infection in Sudanese canal cleaners. Clinical Experimental Immunology 106: 45–54. intestinal nematodes and in urinary schistosomiasis. Acta Trop 72: 15 74. Booth M, Vennervald BJ, Kabatereine NB, Kazibwe F, Ouma JH, et al. (2004) Hepatosplenic morbidity in two neighbouring communities in Uganda with high levels of Schistosoma mansoni infection but very different durations of residence. Trans R Soc Trop Med Hyg 98: 125–136. 62. Dzionek A, Inagaki Y, Okawa K, Nagafune J, Rock J, et al. (2002) Plasmacytoid dendritic cells: from specific surface markers to specific cellular functions. Hum Immunol 63: 1133–1148. 75. Myeloid Dendritic Cells and S.haemtobium Infection Mohamed-Ali Q, Elwali NE, Abdelhameed AA, Mergani A, Rahoud S, et al. (1999) Susceptibility to periportal (Symmers) fibrosis in human schistosoma mansoni infections: evidence that intensity and duration of infection, gender, and inherited factors are critical in disease progression. J Infect Dis 180: 1298–1306. 63. Quinnell RJ, Bethony J, Pritchard DI (2004) The immunoepidemiology of human hookworm infection. Parasite Immunol 26: 443–454. 64. Mutapi F, Mduluza T, Gomez-Escobar N, Gregory WF, Fernandez C, et al. (2006) Immuno-epidemiology of human Schistosoma haematobium infection: preferential IgG3 antibody responsiveness to a recombinant antigen dependent on age and parasite burden. BMC Infect Dis 6: 96. p g J 76. Balazs M, Martin F, Zhou T, Kearney J (2002) Blood dendritic cells interact with splenic marginal zone B cells to initiate T-independent immune responses. Immunity 17: 341–352. 65. Lyke KE, Dabo A, Sangare L, Arama C, Daou M, et al. (2006) Effects of concomitant Schistosoma haematobium infection on the serum cytokine levels elicited by acute Plasmodium falciparum malaria infection in Malian children. Infect Immun 74: 5718–5724. 77. Tuettenberg A, Huter E, Hubo M, Horn J, Knop J, et al. (2009) The role of ICOS in directing T cell responses: ICOS-dependent induction of T cell anergy by tolerogenic dendritic cells. J Immunol 182: 3349–3356. 78. Cella M, Dohring C, Samaridis J, Dessing M, Brockhaus M, et al. (1997) A novel inhibitory receptor (ILT3) expressed on monocytes, macrophages, and dendritic cells involved in antigen processing. J Exp Med 185: 1743–1751. 66. Steinbrink K, Wolfl M, Jonuleit H, Knop J, Enk AH (1997) Induction of tolerance by IL-10-treated dendritic cells. J Immunol 159: 4772–4780. 67. Steinbrink K, Graulich E, Kubsch S, Knop J, Enk AH (2002) CD4(+) and CD8(+) anergic T cells induced by interleukin-10-treated human dendritic cells display antigen-specific suppressor activity. Blood 99: 2468–2476. 79. Colonna M, Samaridis J, Cella M, Angman L, Allen RL, et al. (1998) Human myelomonocytic cells express an inhibitory receptor for classical and nonclassical MHC class I molecules. J Immunol 160: 3096–3100. 68. Zheng Z, Narita M, Takahashi M, Liu A, Furukawa T, et al. (2004) Induction of T cell anergy by the treatment with IL-10-treated dendritic cells. Comp Immunol Microbiol Infect Dis 27: 93–103. J 80. Selenko-Gebauer N, Majdic O, Szekeres A, Hofler G, Guthann E, et al. (2003) B7-H1 (programmed death-1 ligand) on dendritic cells is involved in the induction and maintenance of T cell anergy. J Immunol 170: 3637–3644. References (2012) Schistosoma haematobium infection levels determine the effect of praziquantel treatment on anti-schistosome and anti-mite antibodies. Parasite Immunol. 27. Faveeuw C, Angeli V, Fontaine J, Maliszewski C, Capron A, et al. (2002) Antigen presentation by CD1d contributes to the amplification of Th2 responses to Schistosoma mansoni glycoconjugates in mice. J Immunol 169: 906–912. September 2012 | Volume 6 | Issue 9 | e1824 11 September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org September 2012 | Volume 6 | Issue 9 | e1824 Myeloid Dendritic Cells and S.haemtobium Infection PLOS Neglected Tropical Diseases | www.plosntds.org Myeloid Dendritic Cells and S.haemtobium Infection 69. Torres-Aguilar H, Aguilar-Ruiz SR, Gonzalez-Perez G, Munguia R, Bajana S, et al. (2010) Tolerogenic dendritic cells generated with different immunosup- 81. Sumpter TL, Thomson AW (2011) The STATus of PD-L1 (B7-H1) on tolerogenic APCs. Eur J Immunol 41: 286–290. September 2012 | Volume 6 | Issue 9 | e1824 PLOS Neglected Tropical Diseases | www.plosntds.org 12
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SciRoc_WP2 - ERL-SR Rulebook Update (a) - Deliverable 2.1 - V1.0
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Deliverable 2.1 ERL-SR* Rulebook Update (a) *Note: currently named ERL Consumer Service Robots Project acronym: SCIROC Project number: 780086 Project title European Robotics League plus Smart Cities Robot Competitions WP number and title: WP2 – ERL Service Robots WP leader: IST-ID Organisation responsible for deliverable: Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento (IST-ID) Deliverable author(s): Pedro Lima (IST-ID) Meysam Basiri (IST-ID) Deliverable version number: 1.0 Actual delivery date: 28/09/2018 Dissemination Type Report Dissemination level: Public Change log Version Date Author Reason for change 0.1 11/09/2018 Pedro Lima, Meysam Basiri N/A 1.0 28/09/2018 Pedro Lima, Meysam Basiri Reviewed by Matthew Studley Release approval Version Date Name and organisation Role 1.0 28/09/2018 Matthew Studley Coordinator This project has received funding from the European Union’s European Union’s Horizon 2020 research and innovation programme under grant agreement n° 780086. This project has received funding from the European Union’s European Union’s Horizon 2020 research and innovation programme under grant agreement n° 780086. European Robotics League plus Smart Cities Robot Competitions Horizon 2020 ERL Consumer European Robotic League for Consumer Service Robots Latest Update: Editors: Contributors: September 10, 2018 Meysam Basiri, Pedro Lima Aamir Ahmad, Francesco Amigoni, Iman Awaad, Jakob Berghofer, Rainer Bischo, Andrea Bonarini, Rhama Dwiputra, Giulio Fontana, Frederik Hegger, Nico Hochgeschwender, Luca Iocchi, Gerhard Kraetzschmar, Pedro U. Lima, Matteo Matteucci, Daniele Nardi, Pedro Miraldo, Viola Schiaonati, Sven Schneider, Meysam Basiri, Emanuele Bastianelli, Pedro Resende, João Mendes European Robotics League plus Smart Cities Robot Competitions Horizon 2020 European Robotics League plus Smart Cities Robot Competitions Horizon 2020 Introduction The European Robotic League (ERL) is an innovative concept for robot competitions. The ERL is composed of multiple across-the-year Local Tournaments, held in dierent certied test beds located across Europe, and Major Tournaments, where the competition takes place as part of a major conference or event such as RoboCup. From 2019 on, Smart City tournaments will also take place every other year in European cities. Smart City tournaments are a single annual event. During each across-the-year ERL Season, teams participate in a minimum of two tournaments (Local and/or Major) and get scores based on their performances on Task Benchmarks (TBM) and Functionality Benchmarks (FBM). A nal Season score is computed for each team, using the team best two participations in the Season Tournaments, and teams are ranked based on their nal score. Prizes for the top teams are awarded during the next year's European Robotics Forum (ERF). For more information, please visit: Note: This version of the ERL Consumer rule book is valid until 28.02.2019. Contents Contents v I: ERL Consumer in a Nutshell ix 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 2 The ERL Consumer User Story . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 3 ERL Consumer Scenario . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 3.1 ERL Consumer Environment . . . . . . . . . . . . . . . . . . . . . . . . . 1 3.2 ERL Consumer Benchmarks . . . . . . . . . . . . . . . . . . . . . . . . . . 2 3.2.1 Task Benchmarks . . . . . . . . . . . . . . . . . . . . . . . . . . 2 3.2.2 Functionality Benchmarks . . . . . . . . . . . . . . . . . . . . . . 3 3.3 ERL Consumer Robots . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 II: ERL Consumer Rulebook i 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 2 How to Read and Outline of the Document . . . . . . . . . . . . . . . . . . . . . 1 3 Task Benchmarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 3.1 Task Getting to know my home . . Contents . . . . . . . . . . . . . . . . . . . . . . 1 3.1.1 Task Description . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 3.1.2 Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 3.1.3 Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 2 3.1.4 Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 5 3.1.5 Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 5 3.1.6 Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 5 3.2 Task Welcoming visitors . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 3.2.1 Task Description . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 3.2.2 Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 3.2.3 Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 7 3.2.4 Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 8 3.2.5 Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 9 3.2.6 Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 9 3.3 Task Catering for Granny Annie's Comfort . www.robotics-league.eu The ERL Consumer Service Robots Challenge (ERL Consumer for short) stems from its predecessors, the RoCKIn@Home Challenge, and the ERL Service Robots Challenge, and covers the domain of consumer service robotics, with current focus on domestic applications. This document describes the rules of the ERL Consumer Challenge for the season 2018/2019. Note: The top performing teams from all Challenges (ERL Consumer, ERL Professional and ERL Emergency) of the ERL 2018/19 Season will qualify to participate in the Smart City tournament that will take place in Milton Keynes, United Kingdom in the Fall of 2019. c⃝2018 by ERL Consumer Revision 1.1 iv Contents . . . . . . . . . . . . . . . . 11 3.3.1 Task Description . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 3.3.2 Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 3.3.3 Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 12 3.3.4 Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 12 3.3.5 Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 13 3.3.6 Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 13 3.4 Task Visit my home . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 3.4.1 Task Description . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 3.4.2 Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 3.4.3 Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 14 v Contents Contents 3.4.4 Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 15 3.4.5 Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 16 3.4.6 Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 16 4 Functionality Benchmarks . . . . . Contents . . . . . . . . . . . . . . . . . . . . . . . . . . 17 4.1 Object Perception Functionality . . . . . . . . . . . . . . . . . . . . . . . 17 4.1.1 Functionality Description . . . . . . . . . . . . . . . . . . . . . . 17 4.1.2 Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 4.1.3 Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 17 4.1.4 Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 18 4.1.5 Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 18 4.1.6 Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 19 4.2 Navigation Functionality . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 4.2.1 Functionality Description . . . . . . . . . . . . . . . . . . . . . . 19 4.2.2 Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 4.2.3 Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 19 4.2.4 Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 20 4.2.5 Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 20 4.2.6 Scoring and Ranking . . . . . . . . . . . . . Contents . . . . . . . . . . . . 20 4.3 Speech Understanding Functionality . . . . . . . . . . . . . . . . . . . . . 22 4.3.1 Functionality Description . . . . . . . . . . . . . . . . . . . . . . 22 4.3.2 Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 4.3.3 Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 25 4.3.4 Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 26 4.3.5 Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 26 4.3.6 Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 26 4.4 People Perception Functionality . . . . . . . . . . . . . . . . . . . . . . . . 27 4.4.1 Functionality Description . . . . . . . . . . . . . . . . . . . . . . 27 4.4.2 Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 4.4.3 Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 28 4.4.4 Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 28 4.4.5 Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 28 4.4.6 Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 28 4.5 Person Following Functionality . . Contents . . . . . . . . . . . . . . . . . . . . . . 29 4.5.1 Functionality Description . . . . . . . . . . . . . . . . . . . . . . 29 4.5.2 Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 4.5.3 Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 29 4.5.4 Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 29 4.5.5 Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 30 4.5.6 Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 30 4.6 Object Grasping and Manipulation Functionality . . . . . . . . . . . . . . 30 4.6.1 Functionality Description . . . . . . . . . . . . . . . . . . . . . . 30 4.6.2 Input Provided . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 4.6.3 Expected Robot Behavior or Output . . . . . . . . . . . . . . . . 31 4.6.4 Procedures and Rules . . . . . . . . . . . . . . . . . . . . . . . . 31 4.6.5 Acquisition of Benchmarking Data . . . . . . . . . . . . . . . . . 31 4.6.6 Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . 32 A ERL Consumer Award Categories . . . . . . . . . . . . . . . . . . . . . . . . . Contents . . 33 B The ERL Consumer Test bed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 B.1 Environment Structure and Properties . . . . . . . . . . . . . . . . . . . . 34 B.2 Task-Relevant Objects in the Environment . . . . . . . . . . . . . . . . . . 39 B.2.1 Navigation-Relevant Objects . . . . . . . . . . . . . . . . . . . . 39 c⃝2018 by ERL Consumer vi Contents Contents B.2.2 Manipulation-Relevant Objects . . . . . . . . . . . . . . . . . . . 40 B.2.3 Perception-Relevant Objects . . . . . . . . . . . . . . . . . . . . 42 B.3 Non-Task-Relevant Objects in the Environment . . . . . . . . . . . . . . . 43 B.4 Referee, Scoring and Benchmarking Box . . . . . . . . . . . . . . . . . . . 44 B.4.1 Communication between Benchmarking Equipment and Robots . 46 B.5 Networked Devices in the Environment . . . . . . . . . . . . . . . . . . . . 46 B.6 Benchmarking Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 C Robots and Teams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 C.1 General Specications and Constraints on Robots and Teams . . . . . . . 49 C.2 Safety Check and Robot Inspection . . . . . . . . . . . . . . . . . . . . . . 50 C.3 Benchmarking Equipment and Data Logging on the Robot . . . . . . . . . 51 C.3.1 Setup for the Motion Capture System . . . . Contents . . . . . . . . . . . 51 C.3.2 Internal Data Logging . . . . . . . . . . . . . . . . . . . . . . . . 51 C.4 YAML Data File Specication . . . . . . . . . . . . . . . . . . . . . . . . . 53 C.4.1 File Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 C.4.2 YAML-to-ROSbag Conversion Tool . . . . . . . . . . . . . . . . 54 D General Procedure and Scoring for Task Benchmarks . . . . . . . . . . . . . . . . 55 D.1 Safety check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 D.2 General Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 D.2.1 Start Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 D.2.2 Restart Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . 56 D.2.3 Exit Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 D.3 Scoring and Ranking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 E The ISRoboNet@Home Test Bed at IST . . . . . . . . . . . . . . . . . . . . . . . 58 E.1 Environment Structure and Properties . . . . . . . . . c⃝2018 by ERL Consumer Contents . . . . . . . . . . . 58 E.2 Objects in the Environment . . . . . . . . . . . . . . . . . . . . . . . . . . 59 E.3 Network Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 c⃝2018 by ERL Consumer Revision 1.1 vii Contents Contents c⃝2018 by ERL Consumer Revision 1.1 viii 2 The ERL Consumer User Story Granny Annie is an elderly person, who lives in an in ordinary apartment. Granny Annie is suering from typical problems of ageing people: She has some mobility constraints. She tires fast. She needs to have some physical exercise, though. She needs to take her medicine regularly. She must drink enough. She must obey her diet. She needs to observe her blood pressure and blood sugar regularly. She needs to take care of her pets. She wants to have a vivid social life and welcome friends in her apartment occasionally, but regularly. Sometimes she has days not feeling so well and needs to stay in bed. She still enjoys intellectual challenges and reads books, solves puzzles, and socializes a lot with friends. For all these activities, ERL Consumer is looking into ways to support Granny Annie in mastering her life. The context for performing such activities by technical systems is set in the subsequent scenario description. 3 ERL Consumer Scenario The ERL Consumer scenario description is structured into three sections: environment, tasks and their functionalities, and robots: • The environment section species the environment in which the tasks have to be performed. This information is also relevant for building test beds and simulators. • The environment section species the environment in which the tasks have to be performed. This information is also relevant for building test beds and simulators. • The tasks and functionalities section provides some more detail on the tasks the partic- ipating teams are expected to solve through the use of one or more robots and possibly additional equipment. Since task benchmarks are seen in ERL Consumer as a composition of functionality benchmarks, several functionalities are also introduced. This information tells teams what to prepare for. • The robot section species some constraints and requirements for participating robots, which mainly arise for practical reasons (size and weight limitations, for example) and/or due to the need to observe safety regulations. • The robot section species some constraints and requirements for participating robots, which mainly arise for practical reasons (size and weight limitations, for example) and/or due to the need to observe safety regulations. I: ERL Consumer in a Nutshell 1. Introduction 1. Introduction Contents 1 Introduction ERL Consumer is a competition that aims at bringing together the benets of scientic bench- marking with the attraction of scientic competitions in the realm of consumer service robotics. The objectives are to bolster research in consumer service robotics for home applications and to raise public awareness of the current and future capabilities of such robot systems to meet societal challenges like healthy ageing and longer independent living. Currently, ERL Consumer raises challenges in domestic environments that resemble similar challenges to be posed in smart city environments (e.g., shopping malls), such as recognising and picking objects from shelves, moving outside the home to populated areas, and/or taking elevators between oors, so as to prepare teams for the Smart City Tournaments. Revision 1.1 3.2 ERL Consumer Benchmarks Two types of Benchmarks are dened and used in across-the-year ERL Consumer Local/Major Tournaments: Task Benchmarks and Functionality Benchmarks. 3.1 ERL Consumer Environment The current setup of the ERL Consumer environment reects an ordinary European apartment with all its environmental aspects, like walls, windows, doors or blinds as well as common house- hold items, furniture, decoration and so on. The apartment depicted in Figure 1.1 serves as a guideline. More detailed specications are given in the rule book. The following embedded devices may be installed and are accessible within the apartment's WLAN: Revision 1.1 c⃝2018 by ERL Consumer 1 1 3. ERL Consumer Scenario Contents Figure 1.1: Granny Annie's apartment. Figure 1.1: Granny Annie's apartment. • A networkable, camera-based intercom at the front door. It allows to see who is in front of the door. • A networkable, camera-based intercom at the front door. It allows to see who is in front of the door. • The lamps in the bedroom (e.g. on the bed stand) are accessible and controllable via network. • The lamps in the bedroom (e.g. on the bed stand) are accessible and controllable via network. • The shutters on the bedroom or living room window are accessible and controllable via network. • The shutters on the bedroom or living room window are accessible and controllable via network. Currently, ERL Consumer is not using these networked devices except for possible demos during Local Tournaments in the test beds equipped with them. 3.2.1 Task Benchmarks The following Task Benchmarks will be available in all test beds and Local/Major Tourn 1. Getting to know my home: The robot must detect new changes in the environment, and update the semantic map of the apartment, within a limited time frame. The task shall be performed by the robot autonomously, though it may include moments of symbiotic interaction with a user in the apartment, e.g., to learn more about an object or a location. At the end of the knowledge acquisition phase, the robot must show the understanding of the new environment, namely by handling one of the changed objects. 2. Welcoming visitors: The robot needs to handle a set of known and unknown visitors, who will arrive individually at the home entrance in random sequence. The robot must 2. Welcoming visitors: The robot needs to handle a set of known and unknown visitors, who will arrive individually at the home entrance in random sequence. The robot must c⃝2018 by ERL Consumer 2 Revision 1.1 2 Contents 3. ERL Consumer Scenario correctly recognize the known visitors and interact with the unknown visitors to identify them and understand their purpose of visit. The robot must then perform a set of visitor- specic behaviors that could range from manipulating and delivering of objects to guiding and following the visitors. correctly recognize the known visitors and interact with the unknown visitors to identify them and understand their purpose of visit. The robot must then perform a set of visitor- specic behaviors that could range from manipulating and delivering of objects to guiding and following the visitors. 3. Catering for Granny Annie's comfort: This task aims at providing general purpose requests of Granny Annie inside the apartment. It focuses on the integration of dierent robot abilities such as human-robot interaction, navigation and robot-object interaction. After waking up in the morning, Granny Annie calls the attention of the robot by touching a button on a tablet computer. When the robot arrives, she gives a single speech command composing of three actions from the following three categories: (a) Finding an item or a person in the apartment (b) Manipulating and delivering an object (c) Accompanying a person inside or outside the apartment These three actions are randomly generated into a single command using a command generator in no predened order. The robot is required to understand the actions and execute them accordingly. 3.2.1 Task Benchmarks 4. Visiting my home: This TBM focuses on safe navigation in dynamic environments, obstacle avoidance, tracking and recognizing a person and human following and guiding navigation modes. In this task, the robot should visit a set of predened waypoints while avoiding and/or interacting with dierent obstacles based on the nature of the obstacle. Furthermore, the robot must interact and follow a previously unknown person outside the arena through a small crowd and then guide that person back to the arena. 3.2.2 Functionality Benchmarks The Functionality Benchmarks may be available in Local/Major Tournaments (number and type of Functionalities may vary across test beds). The Functionality Benchmarks may be available in Local/Major Tournaments (number and type of Functionalities may vary across test beds). 1. Object Perception: Evaluates the ability of a robot to recognize and localize a wide range of objects. A set of objects, selected from the list of ERL Consumer items, will be positioned, one at the time, on a table located directly in front of the robot. For each object presented, the robot has to perform the following activities: i) Object detection: perception of the presence of an object on the table and association between the perceived object and one of the object classes. ii) Object recognition: association between the perceived object and one of the object instances belonging to the selected class. iii) Object localization: estimation of the 3D pose of the perceived object with respect to the surface of the table. 1. Object Perception: Evaluates the ability of a robot to recognize and localize a wide range of objects. A set of objects, selected from the list of ERL Consumer items, will be positioned, one at the time, on a table located directly in front of the robot. For each object presented, the robot has to perform the following activities: i) Object detection: perception of the presence of an object on the table and association between the perceived object and one of the object classes. ii) Object recognition: association between the perceived object and one of the object instances belonging to the selected class. iii) Object localization: estimation of the 3D pose of the perceived object with respect to the surface of the table. 1. Object Perception: Evaluates the ability of a robot to recognize and localize a wide range of objects. A set of objects, selected from the list of ERL Consumer items, will be positioned, one at the time, on a table located directly in front of the robot. For each object presented, the robot has to perform the following activities: i) Object detection: perception of the presence of an object on the table and association between the perceived object and one of the object classes. ii) Object recognition: association between the perceived object and one of the object instances belonging to the selected class. 3.2.2 Functionality Benchmarks In particular, it assesses the object picking and placing capabilities of robots suitable for many consumer applications such as setting up a dining table in domestic environments. 6. Grasping and Manipulation: Evaluates the ability of a robot to correctly grasp and manipulate objects. In particular, it assesses the object picking and placing capabilities of robots suitable for many consumer applications such as setting up a dining table in domestic environments. 3.2.2 Functionality Benchmarks iii) Object localization: estimation of the 3D pose of the perceived object with respect to the surface of the table. 2. Navigation: Evaluates the ability of a robot to correctly, safely, and autonomously nav- igate in a ordinary apartment, including: the navigation in a apartment-like environment with furniture, walls, and doors, i.e. in a previously mapped area; avoiding collisions with dierent type of unknown obstacles, in unknown positions (not previously mapped); and navigating in the presence of people in the arena. 3. Speech Understanding: Evaluates the ability of a robot to understand speech com- mands that a user gives to a robot in a consumer environment, including all the related issues, such as background noise caused by other ongoing activities and by the robot mo- tion. A set of spoken sentences, recorded in dierent environments, will be broadcast through a speaker. The robot needs to interpret the commands and produce an output according to a dened representation. c⃝2018 by ERL Consumer Revision 1.1 3 3. ERL Consumer Scenario Contents 4. People Perception: Evaluates the ability of a robot to locate and recognize humans. Similarly to object perception, the robot must recognize a person who is standing inside a target area and to estimate the location of this person. 4. People Perception: Evaluates the ability of a robot to locate and recognize humans. Similarly to object perception, the robot must recognize a person who is standing inside a target area and to estimate the location of this person. 5. Person Following: Evaluates the ability of a robot to eectively follow a human target around and through obstacles and crowd of walking people. The benchmark requires that the robot accompanies a human target and always maintain a desired distance with this person. 5. Person Following: Evaluates the ability of a robot to eectively follow a human target around and through obstacles and crowd of walking people. The benchmark requires that the robot accompanies a human target and always maintain a desired distance with this person. 5. Person Following: Evaluates the ability of a robot to eectively follow a human target around and through obstacles and crowd of walking people. The benchmark requires that the robot accompanies a human target and always maintain a desired distance with this person. 6. Grasping and Manipulation: Evaluates the ability of a robot to correctly grasp and manipulate objects. 3.3 ERL Consumer Robots Participating teams can use one or two robots to solve the tasks. The robots must t through a door of 80cm width and weigh no more than 250kg. They must be fully autonomous, i.e. neither power supply via cable nor any kind of tele-operation is permitted. Each robot must be safe to operate in the environment. Robots polluting or damaging the environment or presenting a threat to humans in the environment are not allowed to participate. A mechanism to stop the robots in case of emergencies must exist. Robots must be properly equipped to be able to solve the tasks at least in principle. For example, it is not permitted to substitute for lack of speech understanding by entering commands on the keyboard. Teams are not allowed to modify the environment, or to install their own embedded devices in the environment, e.g. additional sensors or actuators. c⃝2018 by ERL Consumer Revision 1.1 4 2 How to Read and Outline of the Document This remainder of this part is structured as follows: Section 3 describes in detail the ERL Con- sumer Task Benchmarks, their goals, specic procedures, scoring methods and details. Section 4 does the same for ERL Consumer Functionality Benchmarks. This is the most relevant part of the rulebook, that an experienced ERL Con- sumer participant should read carefully. Sections of former versions of this rulebook providing general information on awards, test beds, robots and teams, as well as the general procedures, scoring and benchmarking methods for Task Benchmarks, were now turned into appendices. Appendix A surveys the number and kind of awards that will be awarded and when, as well as how the ranking of the award categories is determined based on individual benchmark results. The certication requirements for a test bed to be used in ERL Consumer Tournaments are described in some detail in Appendix B). Subsections of this appendix are devoted to the specication of the structure of the environment and its properties (B.1), to the objects in the environment relevant to the tasks on hand (B.2), to other objects not directly related to tasks but possible aecting the robot's behavior in other ways (e.g. need to avoid them in navigation, distractions and perceptual noise caused by them in robot vision) (B.3), to the networked devices embedded in the environment and accessible to the robot (B.5), and to the benchmarking equip- ment which may impose additional constraints to the robot's behavior (equipment presenting obstacles to avoid) or add further perceptual noise (visible equipment) (B.6). In Appendix C), we provide some specications and constraints applying to the robots and teams permitted to participate in ERL Consumer, including the requirements for data logging. The general procedure to run Task Benchmarks, as well as the scoring methods used to rank the teams, are introduced in Appendix D. Appendix E depicts one instance of a ERL Consumer certied testbed. Any ERL Consumer participant should read these appendices at least once. Ex- perienced ERL Consumer participants should use them primarily for consultation of details. 1 Introduction This part of the document describes in detail the actual competition rules for ERL Consumer Benchmarks and it assumes that the reader has already read Part I of the document, with the ERL Consumer nutshell information. The audience for the current part are teams who want to participate in the competition, the organizers of ERL Consumer Tournaments, and the developers of simulation software, who want to provide their customers and users with ready-to-use models of the environment. They all need to know more details on the competition than the nutshell document provides. 3 Task Benchmarks This chapter describes in detail each of the Task and Functionality Benchmarks that will be available during the current ERL Consumer Season. II: ERL Consumer Rulebook II: ERL Consumer Rulebook 1. Introduction Contents Revision 1.1 3.1.1 Task Description Before each task run, some random changes in the environment are made with respect to the nominal conguration given to the teams during the set-up days. These changes involve: • Closing a door connecting two rooms • Closing a door connecting two rooms • Moving two pieces of furniture from one room to another • Moving two known objects from one furniture to another • Placing an unknown object (trash) on the oor The robot has to detect all the changes, either automatically or with some limited help from an untrained user (a person from the technical/organizing committee), and provide an explicit representation of them referred to the map of the environment (that can be either acquired on-line during the task run, o-line before the run, or merge o-line and on-line acquisition). 3.1 Task Getting to know my home This task is focused on acquiring knowledge about the environment and on its explicit representa- tion. The robot is required to identify some changes in the environment either fully autonomously or through some limited interactions with a human user. Revision 1.1 c⃝2018 by ERL Consumer 1 1 3. Task Benchmarks Contents 3.1.2 Input Provided The teams must create a semantic map of the apartment, during the set-up days, and label it with pieces of furniture and objects. The names of rooms, furniture and objects, along with their default locations, will be distributed to the teams before the competition. The objects and furniture will also be available to the teams during the setup days for training purposes. The following information about the object locations is provided in advance to facilitate the robot's searching process: • A list of four candidate locations (four pieces of furniture) where the changed objects could be located will be given in advance. These four furniture are not among the moved furniture and are always at their default locations. • One object is placed on every candidate location. Hence, two locations will contain the changed objects to be found while the other two locations will contain one of the default objects for that location. • An unknown manipulable object, such as an empty water bottle or an empty drink can, acting as the trash, will be placed on the oor of one of the rooms in a noticeable location (away from walls and furniture); • An unknown manipulable object, such as an empty water bottle or an empty drink can, acting as the trash, will be placed on the oor of one of the rooms in a noticeable location (away from walls and furniture); Phase 1: knowledge acquisition. The robot is expected to detect the changes and represent them in an explicit format (see Expected Output below) either fully autonomously or semi-autonomously (with limited help from a user). In case of a semi-autonomous approach the robot must be dominant in the task and interact with an untrained user for assistance. More precisely: • The robot can only interrogate the user about the location and nature of the changed doors and furniture. (Example: what furniture is changed? where to?) • The robot can only interrogate the user about the location and nature of the changed doors and furniture. (Example: what furniture is changed? where to?) • The robot can request the user to guide the robot (through human-following) to the loca- tion of any furniture and/or to point to a furniture. • The robot cannot interrogate or use information spontaneously provided by the user about the nature or location of the changed objects, including the unknown item (trash). c⃝2018 by ERL Consumer 2 Revision 1.1 2 3. Task Benchmarks Contents • The robot cannot ask or follow direct motion commands (i.e. Speech commands: Go to, Turn right, Move forward, Navigate to, etc are no longer allowed) At any time the teams can decide to move to Phase 2, even if not all changes have been detected. However, the task in Phase 2 can refer only to objects acquired during Phase 1. (a) Predicates about doors and their status (a) Predicates about doors and their status • Denition: type (door_ID , door ) . connect (door_ID , room_name , room_name ) . isOpen (door_ID , true | f a l s e ) . • Example: type ( door36 , door ) connects ( door36 , kitchen , o f f i c e ) . isOpen ( door36 , true ) . (b) Predicates about location of pieces of furniture (b) Predicates about location of pieces of furniture Phase 2: knowledge use. The robot has to show the use of the new acquired knowledge. This will be accomplished by moving one of the changed objects recognized in Phase 1 back to its default location. The default location of the trash is considered as the trash bin. Expected output. The output provided by the teams is a set of les that must be saved in a USB stick given to the teams before the test. The USB stick will be formatted with FAT32 le system and all the les should be saved in a folder with the name of the team. The following les are expected: • semantic map le • pictures of changed objects and furniture • metric map les • metric map les 1. Semantic map le: this must be a text le named semantic_map.txt containing a set of Prolog-like statements (or facts) in the following form: 1. Semantic map le: this must be a text le named semantic_map.txt containing a set of Prolog-like statements (or facts) in the following form: predicate ( arg_1 , . . . , arg_n ) . predicate ( arg_1 , . . . , arg_n ) . The following predicates will be considered for evaluation: Revision 1.1 • Denition: • Denition: type ( furniture_ID , furniture_name ) in ( furniture_ID , room_name) picture ( furniture_ID , image_filename ) . • Example: type ( ch1 , kitchen_chair ) . in ( ch1 , living_room ) . picture ( ch1 , image_ch1 . jpg ) . • Example: type ( ch1 , kitchen_chair ) . in ( ch1 , living_room ) . picture ( ch1 , image_ch1 . jpg ) . Note: Only one piece of furniture for each type will be involved in the test and described in the semantic map le. Note: Only one piece of furniture for each type will be involved in the test and described in the semantic map le. c⃝2018 by ERL Consumer Revision 1.1 3 Contents 3. Task Benchmarks (c) Predicates about position, location and properties of objects) • Denition: type ( object_ID , object_category ) . in ( object_ID , room_name ) . on ( object_ID , furniture_name ) . picture ( object_ID , image_filename ) . • Example: type ( obj33 , apple ) . in ( obj33 , kitchen ) . on ( obj33 , kitchen_table ) . picture ( obj33 , image_obj33 . jpg ) . • Example: type ( obj33 , apple ) . in ( obj33 , kitchen ) . on ( obj33 , kitchen_table ) . picture ( obj33 , image_obj33 . jpg ) . • Example: Note: Only the information about the door/furniture/objects that are involved in the change during the test will be evaluated. Additional information about other doors/furniture/objects can be included in the le as well, but they will not be used for determining the score. 2. Pictures of objects: actual images in standard image format (JPEG, PNG, BMP, PPM) named in the picture predicate of the semantic map. These images will be evaluated by a referee through visual inspection. The object named in the semantic map le must be visible in the foreground. 2. Pictures of objects: actual images in standard image format (JPEG, PNG, BMP, PPM) named in the picture predicate of the semantic map. These images will be evaluated by a referee through visual inspection. The object named in the semantic map le must be visible in the foreground. 3. Metric map les: metric map (possibly acquired before the test) should be included, preferably in ROS format (i.e. bitmap (PNG/PPM) + YAML le), using the global reference system provided during the setup days. Note: this map will not be evaluated, but it is useful for benchmarking and statistics. Complete Example: A complete example is illustrated below, where the following changes where executed: • the door connecting the kitchen and the hallway is closed, • a kitchen chair is moved to the living room, • a plant is moved to the hallway, • a can of coke is placed on the kitchen table in the kitchen, • a box of biscuits is placed on the coee table in the living room, and • an empty water bottle is placed on the oor of the dining room. The generated semantic map le which refers to the changes in the environment is given below: The generated semantic map le which refers to the changes in the environment is given below: type ( door_1 , door ) . connects ( door_1 , kitchen , hallway ) . isOpen ( door_1 , f a l s e ) . type ( door_1 , door ) . connects ( door_1 , kitchen , hallway isOpen ( door_1 , f a l s e ) . type ( kitchen_chair_1 , chair ) . in ( kitchen_chair_1 , living_room ) . picture ( kitchen_chair_1 , kitchen_chair_1 . jpg ) . type ( kitchen_chair_1 , chair ) . in ( kitchen_chair_1 , living_room ) . • Example: type ( kitchen_chair_1 , chair ) . type ( kitchen_chair_1 , chair ) . in ( kitchen_chair_1 , living_room ) . picture ( kitchen_chair_1 , kitchen_chair_1 . jpg ) . picture ( kitchen_chair_1 , kitchen_chair_1 . jpg ) . type ( plant_1 , plant ) . Revision 1.1 4 c⃝2018 by ERL Consumer 3. Task Benchmarks Contents in ( plant_1 , hallway ) . picture ( plant_1 , plant_1 . jpg ) . type ( object_1 , coke ) . in ( object_1 , kitchen ) . on ( object_1 , kitchen_table ) . picture ( object_1 , object_1 . jpg ) . picture ( object_1 , object_1 . jpg ) . type ( object_2 , b i s c u i t s ) . in ( object_2 , living_room ) . on ( object_2 , coffee_table ) . picture ( object_2 , object_2 . jpg ) . type ( object_3 , trash ) . in ( object_3 , dining_room ) . on ( object_3 , f l o o r ) . picture ( object_3 , object_3 . jpg ) . picture ( object_3 , object_3 . jpg ) . 3.1.5 Acquisition of Benchmarking Data During this Task Benchmarks, beside the information related to the semantic map of the envi- ronment to be evaluated, the Internal Data described in Section C.3.2 will be collected. 3.1.4 Procedures and Rules Before the robot enters the apartment, any of the doors in the environment will be closed and two randomly-selected pieces of furniture will be moved from their original position. In addition, four randomly-selected objects will be placed in the four candidate locations (above some piece of furniture) where only two of the objects are not in their default locations and need to be identied as the changed objects. Note that the closed door could be also the entrance door. In this case, this door will be closed immediately after the robot has entered the apartment. Phase 1 The robot can move around in the environment for up to the maximum time limit of this task, possibly accompanied by a user (a person from the technical/organizing commit- tee) and interacting with him/her: The robot has to detect the changes specied above, and then represent them in an explicit format as described in sub-subsection 3.1.3. Phase 2 (Assuming that the robot has either nished the task requested in the previous steps, or is incapable to do so) the robot can automatically, or via a speech command, proceed to move one of the objects recognized in Phase 1 back to its default location. The knowledge acquired during Phase 1 must be reported in an explicit way by producing les in the given output format and by automatically saving them on a USB stick given to the team by the Technical Committee before the start of the run, as described in the Expected Output section. No manual intervention on the robot is allowed to save les on the USB stick. c⃝2018 by ERL Consumer 3.2.3 Expected Robot Behavior or Output For each visiting person, the following two phases are expected. 3.1.6 Scoring and Ranking The set A of eight possible achievements for this task are: The set A of eight possible achievements for this task are: • The robot detects the door with changed state. (1) • The robot detects each piece of the moved furniture. (2) c⃝2018 by ERL Consumer 5 Revision 1.1 3. Task Benchmarks Contents • The robot detects each of the changed objects. (2) • The robot detects each of the changed objects. (2) • The robot locates the trash. (1) • The robot locates the trash. (1) • The robot grasps an object in Phase 2. (1) • The robot delivers the object to the default location. (1) • The robot delivers the object to the default location. (1) The set PB of penalized behaviors for this task are: he set PB of penalized behaviors for this task are: • The robot requires repetitions of human gesture/speech. • The robot requires repetitions of human gesture/speech. • If following is used, the robot loses the user and it requires that explicit actions are per- formed by the operator. • The robot bumps into the furniture. • The robot stops working. • The robot drops the object when delivering. • The robot drops the object when delivering. • Pictures are not taken or do not contain the target, for each piece of object/furniture (5) Additional penalized behaviors may be identied and added to this list if deemed necessary. The set DB of disqualifying behaviors for this task are: • The robot hits Annie or another person in the environment. • The robot hits Annie or another person in the environment. • The robot damages the test bed. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. c⃝2018 by ERL Consumer Revision 1.1 6 3. Task Benchmarks Contents 3.2 Task Welcoming visitors This task assesses the robot's capability to interact eectively with humans and to demonstrate dierent behaviors when dealing with known and unknown people. 3.2.2 Input Provided The following information about the people acting as visitors is provided below. • Dr. Kimble is a known person from the Organizing or Technical Committee running all the runs. Pictures of Dr. Kimble will be provided before the competition. • Dr. Kimble is a known person from the Organizing or Technical Committee running all the runs. Pictures of Dr. Kimble will be provided before the competition. • The Postman is a known person from the Organizing or Technical Committee running all the runs. He/she will also wear a known uniform. Images of the uniform and the Postman will be given before the competition. • The Deli Man will be unknown beforehand (the actual person will change in every run). He/she will be carrying a shopping bag with the breakfast inside. • The Deli Man will be unknown beforehand (the actual person will change in every run). He/she will be carrying a shopping bag with the breakfast inside. • The Plumber will be unknown beforehand (the actual person will change in every run). He will carry a toolbox in his hand. Some privileges are given to the four dierent kinds of people, as reported in the following table, and the robot has to act accordingly. Some privileges are given to the four dierent kinds of people, as reported in the following table, and the robot has to act accordingly. Privileges Dr. Kimble Postman Deli Man Plumber Allow to enter the house Yes No Yes Yes Allow to deliver objects No Yes Yes Yes Allow access to bathroom Yes No No Yes Allow access to kitchen Yes No Yes Yes Allow access to bedroom Yes No No No Pictures of the parcel used by the postman will be provided before the competition. The dimensions of the parcel are 9.5 inches / 24.13 cm (width) x 6.5 inches / 16.51 cm (length) x 1.75 inches / 4.45 cm (height) and weights about 30 grams. 3.2.1 Task Description The task involves handling several known and unknown visitors arriving at the home entrance in a random sequence, but separately from each other. The robot must recognize the known visitors and interact with the unknown visitors to identify them. The robot must then perform a set of visitor-specic behaviors. If a visitor has been admitted, the robot should guide him/her out after the visit is over. Phase 2: executing the visitor-specic behavior. The following behaviors are expected depending on the visitor: Dr. Kimble: The robot guides the Doctor to Annie's bedroom; then it waits until the Doctor exits the bedroom, follows him/her to the entrance door, and allows the Doctor to exit. The human-following behavior must be observed. PostMan: The robot receives the postal mail using its manipulator(s), allows the Postman to exit and delivers the mail to Granny Annie in the bedroom. A natural robot-human object handover is preferred, however, the robot could also advise the postman on how to hold or hand over the object. Deli Man: The robot guides the Deli Man to the kitchen, asking him/her to deliver the breakfast box on the table; then it guides the Deli Man back to the entrance door, and allows him/her to exit. The human-guiding behavior must be observed. Plumber: The robot asks the Plumber where he/she would like to visit, guides the Plumber to the desired location, it waits for the plumber to nish his job; then it follows him/her back to the entrance door. The robot must always keep a close eye on the plumber by maintaining a close distance with him/her. The human guiding and following behaviors must be observed. After the execution of the visitor-specic behavior, the robot must return to the initial position and wait for the next visitor. Phase 1: detection and recognition of the visitor. Doorbell: Whenever a person rings the door bell, the robot can use its own on-board audio system to detect the bell ring(s) or the signal from the RSBB. Opening the door: Naturally, the front door will be closed. The robot can either use its own manipulators to open the door or request the visitor to open it (e.g. using speech). An extra achievement is assigned for the former case. Fig. 2.2 shows an example of the type of handle Revision 1.1 c⃝2018 by ERL Consumer 7 3. Task Benchmarks Contents that will be mounted on the entrance door. that will be mounted on the entrance door. Identifying the visitor: Once the door is open, the robot must then use its on-board sensing to correctly identify the person rst as known or unknown visitor. If the visitor is known, the robot should be able to recognize him/her. If the visitor is unknown the robot must interrogate the person to learn who is visiting and what is the purpose of the visit. Greeting the visitor: For each detected visitor, the robot must greet the visitor with a spoken sentence, demonstrating that it has recognized the visitor. For example, "Hi postman, I am coming to get the post mail" or "Hello Plumber, where do you want to visit in the house?". Figure 2.2: Door handle at the main entrance Figure 2.2: Door handle at the main entrance 3.2.4 Procedures and Rules The test starts with the robot being in one of the available rooms. The exact room will be announced at the beginning of the competition and will be same for all the teams. The visitors will be from all the four categories mentioned previously. The following steps will be repeated for each visitor (in a random order). c⃝2018 by ERL Consumer Revision 1.1 8 3. Task Benchmarks Contents Step 1 The door-bell will be rung by the visitor. At this point in time, the robot must recognize the sound or use the RSBB, to see if someone rung the door bell. Step 1 The door-bell will be rung by the visitor. At this point in time, the robot must recognize the sound or use the RSBB, to see if someone rung the door bell. Step 2 The robot must navigate to the entrance and open the entrance door either using its manipulator(s) or by asking the visitor to open the door. Step 3 The robot must correctly identify the visiting person, greet him/her, and proceed to do the behavior-specic actions as instructed in Section 3.2.3. Step 4 Once the visit is over, the robot will return to the initial position. 3.2.5 Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be collected together with the additional information described in the following table Topic Type Frame Id Notes /ERLSCR/command1 std_msgs/String   /ERLSCR/visitor2 std_msgs/String   /ERLSCR/audio3 audio_common_msgs/AudioData   /ERLSCR/notication4 std_msgs/String   NOTE: the images and pointclouds in the Internal Data should contain the sensorial data used to recognize the visitor. 1The event or command causing the activation of the robot. The result of any attempt by the robot to detect and classify a visi 3The audio signals of the conversation with the visitors. 3.3 Task Catering for Granny Annie's Comfort This benchmark aims at assessing the robot's performance for executing general purpose requests of users in the apartment. It focuses on the integration of dierent robot abilities such as human-robot interaction, navigation and robot-object interaction. The task does not have a predened story or a predened set of actions requiring more than the traditional state machine- like behaviors. Note: This task is an updated and merged version of the former ERL-SR Catering for Granny Annie's Comfort and General Purpose Service Robots tasks. 3.2.6 Scoring and Ranking The set A of achievements for this task are: • The robot correctly recognizes Dr. Kimble. • The robot correctly recognizes the Postman. • The robot correctly identies the Deli Man. • The robot correctly identies the plumber. • The robot exhibits the expected behavior for interacting with Dr. Kimble. • The robot exhibits the expected behavior for interacting with the Deli Man. • The robot exhibits the expected behavior for interacting with the Postman. • The robot opens the entrance door using its manipulator at least one time during the task. The set PB of penalized behaviors for this task are: The set PB of penalized behaviors for this task are: • The robot stops working. • The robot fails in making the visitor respect the proper rights. • The robot fails in maintaining the original state of the environment. 1The event or command causing the activation of the robot. 2 2The result of any attempt by the robot to detect and classify a visitor 3The audio signals of the conversation with the visitors. g 4Any notications from the robot (e.g., alarm if a visitor shows anomalous behavior) c⃝2018 by ERL Consumer Revision 1.1 9 3. Task Benchmarks Contents • The robot requires extra repetitions of speech. • The robot requires extra repetitions of speech. he robot requires extra repetitions of speech. • The robot bumps into the furniture. Additional penalized behaviors may be identied and added to this list if deemed necessary. The set DB of disqualifying behaviors for this task are: Additional penalized behaviors may be identied and added to this list if deemed necessary. The set DB of disqualifying behaviors for this task are: • The robot hits Annie or one of the visitors. • The robot hits Annie or one of the visitors. • The robot damages the test bed. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. c⃝2018 by ERL Consumer Revision 1.1 10 3. Task Benchmarks Contents 3.3.1 Task Description The robot is going to help a user with his/her daily tasks. After waking up in the morning, the user calls the attention of the service robot by touching a button on a tablet computer. When the robot arrives, the user gives a single speech command composing of three actions from the following three categories: 1. Searching for an item or a person 1. Searching for an item or a person 2. Manipulating and delivering an object 3. Accompanying a person inside or outside the house These actions are randomly generated into a single sentence in no predened order. The robot is required to understand the actions and execute them accordingly. Revision 1.1 Accompanying guide, take, lead, accompany, follow, escort Searching nd, locate, look for, search for, pinpoint, spot put, place, leave, set, get, grasp, take, retrieve, pick up, bring, deliver, give, hand 3.3.3 Expected Robot Behavior or Output After the robot is called, the robot is expected to reach the room where the user is located, approaching in such a way that spoken communication is possible. The robot should then state its readiness to receive the command. When the command is given, the robot should show that it has understood all the actions in an appropriate way (e.g., by repeating it back to the user and asking if it was correctly understood). The robot is then expected to successfully execute all of the actions in the order that was given in the command. If the robot is unable to perform any of the actions it should announce it and proceed with the other actions. The following are some examples selected from a large set of possible commands: The following are some examples selected from a large set of possible commands: The following are some examples selected from a large set of possible commands: • Locate Tracy, lead her to the bedroom, and bring me an apple from the kitchen cabinet • Locate Tracy, lead her to the bedroom, and bring me an apple from the kitchen cabinet. Find the bottle, place it in the trash bin, and take John from the bedroom to the exit. • Find the bottle, place it in the trash bin, and take John from the bedroom to the exit. Guide me to the bedroom, nd my glasses, and bring me a pear from the kitchen table. • Guide me to the bedroom, nd my glasses, and bring me a pear from the kitchen table. • Give me the cup on the coee table, nd John, and follow him. Give me the cup on the coee table, nd John, and follow him. Calling the Robot for Attention: The initial location of the user will be announced in advance. The user has a tablet computer which runs an application provided by the consortium. It allows the user to call the robot's attention. The communication with the tablet is realized through the RSBB. Further details are specied in the ERL Wiki [1]. Alternatively, if the tablet is unavailable in a testbed, the start signal of the task, sent from the RSBB, will be considered as the calling signal. 3.3.2 Input Provided Objects and names The list of objects and people's names used in the task will be provided before the competition by the local organizers. For every object/person to be found by the robot a set of possible locations with an associated likelihood will be provided: Object/Person Location Likelihood % Object i Furniture 1 60 Furniture 2 30 Furniture 3 10 Person i Room 1 60 Room 2 30 Room 3 10 All of the objects will be made available to the teams for calibration during the setup days. Note: In the case of nding a person, only one person will be present at one of the target locations. Commands: A command will be generated randomly before the task run and is composed of three actions as described in Section 3.3.1. The lexicon used in the commands will consist of the names of people/objects/locations (provided to the teams before the competition), along with the following verbs divided based on the action categories: Manipulating c⃝2018 by ERL Consumer Revision 1.1 11 3. Task Benchmarks Contents 3.3.5 Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in SectionC.3.2 will be collected together with the additional information described in the following table NOTE: the images and pointclouds in the Internal Data should contain the object to be operated. 3.3.4 Procedures and Rules A successful execution of this task would be the robot going to the user (played by a member of the OC/TC) and executing all or some of the actions in the command. The task involves the following activities: 1. User initiates the task by calling the robot's attention. 2. The robot approaches the user in such a way that spoken communication is possible, stating its readiness to receive commands. 3. The user provides the sentence from the predened list of possible commands. 4. The robot conrms that it understood the command and executes the corresponding ac- tions in the command. 5. After completing the task, the robot returns to the user. Teams are allowed to give instructions as to how the user should speak to the robot. If the robot fails to understand the original command after three times a team member can replace the user to repeat the same command. Alternatively, if the robot is incapable of processing and understanding the original command in full, a team member can decompose or interpret the command into a desired format that is understandable by the robot. However, the achievements for "correctly understanding the original command" and "executing the full command without any interruption" will not be obtained. c⃝2018 by ERL Consumer 12 Revision 1.1 3. Task Benchmarks Contents Topic Type Frame Id Notes /erlc/command5 std_msgs/String   /erlc/audio6 audio_common_msgs/AudioData   Revision 1.1 5The command produced by the natural language analysis process. 3.3.6 Scoring and Ranking The set A of achievements for this task are: • The robot enters the room where the user is waiting. • The robot enters the room where the user is waiting. • The robot understands the user's original command without any interpretations. • The robot understands at least one of the actions to be executed. • The robot manages to nd the right object/person. • The robot correctly executes the accompanying action. • The robot grasps and picks up the object to be delivered. • The robot delivers the object to the desired location • The robot completes all three actions continuously without any interruptions. The set PB of penalized behaviors for this task are: • The robot requires multiple repetition of the command • The robot bumps into the furniture. • The robot drops an object. • The robot stops working. • The robot fails to return to user after task completion. • The robot fails to return to user after task completion. Additional penalized behaviors may be identied and added to this list if deemed necessary. The set DB of disqualifying behaviors for this task are: Additional penalized behaviors may be identied and added to this list if deemed necessary. The set DB of disqualifying behaviors for this task are: • The robot hits the user or another person in the environment. • The robot damages or destroys the objects requested to manipulate. • The robot damages the test bed. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. 5The command produced by the natural language analysis process. 3.4 Task Visit my home This task focuses on safe navigation in dynamic environments, obstacle avoidance, obstacle interaction, and tracking and recognizing a previously unknown person. 3.4.2 Input Provided A Path consisting of four waypoints will be selected and announced to the teams during the setup days. The rst waypoint will be reachable via at least two dierent paths, the second waypoint will be blocked by an obstacle and the fourth waypoint will be outside the arena in an unknown location. A human operator will be standing at the third waypoint who will guide the robot to the fourth waypoint. The entrance door to the apartment will be initially closed while all other doors are left open. The following information about the obstacles blocking the path of the robot is provided below: (Objects will be available to the teams during the setup days) • Small object: A small Kraft paper shopping bag • Wheeled object: A rolling chair, cart, wheeled luggage or some other object with wheels. • Wheeled object: A rolling chair, cart, wheeled luggage or some other object with wheels. • Human obstacle: A person who is unknown beforehand. Figure 2.3: The type of shopping bag used as the small obstacle to be removed using the robot's manipulators. (The bag dimensions will be between 10 and 30 cm per edge with weight of less than 300 grams) Figure 2.3: The type of shopping bag used as the small obstacle to be removed using the robot's manipulators. (The bag dimensions will be between 10 and 30 cm per edge with weight of less than 300 grams) Figure 2.3: The type of shopping bag used as the small obstacle to be removed using the robot's manipulators. (The bag dimensions will be between 10 and 30 cm per edge with weight of less than 300 grams) 3.4.1 Task Description In this task, the robot should visit a set of predened waypoints while avoiding obstacles on its path. The robot needs to interact with the obstacles based on the nature of the obstacle. Furthermore, the robot must interact and follow a person to an unknown location outside the arena. Finally the robot needs to nd its way back to the arena. 5The command produced by the natural language analysis process. 6The audio of the conversation between user and the robot. Speech les from all teams and all bench- marks (both Task benchmarks and Functionality benchmarks) will be collected and used to build a public dataset. The audio les in the dataset will therefore include all the defects of real-world audio capture using robot hardware (e.g., electrical and mechanical noise, limited bandwidth, harmonic distortion). Such les will be usable to test speech recognition software, or (possibly) to act as input during the execution of speech recognition benchmarks. c⃝2018 by ERL Consumer Revision 1.1 13 3. Task Benchmarks Contents Phase 4: Human following After reaching Waypoint 2, the robot must navigate to Waypoint 3, in which a person is standing. The robot must memorize this person and follow him/her outside the arena to Way- point 4. This phase can include the following states: After reaching Waypoint 2, the robot must navigate to Waypoint 3, in which a person is standing. The robot must memorize this person and follow him/her outside the arena to Way- point 4. This phase can include the following states: • Training: The robot has to memorize the operator. The robot may instruct the operator to follow a certain setup procedure and instruct the operator on what to do when the robot needs to stop following. • Following: When the robot signals that it is ready to start following, the operator starts walking in a natural way through a designated path outside the arena. The robot needs to follow the operator until the operator asks the robot to stop. • Resuming: If the robot loses the operator, it can ask him/her to come back or give a signal by waving to resume following, but will be penalized for doing so. • Stop following: Upon reaching Waypoint 4, the operator will command the robot to stop following him as instructed in the training phase. • Stop following: Upon reaching Waypoint 4, the operator will command the robot to stop following him as instructed in the training phase. Phase 5: Returning Home After reaching Waypoint 4 the robot must then go back to Waypoint 3. The robot has to open the door of the apartment, closed by the referee after the robot left the arena, in order to reach Waypoint 3. The robot is allowed to use its base to gently push the door open, but only after it used a manipulator to initially open the door by the handle Phase 3: Obstacle interaction After reaching Waypoint 1, the robot must navigate to the second waypoint. The path to this waypoint is blocked by one of the obstacles described in Section 3.4.2. The robot is expected to identify, state the nature of the obstacle and interact with the obstacle accordingly. Possible actions include: • Small object: Remove the small object from the path using the robot's manipulators, or overcome the obstacle in case of bipedal robots. • Wheeled object: Gently push away the object to unblock the path using either the ma- nipulators or the robot's body. • Human obstacle: Kindly ask the human to move away. If the robot is unable to remove the obstacle it can ask the referee to remove it to continue with the task. Otherwise, the obstacle will clear or be cleared after roughly 45 seconds. Phase 2: Navigation and Path Planning After entering the arena, the robot must navigate to the rst waypoint that is reachable via at least two paths. Whatever path the robot initially takes will be blocked as the robot approaches and the robot should take the alternative path. Phase 1: Entering the arena The task starts with the robot waiting outside the arena and when the entrance door is opened by the referee. The robot should detect the door-opening event and enter the arena c⃝2018 by ERL Consumer Revision 1.1 14 3. Task Benchmarks Contents autonomously. Alternatively, the team may start the robot using a start button without getting the respective achievement. autonomously. Alternatively, the team may start the robot using a start button without getting the respective achievement. Revision 1.1 3.4.4 Procedures and Rules The referee starts the test by opening the entrance door. The robot must navigate to the waypoints in sequential order while respecting the expected behaviors described in Section 3.4.3. If a robot is unable to reach a waypoint, it must announce it and proceed to the next waypoint. Revision 1.1 c⃝2018 by ERL Consumer 15 3. Task Benchmarks Contents 3.4.5 Acquisition of Benchmarking Data During this Task Benchmark, the Internal Data described in Section C.3.2 will be collected. 4.1.1 Functionality Description Teams are provided with a list of individual objects (instances), subdivided into classes. The benchmark requires that the robot, when presented with objects from such list, detects their presence and estimates their class, instance, and location. For example, when presented with a bottle of milk, the robot should detect a bottle (class) of milk (instance) and estimate its pose w.r.t. a known reference frame. 4.1.2 Input Provided The set of individual objects, denoted as object instances, that will actually be presented to the robot during the execution of the functionality benchmark will be provided to the teams before the competition. All objects are commonplace items that can be found in domestic or retail environments. Object instances are subdivided into classes of objects that have one or more properties in common, here denoted as object classes. Objects of the same class share one or more properties, not necessarily related to their geometry (for instance, a class may include objects that share their application domain). Each object instance and each object class is assigned a unique ID. More precisely, teams will be provided with the following information: • Descriptions of all the object instances; Subdivision of the object instances into object classes (for instance: boxes, mugs, cutlery • Reference systems associated to the table surface and to each object instance (to be used to express object poses). • Reference systems associated to the table surface and to each object instance (to be used to express object poses). 3.4.6 Scoring and Ranking The set A of achievements for this task are: • The robot enters the arena autonomously when the door is opened. • The robot enters the arena autonomously when the door is opened. • The robot reaches waypoint 1. • The robot reaches waypoint 2. • The robot reaches waypoint 3. • The robot reaches waypoint 4 following the operator. • The robot reaches waypoint 3 after visiting waypoint 4. • The robot recognizes properly the nature of the obstacle. • The robot interacts with obstacle accordingly to their nature. • The robot interacts with obstacle accordingly to their nature. The set PB of penalized behaviors for this task are: The set PB of penalized behaviors for this task are: • The robot bumps into a non-human obstacle. • If the robot loses the operator, it requires that explicit actions are performed by the operator (e.g., waving) to retrieve them. • If the robot loses the operator, it requires that explicit actions are performed by the operator (e.g., waving) to retrieve them. • The robot stops working. • Any behavior towards attendees and/or operator that is deemed as threatening by the referees (e.g., rapidly moving towards a person, then stopping at moderate distance) • Any behavior towards attendees and/or operator that is deemed as threatening by the referees (e.g., rapidly moving towards a person, then stopping at moderate distance) Additional penalized behaviors may be identied and added to this list if deemed necessary. The set DB of disqualifying behaviors for this task are: Additional penalized behaviors may be identied and added to this list if deemed necessary. The set DB of disqualifying behaviors for this task are: • The robot hits the operator or any other human. • The robot damages an object. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. Additional disqualifying behaviors may be identied and added to this list if deemed necessary. These sets will be completed in later rule revisions. c⃝2018 by ERL Consumer Revision 1.1 16 4. Functionality Benchmarks Contents 4.1 Object Perception Functionality This functionality benchmark has the objective of assessing the capabilities of a robot in pro- cessing sensor data in order to extract information about observed objects. Revision 1.1 4.1.3 Expected Robot Behavior or Output The objects that the robot is required to perceive are positioned, one at the time, on a table (benchmark setup area) located directly in front of the robot. The actual pose of the objects presented to the robot is unknown before they are set on the table. For each presented object, the robot must perform all of the following: • Object detection (i.e., class recognition): perception of the presence of an object on the table and association between the perceived object and one of the object classes (see Information provided to the team). • Object recognition (i.e., instance recognition): association between the perceived object and one of the object instances belonging to the selected class (see sub-subsection 4.1.2). • Object localization (i.e., pose estimation): estimation of the 3D pose of the perceived object with respect to the benchmark setup reference frame. c⃝2018 by ERL Consumer Revision 1.1 17 4. Functionality Benchmarks Contents 4.1.4 Procedures and Rules Every run in all the stages of this functionality benchmark will be preceded by a safety-check similar to that described for the task benchmark procedures. Each team is required to perform this functionality benchmark according to the steps men- tioned below. The maximum time allowed for one functionality run is 10 minutes. Step 1 An object of unknown class and unknown instance will be placed on a table in front of the robot. Step 2 The robot must determine the object's class, its instance within that class as well as the 2D pose of the object w.r.t. the reference system specied on the table (see Fig. 2.4). Figure 2.4: Reference frame on the FBM table. Figure 2.4: Reference frame on the FBM table. The preceding steps are repeated until the time runs out or the maximum number of objects have been processed. 7The string with the notication of the perceived object should be in a tab separated string: CLASS OBJECT_ID X Y THETA 4.2.2 Input Provided The following information will be provided in advance: • The starting position. • The number of waypoints that the robot must visit. • The maximum time allowed to the robot to go from each waypoint to the next waypoint, without penalization. • The maximum time allowed to the robot to go from each waypoint to the next waypoint, without penalization. Furthermore, the coordinates of the waypoints that the robot must visit will be communicated sequentially to the robot during the run time. A waypoint encapsulates a X, Y and θ. The coordinates are given in the test bed reference frame (which will be dened on site and provided during the rst day to the teams). 4.2.1 Functionality Description This functionality benchmark aims at assessing the capabilities of a robot to correctly and au- tonomously navigate in a typical apartment, containing furniture and objects spread through the apartment's rooms. The benchmark will use the ERL Consumer test bed (see Sec. B). From a predened starting position, the robot will receive a list of waypoints that it must visit to reach a goal position. 4.1.5 Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be collected together with the additional information described in the following table Topic Type Frame Id Notes /erlc/notication7 std_msgs/String   NOTE: the images and pointclouds in the Internal Data should contain the sensorial data used to recognize each of the presented object, thus we expect to have 10 images (if recognition uses a camera), 10 pointclouds (if recognition uses a depth sensor), and 10 notication strings. 7The string with the notication of the perceived object should be in a tab separated string: CLASS OBJECT_ID X Y THETA c⃝2018 by ERL Consumer Revision 1.1 18 4. Functionality Benchmarks Contents Revision 1.1 4. Execution time (if less than the maximum allowed for the benchmark). The previous criteria are in order of importance: the rst criterion is applied rst and teams will be scored according to the common accuracy metrics; the ties are broken by second criterion which is the position error. Since the position error is aected by the precision of the ground truth system we will use a set of accuracy classes in this as well and in case of ties we will resort to the third criterion and nally the execution time. 4.1.6 Scoring and Ranking Evaluation of the performance of a robot according to this functionality benchmark is based on: 1. The number and percentage of correctly recognized objects. (i.e.,instance recognition) 1. The number and percentage of correctly recognized objects. (i.e.,instance recognition) 2. Pose error for all correctly identied objects. 3. The number and percentage of correctly classied objects. (i.e.,class recognition) 4. Execution time (if less than the maximum allowed for the benchmark). 4.2.4 Procedures and Rules All teams are required to perform this functionality benchmark according to the steps mentioned below. The task must be performed exclusively in autonomous mode. No teleoperation is allowed. Teams will have up to ten minutes to complete the functionality benchmark. Step 1 The team is required to start their robot on a pre-dened starting position. This starting position will be given to the teams before each run. Step 1 The team is required to start their robot on a pre-dened starting position. This starting position will be given to the teams before each run. Step 2 When the procedure starts, the robot receives a sequence of waypoints, one by one, that it must follow in the respective order, sending back a signal through the RSBB, each time it reaches a waypoint. The robot must avoid hitting any obstacle it encounters in its path. Step 2 When the procedure starts, the robot receives a sequence of waypoints, one by one, that it must follow in the respective order, sending back a signal through the RSBB, each time it reaches a waypoint. The robot must avoid hitting any obstacle it encounters in its path. Step 3 The procedure stops when the robot noties it has reached the last waypoint, when the time given to complete the test expires, or when the robot hard-hits an obstacle. Step 3 The procedure stops when the robot noties it has reached the last waypoint, when the time given to complete the test expires, or when the robot hard-hits an obstacle. It is considered a hard hit when: It is considered a hard hit when: • A collision damages any of the obstacles; • The robot pushes or continually touches an obstacle for more than 3 seconds; • The robot forces its path through an obstacle; The obstacles can be of three types: • Static and previously mapped: Hardware already present in the house such as furni- ture, doors, walls, dened in B.2.1. The teams should already have this obstacles mapped from set-up days. These items will not change during this functionality benchmark. • Static and previously mapped: Hardware already present in the house such as furni- ture, doors, walls, dened in B.2.1. The teams should already have this obstacles mapped from set-up days. These items will not change during this functionality benchmark. 4.2.3 Expected Robot Behavior or Output Teams are required to set their robot on a specic starting position. Then, the robot receives, through the RSBB, the start signal, as well as the rst waypoints that it must reach. The robot must navigate to this waypoint and send back a signal to the RSBB, indicating that it has reached the waypoint. At this time the RSBB will issue a new waypoint. This process is repeated until the robot has reached the nal waypoint and a stop signal is issued by the RSBB. c⃝2018 by ERL Consumer Revision 1.1 19 4. Functionality Benchmarks Contents 4.2.5 Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in SectionC.3.2 will be collected together with the additional information described in the following table Topic Type Frame Id Notes /erlc/robot_pose_waypoint8 geometry_msgs/PoseStamped /map when reached /erlc/marker_pose_waypoint9 geometry_msgsPoseStamped /map when reached This functionality benchmark will be fully automated (no human operation will be allowed) and, for that, the robot has to communicate with the RSBB. It will receive the list of target waypoints from the RSBB and it must send back a signal, each time it reaches a waypoint. 4.2.4 Procedures and Rules • Static: Items Granny Annie left lying on the ground. The obstacles may be of dierent shapes and sizes, are not previously known by the teams, and may be dierent in between runs. • Static: Items Granny Annie left lying on the ground. The obstacles may be of dierent shapes and sizes, are not previously known by the teams, and may be dierent in between runs. • Dynamic: Granny Annie's visitors. People moving inside the house. 8The 2D robot pose, once each waypoint is reached, at the oor level, i.e., z = 0 and only yaw rotation. 9The 3D pose of the marker in 6 degrees of freedom once each waypoint is reached. Revision 1.1 4.2.6 Scoring and Ranking At each run and for each team, three metrics will be used to score the performance: Accuracy, number of obstacle hits, execution time. 8The 2D robot pose, once each waypoint is reached, at the oor level, i.e., z = 0 and only yaw rotation. 9The 3D pose of the marker in 6 degrees of freedom once each waypoint is reached. c⃝2018 by ERL Consumer Revision 1.1 20 4. Functionality Benchmarks Contents Topic Type Notes /roah_rsbb/goal geometry_msgs/Pose2D List of waypoints, sent by the RSBB to the robot, when start- ing the task. /roah_rsbb/reached_waypoint roah_rsbb_comm_ros/UInt8 Message sent by the robot to the RSBB, when reaching a point. It must include the number of the respective waypoint in the se- quence (starting from zero). Figure 2.5: Depiction of the sequence of waypoints that the robot must follow, during the navigation functionality benchmark. Topic Type Notes /roah_rsbb/goal geometry_msgs/Pose2D List of waypoints, sent by the RSBB to the robot, when start- ing the task. /roah_rsbb/reached_waypoint roah_rsbb_comm_ros/UInt8 Message sent by the robot to the RSBB, when reaching a point. It must include the number of the respective waypoint in the se- quence (starting from zero). Figure 2.5: Depiction of the sequence of waypoints that the robot must follow, during the navigation functionality benchmark. Figure 2.5: Depiction of the sequence of waypoints that the robot must follow, during the navigation functionality benchmark. • Accuracy scoring will be based on the the mathematical means of the distance from the waypoints and and the corresponding orientation error. The distance mean from the robot to the target waypoint follows the equation • Accuracy scoring will be based on the the mathematical means of the distance from the waypoints and and the corresponding orientation error. The distance mean from the robot to the target waypoint follows the equation A = 1 N N X i d (pi, ri) , (2.1) (2.1) where d (pi, ri) is the Euclidean distance from the robot's position ri to the target waypoint pi (as shown in Figure 2.5) and N the total number of points. where d (pi, ri) is the Euclidean distance from the robot's position ri to the target waypoint pi (as shown in Figure 2.5) and N the total number of points. 4.3.1 Functionality Description This functionality benchmark aims at evaluating the ability of a robot to understand speech commands from users. A set of spoken sentences, recorded in dierent consumer environments, will be broadcast through a speaker. All robots should be able to capture audio from an on-board microphone, to record the captured audio in a le and to interpret the corresponding commands. The system should produce an output according to a nal representation dened in the following sections. Such a representation will have to respect a command/arguments structure, where each argument is instantiated according to the arguments of the command evoking verb. It is referred to as Command Frame Representation (CFR) (e.g., go to the living room will correspond to MOTION(goal:living room )). 4.2.6 Scoring and Ranking Considering the orientation, the mean is B = 1 N N X i δ (αi, βi) , (2.2) (2.2) where δ (α, β) is the absolute value of the dierence between the desired waypoint orien- tation α and the robot's orientation β, such that δ (α, β) = |α −β| where δ (α, β) is the absolute value of the dierence between the desired waypoint orien- tation α and the robot's orientation β, such that δ (α, β) = |α −β| After the computation of these accuracy scorings, they will be discretized and tted in one of the following groups:  1: A < 10cm AND B < 20◦;  2: A < 30cm AND B < 45◦;  3: A < 50cm AND B < 90◦;  4: A < 80cm AND B > 90◦; 21 c⃝2018 by ERL Consumer c⃝2018 by ERL Consumer Revision 1.1 21 4. Functionality Benchmarks Contents A lower group number corresponds to the better performance. Therefore, teams will be ranked starting from group 1. Note that for a team to be placed in any of the groups, it must respect the limits for A and B. If a team has a score that does not t any of groups dened above (e.g. mean of the error above 80cm), it will not receive scoring in the respective Functionality Benchmark run; • If more than one team is found inside each of the previously dened group, the number of obstacle hits will be used as a tie breaker, where the team with less hits will be ranked rst and so on. Note that hits will only be considered as a tie breaker, i.e., a team in group 2 will never be ranked rst than any team in 1, despite of the number of hits (note that a class of hard hits was dened which, if they happen, the procedure stops); • If teams are still tied, time will be the decisive tie breaker. • If teams are still tied, time will be the decisive tie breaker. Note that throughout the competition and according to the teams performance, the thresh- olds for the classes of A and B can be changed. 4.3.2 Input Provided Some information about the lexicon (verbs and nouns of objects) used in the benchmark and a sample audio le can be found in the ERL Wiki [1]. In order to evaluate the correct understanding of a command expressed in natural language (e.g. through a sentence), a semantic representation formalism based on semantic frame has been selected. Each frame corresponds to an action, namely a robot command. A set of arguments is associated to each frame, specifying part of the command playing a particular role with respect to the action expressed by the frame. For example, in the command go to the dining room the Motion frame is expressed by the verb go, while the part of the sentence to the dining room corresponds to the Goal argument, indicating the destination of the Motion action. The set of frames dened and selected for this Benchmark is reported in the following list, together with the set of associated arguments (current arguments are reported in bold italic inside the example commands): • Motion: the action performed by the robot itself of moving from one position to another, occasionally specifying a specic path followed during the motion. The starting point is always taken as the current position of the robot. • Motion: the action performed by the robot itself of moving from one position to another, occasionally specifying a specic path followed during the motion. The starting point is always taken as the current position of the robot.  Goal: the nal position in the space to be occupied at the end of the motion action, e.g. Go to the kitchen; Go to the right of the sofa.  Path: the trajectory followed while performing the motion towards the Goal, e.g. Move along the wall. c⃝2018 by ERL Consumer Revision 1.1 22 4. Functionality Benchmarks Contents • Searching: the action of inspecting an environment or a general location, with the aim of nding a specic entity.  Theme: the entity (most of the time an object) to be searched during the searching action, e.g. Search for the glass.  Ground: the environment or the general location in the space where to search for the Theme, e.g. Find the glass in the living room. • Taking: the action of removing an entity from one place, so that the entity is in robot possession. 4.3.2 Input Provided  Theme: the entity (typically an object) taken through the action, e.g. Take the cereal box.  Source: the location occupied by the Theme before the action is performed and from which the Theme is removed, e.g. Grab the mayo on the table; Remove the sheets from the bed. • Placing: the action of placing an entity that the robot already posses in a place or position in the space.  Theme: the entity (typically an object) placed through the action, e.g. Drop the jar.  Goal: the location that should be occupied by the Theme after the action is per- formed, e.g. Put the can on the counter. • Bringing: the action of changing the position of an entity in the space from a location to another.  Theme: the entity (typically an object), being carried during the bringing action, e.g. Bring the garbage to the kitchen.  Goal: the endpoint of the path along which the carrier (e.g. the robot - and thus the Theme) travels, e.g. Bring the garbage to the kitchen.  Source: the beginning of the path along which the carrier (e.g. the robot - and thus the Theme) travels, e.g. Bring the garbage from the dining room to the kitchen.  Beneficiary: the person to whom the Theme must be brought, e.g. Bring me the mobile phone. Composition of actions is also possible in the CFR, corresponding to more complex action as the Pick_and_place action, represented by a sequence of Taking frame followed by a Bringing frame (e.g. for the command take the box and bring it to the kitchen). Composition of actions is also possible in the CFR, corresponding to more complex action as the Pick_and_place action, represented by a sequence of Taking frame followed by a Bringing frame (e.g. for the command take the box and bring it to the kitchen). The grammar specifying the correct syntax for a CFR will be also provided, and is reported in the following. In order to represent the semantic frames extracted from the commands in a compact way, a specic syntax has been dened, called Command Frame Representation (CFR). Such a representation will have to respect a command/arguments structure, resembling the common syntax for a programming language method: the frame represents the method name, while the arguments represent the method arguments. MOTION(goal:to the kitchen)#TAKING(theme:the tea cup). Frames can have more than one single arguments, as for the command take a towel from the bathroom, corresponding to the following tagging and CFR: [take]Taking [a towel]Theme [from the bathroom]Source [take]Taking [a towel]Theme [from the bathroom]Source go to the kitchen and [take]Taking [the tea cup]Theme. go to the kitchen and [take]Taking [the tea cup]Theme. go to the kitchen and [take]Taking [the tea cup]Theme. The frame are associated to the verbs as they evoke the action expressed by the frames. This double tagging of the semantic information will correspond to the conjunction of the CFR of the two frames, that is: [go]Motion [to the kitchen]Goal and take the tea cup [go]Motion [to the kitchen]Goal and take the tea cup Action →MOTION | TAKING | BRINGING | SEARCHING | PLACING Action →MOTION | TAKING | BRINGING | SEARCHING | PLACING Arguments →Argument | Argument, Arguments Argument →Argument_name:Role_filler Argument_name →theme | goal | source | path | ground | beneficiary Role_filler →Defined_lexicon where Defined_lexicon is the lexicon that will be released to the team before the competition, including names of rooms (e.g. hallway, living room, etc.) and objects (e.g. cereal box, jar, etc.). where Defined_lexicon is the lexicon that will be released to the team before the competition, including names of rooms (e.g. hallway, living room, etc.) and objects (e.g. cereal box, jar, etc.). Composition of actions is also possible in the CFR, corresponding to more complex action as the Pick_and_place action, represented by a sequence of Taking frame followed by a Placing frame (e.g. for the command take the box and put it on the table). The corresponding CFR will be: TAKING(theme:the box)#PLACING(theme:it,goal:on the table) A parser is available in the ERL Wiki [1] in order to check the format compliance of the produced output in terms of interpretation. Here we provide some annotation examples. Considering the command go to the kitchen and take the coee mug, where two frames are evoked (e.g. Motion, the two associated annotation will be: 4.3.2 Input Provided For example, for the go to the dining room command, where a Motion frame is expressed and the Goal argument is instantiated with to the dining room, the corresponding CFR will be: MOTION(goal:to the dining room). It is worth underlying that more than one argument can be expressed in a command. c⃝2018 by ERL Consumer Revision 1.1 23 4. Functionality Benchmarks Contents Results of the Speech Understanding Functionality must be presented according to the CFR formalism. The grammar specifying the correct syntax for a CFR will be also provided, and is reported in the following. Command →Single_command | Composed_command Command →Single_command | Composed_command Composed_command →Single_command#Command Single_command →Action(Arguments) Single_command →Action(Arguments) Revision 1.1 SEARCHING(theme:my jacket). More detailed information about the available audio datasets, the parser and the lexicon can be found in the ERL Wiki [1]. SEARCHING(ground:the bedroom,theme:for my wristwatch). Finally, some commands have been enriched with colloquial forms, as the use of modal verbs, e.g. could you please nd my jacket?. These particles are not considered in the tagging, as they represent only inections that, in this case, don't aect the general meaning of the command: could you please [find]Searching [my jacket]Theme ? Revision 1.1 TAKING(theme:a towel,source:from the bathroom). In a sentence, it will be possible to nd some arguments that have not been tagged. These will be only arguments not dened for this task (and thus not reported in the list in Section 4.3.2) as, for example, the Manner argument, representing the manner in which the action c⃝2018 by ERL Consumer 24 Revision 1.1 4. Functionality Benchmarks Contents take place. For example, in the command Search carefully the bedroom for my wristwatch, the adverb carefully, representing the Manner, is not tagged: [search]Searching carefully [the bedroom]Ground [for my wristwatch]Theme 4.3.3 Expected Robot Behavior or Output The robot should be able to understand a command starting from the speech input. The robot should correctly transcribe the command and recognize the action to perform, resulting in the correct command frame (e.g. MOTION for a motion command) and the arguments involved (e.g. the goal of a motion command). The output of the robot should provide the CFR format for each command, as reported in Section 4.3.1 and dened in Section 4.1.2. For each command, the system should generate the corresponding transcription and the interpretation in the CFR format. This information have to be saved in an output text le called results.txt. In this le, a line has to be added for each command, following the format 4.3.4 Procedures and Rules The robots will be disposed in circle around a 360◦speaker that will broadcast a set of spoken sentences. These sentences are pre-recorded commands in dierent consumer environments and are played continuously while containing a small pause between the commands. For every com- mand the command number is also announced in advance. An example can be downloaded from: https://sites.google.com/site/erlsrlisbon/resources/test.mp3 NOTE: An autonomous detection of the command number is highly preferred, however, teams can also indicate the start of a new command by pressing a single button (either a button in a GUI or a key on the keyboard). The benchmarking procedure is performed for all the teams in parallel. Each team receives a USB stick before the benchmark begins to connect to their robots. Once the benchmark is over, only one button can be pressed to store the output le and all teams must then deliver their USB sticks. 4.3.5 Acquisition of Benchmarking Data During the execution of the benchmark, the following data will be collected: During the execution of the benchmark, the following data will be collected: • Sensor data (in the form of audio les) used by the robot to perform speech recognition10 • Sensor data (in the form of audio les) used by the robot to perform speech recognitio • The set of all possible transcription for each user utterance; • The nal command produced during the natural language analysis process; • Intermediate information produced or used by the natural language understanding system during the analysis as, for example, syntactic information. 10Speech les from all teams and all benchmarks (both Task benchmarks and Functionality bench- marks) will be collected and used to build a public dataset. The audio les in the dataset will therefore include all the defects of real-world audio capture using robot hardware (e.g., electrical and mechani- cal noise, limited bandwidth, harmonic distortion). Such les will be usable to test speech recognition software, or (possibly) to act as input during the execution of speech recognition benchmarks. command_numberi|command_transcriptioni|CFRi where Command_number, command_transcription and CFR represent respectively the number, the transcription and the interpretation of the i-th audio le, separated by a pipe (|). The results.txt le must be encoded using standard UTF-8 character encoding: les with a dierent encoding will be automatically rejected. where Command_number, command_transcription and CFR represent respectively the number, the transcription and the interpretation of the i-th audio le, separated by a pipe (|). The results.txt le must be encoded using standard UTF-8 character encoding: les with a dierent encoding will be automatically rejected. NOTE: the correspondence between the data in the results le and the audio command numbers must be consistent. If the Automatic Speech Recognition fails in transcribing a sentence, the label BAD_RECOGNITION must be used. Similarly, if the semantic frame extraction does not produce any correct result, the NO_INTERPRETATION label must be reported. An example of results.txt le is reported in the following: command_1|move to the living room|MOTION(goal:living room ) command_2|BAD_RECOGNITION|NO_INTERPRETATION command_1|move to the living room|MOTION(goal:living room ) command_2|BAD_RECOGNITION|NO_INTERPRETATION NOTE: every line not respecting the format required and described above will be skipped during the evaluation phase. In addition to saving the output on the text le, which will be used for scoring, the organizing committee might ask the teams to also send the output to the RSBB, after every command, in order to visualize the results in real-time for the audience. Revision 1.1 c⃝2018 by ERL Consumer 25 4. Functionality Benchmarks Contents 3. Time utilized (if less than the maximum allowed for the benchmark). 3. Time utilized (if less than the maximum allowed for the benchmark). The nal score will be evaluated considering both the AcC and the AgC. Only the F-Measure will be considered for both measures, each one contributing for 50% of the score. The AgC F-Measure will be evaluated for each argument, and the nal F-Measure for the AgC will be the sum of the single F-Measure of the single arguments divided by the number of arguments. This nal score has to be considered as an equivalence class. If this score will be the same for two or more teams, the WER will be used as penalty to evaluate the nal ranking. This means that a team belonging to an equivalence class can not be ranked lower than one belonging to a lower one, even though the nal score, considering the WER of the rst is lower than the score of the second. 4.4 People Perception Functionality This functionality benchmark aims at assessing the capabilities of a robot to correctly detect, locate and recognize humans. Human perception is one of the most important capabilities re- quired for human-robot interactions and essential for a successful deployment of robots in many consumer environments. 4.4.1 Functionality Description The benchmark requires that the robots correctly detects the presence of a human inside a predened target area, recognizes the person and accurately estimates his/her position. Revision 1.1 4.3.6 Scoring and Ranking During the functionality benchmark, dierent aspects of the speech understanding process will be assessed: During the functionality benchmark, dierent aspects of the speech understanding process will be assessed: 1. The Word Error Rate on the transcription of the user utterances, in order to evaluate the performance of the speech recognition process. 2. For the generated CFR, the performance of the system will be evaluated against the provided gold standard version of the CFR, that is conveniently paired with the analyzed audio le and transcription. Two dierent performances will be evaluated at this step. One measuring the ability of the system in recognizing the main action, called Action Classication (AcC), and one related to the classication of the action arguments, called Argument Classication (AgC). In both cases the evaluations will be carried out in term of Precision, Recall and F-Measure. This process is inspired to the Semantic Role Labeling evaluation scheme proposed in [2]. For the AcC this measures will be dened as follow: • Precision: the percentage of correctly tagged frames among all the frames tagged by the system; • Precision: the percentage of correctly tagged frames among all the frames tagged by the system; • Recall: the percentage of correctly tagged frames with respect to all the gold standard frames; • Recall: the percentage of correctly tagged frames with respect to all the gold standard frames; c⃝2018 by ERL Consumer Revision 1.1 26 4. Functionality Benchmarks Contents • F-Measure: the harmonic mean between Precision and Recall. • F-Measure: the harmonic mean between Precision and Recall. • F-Measure: the harmonic mean between Precision and Recall. Similarly, for the AgC, Precision, Recall and F-Measure will be evaluated, given an action f, as: • Precision: the percentage of correctly tagged arguments of f with respect to all the arguments tagged by the system for f. • Precision: the percentage of correctly tagged arguments of f with respect to all the arguments tagged by the system for f. • Recall: the percentage of correctly tagged arguments of f with respect to all the gold standard arguments for f. • Recall: the percentage of correctly tagged arguments of f with respect to all the gold standard arguments for f. • F-Measure: the harmonic mean between Precision and Recall. 4.4.3 Expected Robot Behavior or Output The participating team is required to position their robot on any desired initial position, that could be anywhere outside the specied target area, from which it can best perceive this area. The human targets that the robot is required to perceive will move into the target area one at the time. The identity and location of the person presented to the robot is unknown before he/she moves and stands inside the area. For each presented person, the robot must perform the following: • Person localization: Locate the 2D position of the person with respect to the benchmark setup reference frame. • Person localization: Locate the 2D position of the person with respect to the benchmark setup reference frame. • Person recognition: Recognize the person inside the target area. For each person, the robot must communicate the results to the RSBB, or announce that it is incapable of perceiving the person. In addition, for the interest of the audience, the robot must announce the name of the recognized person after recognition. 4.4.2 Input Provided A bounded rectangular target area, of approximately 3m×3m, will be dened on the oor that will accommodate humans during the benchmark. The coordinates of the target area along with the reference frame will be communicated to the teams during the setup days. This area will only accommodate one person at a time. The test area will be surrounded by motion tracking cameras, such as an Optitrack system, to locate the precise position of the person and automatically evaluate the performance of the robots in locating people. Up to 10 persons will be chosen from the technical and organizing committee as well as from the team members of the competing teams during the setup days. Each team will be given the opportunity to meet the people and to collect training data before the beginning of the benchmark. c⃝2018 by ERL Consumer Revision 1.1 27 4. Functionality Benchmarks Contents 4.4.4 Procedures and Rules All teams are required to perform this functionality benchmark according to the steps mentioned below: Step 1 The participating team is required to set their robot on any desired initial position outside the target area. Step 1 The participating team is required to set their robot on any desired initial position outside the target area. Step 2 Once the start signal is sent out from the RSBB, the robot is required to detect and localize the person standing inside the target area. 3 The robot sends the results to the RSBB and announces its readiness for the next person Step 3 The robot sends the results to the RSBB and announces its readiness for the next person. Step 4 The RSBB requests the person to move out of the area and the randomly selects the next person to move into the area. Step 4 The RSBB requests the person to move out of the area and the randomly selects the next person to move into the area. This process is repeated until all people are presented to the robot. Teams will have up to ten minutes to complete the functionality benchmark. This process is repeated until all people are presented to the robot. Teams will have up to ten minutes to complete the functionality benchmark. 4.4.5 Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be collected. 4.5.3 Expected Robot Behavior or Output Initially, a human will stand in front of the robot that is placed at a previously dened location in the arena. Once the benchmark starts, the person will start to walk and visit dierent regions of the arena. The robot is expected to follow and maintain its original distance with this person at all times while avoiding obstacles and other people that will interrupt the motion of the robot. If the robot loses or cant keep up with the target, it can request the person to come back, walk slower, wait or stand in front of the robot to resume the walking behavior. However, such interruptions will have a direct impact on the performance score that is computed automatically by the system. 4.4.6 Scoring and Ranking Evaluation of the performance of a robot according to this functionality benchmark is based on: Evaluation of the performance of a robot according to this functionality benchmark is based on: 1 The number and percentage of correctl recogni ed persons 1. The number and percentage of correctly recognized persons. 1. The number and percentage of correctly recognized persons. 2. Location error for all detected persons. 3. Execution time (if less than the maximum allowed for the benchmark). The previous criteria are in order of importance: the rst criterion is applied rst and teams will be scored according to the common accuracy metrics; the ties are broken by second criterion which is the position error. Since the position error is slightly aected by the precision of the ground truth system we will use a set of accuracy classes, and in case of ties we will resort to the third criterion. c⃝2018 by ERL Consumer Revision 1.1 28 4. Functionality Benchmarks Contents 4.5 Person Following Functionality Human accompanying is an important capability required by many service robots for human- robot interactions. This functionality benchmark aims at assessing the capabilities of mobile robots in eectively following humans. The human following capability is expected to be one of the essential capabilities required for the robots planning to take part in the upcoming Smart City Major Competitions. 4.5.1 Functionality Description The benchmark requires that the robot accompanies a human and always maintain a desired distance with this person. In this benchmark, a person will initially stand in front of the robot and then will start to walk around the arena. The robot must always follow this person while avoiding obstacles or other humans who are passing by. 4.5.2 Input Provided The test is executed inside an apartment-like arena that will include stationary and dynamic obstacles such as furniture or people. The initial pose of the robot and the person will be communicated to the teams before the competition. Since the main aim of this benchmark is to evaluate the following capabilities of robots, and the human-perception is not the main focus of the test, teams are open to exploit any preferred perceptual technique for their robots to display an ecient following behavior. This can range from anything such as laser range scanners, ultrasound sensors to vision-based perception systems. Furthermore, teams are allowed to instruct the person to wear tags, markers, colored shirt or anything that will minimize the perceptual errors. 4.5.6 Scoring and Ranking The evaluation of the performance of a robot is performed autonomously with the aid of a motion capture system that precisely measures the true pose of the robot and the person at all times. The performance score is computed based on: 1. The accuracy in keeping the desired relative distance to the target. 1. The accuracy in keeping the desired relative distance to the target. 2. The total distance covered by the robot when it is following the target. The robot is automatically considered to be following when it is within a tolerance distance from the desired relative distance. 2. The total distance covered by the robot when it is following the target. The robot is automatically considered to be following when it is within a tolerance distance from the desired relative distance. The previous criteria are considered to be of equal importance, encouraging both accurate and fast solutions with minimum interruptions. 4.5.4 Procedures and Rules All teams are required to perform this functionality benchmark according to the steps described below. The task must be done exclusively in autonomous mode and no teleoperation is permitted. Step 1 The robot is placed on the starting position facing a standing human. Step 2 The benchmark starts after the start signal is communicated by the RSBB. Step 2 The benchmark starts after the start signal is communicated by the RSBB. Step 3 The person starts to walks in normal walking speed and visits dierent areas of the apartment, occasionally stopping and then resuming the walking. The robot must exhibit the following behaviour as described in Section 4.5.3 . Step 4 The benchmark will stop automatically after the timeout. An End signal will be issued by the RSBB at timeout. Step 4 The benchmark will stop automatically after the timeout. An End signal will be issued by the RSBB at timeout. This benchmark will last 5 minutes. This benchmark will last 5 minutes. c⃝2018 by ERL Consumer Revision 1.1 29 4. Functionality Benchmarks Contents 4.5.5 Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be collected. 4.6 Object Grasping and Manipulation Functionality This functionality benchmark evaluates the capabilities of a robot to correctly grasp and ma- nipulate objects. In particular, it assesses the object picking and placing capabilities of service robots that is an essential requirement for many consumer applications, for example to set up a dining table. 4.6.3 Expected Robot Behavior or Output The participating team is required to set their robot in front of the working table. After an object is placed on the table and the benchmark starts, the robot must grasp and pick up the object from the table surface and then deliver and place it on the target position specied by the RSBB. If required, the robot can further manipulate the object to improve the pose of the object. Once the robot has completed the task, or it is incapable of completing it, it must send the end command to the RSBB for the next object to be placed on the table. 4.6.1 Functionality Description In this benchmark the robots are required to correctly grasp, lift and move a set of objects over a tabletop. Objects will be placed one by one on top of a table located in front of the robot. The initial pose of the object is not known beforehand. The robot must grasp the object and deliver it to a target position over the table that is specied and communicated by the RSBB. Figure 2.6 describes an illustration of the benchmarking procedure. Figure 2.6: Illustration of the Grasping and manipulation functionality benchmark where the robot is required to grasp, pick up and place the object on a dened target position. Motion capture markers are attached on the object and are used for measuring the object pose and automatic evaluation Figure 2.6: Illustration of the Grasping and manipulation functionality benchmark where the robot is required to grasp, pick up and place the object on a dened target position. Motion capture markers are attached on the object and are used for measuring the object pose and automatic evaluation c⃝2018 by ERL Consumer Revision 1.1 30 4. Functionality Benchmarks Contents 4.6.4 Procedures and Rules All teams are required to perform this functionality benchmark according to the steps mentioned below: Step 1 The participating team is required to set their robot on any desired initial position in front of the working table. Step 2 The start signal will be communicated to the robot by the RSBB to indicate the start of the benchmark. Step 2 The start signal will be communicated to the robot by the RSBB to indicate the start of the benchmark. Step 3 Once the robot announces its readiness to the RSBB by sending the Prepared signal, an object is randomly selected by the RSBB, from the list of possible objects, and is manually placed over the table by the referee. Step 3 Once the robot announces its readiness to the RSBB by sending the Prepared signal, an object is randomly selected by the RSBB, from the list of possible objects, and is manually placed over the table by the referee. Step 4 The execution command along with the target position of the object will be issued from the RSBB. Step 4 The execution command along with the target position of the object will be issued from the RSBB. Step 4 The execution command along with the target position of the object will be issued from the RSBB. Step 5 The robot must grasp, pick up and place the object on the specied target location. Step 5 The robot must grasp, pick up and place the object on the specied target location. Step 6 The robot sends the end signal to the RSBB and announces its readiness for the next object. Step 6 The robot sends the end signal to the RSBB and announces its readiness for the next object. This process is repeated until all objects are presented to the robot. Teams will have up to ten minutes to complete the functionality benchmark. This process is repeated until all objects are presented to the robot. Teams will have up to ten minutes to complete the functionality benchmark. 4.6.2 Input Provided A set of 3D-printed objects of dierent shapes will be used for this benchmark. The 3D models of all objects, in digital format, will be available to the teams before the competition allowing them to train their robots in simulation or in real-world by 3D-printing the objects. Furthermore, objects are also provided to the teams during the setup days. As the focus of this benchmark is on evaluation of the grasping and manipulation capabilities of robots and object, object perception is simplied by using 3D printed single-color objects over a white table. Furthermore, the nature of objects will be communicated to the robot through the RSBB to further assist the robot with the perception. The reference frame will be marked on the table as in the object perception functionality, see Figure 2.4, and the test area will be surrounded by motion tracking cameras, such as an Optitrack system, to precisely locate the objects and evaluate the performance of robots. 12Internal robot data referring to end eector 3D position 11Any notication from the robot 4.6.5 Acquisition of Benchmarking Data During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be collected together with the additional information described in the following table During the execution of the benchmark, the Internal Data dened in Section C.3.2 will be collected together with the additional information described in the following table c⃝2018 by ERL Consumer 31 Revision 1.1 Contents 4. Functionality Benchmarks Topic Type Frame Id Notes /erlc/notication11 std_msgs/String   /erlc/gripper_pose12 geometry_msgs/Pose   Individual tournament awards: Awards will be given to the best teams for each of the Task Benchmarks (TBMs) and Function- ality Benchmarks (FBMs) per tournament by the local organizers. In every Local/Major Tournament, each team is requested to perform several trials of the available TBMs and FBMs. The team score for a given TBM/FBM in a Local/Major Tournament is computed as follows: 1. Select the best ve trials of the TBM/FBM by the team (all the trials if less than ve trial attempts are oered by the local organizers) 1. Select the best ve trials of the TBM/FBM by the team (all the trials if less than ve trial attempts are oered by the local organizers) 2. The team score is the median of the scores of the trials selected in 1. The team with the highest score in each of the task benchmarks will be awarded the title (ERL Consumer Best-in-class Task Benchmark <task benchmark title>). The teams with the highest score ranking for each of the functionality benchmarks will be awarded the title (ERL Consumer Best-in-Class Functionality Benchmark <functionality benchmark title> and 'ERL Consumer Second-Best-in-Class Functionality Benchmark <functionality benchmark title>). The team with the highest score in each of the task benchmarks will be awarded the title (ERL Consumer Best-in-class Task Benchmark <task benchmark title>). The teams with the highest score ranking for each of the functionality benchmarks will be awarded the title (ERL Consumer Best-in-Class Functionality Benchmark <functionality benchmark title> and 'ERL Consumer Second-Best-in-Class Functionality Benchmark <functionality benchmark title>). Notes: • The number of TBM/FBM trial attempts oered in a tournament is recommended to be a minimum of 3 and a maximum of 7 trials. • The number of TBM/FBM trial attempts oered in a tournament is recommended to be a minimum of 3 and a maximum of 7 trials. • When a single team participates in a given benchmark, the corresponding benchmark award will only be given to that team if the Executive and Technical Committees consider the team performance of exceptional level. • When a single team participates in a given benchmark, the corresponding benchmark award will only be given to that team if the Executive and Technical Committees consider the team performance of exceptional level. 4.6.6 Scoring and Ranking Evaluation of the performance of a robot for this functionality benchmark is performed au- tonomously and is based on: 1. The number and percentage of correctly grasped objects. An object is considered to be grasped by the RSBB system once it is lifted completely from the table. 1. The number and percentage of correctly grasped objects. An object is considered to be grasped by the RSBB system once it is lifted completely from the table. 2. Final pose error of the object with respect to the specied target location. 3. Execution time (if less than the maximum allowed for the benchmark). The rst criterion is applied rst and teams will be scored according to the common accuracy metrics; the ties are broken by second criterion which is the position error. Since the position error can be slightly aected by the precision of the ground truth system, a set of accuracy classes is dened and used, in case of ties we will resort to the the execution time. c⃝2018 by ERL Consumer Revision 1.1 32 A. ERL Consumer Award Categories Contents Individual tournament awards: • When less than three teams participate in a given functionality benchmark, only the ERL Consumer Best-in-class Functionality Benchmark <functionality benchmark title> award will be given to a team, and only if the Executive and Technical Committees consider that team's performance as excellent A ERL Consumer Award Categories Individual tournament awards: Best ERL Consumer team award: Only one nal Best ERL Consumer team award will be awarded to the best performing team at the end of the Season. The Season ranking is computed as follows: Only one nal Best ERL Consumer team award will be awarded to the best performing team at the end of the Season. The Season ranking is computed as follows: • To be eligible for an award, a team must have executed valid (i.e., scored) trials of at least one TBM in minimum two Local/Major Tournaments of the Season; • Only TBMs are considered for computing the nal score; • A score is computed for every TBM as the median of the pooled trials used for scoring the best two performances of a team in the Local/Major Tournaments of the Season (see above); • A score is computed for every TBM as the median of the pooled trials used for scoring the best two performances of a team in the Local/Major Tournaments of the Season (see above); • The team nal score is then calculated by summing up all the TBM scores; • A minimum score value will be required in order for the award to be given. c⃝2018 by ERL Consumer Revision 1.1 33 B. The ERL Consumer Test bed Contents B The ERL Consumer Test bed The test bed for ERL Consumer consists of the environment in which the competition will happen, including all the objects and artefacts in the environment, and the equipment brought into the environment for benchmarking purposes. An environment tting quite well the user story is depicted by Figure 7. Figure 7: Granny Annie's apartment. Figure 7: Granny Annie's apartment. Note: There is considerable discussion in the community, as to how specic and precise the description of the environment should be, especially in the light of benchmarking. In order to require teams to develop robots which can be easily and exibly adapted to a wide range of dif- ferent environments, can deal with a wide variety of objects, etc., and to avoid overengineering of solutions, it would be highly advisable to keep the description as exible as possible. We reect this in the specications below by providing comparatively generous boundary conditions, e.g. on room sizes, and by complementing them by a recommendation, which should be understood as a default size and the size we target to use at least for the rst iteration of the competition. Com- petition organizers should plan with these recommended sizes and objects, while the developers of simulation software should provide means to easily modify models, e.g. by resizing rooms or by changing the properties of the environment or replacing objects, etc. The recommended environment for the ERL Consumer Challenge is illustrated in Figure 8. Participating teams should assume the competition environment to be as illustrated; deviations should only occur if on-site constraints (space available, safety regulations) enforce them. An example of a certied ERL Consumer test bed and its corresponding environment is provided in Appendix E. Environment Specication B.4 (List of Rooms) The environment features the following ve spatial areas: hallway, living room, dining room, kitchen, and bedroom. Environment Specication B.2 (Flat Environment) All spatial areas all located on the same level, except where specied otherwise. There are no stairs in the environment. Environment Specication B.3 (Spatial Areas and Rooms) Spatial areas completely enclosed by walls are referred to as rooms. The apartment follows an open plan architecture, i.e. several spatial areas are connected to each other by open space (openly connected) and are only jointly surrounded by walls. In human-robot interaction, such spatial areas may still referred to as rooms. B.1 Environment Structure and Properties The following set of scenario specications must be met by the ERL Consumer environment. Environment Specication B.1 (Structured Environment) The environment consist of an ensemble of ve spatial areas. c⃝2018 by ERL Consumer Revision 1.1 34 B. The ERL Consumer Test bed Contents Hallway Kitchen Living Room Bathroom Bedroom Dining Room Patio Figure 8: The test bed for the ERL Consumer Competition (Patio and Bathroom will not be accessible to the robots in this edition). Bathroom Bedroom Kitchen Living Room Dining Room Patio Figure 8: The test bed for the ERL Consumer Competition (Patio and Bathroom will not be accessible to the robots in this edition). Kitchen Living Room Figure 8: The test bed for the ERL Consumer Competition (Patio and Bathroom will not be accessible to the robots in this edition). c⃝2018 by ERL Consumer Revision 1.1 35 B. The ERL Consumer Test bed Contents Two additional areas are foreseen for future extensions; they may be provided as part of a test bed, but they are not foreseen and not accessible to the robots, yet. We do not further consider them in the following specications. Robots are expected to cope with rooms and spatial areas of dierent sizes. Robots are expected to cope with rooms and spatial areas of dierent sizes. Robots are expected to cope with rooms and spatial areas of dierent sizes. The minimum sizes of the spatial areas are as follows: hallway 120cm × 200cm, bedroom 400cm × 300cm, kitchen 200cm × 240cm, dining room 300cm × 300cm, living room 400cm × 400cm. The whole apartment should t into bounding rectangular box having a minimum are f 50m2 and a maximum area of 200m2. The recommended sizes of the spatial areas are as follows: hallway 120cm × 200cm, bedroom 400cm × 300cm, kitchen 300cm × 260cm, dining room 300cm × 300cm, living room 400cm × 580cm. Bedroom Dining Room Living Room Inside Hallway Outside Hallway Kitchen area accessible to the robot door area not accessible to the robot open space Figure 9: Graph showing the topological structure of environment. Figure 9: Graph showing the topological structure of environment. Environment Specication B.8 (Walls) The walls of the environment must meet the following criteria: Material features: The bedroom walls have to be made of some sti material, such as wood, wood-based materials (chipboards), stone, concrete, or metal. For competition arenas, walls will usually be made of chipboards in combination with wood or metallic frames. The color of the walls will usually be some light color (such as white, ivory, yellow, light green, to name a few examples). One or two walls per room may be painted with some darker color (such dark red, aubergine, mocca, dark grey, dark brown, to name a few examples) for decorative purposes. Patterned wallpaper may be used for nishing the walls. The walls are not translucent. If some kind of translucent material, such as glass, Plexiglass R ⃝, Perspec R ⃝, or Lucite R ⃝is used, then these wall areas are dened as windows. Shape/form: The walls are upright. No slanted walls will be used. Osets up to 5cm are allowed to ease construction of test beds. Shape/form: The walls are upright. No slanted walls will be used. Osets up to 5cm are allowed to ease construction of test beds. Size: The minimum height of the walls is 80cm. The recommended wall height is 240cm. Exceptions may be made for up to two connecting walls of each room in order to allow better visibility for the audience at competitions. The length of the walls is dened by the connecting oor shapes. The width (thickness) of the walls must be large enough to ensure sucient stability. The drawings assume a wall thickness of 20cm. If the construction of an environment foresees inside walls with less thickness, then the space of the connecting spatial areas will grow accordingly. Uniqueness: The walls may be unique or not, i.e. the wall colors and patterns may be the same as in other spatial areas of the apartment or they may be dierent. Environment Specication B.7 (Floors) The oor of each spatial area must be such that safe operation of robots meeting the specications laid down in Section C is possible. The following criteria must be met: Material features: The oor is either carpet or parquet oor. No constraints exist with respect to the colors or patterns used. Slope: The oor should be well-leveled, but slopes of up to 2◦and unevenness of up to 5mm are acceptable. Uniqueness: The oor may be unique or not, i.e. a oor in a room be the same as in other room, or it may be dierent. Environment Specication B.6 (Connectivity of Spatial Areas) The environment is accessible from outside through a front door to the hall way. The hallway is openly connected to the living room by a portal. The living room is connected to the bedroom by a door. The living room is openly connected to the kitchen. The living c⃝2018 by ERL Consumer Revision 1.1 36 B. The ERL Consumer Test bed Contents room is openly connected to the dining room. The dining room is openly connected to the kitchen. room is openly connected to the dining room. The dining room is openly connected to the kitchen. room is openly connected to the dining room. The dining room is openly connected to the kitchen. connectivity of the spatial areas is illustrated by the topological graph depicted in Figure he connectivity of the spatial areas is illustrated by the topological graph depicted in Figure 9. nvironment Specication B.7 (Floors) The connectivity of the spatial areas is illustrated by the topological graph depicted in Figure 9. Environment Specication B.7 (Floors) Environment Specication B.7 (Floors) Environment Specication B.9 (Ceilings) p ( g ) The rooms may or may not be covered by a ceiling. If it is not covered by a ceiling, then special constructions may be foreseen for xing lamps, sensors, or other objects. If it is covered by a ceiling, the following specications apply: Material features: The ceiling can be of any material. Slope: The ceiling may be (partially or completely) sloped. Uniqueness: The ceiling is not unique. The rooms may or may not be covered by a ceiling. If it is not covered by a ceiling, then special constructions may be foreseen for xing lamps, sensors, or other objects. If it is covered by a ceiling, the following specications apply: Material features: The ceiling can be of any material. Slope: The ceiling may be (partially or completely) sloped. Material features: The ceiling can be of any material. Slope: The ceiling may be (partially or completely) sloped. Uniqueness: The ceiling is not unique. c⃝2018 by ERL Consumer 37 Revision 1.1 B. The ERL Consumer Test bed Contents Environment Specication B.12 (Dining Room) The dining room has a window and the furniture includes a dining table seating four, and four chairs. The dining room has a window and the furniture includes a dining table seating four, and four chairs. Environment Specication B.11 (Living Room) Environment Specication B.11 (Living Room) The living room has a large window front side to the patio. These windows cannot be opened. These windows have inside blinds that are operated electrically. The furniture includes a large carpet, a coee table, a couch, two armchairs, a low-height sideboard, and a bookshelf. A TV set is located on the sideboard. The lighting includes central ceiling lights, a band of dimmable ceiling spots, and a large oor light. Environment Specication B.10 (Bedroom) The furniture includes a double bed, two bedside tables, a large wardrobe, a large mirror, a dressing table, and a carpet. The lighting includes two bedside lamps. n example conguration of the bedroom is depicted in Figure 10. An example conguration of the bedroom is depicted in Figure 10. Figure 10: An example bedroom created with the IKEA bedroom planner. Figure 10: An example bedroom created with the IKEA bedroom planner. Environment Specication B.13 (Kitchen) The kitchen has no window and no door. The furniture includes several cupboards with drawers and doors. The installation include a fridge/freezer combination, a sink, a dish- washer, a stove, a baking oven, and an exhaust hood. Two rows of ceiling lights are available for the lighting. (Details of the kitchen will be specied in more detail as needed.) Environment Specication B.14 (Hallway) The hallway has no windows. The furniture consists of a coat rack. The lighting consists of lamps mounted on the walls. The hallway has no windows. The furniture consists of a coat rack. The lighting consists of lamps mounted on the walls. c⃝2018 by ERL Consumer Revision 1.1 38 B. The ERL Consumer Test bed Contents Environment Specication B.15 (Navigation-Relevant Object Types) The navigation-relevant objects that may be present in the environment include the following types of objects: • Rugs, which may be placed on top of oors, covering the oor usually only partially. • Rugs, which may be placed on top of oors, covering the oor usually only partially. F i hi h i l d i h i • Rugs, which may be placed on top of oors, covering the oor usually only partially. • Furniture, which is placed in the environment. • Furniture, which is placed in the environment. • Furniture, which is placed in the environment. • Doors, which connect rooms and may be in various dierent states. • Doors, which connect rooms and may be in various dierent states. • Any other kind of object, task-relevant or not, and including networked embedded devices and benchmarking equipment, if placed in the environment such that the object occupies space in the robot's workspace. • Any other kind of object, task-relevant or not, and including networked embedded devices and benchmarking equipment, if placed in the environment such that the object occupies space in the robot's workspace. B.2 Task-Relevant Objects in the Environment The test bed environment will contain numerous objects, some of which are explicitly relevant for one or more of the task benchmarks or functionality benchmarks described in Section 3 and 4, respectively. We distinguish three major categories of task relevance: Navigation-Relevant Objects: This class of objects comprises of all objects which have extent in physical space and do (or may) intersect (in 3D) with the robot's navigation space. All such objects must be avoided during navigation, i.e. whenever the robot moves, it may not bump into these objects or touch them, unless otherwise specied by a task. Navigation- relevant objects may be known by name or not. If these objects have a unique name, then the object may occur as a destination, e.g. for a navigation or manipulation operation. Manipulation-Relevant Objects: This class contains all objects that the robot may have manipulative interactions with, which may include touching (a switch), grasping (a glass), lifting (a book), holding (a cup), placing (a parcel), dropping (waste), carrying (a glass), pushing (a drawer), pulling (a drawer), turning (a book), lling ( a glass), pouring (from a cup), etc. For these objects, the most comprehensive information will be provided. Perception-Relevant Objects: These are objects that the robot must only be able to per- ceive. By perceive we mean that the robot should be able to recognize if such an object is in its view, that it should be able to identify the object if it is unique or to classify it if not (e.g. an instance of a cup, if several non-unique instances exist), and that it should be able to localize the object. Objects that are only perception-relevant usually occur in tasks where the robot is supposed to nd and localize these objects, but is not required to manipulate them. Perception-Relevant Objects: These are objects that the robot must only be able to per- ceive. By perceive we mean that the robot should be able to recognize if such an object is in its view, that it should be able to identify the object if it is unique or to classify it if not (e.g. an instance of a cup, if several non-unique instances exist), and that it should be able to localize the object. Objects that are only perception-relevant usually occur in tasks where the robot is supposed to nd and localize these objects, but is not required to manipulate them. B.2 Task-Relevant Objects in the Environment Subsequently, we describe a complete collection of all objects relevant for the task benchmarks and functionality benchmarks. Object Specication B.1 (Rugs) The ERL Consumer Competition does not foresee any rugs in the environment, yet The ERL Consumer Competition does not foresee any rugs in the envir Object Specication B.2 (Furniture) Object Specication B.2 (Furniture) The furniture placed in each room or spatial area is listed in the environment specications B.10 to B.14. Further details on the furniture are provided in the ERL wiki. The furniture placed in each room or spatial area is listed in the environment specications B.10 to B.14. Further details on the furniture are provided in the ERL wiki. The furniture placed in each room or spatial area is listed in the environment specications B.10 to B.14. Further details on the furniture are provided in the ERL wiki. Environment Specication B.16 (Manipulation-Relevant Object Types) The manipulation-relevant objects that may be present in the environment include the following types of objects: • Personal items, like keys connected by key rings, mobile phones, tablet computers, MP3 players, eyeglasses/spectacles and their cases, wallets/purses and billfolds, watches, bracelets and rings. • Personal items, like keys connected by key rings, mobile phones, tablet computers, MP3 players, eyeglasses/spectacles and their cases, wallets/purses and billfolds, watches, bracelets and rings. • Mail items, like letters and parcels, and print material, like newspapers, magazines, journals, paperbacks and books. • Mail items, like letters and parcels, and print material, like newspapers, magazines, journals, paperbacks and books. • Household items, such as glasses, cups, plates, knifeware, and such. • Groceries in containers of various forms, like cartons, cans, bottles, tubes, bags. • Switches for lighting and electronic appliances. • Handles of doors, including handles of wardrobe doors and drawers. • Any other kind of object provided that it meets all of the object constraints B.1 to B.4. Object Specication B.3 (Doors) ( ) The doors used in the environment have a door handle on both sides. Doors are dynamic objects that can be in dierent states at dierent times. At any time, a door may be in one of Revision 1.1 39 c⃝2018 by ERL Consumer The doors used in the environment have a door handle on both sides. Doors are dynamic objects that can be in dierent states at dierent times. At any time, a door may be in one of Revision 1 1 39 c⃝2018 by ERL Consumer Revision 1.1 c⃝2018 by ERL Consumer 39 B. The ERL Consumer Test bed Contents the following four states: open, ajar, closed, locked. A door is considered open if its opening angle is 80◦or more. A door is considered closed, if its opening angle is 0◦and the door is latched but not locked. In case the door is locked as well, the door state obviously is locked. In all other cases, the door is considered to be ajar. the following four states: open, ajar, closed, locked. A door is considered open if its opening angle is 80◦or more. A door is considered closed, if its opening angle is 0◦and the door is latched but not locked. In case the door is locked as well, the door state obviously is locked. In all other cases, the door is considered to be ajar. The personal items to be used include: The personal items to be used include: • keys with a key ring and lanyard. • mobile phones. • tablet computers (e.g. iPad). • eyeglasses with cases, e.g. rimless, horn-rimmed or sunglasses. • purses with dierent colors. • wristwatches. Object Specication B.5 (Mail Items and Print Material) The mail items to be used include: • A parcel as specied in Section 3.2.2. Object Specication B.6 (Household Items) The household items to be used include: • coee mugs, in a dierent color or pattern • coee cups with saucers, all identical. • dessert plates • cake plates • small and large glasses • water jugs c⃝2018 by ERL Consumer 40 Revision 1.1 The mail items to be used include: c⃝2018 by ERL Consumer Revision 1.1 40 B. The ERL Consumer Test bed Contents • coee machine • electric kettle • electric kettle c⃝2018 by ERL Consumer Object Specication B.8 (Switches) Switches are buttons and may be latching (e.g. power button of a washing machine) or non-latching (e.g. power button of a PC). Digital switches are connected to either lamps or shutters. Switches are used as follows: • Switches embedded into walls for operating the lighting. These may be simple on/o switches, changeover switches, or intermediate switches. • Switches embedded into walls for operating the lighting. These may be simple on/o switches, changeover switches, or intermediate switches. • Switches embedded into walls for operating blinds or shutters. These switches come as a pair of pushbuttons, one for each direction of operation, and require to remain pushed for the duration of the operation. • Switches embedded into walls for operating blinds or shutters. These switches come as a pair of pushbuttons, one for each direction of operation, and require to remain pushed for the duration of the operation. Object Specication B.7 (Groceries) The grocery items to be used include: • cartons of dierent size and coloring, containing food items such as cornakes, cereal, pasta, salt, cornstarch, • cartons of dierent size and coloring, containing food items such as cornakes, cereal, pasta, salt, cornstarch, • tin cans in at least three dierent sizes, containing tinned food such as tomato paste, sauerkraut, tuna, and fruits such as pears, peaches, and pineapples • tin cans in at least three dierent sizes, containing tinned food such as tomato paste, sauerkraut, tuna, and fruits such as pears, peaches, and pineapples • tin cans, all of the same size, but dierently colored, containing soft drinks. • glass jars in at least two dierent sizes, containing food such as pickled vegetables like cucumber, onions, corn, and beetroot, or pasta sauces, mustard, mayonnaise, or jams and jellies. • PET bottles, containing water, soft drinks, or juices. • No tubes or bags are foreseen yet. The next two object specications concern objects relevant for manipulation, which themselves are embedded either directly into the environment or into objects placed into the environment, like furniture. c⃝2018 by ERL Consumer Revision 1.1 41 B. The ERL Consumer Test bed Contents Object Constraint B.3 (Object Consistency, Rigidity, Stiness) Object Constraint B.3 (Object Consistency, Rigidity, Stiness) Any objects foreseen for manipulation tasks must be suciently rigid such that grasping by a robot is possible. There may be constraints on where objects can or may be grasped. Some objects may be foreseen which can appear in dierent shapes, e.g. glasses or a bunch of keys. Object Constraint B.4 (Object Content) Objects may not consist of or contain any kind of hazardous material. The content of objects may be solid matter (e.g. paper, nutrition), uids (e.g. water or juices), or gases (e.g. air). If the object contains uids or solid matter in the form of loose material (e.g. cornakes or chips), the object must have a lid or other kind of xture which ensures that the content is properly contained in the object and not spilled. Object Constraint B.1 (Object Weight) The objects foreseen for manipulation can have a maximum weight of 1kg. The objects foreseen for manipulation can have a maximum weight of 1kg. The door handles to be used include: • Each of the doors in the environment has a door handle on each side of the door. • Furniture features some handles, but they will not be relevant for manipulation. • Furniture features some handles, but they will not be relevant for manipulatio Fig. 2.2 illustrates the look and feel of one door handle in the environment. Fig. 2.2 illustrates the look and feel of one door handle in the environment. Object Constraint B.2 (Object Size) The default minimum width/length/depth/diameter/thickness (henceforth: size) of an ob- ject foreseen for manipulation is 2cm, and the default sum of the length, width, and height of the smallest bounding box around the object (henceforth: box sum) is 6cm. An object may have a lower size than 2cm, down to 5mm, in up to two dimensions, if the other dimensions compensate for it, i.e. if the box sum is still at least 6cm. The default minimum width/length/depth/diameter/thickness (henceforth: size) of an ob- ject foreseen for manipulation is 2cm, and the default sum of the length, width, and height of the smallest bounding box around the object (henceforth: box sum) is 6cm. An object may have a lower size than 2cm, down to 5mm, in up to two dimensions, if the other dimensions compensate for it, i.e. if the box sum is still at least 6cm. Object Constraint B.3 (Object Consistency, Rigidity, Stiness) B.2.3 Perception-Relevant Objects This section provides some clarications with respect to perception. This section provides some clarications with respect to perception. Environment Specication B.17 (Perception-Relevant Object Types) Environment Specication B.17 (Perception-Relevant Object Types) Environment Specication B.17 (Perception-Relevant Object Types) The perception-relevant objects in the environment include the following types of objects: The perception-relevant objects in the environment include the following types of objects The perception-relevant objects in the environment include the following types o • The basic environment structure including oors, walls, and ceilings. • The basic environment structure including oors, walls, and ceilings. • All navigation-relevant objects, including rugs, furniture, and any other physical object in the workspace. • All navigation-relevant objects, including rugs, furniture, and any other physical object in the workspace. c⃝2018 by ERL Consumer Revision 1.1 42 B. The ERL Consumer Test bed Contents • All dynamic navigation-relevant objects, i.e. objects with changeable state, like doors, windows, and some furniture. • All dynamic navigation-relevant objects, i.e. objects with changeable state, like doors, windows, and some furniture. • All manipulation-relevant objects, some of which may be uniquely identiable while others are not (identical copies present) • All manipulation-relevant objects, some of which may be uniquely identiable while others are not (identical copies present) • Target locations for navigation and manipulation may require the capability to identify objects (such as furniture items) that are not manipulation-relevant. Examples include objects the robot is supposed to move nearby (e.g. the bedside table) or objects the robot is supposed to grasp or place objects (e.g. the kitchen counter) • Non-task-relevant objects (see Section B.3) will not have to be perceived as part of task benchmarks or functionality benchmarks, but due to their presence in the environment, they will present perceptual noise. • Non-task-relevant objects (see Section B.3) will not have to be perceived as part of task benchmarks or functionality benchmarks, but due to their presence in the environment, they will present perceptual noise. The perception-relevant objects are already specied in various other sections. Further details on the target locations (and respective objects) are provided in the ERL wiki. The perception-relevant objects are already specied in various other sections. Further details on the target locations (and respective objects) are provided in the ERL wiki. Environment Specication B.18 (Non-Task-Relevant Object Types) Environment Specication B.18 (Non-Task-Relevant Object Types) The non-task-relevant objects that may be present in the environment include the following types of objects: The non-task-relevant objects that may be present in the environment include the following types of objects: • Textile objects, like curtains, tablecloth, placesets, napkins, and pillows, either axed to walls/ceilings or sitting on top of furniture. • Textile objects, like curtains, tablecloth, placesets, napkins, and pillows, either axed to walls/ceilings or sitting on top of furniture. • Mirrors, usually xed to walls or furniture. • Mirrors, usually xed to walls or furniture. • Lamps, on the oor or on top of furniture. • Floristic objects, like owers and plants, and associated objects like ower pots and vases, which may be on the oor, on window sills, or on top of furniture. • Floristic objects, like owers and plants, and associated objects like ower pots and vases, which may be on the oor, on window sills, or on top of furniture. • Pictorial objects, like posters, photographs, drawings, and paintings, either axed to walls or sitting on furniture. • Pictorial objects, like posters, photographs, drawings, and paintings, either axed to walls or sitting on furniture. • Other decorative objects, like plates and bowls, candles, and miniatures, usually sitting on top of furniture items. • Other decorative objects, like plates and bowls, candles, and miniatures, usually sitting on top of furniture items. B.3 Non-Task-Relevant Objects in the Environment The test bed environment for ERL Consumer is supposed to resemble a realistic apartment inhabited by an elderly person.Aside of the already listed and specied objects, which make up the environment itself, and objects relevant for navigation and manipulation, as well as networked embedded devices (see Section B.5) and benchmarking equipment (see Section B.6), the environment will contain numerous other objects, mostly for decoration and providing the required realism. The decoration objects to be used include: • plates • bowls • triplets of candles. • miniatures or other decorative objects. The oristic objects to be used include: • small plants in pots, e.g. on the bedroom window sill. • herbal plants in pots, e.g. on the kitchen window sill. • large plants in pots, e.g in the living or dining room. • small vases with owers, e.g. on the kitchen counter. • large vases with xerophytes, e.g. on the oor of the living room. • small plants in pots, e.g. on the bedroom window sill. • herbal plants in pots, e.g. on the kitchen window sill. • large plants in pots, e.g in the living or dining room. • small vases with owers, e.g. on the kitchen counter. • large vases with xerophytes, e.g. on the oor of the living room. B.4 Referee, Scoring and Benchmarking Box The Referee, Scoring and Benchmarking Box (RSBB) software is available at the following repos- itory: The pictorial objects to be used include: The pictorial objects to be used include: • small framed pieces of photographs or drawings, each sized less than A4. • medium-sized pieces of posters or prints, each sized about A3. • small framed pieces of photographs or drawings, each sized less than A4. • medium-sized pieces of posters or prints, each sized about A3. • large pieces of paintings or posters, each sized about A1. • large pieces of paintings or posters, each sized about A1. • large pieces of paintings or posters, each sized about A1. Object Specication B.11 (Mirrors) The mirror objects to be used include: • a tall mirror, e.g. in the hallway. Object Specication B.12 (Lamps) The lamps to be used include: • small lamp(s), e.g. on top of the bedside tables. • oor lamp(s), e.g. in the living room. • oor uplighters, e.g. in the living room. Note that ceiling lamps are already specied with the environment. Note that ceiling lamps are already specied with the environment. The textile objects to be used include: B.4 Referee, Scoring and Benchmarking Box Object Specication B.11 (Mirrors) The mirror objects to be used include: • a tall mirror, e.g. in the hallway. • a large mirror, e.g. in the bedroom The textile objects to be used include: The textile objects to be used include: The textile objects to be used include: • curtains for the bedroom windows. • tablecloths for the dining table. • dierently colored sets of textile placesets, each set consisting of four items. • dierently colored sets of textile napkins, each set consisting of four items. • pillows for couch and chairs in the living room. • linens, pillows, and coverlets for the bed in the bedroom. • curtains for the bedroom windows. • tablecloths for the dining table. • dierently colored sets of textile placesets, each set consisting of four items. • dierently colored sets of textile placesets, each set consisting of four items. • dierently colored sets of textile napkins, each set consisting of four items. • pillows for couch and chairs in the living room. • linens, pillows, and coverlets for the bed in the bedroom. c⃝2018 by ERL Consumer Revision 1.1 43 B. The ERL Consumer Test bed Contents Object Specication B.11 (Mirrors) The mirror objects to be used include: • a tall mirror, e.g. in the hallway. • a large mirror, e.g. in the bedroom Object Specication B.12 (Lamps) The lamps to be used include: • small lamp(s), e.g. on top of the bedside tables. • oor lamp(s), e.g. in the living room. • oor uplighters, e.g. in the living room. Note that ceiling lamps are already specied with the environment. Object Specication B.13 (Floristic Objects) The oristic objects to be used include: • small plants in pots, e.g. on the bedroom window sill. • herbal plants in pots, e.g. on the kitchen window sill. • large plants in pots, e.g in the living or dining room. • small vases with owers, e.g. on the kitchen counter. • large vases with xerophytes, e.g. on the oor of the living room. Object Specication B.14 (Pictorial Objects) The pictorial objects to be used include: • small framed pieces of photographs or drawings, each sized less than • medium-sized pieces of posters or prints, each sized about A3. • large pieces of paintings or posters, each sized about A1. Object Specication B.15 (Decoration Objects) The decoration objects to be used include: • plates • bowls • triplets of candles. • miniatures or other decorative objects. Revision 1.1 https://github.com/rockin-robot-challenge/rsbb During the benchmarks, a human referee enforces the rules. This referee must have a way to transmit his decisions to the robot, and receive some progress information. To achieve this c⃝2018 by ERL Consumer 44 Revision 1.1 B. The ERL Consumer Test bed Contents in a practical way, an assistant referee is seated at a computer communicating verbally with the main referee. The assistant referee uses the Referee, Scoring and Benchmarking Box (RSBB). Besides basic starting and stopping functionality, the RSBB is also designed to receive scoring input and provide ne grained benchmark control for functionality benchmarks that require so. in a practical way, an assistant referee is seated at a computer communicating verbally with the main referee. The assistant referee uses the Referee, Scoring and Benchmarking Box (RSBB). Besides basic starting and stopping functionality, the RSBB is also designed to receive scoring input and provide ne grained benchmark control for functionality benchmarks that require so. g y The Referee, Scoring and Benchmarking Box was designed to support the following feature Benchmark starting and stopping: Benchmark can only start if robot clock skew is below 100 milliseconds. Stop can be issued manually by the referee, by the robot if it completed the benchmark or automatically by the RSBB if the time for the benchmark is over or if the robot does not declare that it is saving oine data. Benchmark starting and stopping: Benchmark can only start if robot clock skew is below 100 milliseconds. Stop can be issued manually by the referee, by the robot if it completed the benchmark or automatically by the RSBB if the time for the benchmark is over or if the robot does not declare that it is saving oine data. Devices communication: the ERL Consumer competition area includes automated home de- vices such as lights and window blinds. The RSBB provides an interface to control these devices, enabled only in certain benchmarks, so that the robot does not command the devices directly. The assistant referee can control the devices from his graphical interface. Tablet communication: the ERL Consumer competition area includes a tablet device that can be used to communicate with the robot. Tablet communication passes through the RSBB and is enabled only for certain benchmarks. Schedule: the full schedule of the competition is stored in the RSBB, allowing for automated progression with no setup time before each benchmark. B.4.1 Communication between Benchmarking Equipment and Robots For some types of internal benchmarking data (i.e. provided by the robot), logging is done on board the robot, and data are collected after the benchmark (for instance, via USB stick). Other types of internal benchmarking data, instead, are communicated by the robot to the test bed during the benchmark. In such cases, communication is done by interfacing the robot with standard wireless network devices (IEEE 802.11n) that are part of the test bed, and which therefore become a part of the benchmarking equipment of the test bed. However, it must be noted that network equipment is not strictly dedicated to benchmarking: for some benchmarks, in fact, the WLAN may be also (or exclusively) used to perform interaction between the robot and the test bed. Due to the need to communicate with the test bed via the WLAN, all robots participating to the ERL Consumer Competition are required to: 1. possess a fully functional IEEE 802.11n network interface13; 1. possess a fully functional IEEE 802.11n network interface13; 2. be able to keep the wireless network interface permanently connected to the test bed WLAN for the whole duration of the benchmarks 2. be able to keep the wireless network interface permanently connected to the test bed WLAN for the whole duration of the benchmarks https://github.com/rockin-robot-challenge/rsbb Schedule: the full schedule of the competition is stored in the RSBB, allowing for automated progression with no setup time before each benchmark. Online data: data produced by the robot during benchmarks falls in two categories: online and oine. Oine data is saved in a USB stick for latter analysis. Online data is transmitted to the RSBB. The RSBB displays and saves the data. Online data: data produced by the robot during benchmarks falls in two categories: online and oine. Oine data is saved in a USB stick for latter analysis. Online data is transmitted to the RSBB. The RSBB displays and saves the data. Logging: the RSBB saves a full log for each benchmark. Logging: the RSBB saves a full log for each benchmark. Referee interface: the RSBB includes a fully featured graphical interface to be used by the assistant referee. Referee interface: the RSBB includes a fully featured graphical interface to be used by the assistant referee. Single client communication interface: the RSBB includes all features in a single communi- cation interface. This way, participating teams only have to implement one communication mechanism. State information: the RSBB continuously displays what state the benchmark is in. Client libraries are available and should be integrated in the teams software https://github. com/rockin-robot-challenge/at_home_rsbb_comm_ros. This repository also includes the pro- tocol to access the home automation devices and as well as the tablet application. Passwords: a password will be given to each team at the beginning of the competition. These can be used to set up the private communication channel with the RSBB and to get access to the home automation devices. Security note: the password security mechanism is only designed to prevent unintentional honest mistakes from the teams, like accessing the camera over WLAN, while another team is executing a benchmark. Any team caught trying to hack, circumvent or change the behaviour of any component described here for any purpose will be punished. c⃝2018 by ERL Consumer Revision 1.1 45 B. The ERL Consumer Test bed Contents B.5 Networked Devices in the Environment Networked sensors and actuators may be provided as a part of the environment. These devices are as enumerated and described below. (Note: Currently, ERL consumer is not using these networked devices except for possible demos during Local Tournaments in the test beds equipped with them. Furthermore, the use of the xed IP camera at the entrance is no longer permitted for any of the tasks) Home automation controller: This device will run as a server on the local area network within the test bed. It will be accessible from all `permitted' devices (wi-enabled laptop- s/single board computers, etc. on the robots) on the same network. Using this controller, devices such as motorized window blinds/shutters, some of the room lights, motorized tilt- able windows, etc. can be controlled. The controller will be able to receive messages (in a specic format provided to the teams) from the `permitted' devices in order to control all the aforementioned devices. An example of such a controller can be found here14. Ethernet Camera: There will be a standard IP camera mounted a the front door, e.g. to retrieve images from the ringing visitors. The camera can have its parameters (frame rate, resolution, color gains) changed over Ethernet and it is not motor-controlled (no pan-tilt). One way to access the camera is by receiving the MJPEG stream published by the cam- era15. During the setup days, the camera can be congured directly by each team to t the needs (with admin but not root access). The OC/TC will save the conguration of each team and load them before each benchmark. Teams are free to use any protocol or conguration which the camera supports. A ROS package that can be used to acquire images from the camera is available16 Ethernet Camera: There will be a standard IP camera mounted a the front door, e.g. to retrieve images from the ringing visitors. The camera can have its parameters (frame rate, resolution, color gains) changed over Ethernet and it is not motor-controlled (no pan-tilt). One way to access the camera is by receiving the MJPEG stream published by the cam- era15. During the setup days, the camera can be congured directly by each team to t the needs (with admin but not root access). The OC/TC will save the conguration of each team and load them before each benchmark. B.5 Networked Devices in the Environment Teams are free to use any protocol or conguration which the camera supports. A ROS package that can be used to acquire images from the camera is available16. A ROS package that can be used to acquire images from the camera is available16. A ROS package that can be used to acquire images from the camera is available16 The diagram in Fig. 11 illustrates the network infrastructure which will be used throughout the competition. The network consists of the following devices: The diagram in Fig. 11 illustrates the network infrastructure which will be used throughout the competition. The network consists of the following devices: • Server: computer used to manage the network. 13It must be stressed that full functionality also requires that the network interface must not be hampered by electromagnetic obstacles, for instance by mounting it within a metal structure and/or by employing inadequate antenna arrangements. Network spectrum in the Competition area is typically very crowded, and network equipment with impaired radio capabilities may not be capable of accessing c⃝2018 by ERL Consumer Revision 1.1 46 B. The ERL Consumer Test bed Contents AP SMARTIF Server Ethernet Camera Server SMARTIF IO Device1 Switch Ethernet Non-Ethernet Device2 DeviceN (...) Figure 11: Network infrastructure of the ERL Consumer Competition AP Switch Ethernet Camera Figure 11: Network infrastructure of the ERL Consumer Competition • Switch: Ethernet switch used to connect all the devices. • Switch: Ethernet switch used to connect all the devices. • AP: access point where the robot is supposed to connect to. This is the only connec between the robot and the network. • AP: access point where the robot is supposed to connect to. This is the only connection between the robot and the network. • Ethernet Camera: perspective camera outside at the main entrance door. • Devices: dierent devices may exist in the environment, such as a motor to control the window blinds, controlled power plugs, light dimmers or a door bell button. • Devices: dierent devices may exist in the environment, such as a motor to control the window blinds, controlled power plugs, light dimmers or a door bell button. • SMARTIF IO: module to control the dierent devices/sensors existing in the house. They can only be accessed via the SMARTIF server. Teams do not have to interact with each device separately. the test bed WLAN, even if correctly working in less critical conditions. 14http://rollertrol.com/store/en/vera-home-automation-control/87-vera-v3.html 15For example by using http://team_name:PASSWORD@10.0.0.2/mjpg/video.mjpg 16https://github.com/rockin-robot-challenge/at_home_ipcam 17http://www.smartif.com B.5 Networked Devices in the Environment • SMARTIF Server: device which is responsible for the communication between the SMARTIF IO and the network. It can only be accessed from the server. Teams do not have to interact directly with it. Technical details regarding SMARTIF products can be found at the ocial site17. p g 17http://www.smartif.com B.6 Benchmarking Equipment ERL benchmarking is based on the processing of data collected in two ways: ERL benchmarking is based on the processing of data collected in two ways: Internal benchmarking data, collected by the robot system under test (see Section C • Internal benchmarking data, collected by the robot system under test (see Sect • External benchmarking data, collected by the equipment embedded into the test bed. External benchmarking data, collected by the equipment embedded into the test bed External benchmarking data is generated by the ERL test bed in dierent ways depending on their nature. One of the types of external benchmarking data used by ERL are pose data about robots and/or their constituent parts. To acquire these, ERL uses a camera-based commercial motion capture system composed of dedicated hardware and software. Benchmarking data has the form of a time series of poses of rigid elements of the robot (such as the base or a marker mounted in a known position). Pose data are acquired and logged by a customized external software system based on ROS (Robot Operating System): more precisely, logged data is saved as bagles created with the rosbag utility provided by ROS. Other types of external benchmarking data are usually collected using devices that are specic to the benchmark and they are described in the context of the associated benchmark. Equipment c⃝2018 by ERL Consumer Revision 1.1 47 B. The ERL Consumer Test bed Contents to collect external benchmarking data includes any server which is part of the test bed and that the robot subjected to a benchmark has to access as part of the benchmark. Communication between servers and robot is performed via the test bed's own wireless network (see Section C.3). to collect external benchmarking data includes any server which is part of the test bed and that the robot subjected to a benchmark has to access as part of the benchmark. Communication between servers and robot is performed via the test bed's own wireless network (see Section C.3). c⃝2018 by ERL Consumer Revision 1.1 48 C. Robots and Teams Contents Robot Specication C.3 (Sensor Subsystems) Any robot used by a team may use any kind of onboard sensor subsystem, provided that the sensor system is admitted for use in the general public, its operation is safe at all times, and it does not interfere with other teams or the environment infrastructure. A team may use any kind of sensor system provided as part of the environment, e.g. the networked camera specied in Section B.5, by correctly using a wireless communica- tion protocol specied for such purpose and provided as part of the scenario. Sensor systems used for benchmarking and any other systems intended for exclusive use of the organisers are not accessible by the robot system. Any robot used by a team may use any kind of onboard sensor subsystem, provided that the sensor system is admitted for use in the general public, its operation is safe at all times, and it does not interfere with other teams or the environment infrastructure. A team may use any kind of sensor system provided as part of the environment, e.g. the networked camera specied in Section B.5, by correctly using a wireless communica- tion protocol specied for such purpose and provided as part of the scenario. Sensor systems used for benchmarking and any other systems intended for exclusive use of the organisers are not accessible by the robot system. Robot Specication C.1 (Type/Class) A competition entry may use a single robot or multiple robots acting as a team. Robot Specication C.2 (Mobility Subsystems) At least one of the robots entered by a team must be mobile and able to visit dierent task- relevant locations by autonomous navigation. Teleoperation (using touch screens, tablets, mouse, keyboard, etc.) of robots for navigation is not permitted (except when otherwise specied, e.g., in particular instances of task and functionality benchmarks). The robot mobility must work in the kind of environments specied for ERL Consumer and on the kind of oors dened in the ERL Consumer environment specications. C Robots and Teams The purpose of this section is threefold: 1. It species information about various robot features that can be derived from the environ- ment and the targeted tasks. These features are to be considered at least as desirable, if not required for a proper solution of the task. Nevertheless, we will try to leave the design space for solutions as large as possible and to avoid premature and unjustied constraints. 1. It species information about various robot features that can be derived from the environ- ment and the targeted tasks. These features are to be considered at least as desirable, if not required for a proper solution of the task. Nevertheless, we will try to leave the design space for solutions as large as possible and to avoid premature and unjustied constraints. 2. The robot features specied here should be supplied in detail for any robot participating in the competition. This is necessary in order to allow better assessment of competition and benchmark results later on. 2. The robot features specied here should be supplied in detail for any robot participating in the competition. This is necessary in order to allow better assessment of competition and benchmark results later on. 3. It species the benchmarking equipment and data logging facilities required to perform benchmarking. 3. It species the benchmarking equipment and data logging facilities required to perform benchmarking. Robot Specication C.4 (Communication Subsystems) Any robot used by a team may internally use any kind of communication subsystem, provided that the communication system is admitted for use in the general public, its op- eration is safe at all times, and it does not interfere with other teams or the environment infrastructure. A robot team must be able to use the communication system provided as part of the environment by correctly using a protocol specied for such purpose and provided as part of the scenario. Any robot used by a team may internally use any kind of communication subsystem, provided that the communication system is admitted for use in the general public, its op- eration is safe at all times, and it does not interfere with other teams or the environment infrastructure. A robot team must be able to use the communication system provided as part of the environment by correctly using a protocol specied for such purpose and provided as part of the scenario. infrastructure. A robot team must be able to use the communication system provided as part of the environment by correctly using a protocol specied for such purpose and provided as part of the scenario. Robot Constraint C.3 (Environmental Aspects) ( p ) Robots, devices, and apparatus causing pollution of air, such as combustion engines, or other mechanisms using chemical processes impacting the air, are not allowed. Robots, devices, and any apparatus used should minimize noise pollution. In particular, very loud noise as well as well-audible constant noises (humming, etc.) should be avoided. The regulations of the country in which a competition or benchmark is taking place must be obeyed at all times. The event organizers will provide specic information in advance, if applicable. Robots, devices, and any apparatus used should not be the cause of eects that are perceived as a nuisance to the humans in the environment. Examples of such eects in- clude causing wind and drafts, strong heat sources or sinks, stenches, or sources for allergic reactions. Robots, devices, and apparatus causing pollution of air, such as combustion engines, or other mechanisms using chemical processes impacting the air, are not allowed. Robots, devices, and any apparatus used should minimize noise pollution. In particular, Robots, devices, and apparatus causing pollution of air, such as combustion engines, or other mechanisms using chemical processes impacting the air, are not allowed. Robots, devices, and any apparatus used should minimize noise pollution. In particular, very loud noise as well as well-audible constant noises (humming, etc.) should be avoided. The regulations of the country in which a competition or benchmark is taking place must be obeyed at all times. The event organizers will provide specic information in advance, if applicable. Robots, devices, and any apparatus used should not be the cause of eects that are perceived as a nuisance to the humans in the environment. Examples of such eects in- clude causing wind and drafts, strong heat sources or sinks, stenches, or sources for allergic reactions. Robot Specication C.5 (Power Supply) Any mobile device (esp. robots) must be designed to be usable with an onboard power supply (e.g. a battery). The power supply should be sucient to guarantee electrical autonomy for a duration exceeding the periods foreseen in the various benchmarks, before recharging of Revision 1.1 c⃝2018 by ERL Consumer 49 C. Robots and Teams Contents batteries is necessary. Charging of robot batteries must be done outside of the competition environment. The team members are responsible for safe recharging of batteries. If a team plans to use inductive power transmission devices for charging the robots, they need to request permission from the event organizers in advance and at least 3 months before the competition. Detailed specications about the inductive device need to be supplied with the request for permission. Robot Constraint C.2 (Safety and Security Aspects) For any device a team brings into the environment and/or the team area, and which fea- tures at least one actuator of any kind (mobility subsystems, robot manipulators, grasping devices, actuated sensors, signal-emitting devices, etc.), a mechanisms must be provided to immediately stop its operation in case of an emergency (emergency stop). For any device a team brings into the environment and/or the team area, it must guarantee safe and se- cure operation at all times. Event ocials must be instructed about the means to stop such devices operating and how to switch them o in case of emergency situations. Robot Constraint C.1 (Computational Subsystems) Any robot or device used by a team as part of their solution approach must be suitably equipped with computational devices (such as onboard PCs, microcontrollers, or similar) with sucient computational power to ensure safe autonomous operation. Robots and other devices may use external computational facilities, including Internet services and cloud com- puting to provide richer functionalities, but the safe operation of robots and devices may not depend on the availability of communication bandwidth and the status of external services. C.3.1 Setup for the Motion Capture System During all task benchmarks, the pose of the robot will be captured by a motion capture system. For this, a Marker Set, similar to the one depicted in Fig. 12, which was used during the RoCKIn 2014 Competition, will be provided by ERL to be tted on the robot. (a) Perspective view (b) Top view Figure 12: RoCKIn Marker Set used during the RoCKIn 2014 Competition (the motion capture markers are illustrated as red spheres) (b) Top view (b) Top view (b) To (a) Perspective view Figure 12: RoCKIn Marker Set used during the RoCKIn 2014 Competition (the motion capture markers are illustrated as red spheres) As part of robot internal data (see Section C.3.2) Teams must provide the position of the Marker Set in the test bed reference frame together with the robot estimated pose in the same reference frame. To do so, the static transformation between the origin of the reference frame of the base of the robot and the Marker Set, acquired through the motion capture system, will be provided to the Teams during the setup days. The Marker Set will be provided to the Teams in advance with respect to the competition and the Teams require to mount it on the robot so to be above the robot and completely visible from the motion capture system. The robot must avoid collisions between the Marker Set and other objects (when assessing collisions for scoring, the Marker Set is considered as a part of the robot). C.3 Benchmarking Equipment and Data Logging on the Robot Whenever teams are required to install some element provided by ERL on (or in) their robots, such element will be carefully chosen in order to minimize the work required from teams and the impact on robot performance. C.2 Safety Check and Robot Inspection During the set-up days, all robots will be checked by the TC/OC for compliance with the specications and constraints described in Section C.1. Teams will be asked to show the safety mechanisms of their robots and to demonstrate their use. A live demonstration is necessary: for example, pushing an emergency stop button while the robot is moving and verifying that the robot immediately stops. If the robot has other mechanical devices (e.g. a manipulator), their safety must be demonstrated as well. This inspection can be done at any time during the set-up days. When teams are ready for an inspection, they can request one of the TC/OC members. The inspection can be repeated at any time during the competition days, upon request of the TC/OC. Referees, TC/OC members, team members and any other user who is interacting with the robot are always allowed to operate the safety mechanisms when there is a clear risk for the safety of any person or for the damage of any part of the environment. c⃝2018 by ERL Consumer c⃝2018 by ERL Consumer 50 Revision 1.1 C. Robots and Teams Contents Robots that are not considered safe by the TC/OC are not allowed to participate in the competition! Revision 1.1 C.3.2 Internal Data Logging During all task benchmarks, robots are required to log Internal data according to the following specications. This data must be expressed in the reference frame of the test bed which will be clearly marked on it. It will be possible for teams to dene such frame in their robot before the start of the competition. Fig. 13 illustrates one possible position of the test bed reference frame. Only relevant data is expected to be logged (i.e. pointcloud used to recognize an object, more than one if an algorithm requiring multiple pointclouds is used). There are no restriction about the framerate: data can be saved, for the relevant parts of the benchmark, at the rate they are acquired or produced. The log may be a rosbag or the corresponding YAML representation, as c⃝2018 by ERL Consumer Revision 1.1 51 Contents C. Robots and Teams Figure 13: Example of a test bed reference frame for ERL Consumer. The z-axis points towards the reader. Figure 13: Example of a test bed reference frame for ERL Consumer. The z-axis points towards the reader. specied in Section C.4, here we refer to the rosbag version, the corresponding YAML translation should be direct. The list of topics to be logged (i e for all tasks and functionality benchmarks) is reported specied in Section C.4, here we refer to the rosbag version, the corresponding YAML translation should be direct. The list of topics to be logged (i.e., for all tasks and functionality benchmarks) is reported in the following table Topic Type Frame Id Notes /erlc/robot_pose18 geometry_msgs/PoseStamped /map 10 Hz /erlc/marker_pose19 geometry_msgsPoseStamped /map 10 Hz /erlc/trajectory20 nav_msgs/Path /map Each (re)plan /erlc/<device>/image21 sensor_msgs/Image /<device>_frame  /erlc/<device>/camera_info22 sensor_msgs/CameraInfo   /erlc/depth_<id>/pointcloud23 sensor_msgs/PointCloud2 /depth_<id>_frame  /erlc/scan_<id>24 sensor_msgs/LaserScan /laser_<id>_frame 10-40Hz tf25 tf   The format for the name of the bag le to be saved by the Teams on their robot is the following: The 2D robot pose at the oor level, i.e., z = 0 and only yaw rotation. 18The 2D robot pose at the oor level, i.e., z = 0 and only yaw rotation. 19The 3D pose of the marker in 6 degrees of freedom. 20 Trajectories planned by the robot, referred to the robot base, including when replanning. 20Trajectories planned by the robot, referred to the robot base, including when replanning. 19The 3D pose of the marker in 6 degrees of freedom. 20 23Point cloud processed for object perception; <id> is a counter starting from 0 to take into account the fact that multiple depth camera could be present on the robot: e.g., "depth_0", "depth_1", and so on. 24Laser scans, <id> is a counter starting from 0 to take into account the fact that multiple laser range nders could be present on the robot: e.g., "scan_0", "scan_1", and so on. g _ _ 25The tf topic on the robot; the tf tree needs to contain the frames described in this table properly connected through the /base_frame which is the odometric center of the robot. Trajectories planned by the robot, referred to the robot base, including when replanning. 21Image processed for object perception; <device> must be any of stereo_left, stereo_right, rgb; if multiple devices of type <device> are available on your robot, you can append "_0", "_1", and so on to the device name: e.g., "rgb 0", "stereo left 2", and so on. 19The 3D pose of the marker in 6 degrees of freedom. 20Trajectories planned by the robot, referred to the robot base, including when replanning. 21Image processed for object perception; <device> must be any of stereo_left, stereo_right, rgb; if multiple devices of type <device> are available on your robot, you can append "_0", "_1", and so on to the device name: e.g., "rgb_0", "stereo_left_2", and so on. 22Calibration info for /erlc/<device>/image. 23Point cloud processed for object perception; <id> is a counter starting from 0 to take into account the fact that multiple depth camera could be present on the robot: e.g., "depth_0", "depth_1", and so on. 24Laser scans, <id> is a counter starting from 0 to take into account the fact that multiple laser range nders could be present on the robot: e.g., "scan_0", "scan_1", and so on. 25The tf topic on the robot; the tf tree needs to contain the frames described in this table properly connected through the /base_frame which is the odometric center of the robot. g j y _ _ g g multiple devices of type <device> are available on your robot, you can append "_0", "_1", and so on to the device name: e.g., "rgb_0", "stereo_left_2", and so on. 22Calibration info for /erlc/<device>/image. 23Point cloud processed for object perception; <id> is a counter starting from 0 to take into account the fact that multiple depth camera could be present on the robot: e.g., "depth_0", "depth_1", and so on. 18The 2D robot pose at the oor level, i.e., z = 0 and only yaw rotation 19 C.4 YAML Data File Specication The subsequent paragraphs specify the YAML le format that can be converted to ROS bag les. This closely follows the data items described in D-2.1.7 [3]. The YAML format was chosen because it is a simple format, easy to produce without using any special library. Furthermore, the ROS messages format is already dened: as produced by the rostopic echo command. {F|T}BM{H|W}{1|2|3}_YYYYMMDDhhmm_{teamname}.bag {F|T}BM{H|W}{1|2|3}_YYYYMMDDhhmm_{teamname}.bag e.g., FBMH1_201503041356_myteam.bag, TBMH3_201503041156_myteam.bag, etc What data must be saved? Beside the data in the table, additional data the robot must save is specied in the particular benchmark subsection. Please note that some data streams (those with the highest bitrate) must be logged only in the time intervals when they are actually used by the robot to perform the activities required by the benchmark. In this way, system load and data bulk are minimized. For instance, whenever a benchmark includes object recognition activities, video and point cloud data must be logged by the robot only in the time intervals when it is actually performing object recognition. What we do with the data? This data is not used during the competition. In particular, they are not used for scoring. The data are processed by ERL after the end of the competition for in-depth analyses and/or to produce datasets to be published for the benet of the robotics community. Where and when the robot must save the data? Robots must save the data, as specied in the particular benchmark subsection, on a USB stick provided by ERL. The USB stick is given to the team immediately before the start of the benchmark, and must be returned (with the required data on it) at the end of the benchmark. NOTE: while the content of the data les saved by the robot is not used for scoring, the existence of such les and their compliance to the specications does inuence the score of the robot. Teams have the responsibility of ensuring that the required data les are saved, and of delivering them to the referee at the end of the benchmark. These aspects will be noted on the score sheet and considered for team ranking. C.3.2 Internal Data Logging 21 j p y , , g p g 21Image processed for object perception; <device> must be any of stereo_left, stereo_right, rgb; if multiple devices of type <device> are available on your robot, you can append "_0", "_1", and so on to the device name: e.g., "rgb_0", "stereo_left_2", and so on. 23Point cloud processed for object perception; <id> is a counter starting from 0 to take into account the fact that multiple depth camera could be present on the robot: e.g., "depth_0", "depth_1", and so on. 24Laser scans, <id> is a counter starting from 0 to take into account the fact that multiple laser range nders could be present on the robot: e.g., "scan_0", "scan_1", and so on. 24Laser scans, <id> is a counter starting from 0 to take into account the fact that multiple laser range nders could be present on the robot: e.g., "scan_0", "scan_1", and so on. p g , _ , _ , 25The tf topic on the robot; the tf tree needs to contain the frames described in this table properly connected through the /base_frame which is the odometric center of the robot. 25The tf topic on the robot; the tf tree needs to contain the frames described in this table properly connected through the /base_frame which is the odometric center of the robot. c⃝2018 by ERL Consumer 52 Revision 1.1 C. Robots and Teams Contents Revision 1.1 C.4.1 File Format The YAML le should be composed of a single list of messages. Each message should have four items: • topic - The topic name. • topic - The topic name. • secs - Timestamp of the message, in number of seconds since 1970. • nsecs - Nanoseconds component of the timestamp. • message - The message, according to the topic type. The message should be formatted in YAML, according to its structure. This is the same as the output of rostopic echo. However, binary elds may be specied in base 64 encoding for much smaller les. You can copy the le src/base64.hpp to your project, it depends only on boost to encode base 64. And example for a le generated according to above specication could look as follow Revision 1.1 c⃝2018 by ERL Consumer 53 Contents C. Robots and Teams - topic: pose2d secs: 1397024209 nsecs: 156423000 message: x: 5.5 y: 6 theta: 6.4 - topic: image secs: 1397024210 nsecs: 53585000 message: header: seq: 306 stamp: secs: 1397024210 nsecs: 53585000 frame_id: '' height: 4 width: 4 encoding: bgr8 is_bigendian: 0 step: 12 data: !!binary JaU8JY0kGXUIAZ0UDWzgAXjgAb0kIglwbkGsnkWwoiWUfiGUhi2olhmUgc1YRaUw - topic: pose2d secs: 1397024209 nsecs: 156423000 message: !!binary JaU8JY0kGXUIAZ0UDWzgAXjgAb0kIglwbkGsnkWwoiWUfiGUhi2olhmUgc1YRaUw C.4.2 YAML-to-ROSbag Conversion Tool D.1 Safety check Every run of each of the task benchmark will be preceded by a safety-check, outlined as follows: 1. The team members must ensure and inform at least one of the Organizing Committee (OC) or Technical Committee (TC) member, present during the execution of the task, that they have an emergency stop button on the robot which is fully functional. Any member of the OC/TC can ask the team to stop their robot at any time which must be done immediately. 1. The team members must ensure and inform at least one of the Organizing Committee (OC) or Technical Committee (TC) member, present during the execution of the task, that they have an emergency stop button on the robot which is fully functional. Any member of the OC/TC can ask the team to stop their robot at any time which must be done immediately. 2. A member of the OC/TC present during the execution of the task will make sure if the robot complies with the other safety-related rules and robot specications presented in C. 2. A member of the OC/TC present during the execution of the task will make sure if the robot complies with the other safety-related rules and robot specications presented in C. C.4.2 YAML-to-ROSbag Conversion Tool A tool to convert ERL Consumer YAML les into ROS bag les is available at the following Github repository: https://github.com/rockin-robot-challenge/benchmark_and_scoring_converter c⃝2018 by ERL Consumer Revision 1.1 54 D. General Procedure and Scoring for Task Benchmarks Contents D General Procedure and Scoring for Task Benchmarks General procedures, as well as scoring methods, are common to all Task Benchmarks. Those are detailed in this Appendix. D.2 General Procedures This section species the procedures that will be followed for the start, restart or exit of each TBM. All teams are required to perform each task according to the steps mentioned in the rules and procedures sections for the tasks. Revision 1.1 D.2.2 Restart Procedure Within the rst 2 minutes after the robot enters the apartment and within the rst 5 minutes from the start a test, the team can request for a restart. In this case the team is allowed to enter the apartment, bring the robot outside and perform any operation on the robot. It is not allowed to work on the robot inside the apartment (even if it is a quick and simple operation). Whenever the robot is ready, it can re-enter the arena and restart the test. The restart can be done only once for each run of the test. No penalties will be given for a restart. But any score achieved before the restart will be canceled and the time will not be stopped during the restart procedure. D.2.1 Start Procedure The robots must be prepared outside of the apartment, in particular in a preparation area outside at one of the doors that has been designed to start the test. This preparation area is reserved for the next team in the schedule and can be accessed about 5 minutes before the start of the test. Any other preparation must be done at the own team area or in any other location that does not interfere with the competition. The referee will inform the two participating team 2 minutes before the start of the test. After 2 minutes, the referee will start the test, i.e. s/he starts the timer (no delays for any reason). From this moment on, the robot is allowed to enter the apartment. If the robot is not ready and team members are still working on it after the test is started, there will be no penalty. But the time will run on. Whenever the robot enters the apartment, the team is not allowed to operate the robot in any way (e.g., touching any device, using a mouse, keyboard or touch screen, also remotely). In some task benchmarks it may be required that a person, e.g. guides the robot through the environment. In such a case the description of the respective task benchmark will relax the previous rule. Only those actions described in the particular test are allowed inside the apartment. For each test, a desired location that the robot has to reach inside the apartment will be communicated to the teams during the set-up days. Entering the apartment must be done with a natural behavior (no joystick, keyboard, remote control, etc.). Autonomous navigation is the preferred solution, but following a person (e.g. a team member) is also an alternative way to guide the robot into the apartment. Using an easy-to-use interface may be considered as a natural behavior, however this must be approved beforehand by the by TC. In case of non-fully autonomous behaviors, the teams must verify with the TC in advance that their solution is suitable. If a team prepares a behavior which is not within the scope for a particular test, it should contact the TC by e-mail at least one week before the competition. c⃝2018 by ERL Consumer Revision 1.1 55 D. General Procedure and Scoring for Task Benchmarks Contents D.2.3 Exit Procedure After the end of the test, as communicated by the referee(s), the robot must quickly exit the apartment from the door designated for the test (which is usually dierent from the entrance door). The team members are allowed to manually drive, push or lift the robot. A penalty (in terms of an absolute negative score) will be given to the team if the robot is not outside the arena 2 minutes after the end of the test. D.3 Scoring and Ranking Evaluation of the performance of a robot (a.k.a. scoring) in Task Benchmarks is based on performance equivalence classes. The criterion dening the performance equivalence class of robots is based on the concept of tasks required achievements, while the ranking of the robot within each equivalence class is obtained by looking at the performance criteria. In particular: • The performance of any robot belonging to performance class N is considered as better than the performance of any robot belonging to performance class M whenever M < N • Considering two robots belonging to the same class, then a penalization criterion (penalties are dened according to task performance criteria) is used and the performance of the one which received less penalization is considered as better • If the two robots received the same amount of penalization, the performance of the one which nished the task more quickly is considered as better (unless not being able to reach a given achievement within a given time is explicitly considered as a penalty). Performance equivalence classes and in-class ranking of the robots are determined according o three sets: Performance equivalence classes and in-class ranking of the robots are determined according o three sets: • A set A of achievements, i.e. things that should happen (what the robot is expected to do). • A set PB of penalized behaviors, i.e. robot behaviors that are penalized, if they happen, (e.g., hitting furniture). • A set DB of disqualifying behaviors, i.e. robot behaviors that absolutely must not happen (e.g. hitting people). oring is implemented with the following 3-step sorting algorithm: Scoring is implemented with the following 3-step sorting algorithm: 1. If one or more of the elements of set DB occur during task execution, the robot gets disqualied (i.e. assigned to the lowest possible performance class, called class 0), and no further scoring procedures are performed. c⃝2018 by ERL Consumer 56 Revision 1.1 D. General Procedure and Scoring for Task Benchmarks Contents 2. Performance equivalence class X is assigned to the robot, where X corresponds to the number of achievements in set A that have been accomplished. 2. Performance equivalence class X is assigned to the robot, where X corresponds to the number of achievements in set A that have been accomplished. 3. Whenever an element of set PB occurs, a penalization is assigned to the robot (without changing its performance class). 3. c⃝2018 by ERL Consumer D.3 Scoring and Ranking Whenever an element of set PB occurs, a penalization is assigned to the robot (without changing its performance class). One key property of this scoring system is that a robot that executes the required task completely will always be placed into a higher performance class than a robot that executes the task partially. Moreover the penalties do not make a robot change class (also in the case of incomplete task). c⃝2018 by ERL Consumer Revision 1.1 57 E. The ISRoboNet@Home Test Bed at IST Contents E The ISRoboNet@Home Test Bed at IST Bedroom Bathroom O u t s i d e H a l l w a y Inside Hallway Patio C o u c h Center Table T V Kitchen Table Kitchen cabinet Glass-top Dining Table L i v i n g c u m d i n i n g r o o m 3.5 m m 3.0 m 2.0 m 1.0 m 2.5 m 6.0 m 1.0 m 1.75 m 2.50 m 1.5 m A B C D E F G H I A B C D E F G H I 1.75 m 3.50 m 2.50 m 5.00 m 3.50 m 3.00 m 2.00 m 2.50 m 1.50 m a b c d a + b + c + d 1.00 m Width Height 1.50 m 1.00 m * Only wall A is the high wall * A - I in blue are wall segments * a - d in red are doors * doors c,b and d should have a minimum width of 80 cm Arm chair Arm chair chairs chairs chairs chairs Large Double-Bed Side table Side table Wardrobe with mirror Figure 14: Layout and dimensions of the @Home test bed at ISR/IST, Lisbon. E The ISRoboNet@Home Test Bed at IST Bedroom 3.5 m 3.0 m 6.0 D E c Large Double-Bed Side table Side table Wardrobe with mirror Figure 14: Layout and dimensions of the @Home test bed at ISR/IST, Lisbon. Based on the general design and specications of the ERL Consumer test bed detailed pre- viously in this text, in this sub-section we present the exact design specications of the IS- RoboNet@Home test bed installed at the premises of the Institute for Systems and Robotics (ISR) of IST, University of Lisbon. D.3 Scoring and Ranking Note that this test bed is not an exact replica of the actual ERL Consumer Competition test bed but ts its general specications and, as such, can be seen as a concrete example of using them for an actual implementation. Pictures of this test bed are presented in Figures 1517. E.1 Environment Structure and Properties • Ensemble of ve spatial areas accessible to the robots and three others inaccessible. Rooms and spatial areas (accessible to the robot): Living room, dining room, kitchen, inside hallway, bedroom. Spatial areas (inaccessible to the robot): outside hallway, bathroom, patio. • Flat with no stairs • Open-plan architecture followed for the living room, dining room and kitchen. The bed- room is separated by walls. • Open-plan architecture followed for the living room, dining room and kitchen. The bed- room is separated by walls. • Sizes of spatial areas: Please refer to Figure 14. • Sizes of spatial areas: Please refer to Figure 14. Revision 1.1 58 c⃝2018 by ERL Consumer E. The ISRoboNet@Home Test Bed at IST Contents • Connectivity of spatial areas: Same as depicted in Figure 9. • Connectivity of spatial areas: Same as depicted in Figure 9. • Floor: Parquet, well-leveled and uniform all over the test bed. • Walls: Final version not yet in place  will be reported in version 3 of this document. • Ceilings: Uniform false roof made of coated and perforated aluminum segments without slopes. • Ceilings: Uniform false roof made of coated and perforated aluminum segments without slopes. • Bedroom specications (and furniture): one open-able and tilt-able window, a double bed, two side tables, two table lamps and one large wardrobe with mirror. • Bedroom specications (and furniture): one open-able and tilt-able window, a double bed, two side tables, two table lamps and one large wardrobe with mirror. • Living room specication (and furniture's): contains windows that cannot be opened, couch, two armchairs, one coee table, one TV table and one large oor lamp. • Living room specication (and furniture's): contains windows that cannot be opened, couch, two armchairs, one coee table, one TV table and one large oor lamp. • Dining room specication (and furniture's): One glass-top dining table and 2 dining chairs. • Dining room specication (and furniture's): One glass-top dining table and 2 dining chairs. • Kitchen specication (and furniture's): One kitchen table and 2 chairs, kitchen cabinet with multiple drawers and wash sink, two wall-mounted kitchen shelves. • Kitchen specication (and furniture's): One kitchen table and 2 chairs, kitchen cabinet with multiple drawers and wash sink, two wall-mounted kitchen shelves. • Hallway: consists of one coat rack. 26www.ikea.pt 27http://www.cisco.com/c/en/us/products/collateral/wireless/aironet-1140-series/data_ sheet_c78-609338.html 28http://www.axis.com/products/cam_p1344 E.2 Objects in the Environment A list of all objects present in the environment of this test bed is given below through Tables 1 to 3. As most of the objects were purchased from the IKEA furniture store, the IKEA-reference code of the objects are provided to facilitate the readers of this documents. Note that this reference code is from the Portuguese version of IKEA's homepage26. 26www.ikea.pt ikea.pt p://www.cisco.com/c/en/us/products/collateral/wireless/aironet-1140-series/data_ 78-609338.html p://www.axis.com/products/cam_p1344 Table 1: List of task-relevant navigation-related objects in the environment E.3 Network Devices The @Home test bed at IST is equipped with network devices capable of opening/closing the blind and turning on/o the lamps. The network is organized as shown in Figure 11 followed by a description of each block. • Server: A computer used to manage the network. • Switch: An Ethernet switch used to connect all the devices. • AP: An Access Point where the robot is supposed to connect. This is the only connection between the robot and the network. Acts as a bridge between WLAN and LAN. The Access Points used work in Dual-band Standalone 802.11a/g/n. The models used are Cisco AIR - AP1042N-E-K9 27. • Ethernet Camera: Perspective camera facing the Outside Hallway. The camera can have its parameters (frame rate, resolution, color gains) changed over Ethernet and it is not motor controlled (no pan-tilt). The model of the camera can be found here 28. • Devices: Dierent devices may exist in the house. In our test bed the devices are: a motor to control the window blinds, 3 controlled power plugs, 1 light dimmer, and 1 door bell button. c⃝2018 by ERL Consumer 59 Revision 1.1 E. E.3 Network Devices The ISRoboNet@Home Test Bed at IST Contents Task-relevant Objects Navigation-related Object Quantity IKEA Code Size (cm) Ref-code Observations Double bed 1 BRUSALI 140x200 702.499.07 bed-frame 1 BRUSALI 140x200 901.245.34 bars Matress 1 HAFSLO 140x200x18 602.443.64 Slatted bed base 1 SULTAN LÖDINGEN 140x200 401.602.37 Bedside ta- bles 2 BRUSALI 44x36 502.501.57 Wardrobe + mirror 1 BRUSALI 131x190 402.501.67 Rug 1 HAMPEN 80x80 502.037.88 green 1 HAMPEN 80x80 102.037.90 red Coee ta- ble 1 LACK 90x55 401.042.94 black Couch 1 KLIPPAN 100.722.56 couch 1 202.788.55 cover Armchairs 2 PELLO 500.784.64 Bookshelf 1 BORGSJÖ 75x181 cm 002.209.50 shelf 202.209.54 doors in glass Dining ta- ble 1 INGATORP 59/88/117x78 802.214.27 without glass Dining Chairs 3 SIGURD 002.522.48 black 1 KAUSTBY 400.441.96 brown Kitchen cupboard FYNDIG white 1 80x60x86 702.266.80 closet with doors 1 126x60.6 502.375.33 top cover 1 40x60x86 702.266.75 closet with 1 door and 1 drawer 1 70x50 502.021.33 sink 1 SUNDSVIK 800.318.61 tap 2 SATTA 602.700.70 (1 red and 1 transparent) Coat Rack 1 KROGKIG 128 (height) 201.745.08 multi-color 1 HEMNES 185 (height) 002.468.70 black TV table 1 BYAS 160x42x45 802.277.97 with drawers Kitchen Shelf 2 EKBY JARPEN / VALTER 119x28 699.265.93 Glass Din- ing table 1 GLIVARP 75/110x70 802.423.02 with glass Table 1: List of task-relevant navigation-related objects in the environment Task-relevant Objects Revision 1.1 c⃝2018 by ERL Consumer 60 E. The ISRoboNet@Home Test Bed at IST Contents Task-relevant Objects Manipulation-related Object Quantity IKEA Code Ref-code Observations Coee Mugs 8 FÄRGRIK (2) + OMBYTLIG (1) + TECKEN (1) + UNGDOM (1 pack of 4) 401.439.93 + 202.099.80 + 702.160.49 + 702.348.97 Coee cups 6 DINERA 001.525.50 Dessert plates 1 ÖVERENS 202.097.20 (1 pack of 6) Cake plate 1 ARV BRÖLLOP 401.255.50 Small glasses 6 GODIS 800.921.09 Large glasses 6 POKAL + KROKETT 102.704.78 + 201.952.52 Water jug 1 LÖNSAM + VÄNLIG 202.135.43 + 101.316.99 Table 2: List of task-relevant manipulation-related objects in the environment Task-relevant Objects • SMARTIF IO: This module controls the dierent devices/sensors existing in the house. It is prepared to add more devices in case of need. • SMARTIF Server: Device responsible for the communication between the SMARTIF IO mentioned above and the network. It is also where the system congurations (through the SMARTIF Cong Too) are stored and changed. Technical details regarding SMARTIF products can be found at the ocial site 29. 29http://www.smartif.com/smarthome/techspecs.html c⃝2018 by ERL Consumer Revision 1.1 E.3 Network Devices In our network, robots are supposed to communicate with the devices by sending a message to a specic IP and port. A SDK existent on the server will receive that message and transmit it to the SMARTIF IO witch will then control the device. Images from the Ethernet camera are also available through the AP. The quick set-up in the SMARTIF Conguration Tool, along with the possibility of adding/removing more devices, allows us to change the network if needed and with ease. c⃝2018 by ERL Consumer Revision 1.1 61 E. The ISRoboNet@Home Test Bed at IST Contents Non-task-relevant Objects Object Quantity IKEA Code Ref-code Observations Curtains 1 RITVA 145x300 24 - number in the curtains' sec- tion. 1 pack of 2 Table mats 8 102.361.11 Napkins 1 101.012.73 pack of 50 Couch Pillows 3 FJADRAR 400.667.39 inside of the pil- low 1 STOCKHOLM 302.366.76 cover of the pil- low (multi-color, squares) 1 GURLI 202.496.03 cover (plain blue) 1 SVARTTALL 002.897.13 cover (spots) Linien for bed 1 DVALA 401.499.52 1 SVARTTALL 602.911.38 Pillow for bed 2 GOSA VADD 501.291.66 Lamp (small, bed side) 2 KVART 601.524.58 Lamp (oor, liv- ing room) 1 SAMTID 202.865.63 white Plants in pots (small) 3 FEJKA 702.514.72 Plants in pots (large) 1 FEJKA 302.340.07 Small picture frames with pics 6 NYTTJA 601.674.93 Medium pic frames 5 NYTTJA 601.170.35 Large paintings 1 102.340.46 each pack con- tains 3 pics with- out frame Decoration bowl 2 901.244.02 bowl 2 902.508.86 stung for the bowl (dry ow- ers) Triples of can- dles 3 FLORERA 302.514.69 Flower Jar 2 BLOMSTER 301.136.18 jar 12 SNARTIG 101.391.91 owers Table 3: List of Non-task-relevant objects in the environment Table 3: List of Non-task-relevant objects in the environment c⃝2018 by ERL Consumer 62 Revision 1.1 E. The ISRoboNet@Home Test Bed at IST Contents Figure 15: Living room in the @Home test bed at IST Figure 15: Living room in the @Home test bed at IST Figure 16: Living room, kitchen and dining area in the @Home test bed at IST Figure 16: Living room, kitchen and dining area in the @Home test bed at IST c⃝2018 by ERL Consumer Revision 1.1 63 Contents E. The ISRoboNet@Home Test Bed at IST Figure 17: Bedroom in the @Home test bed at IST Figure 17: Bedroom in the @Home test bed at IST c⃝2018 by ERL Consumer Revision 1.1 64 Bibliography [1] (2015) The RoCKIn Wiki. [Online]. Available: http://thewiki.rockinrobotchallenge.eu [2] D. Croce, G. Castellucci, and E. Bastianelli, Structured learning for semantic role labeling. Intelligenza Articiale, vol. 6, no. 2, pp. 163176, 2012. [3] A. Ahmad, I. Awaad, F. Amigoni, J. Berghofer, R. Bischo, A. Bonarini, R. Dwiputra, G. Fontana, F. Hegger, N. Hochgeschwender, L. Iocchi, G. Kraetzschmar, P. Lima, M. Mat- teucci, D. Nardi, V. Schaonati, and S. Schneider, Description of Ground Truth System, Politecnico di Milano, Milan, Italy, Deliverable D-2.1.7 (public), The RoCKIn Project (FP7- ICT-601012 grant agreement number 601012), 2014. 65
https://openalex.org/W2027692179
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0071078&type=printable
English
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The E3 Ligase AtRDUF1 Positively Regulates Salt Stress Responses in Arabidopsis thaliana
PloS one
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Introduction (ABA), an important phytohormone that can protect plants from damage induced by drought, salinity, and pathogenic attack [16,17]. The accumulation of compatible osmolytes such as proline under dehydration conditions allow cells to maintain osmotic balance with the extracellular space and help to protect the activities of the enzyme activity [18]. Ubiquitination is a mechanism of post-translational regulation. The ubiquitination cascade is catalyzed by ubiquitin-activating enzyme (E1), ubuiquitin-conjugating enzyme (E2) and ubiquitin protein ligase (E3). There are .1300 predicted E3 ligases in the Arabidopsis genome, including .450 RING type E3s [1,2]. The vast majority of E3 uibiquitin ligases in the Arabidopsis genome facilitate the identification of specific substrates and their subsequent ubiquitination [1,3]. The E3 ubiquitin ligases are a huge and varied family of proteins and protein complexes which contain either a HECT domain or a U-box/RING domain. The HECT domain subfamily of E3s is relatively small in Arabidopsis. The RING domain subfamily of E3s is large in Arabidopsis and can be further divided into single subunit RING E3s, such as Constitutive Photomorphogenesis1 (COP1) [4], SEVEN IN ABSENTIA IN ARABIDOPSIS THALIANA 5 (SINAT5) [5], and Arm Repeat-Containing 1 (ARC1) [6], and multisubunit RING E3s including the SCF, CUL3-BTB, and APC complexes [7]. The RING E3s typically contain a cross-brace structure formed of eight Cys and His residues that coordinates two zinc ions [8,9,10]. E3 ligases are involved in various aspects of plant biological processes, including growth, development, and protec- tion from biotic and abiotic stresses [11,12]. AtRDUF1 and AtRDUF2 are homologous proteins with a domain-of-unknown-function (DUF) 1117 motif in their C- terminal regions. Both proteins were identified as ABA-, salt-, and drought-inducible RING finger domain-containing E3 ligases [19]. A study using knock-out mutations revealed that AtRDUFs are positive regulators of ABA response and drought tolerance [19]. Here, through the use of overexpression and knock-out materials, we show that AtRDUF1 positively participates in the response of plants to salt stress. Abstract Ubiquitination is an important post-translational protein modification that is known to play critical roles in diverse biological processes in eukaryotes. The RING E3 ligases function in ubiquitination pathways, and are involved in a large diversity of physiological processes in higher plants. The RING domain-containing E3 ligase AtRDUF1 was previously identified as a positive regulator of ABA-mediated dehydration stress response in Arabidopsis. In this study, we report that AtRDUF1 is involved in plant responses to salt stress. AtRDUF1 expression is upregulated by salt treatment. Overexpression of AtRDUF1 in Arabidopsis results in an insensitivity to salt and osmotic stresses during germination and seedling growth. A double knock-out mutant of AtRDUF1 and its close homolog AtRDUF2 (atrduf1atrduf2) was hypersensitive to salt treatment. The expression levels of the stress-response genes RD29B, RD22, and KIN1 are more sensitive to salt treatment in AtRDUF1 overexpression plants. In summary, our data show that AtRDUF1 positively regulates responses to salt stress in Arabidopsis. Citation: Li J, Han Y, Zhao Q, Li C, Xie Q, et al. (2013) The E3 Ligase AtRDUF1 Positively Regulates Salt Stress Responses in Arabidopsis thaliana. PLoS ONE 8(8): e71078. doi:10.1371/journal.pone.0071078 Editor: Miguel A. Blazquez, Instituto de Biologı´a Molecular y Celular de Plantas, Spain Editor: Miguel A. Blazquez, Instituto de Biologı´a Molecular y Celular de Plantas, Spain Editor: Miguel A. Blazquez, Instituto de Biologı´a Molecular y Celular de Plantas, Spain Received March 14, 2013; Accepted June 26, 2013; Published August 12, 2013 Received March 14, 2013; Accepted June 26, 2013; Published August 12, 2013 Received March 14, 2013; Accepted June 26, 2013; Published August 12, 2013 Copyright:  2013 Li 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 by the Program from the Chinese Ministry of Agriculture (2011ZX0 8009-003-002), the Natural Science Foundation of China for the innovation team (31121065) and the Innovation Grant of CAS (KSCX2-EW-N-07-3). 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. * E-mail: xuyy@ibcas.ac.cn Competing Interests: The authors have declared that no competing interests exist. * E-mail: xuyy@ibcas.ac.cn . These authors contributed equally to this work. unhua Li1,2., Yingying Han1,4., Qingzhen Zhao3, Chunhua Li1, Qi Xie3, Kang Chon Junhua Li1,2., Yingying Han1,4., Qingzhen Zhao3, Chunhua Li1, Qi Xie3, Kang Chong1, Yunyuan Xu1* 1 Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China, 2 College of Life Sciences, Henan Normal University, Xinxiang, Henan, China, 3 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China, 4 Key Laboratory of Molecular Biology, College of 1 Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China, 2 College of Life Sciences, Henan Normal University, Xinxiang, Henan, China, 3 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China, 4 Key Laboratory of Molecular Biology, College of Life Sciences, Heilongjiang University, Harbin, Heilongjiang, China Expression pattern of AtRDUF1 p p To investigate the tissue-specific expression pattern of AtR- DUF1, a fusion gene comprising the native AtRDUF1 promoter, a 1.3-kb fragment upstream of the start codon of AtRDUF1 CDS, and the b-glucuronidase (GUS) gene [26] coding sequence as the reporter gene were constructed and transformed into wild-type Arabidopsis. Histochemical staining showed that AtRDUF1 ex- pressed abundantly in seeds, but was also locally detectable in flowers, hypocotyls, leaves and roots (Figure 2). The staining was strong in immature seeds (Figure 2A), whereas in intact desiccated seeds, the GUS expression was only detectable at the funiculus attachment region (Figure 2B). In broken seeds, GUS staining was uniformly presented throughout the seed (Figure 2C), indicating that the limitation of GUS staining in intact seeds was due to blocking by the seed coat. To exclude possible false observations caused by the diffusion of the soluble intermediate of GUS substrates [27,28], seeds were dissected and stained separately. The GUS staining signal could be observed uniformly throughout the embryo, but only in the funiculus attachment region of the seed coat (Figure 2D). During germination, a reduction in GUS staining was detectable early on (Figure 2E–H), which is consistent with the decrease of AtRDUF1 expression detected by real-time qRT-PCR (Figure S2 in File S1). In 4-d-old seedlings, the GUS expression was mainly detected in the junction of the root and hypocotyl, in leaf tips, and around the meristem (Figure 2H). In 2- week old seedlings, the GUS staining was only detectable in leaf tips and root tips (Figure 2I and 2J). In reproductive tissue, The AtRDUF1 protein contains a conserved C3H2C3-type RING domain, which shows similarity with many known proteins in Arabidopsis (Figure 1A), including several proteins known to be involved in ABA and/or stress signaling pathways, such as ABI3- interacting protein 2 (AIP2) [21], SALT- AND DROUGHT- INDUCED RING FINGER 1 (SDIR1) [22] and ATLs [23,24]. One of these homologous proteins, RING finger protein for embryogenesis (RIE1), is required for normal development of seeds [25]. Subcellular studies using a 35S::AtRDUF1:GFP fusion protein in Arabidopsis leaf protoplast cells showed that the fusion protein was mainly found in the cytosol and in the nuclei (Figure 1B). We examined whether AtRDUF1 is an E3 ligase using in vitro methods. E3 Ligase Positively Regulates Salt Responses At5g59550 and At3g46620 were up-regulated 5.5 and 2.9-fold, respectively, after salt treatment for 6–24 h. At5g59550 and At3g46620 were previously designated as AtRDUF2 and AtRDUF1, respectively [19]. Characterization of AtRDUF1 protein Characterization of AtRDUF1 protein In order to identify stress-related genes, we analyzed several publicly available databases of Arabidopsis microarray experiments. A gene family with three genes (At5g59550, At3g46620 and At2g39720) that encode DUF1117 containing RING finger proteins from stress-specific expression profiles in Genevestigator [20] attracted our interest. The microarray data showed that the expression of these genes was up-regulated by several kinds of abiotic stresses. Of particular interest were the data showed that To adapt to stressful conditions such as drought, cold, and salinity, plants have developed redundant and sophisticated response strategies which function throughout their life cycle [13,14,15]. Plants subjected to stress often accumulate abscisic acid August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org 1 E3 Ligase Positively Regulates Salt Responses Expression pattern of AtRDUF1 As shown in Figure 1C, in the presence of E1 and E2, autoubiquitination of MBP:AtRDUF1 can be detected in the presence of E1 and E2 by both nickel-horseradish peroxidase as well as by anti-MBP antibody assay, indicating that AtRDUF1 is an active E3 ligase. A mutant allele with substitution of metal ligand positions Cys-3, His-4, and His-5 of the RING motif with Tyr (CH/Y) was completely inactive (Figure 1C), indicating that an intact RING motif is essential for the E3 ligase activity of AtRDUF1. Figure 1. Analysis of the AtRDUF1 protein. (A) Alignment of the RING finger domains of the AtRDUF1 homologs in Arabidopsis. Black and gray indicate 100% and $50% identities, respectively. (B) Subcellular localization of AtRDUF1:GFP fusion protein in Arabidopsis leaf protoplast cells. Bars represent 20 mm. The green and blue fluorescenece are GFP and 49,6-diamidino-2-phenylindole (DAPI) signals, respectively. (C) Verification of E3 ligase activity of AtRDUF1 by in vitro autoubiquitination assay. CH/Y represents the mutant form of the MBP:AtRDUF1 fusion protein, with substitution of metal ligand positions Cys-3, His-4, and His-5 of the RING motif with Tyr. The numbers at left denote the molecular masses of marker proteins in kilodaltons. Nichel-HRP (Ub), the nickel-horseradish peroxidase used to detect His-tagged ubiquitin. Anti-MBP, the anti-MBP antibody to detect maltose fusion proteins. doi:10.1371/journal.pone.0071078.g001 Figure 1. Analysis of the AtRDUF1 protein. (A) Alignment of the RING finger domains of the AtRDUF1 homologs in Arabidopsis. Black and gray indicate 100% and $50% identities, respectively. (B) Subcellular localization of AtRDUF1:GFP fusion protein in Arabidopsis leaf protoplast cells. Bars represent 20 mm. The green and blue fluorescenece are GFP and 49,6-diamidino-2-phenylindole (DAPI) signals, respectively. (C) Verification of E3 ligase activity of AtRDUF1 by in vitro autoubiquitination assay. CH/Y represents the mutant form of the MBP:AtRDUF1 fusion protein, with substitution of metal ligand positions Cys-3, His-4, and His-5 of the RING motif with Tyr. The numbers at left denote the molecular masses of marker proteins in kilodaltons. Nichel-HRP (Ub), the nickel-horseradish peroxidase used to detect His-tagged ubiquitin. Anti-MBP, the anti-MBP antibody to detect maltose fusion proteins. doi:10.1371/journal.pone.0071078.g001 August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org 2 E3 Ligase Positively Regulates Salt Responses Figure 2. Histochemical localization of GUS activity in AtRDUF1::GUS transgenic plants. (A) Developing seed at 12 days after pollination. (B) Desiccated mature seed. (C) Broken mature seed. (D) Dissected seed after imbibition. Expression pattern of AtRDUF1 (E–H) Germinating seedlings at 1-day (E), 2-days (F), 3-days (G), and 4-days (H) after germination. (I) Leaf. (J) Root. (K) Flower. (L) Pollen. (M) Siliques. Bars represent 0.25 mm in A-D; 0.1 mm in J; 10 mm in L; and 1 mm in E-I, K, and M. doi:10.1371/journal.pone.0071078.g002 Figure 2. Histochemical localization of GUS activity in AtRDUF1::GUS transgenic plants. (A) Developing seed at 12 days after pollination. (B) Desiccated mature seed. (C) Broken mature seed. (D) Dissected seed after imbibition. (E–H) Germinating seedlings at 1-day (E), 2-days (F), 3-days (G), and 4-days (H) after germination. (I) Leaf. (J) Root. (K) Flower. (L) Pollen. (M) Siliques. Bars represent 0.25 mm in A-D; 0.1 mm in J; 10 mm in L; and 1 mm in E-I, K, and M. doi:10.1371/journal.pone.0071078.g002 (CaMV) 35S promoter. Six transgenic lines of AtRDUF1 were obtained (Figure S1D and S1E in File S1). The 35S::AtRDUF1 plants showed a wild-type growth phenotype under normal conditions. AtRDUF1::GUS activity was observed at the junction of carpels and pedicels, as well as in stigma, anthers, and pollen, and low levels were detected in the vascular tissues of sepals and petals (Figure 2K–M). The expression of the AtRDUFs had been shown to be induced by salt treatment [19]. We therefore tested whether AtRDUF1 plays a role in plant responses to salt. Seeds of wild-type (WT), atrduf1atrduf2, atrduf1, and AtRDUF1 overexpression lines were germinated vertically in 1/2 MS medium. 3-day-old seedlings were transferred to 1/2 MS medium supplemented with 110, 120 or 150 mM NaCl. In the control condition, no significant difference in the length of primary roots was observed among any of the materials (Figure 3A and 3D). Under salt stress conditions, the primary roots of 35S::AtRDUF1 seedlings grew faster than did wild-type seedlings, and the atrduf1atrduf2 double mutants showed inhibited growth (Figure 3A and 3D). AtRDUF1 positively regulates plant salt and osmotic stress responses To investigate the function of AtRDUFs, mutants with T-DNA insertions within the exons of the AtRDUFs were obtained and verified (Figure S1A–B in File S1). Expression of the mutant genes was not detected by RT-PCR with primers spanning the T-DNA in the respective homozygous mutants (Figure S1C in File S1). The mutants for AtRDUF1 and AtRDUF2 were named atrduf1-2 and atrduf2-1, respectively (hereinafter called ‘‘atrduf1’’ and ‘‘atrduf2’’). The double mutant atrduf1atrduf2 was generated by crossing. Germinated atrduf1atrduf2, atrduf1 and 35S::AtRDUF1 lines were transplanted to soil for two weeks, and watered with 200 mM We generated transgenic Arabidopsis plants with constitutive expression of AtRDUF1, driven by cauliflower mosaic virus August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org August 2013 | Volume 8 | Issue 8 | e71078 3 E3 Ligase Positively Regulates Salt Responses Figure 3. Salt tolerance of AtRDUF overexpression plants and mutants. (A) WT, atrduf1atrduf2, atrduf1, RDUF1-L1 (Line 1 of 35S::AtRDUF1 transgenic plants), RDUF1-L2 and RDUF1-L3 seedlings with or without salt treatment. 3-day-old seedlings were transferred to 1/2 MS medium containing 0, 110, 120 or 150 mM NaCl, and vertically cultured for 6 days. Bars represent 1 cm. (B) Soil-grown plants under salt treatment. 2-week-old soil-grown plants were treated with 200 mM NaCl for 15 days. (C) Germination of seeds at 10 days after imbibition on medium supplemented with 0, 200, or 250 mM NaCl, respectively. (D-F) Primary root length (D), survival rates (E) and germination rates (F) of materials under the conditions described in (A), (B), and (C), respectively. Data are presented as means 6 SD. Asterisks indicate significance (*, P,0.05 versus WT control). doi:10.1371/journal.pone.0071078.g003 Figure 3. Salt tolerance of AtRDUF overexpression plants and mutants. (A) WT, atrduf1atrduf2, atrduf1, RDUF1-L1 (Line 1 of 35S::AtRDUF1 transgenic plants), RDUF1-L2 and RDUF1-L3 seedlings with or without salt treatment. 3-day-old seedlings were transferred to 1/2 MS medium containing 0, 110, 120 or 150 mM NaCl, and vertically cultured for 6 days. Bars represent 1 cm. (B) Soil-grown plants under salt treatment. 2-week-old soil-grown plants were treated with 200 mM NaCl for 15 days. (C) Germination of seeds at 10 days after imbibition on medium supplemented with 0, 200, or 250 mM NaCl, respectively. (D-F) Primary root length (D), survival rates (E) and germination rates (F) of materials under the conditions described in (A), (B), and (C), respectively. Data are presented as means 6 SD. PLOS ONE | www.plosone.org Discussion In the course of our investigation of likely stress-related genes, we identified AtRDUFs from in silico data. Their putative proteins contain both RING finger and DUF1117 domains, and represent a novel E3 ligase family in plants. Real time qRT-PCR and promoter-GUS analyses confirmed that the transcription of AtRDUF1 was indeed salt inducible (Figure 5B). We analyzed the phenotypes of wild-type as well as overexpression and loss-of- function mutants of AtRDUFs following salt treatment. Our results showed that AtRDUF1 positively regulates plant responses to salt treatment during both germination and post-germination growth (Figure 3). Furthermore, AtRDUF1 also positively regulates plant tolerance to osmotic and dehydration stress (Figure 4). The fluorescence of AtRDUF1:GFP fusion protein was detectable in our subcellular localization study (Figure 1B), and 35S::AtRDUF1 transgenic plants showed obvious tolerance to salt, osmotic, and water loss stresses (Figure 3 and 4). In a similar report, a fusion protein approach was used to develop transgenic plants that overexpressed AtRDUF1. However, the authors were unsuccessful in detecting significant accumulation of the fusion protein, in spite of expression of significant amounts of AtRDUF1 mRNA, so the plants were not extensively analyzed [19]. The discrepancy of detection may be attributable to distinctions in vector efficiency or differences in the sensitivity of the assay methods employed in these independent studies. In addition to the results reported here, AtRDUF1 and AtRDUF2 are also known to be up-regulated by chitin treatment [32]. Among the homologous proteins of the AtRDUFs subfamily, the E3 ligases KEG [12] and AIP2 [21] are negative regulators of ABA signaling, acting by targeting and degrading ABI5 and ABI3, respectively. The E3 ligase SDIR1 positively regulates ABA signaling, and the sdir1 mutant is resistant to salt and drought stress [22]. Therefore, it is apparent that AtRDUFs and their homologous proteins are widely involved in plant adaptations to stress. We were able to confirm that AtRDUF1 has E3 ligase activity by ubiquitination assays (Figure 1C). Ubiquitination has been shown to play an important role in the perception and transduction of various internal and external environmental signals [33,34]. To test whether AtRDUF1 affects the expression of known stress pathway genes, several marker genes in the stress- responsive pathways were analyzed, RD29B, RD22, and KIN1 showed a hypersensitive salt response in transgenic plants (Figure 5A). RD29B is a cold-, high salt-, and dessication-inducible gene with two ABA-responsive elements (ABREs) present in its promoter region [35]. E3 Ligase Positively Regulates Salt Responses E3 Ligase Positively Regulates Salt Responses Water-loss rate is calculated as the ratio between water loss and plant initial fresh weight (FW), expressed in %. Data are presented as means 6 SD. Asterisks indicate significance (*, P,0.05 versus WT control). doi:10.1371/journal.pone.0071078.g004 Water-loss rate is calculated as the ratio between water loss and plant initial fresh weight (FW), expressed in %. Data are presented as means 6 SD. Asterisks indicate significance (*, P,0.05 versus WT control). doi:10.1371/journal.pone.0071078.g004 2 MS agar plates were sprayed with 200 mM NaCl solution, the seedlings were harvested after 1 h and 2 h, for extraction of total RNA. The result showed that in RDUF1-L1 seedlings, the transcription levels of RD29B, RD22, and KIN1 increased more than those of the WT after 2 h of salt treatment (Figure 5A), suggesting that AtRDUF1 may directly or indirectly interact with known abiotic stress response pathways. When the AtRDUF1::GUS transgenic plants were subjected to salt treatment, the GUS staining was enhanced compared with control plants (Figure 5Ba– 5Bd), which is consistent with the real-time qRT-PCR results (Figure 5Be). AtRDUF1 positively regulates plant salt and osmotic stress responses Asterisks indicate significance (*, P,0.05 versus WT control). doi:10.1371/journal.pone.0071078.g003 NaCl solution for 15 days to induce salt stress. 35S::AtRDUF1 seedlings exhibited higher survival rates than did WT seedlings. Contrastingly, the survival rate of the salt treated atrduf1atrduf2 double mutant seedlings was lower than the WT control seedlings (Figure 3B and 3E). NaCl solution for 15 days to induce salt stress. 35S::AtRDUF1 seedlings exhibited higher survival rates than did WT seedlings. Contrastingly, the survival rate of the salt treated atrduf1atrduf2 double mutant seedlings was lower than the WT control seedlings (Figure 3B and 3E). known to be used as an osmotic agent in some studies [29,30,31]. The root growth of 35S::AtRDUF1 seedlings was less severely inhibited by mannitol than that of WT seedlings (Figure 4A and 4B). Therefore, the tolerance of 35S::AtRDUF1 seedlings to salt treatment is at least partly osmotic in nature. After imbibition on 1/2 MS medium containing NaCl and transfer to a growth chamber for 10 days, the germination rates of 35S::AtRDUF1 seeds were higher than that of WT seeds (Figure 3C and 3F). Therefore, the germination ability of AtRDUF1 overex- pression seeds is insensitive to salt treatment. In our salt tolerance tests, no significant difference was observed between WT and the atrduf1 mutant. In contrast with the accelerated water loss in detached leaves of the atrduf1 mutant [19], the water loss of rosette leaves in the overexpression lines was slower than that of WT leaves (Figure 4C). The overexpression plants also showed a sensitive response to ABA in terms of primary root length (Figure S3 in File S1). Our results support that AtRDUF1 positively participates in ABA-mediated dehydration stress responses. Salinity causes ionic and osmotic stresses in plant cells. Germinated transgenic seedlings were transferred to MS medium supplemented with mannitol, a nonmetabolizable sugar, which is We investigated the expression profiles of several stress- responsive genes in the AtRDUF1 overexpression lines grown under salt stress conditions. 10-day-old seedlings grown on 1/ August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org August 2013 | Volume 8 | Issue 8 | e71078 4 Discussion Compared with the mock treated plants (a and c), GUS expression was enhanced in AtRDUF1::GUS plants treated with 300 mM NaCl for 5 h (b and d). (c) and (d) are close-up views of partial regions of (a) and (b), respectively. Transcript expression values of AtRDUF1 were also determined by real-time qRT-PCR in 2-week-old plants treated with 300 mM NaCl (e). Bars represent 1 mm. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control Figure 5. Induction studies of salt-responsive genes and AtRDUF1. (A) Induction profiles of salt-responsive genes in wild-type and AtRDUF1 overexpression plants under salt stress. Transcript levels of RD29B, RD22, and KIN1 were determined by real-time qRT-PCR analysis of seedlings treated with 200 mM NaCl. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control TUBULIN. Asterisks indicate significance (*, P,0.05 versus WT control). (B) Induction of AtRDUF1 expression by salt treatment. Compared with the mock treated plants (a and c), GUS expression was enhanced in AtRDUF1::GUS plants treated with 300 mM NaCl for 5 h (b and d). (c) and (d) are close-up views of partial regions of (a) and (b), respectively. Transcript expression values of AtRDUF1 were also determined by real-time qRT-PCR in 2-week-old plants treated with 300 mM NaCl (e). Bars represent 1 mm. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control TUBULIN. Asterisks indicate significance (*, P,0.05 versus 0 h control). doi:10.1371/journal.pone.0071078.g005 The vegetative tissues of 35S::RDUF1 seedlings contained a higher content of triglycerides (the ester of glycerol) than did WT control tissues (Figure S4C in File S1). Finally, the oleosin maker gene OleS3 and triglycerides content change in response to salt stress (Figure S4D and S4E in File S1). We speculate that a mechanism by which AtRDUF1 increases salt tolerance is through the positively regulation of either the delayed catabolism or the increased accumulation of the storage lipids. region [22,36]. KIN1, which contains the C repeat/dehydration- responsive element (CRT/DRE) motif in its promoter, can be induced by cold, ABA and dehydration treatment [37]. Discussion According to our data and published results [19], AtRDUF1 may be involved in the up-regulation of stress responses in Arabidopsis seedlings, in this respect, AtRDUF1, may be similar to SDIR1 and AtSAP5, both of which have been shown to be E3 ligases and are known in promoting stress gene expression and stress tolerance [22,38,39]. The vegetative tissues of 35S::RDUF1 seedlings contained a higher content of triglycerides (the ester of glycerol) than did WT control tissues (Figure S4C in File S1). Finally, the oleosin maker gene OleS3 and triglycerides content change in response to salt stress (Figure S4D and S4E in File S1). We speculate that a mechanism by which AtRDUF1 increases salt tolerance is through the positively regulation of either the delayed catabolism or the increased accumulation of the storage lipids. Glycerol, a compatible osmolyte, is used in defending against dehydration stresses in yeast, marine algae, insects, and amphib- ians [40,41,42,43]. Accumulation of intracellular glycerol was observed during the salt adaptation processes of many microor- ganism such as Aspergillus nidulans [44] and Aureobasidium pullulans [45]. In Arabidopsis, the results from studies in mutants with defects in storage lipid accumulation prior to seed maturation or lipid catabolism following germination [29,30,31] suggest that glycerol or glycerol-derived lipids could serve as compatible osmolytes in dehydration stress conditions in plants. As AtRDUF1 expressed primarily in embryos of matured seeds (Figure 2), we tested the correlation of AtRDUF1 expression with storage lipids (Text S1 in File S1). In young seedlings, the staining of GUS driven by the AtRDUF1 promoter partially coincided with staining of Sudan red 7B, a fat-soluble dye that stains lipids red, and the Sudan red 7B staining was darker in the 35S::RDUF1 seedlings (Figure S4A in File S1). The levels of triacylglycerol (TAG), the primary seed oil in Arabidopsis were higher in seeds and young seedlings of 35S::AtRDUF1 lines than in WT seedlings (Figure S4B in File S1). In conclusion, our data show that AtRDUF1 is a functional E3 ligase and a positive regulator of the Arabidopsis response to salt stress. This study contributes to our understanding of the molecular factors involved in the responses of plants to abiotic stresses. Plant materials All Arabidopsis plants used in this study were of the Columbia (Col- 0) ecotype. T-DNA insertion lines SALK_131634 (for AtRDUF1) and N471914 (for AtRDUF2) were obtained from ABRC [46] and NASC [47], respectively. Seedlings were grown under long-day conditions (16 h light/8 h dark) at 22uC, 40 to 60% RH and 63 mE?s21?m22 light intensity. Discussion RD22 transcription is induced by salt and ABA treatment, but no ABRE was identified in its promoter Figure 4. Osmotic tolerance and detached leaf water-loss rates of AtRDUF1 overexpression plants. (A) WT, atrduf1atrduf2, atrduf1, RDUF1-L1, RDUF1-L2 and RDUF1-L3 with or without osmotic stress treatment. 3-day-old seedlings were transferred to 1/2 MS medium containing 0, 200, or 350 mM mannitol, and vertically cultured for 6 d. Bars represent 1 cm. (B) Statistical comparison of root lengths of seedlings under the conditions described in (A). (C) Water loss rates of detached leaves. Detached rosette leaves from wild-type and AtRDUF1 overexpression seedlings were incubated for 6 h at room temperature. August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org 5 E3 Ligase Positively Regulates Salt Responses Figure 5. Induction studies of salt-responsive genes and AtRDUF1. (A) Induction profiles of salt-responsive genes in wild-type and AtRDUF1 overexpression plants under salt stress. Transcript levels of RD29B, RD22, and KIN1 were determined by real-time qRT-PCR analysis of seedlings treated with 200 mM NaCl. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control TUBULIN. Asterisks indicate significance (*, P,0.05 versus WT control). (B) Induction of AtRDUF1 expression by salt treatment. Compared with the mock treated plants (a and c), GUS expression was enhanced in AtRDUF1::GUS plants treated with 300 mM NaCl for 5 h (b and d). (c) and (d) are close-up views of partial regions of (a) and (b), respectively. Transcript expression values of AtRDUF1 were also determined by real-time qRT-PCR in 2-week-old plants treated with 300 mM NaCl (e). Bars represent 1 mm. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control TUBULIN. Asterisks indicate significance (*, P,0.05 versus 0 h control). doi:10.1371/journal.pone.0071078.g005 E3 Ligase Positively Regulates Salt Responses Figure 5. Induction studies of salt-responsive genes and AtRDUF1. (A) Induction profiles of salt-responsive genes in wild-type and AtRDUF1 overexpression plants under salt stress. Transcript levels of RD29B, RD22, and KIN1 were determined by real-time qRT-PCR analysis of seedlings treated with 200 mM NaCl. Data represent means 6 SD. Mean values were normalized to the transcript levels of an internal control TUBULIN. Asterisks indicate significance (*, P,0.05 versus WT control). (B) Induction of AtRDUF1 expression by salt treatment. E3 Ligase Positively Regulates Salt Responses E3 Ligase Positively Regulates Salt Responses E3 Ligase Positively Regulates Salt Responses promoter. The primers used for AtRDUF1 overexpression were R1BamHIF and R1KpnIR (all primer sequences used in this study are listed in Table S1 in File S1). The 1.3 kb promoter sequence of AtRDUF1 was amplified with primers R1PKpnIF and R1PBamHIR, and cloned into the pGUS1301 vector [49]. The constructed plasmid was introduced into Agrobacterium tumefaciens strain C58. Arabidopsis was transformed using the floral dip method [50]. Transgenic plants were first screened on medium containing 40 mg/l hygromycin and subsequently transferred to soil. To produce a AtRDUF1:GFP fusion gene driven by 35S promoter, the AtRDUF1 CDS sequence with the stop codon deleted was amplified with primers R1GXhoIF and R1GKpnIR, and cloned in frame into pBI121GFP. To generate the MBP:AtRDUF1 fusion, the AtRDUF1 CDS was cloned in frame into pMAL-c2 (NEB, Berverly, MA, USA) with primers R1MBamHIF and R1MSalIR. A mutant allele with substitution of metal ligand positions Cys-3, His-4, and His-5 of the RING motif with Tyr (CH/Y) was introduced with primers R1mF and R1mR. DpnI mediated site-directed mutagenesis in the plasmid was performed as described previously [51]. promoter. The primers used for AtRDUF1 overexpression were R1BamHIF and R1KpnIR (all primer sequences used in this study are listed in Table S1 in File S1). The 1.3 kb promoter sequence of AtRDUF1 was amplified with primers R1PKpnIF and R1PBamHIR, and cloned into the pGUS1301 vector [49]. The constructed plasmid was introduced into Agrobacterium tumefaciens strain C58. Arabidopsis was transformed using the floral dip method [50]. Transgenic plants were first screened on medium containing 40 mg/l hygromycin and subsequently transferred to soil. To produce a AtRDUF1:GFP fusion gene driven by 35S promoter, the AtRDUF1 CDS sequence with the stop codon deleted was amplified with primers R1GXhoIF and R1GKpnIR, and cloned in frame into pBI121GFP. To generate the MBP:AtRDUF1 fusion, the AtRDUF1 CDS was cloned in frame into pMAL-c2 (NEB, Berverly, MA, USA) with primers R1MBamHIF and R1MSalIR. A mutant allele with substitution of metal ligand positions Cys-3, His-4, and His-5 of the RING motif with Tyr (CH/Y) was introduced with primers R1mF and R1mR. DpnI mediated site-directed mutagenesis in the plasmid was performed as described previously [51]. The water loss assay was performed as described previously [54]. Eight rosette leaves per plant were detached from 3-week-old plants. 2. Stone SL, Hauksdottir H, Troy A, Herschleb J, Kraft E, et al. (2005) Functional analysis of the RING-type ubiquitin ligase family of Arabidopsis. Plant Physiol 137: 13–30. Stress and ABA treatment After surface sterilization, seeds were imbibed at 4uC for 3 d in the dark. The seeds were sown on half-strength Murashige and Skoog medium [53] supplemented with 1% sucrose and 0.7% agar. 3-day-old seedlings were transferred to 1/2 MS medium containing NaCl, mannitol, or ABA. Primary root length was measured after 6 d. 4-day-old seedlings were transplanted to soil and cultured for two weeks, and treated with 200 mM NaCl for 15 days to induce salt stress. For the germination test, all seeds were harvested simultaneously and stored for 5 weeks after harvest. Germination was determined as penetration of the radicle through the seed coat 10 days after imbibition. Each assay was repeated three times. The data in the graphs (Figure 3D-F, 4B– C, S3B, S4C and S4E in File S1) were subjected to analysis of variance (ANOVA) and means were compared by t-test at the 5% level. All analyses were performed with version 13.0 of SPSS software. Acknowledgments We thank Jia Zhao for plant care and Huanhuan Liu for help with microscope. The authors would like to thank two anonymous reviews for their valuable comments and suggestions for improving the quality of this paper. 1. Smalle J, Vierstra RD (2004) The ubiquitin 26S proteasome proteolytic pathway. Annu Rev Plant Biol 55: 555–590. E3 Ligase Positively Regulates Salt Responses The leaves were exposed to air and the fresh weights were measured at the indicated time points shown in Figure 4C. Water- loss rate is calculated as the ratio between water loss and plant initial fresh weight, expressed in %. GUS histochemical assays Tissues of transgenic seedlings harboring AtRDUF1::GUS at various growth stages were used for the GUS activity assays. Fixation of the tissues by acetone and incubation in staining solution was performed as described by Sieburth and Meyerowitz [55]. For staining of pollen, the pollen was isolated from stamens by vortexing in acetone and enriched using centrifugation at rcf 3000. E3 ubiquitin ligase activity assay The MBP:AtRDUF1 fusion protein was expressed in Escherichia coli strain BL21 (DE3), and subsequently purified using amylose resin (NEB). The in vitro E3 ubiquitin ligase activity assay was performed as described previously [5]. Following the assay reactions, proteins were separated by SDS-PAGE, blotted, and probed by either HisDetector Nickel-HRP (KPL company, USA) for the detection of His-tagged ubiquitin or antibody to MBP (antiserum; NEB) for detection of the MBP-tagged AtRDUF1 protein. Results were visualized using chemiluminescence as per the instructions of the manufacturer (ECL; Amersham Pharmacia, Amersham, UK). Author Contributions Conceived and designed the experiments: QX KC YX. Performed the experiments: JL YH QZ CL. Analyzed the data: JL YH QZ CL QX KC YX. Contributed reagents/materials/analysis tools: QZ QX CL. Wrote the paper: JL QZ KC YX. Conceived and designed the experiments: QX KC YX. Performed the experiments: JL YH QZ CL. Analyzed the data: JL YH QZ CL QX KC YX. Contributed reagents/materials/analysis tools: QZ QX CL. Wrote the paper: JL QZ KC YX. Subcellular localization Plasmid 35S::AtRDUF1:GFP and 35S::GFP were purified by the use of Tiangen kits according to the manufacturer’s protocols. Arabidopsis protoplasts transformations were performed as de- scribed previously [52]. For detection of nuclei, samples were stained with DAPI at a final concentration of 1 mg/mL. Expression analysis Total RNA was extracted from tissues with Trizol reagent (Invitrogen, Carlsbad, CA, USA), and treated with RNase-free DNase (Takara, Dalian, China) according to the manufacturer’s instructions. 2 mg of total RNA was used for cDNA synthesis with avian myeloblastosis virus (AMV) reverse transcriptase (Promega, Madison, WI, USA) according to the manufacturer’s protocol. Real-Time qRT-PCR was performed as described previously [56]. Three independent experiments were performed. The relative quantification method (Delta-Delta CT) was used to evaluate variation in expression. Significance of differences was determined by x2-test. The primer sets for PCR were: R1realtimeF and R1realtimeR for AtRDUF1; RD29BF and RD29BR for RD29B; RD22F and RD22R for RD22; KIN1F and KIN1R for KIN1; TubulinF and TubulinR for TUBULIN; OleS3F and OleS3R for OleS3; ACTINF and ACTINR for ACTIN. Supporting Information File S1 Text S1, lipid detection. Figure S1, verification of T-DNA insertion mutants of AtRDUFs and AtRDUF1 overexpres- sion lines. Figure S2, relative quantification of AtRDUF1 transcription during germination assayed by real-time qRT- PCR. Figure S3, response of AtRDUF1 overexpression plants to ABA. Figure S4, effects of AtRDUF1 and salt treatment on plant lipids. Table S1, sequences of the oligonucleotides used in this study. (DOC) Vector construction and Arabidopsis transformation The cDNA of AtRDUF1 was amplified and cloned into the pSN1301 expression vector [48] driven by the CaMV 35S August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org 6 E3 Ligase Positively Regulates Salt Responses p p 18. 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(2007) RNAi knockdown of Oryza sativa root meander curling gene led to altered root development and coiling which were mediated by jasmonic acid signalling in rice. Plant Cell Environ 30: 690–699. E3 Ligase Positively Regulates Salt Responses August 2013 | Volume 8 | Issue 8 | e71078 PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org 8
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Supplementary Figure 6 from Bcl3 Selectively Promotes Metastasis of ERBB2-Driven Mammary Tumors
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Supplementary Figure 2 Bcl3-/-/MMTV/N2 Bcl3+/+/MMTV/N2 Bcl3+/-/MMTV/N2 A Bcl3+/+ N2 Bcl3+/- N2 Bcl3-/- N2 x4 x40 x4 x40 Bcl3-/N2 Bcl3+/N2 Ki67 B Cl. Casp.3 Neu 185kda C Bcl3+/N2 Bcl3-/N2 Tubulin EGFR 175kda 50kda A Bcl3-/-/MMTV/N2 Bcl3+/+/MMTV/N2 Bcl3+/-/MMTV/N2 A Bcl3+/+ N2 Bcl3+/- N2 Bcl3-/- N2 x4 x40 x4 x40 B Bcl3-/N2 Bcl3+/N2 Ki67 B Cl. Casp.3 Neu 185kda C Bcl3+/N2 Bcl3-/N2 Tubulin EGFR 175kda 50kda C
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Focal adhesion protein vinculin inhibits Mef2c-driven sclerostin expression in osteocytes to promote bone formation in mice
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. CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Focal adhesion protein vinculin inhibits Mef2c-driven sclerostin expression in osteocytes to promote bone formation in mice Yishu Wang1#, Jianmei Huang1#, Sixiong Lin2,1#, Lei Qin3, Dingyu Hao1, Peijun Zhang1, Shaochuan Huo1,4, Xuenong Zou2, Di Chen3,5, Guozhi Xiao1* 1Department of Biochemistry, School of Medicine, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen, 518055, China. 2Department of Spine Surgery, Orthopedic Research Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou 510080, China. Orthopedics and Traumatology, Guangzhou 510080, China. 3Department of Orthopedics, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518000, China. 4Research Institute, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen 518000, China. 5Research Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China. #These authors contributed equally to this work. *Address correspondence to: G. X. (email: xiaogz@sustech.edu.cn). . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Keywords: focal adhesion; vinculin; Mef2c; sclerostin; bone formation. Running title: Vinculin regulation of bone formation. . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Abstract The focal adhesion (FA) is the structural basis of the cell-extracellular matrix The focal adhesion (FA) is the structural basis of the cell-extracellular matrix crosstalk and plays important roles in control of organ formation and function. Here we show that expression of FA protein vinculin is dramatically reduced in osteocytes in patients with aging-related osteoporosis. Deleting vinculin using the mouse 10-kb Dmp1-Cre transgenic mice causes a severe osteopenia in both young and aged mice by impairing osteoblast function without affecting bone resorption. Vinculin loss impairs the anabolic response of skeleton to mechanical loading in mice. At the molecular level, vinculin knockdown increases, while vinculin overexpression decreases, sclerostin expression in osteocytes without impacting expression of Mef2c, a major transcriptional regulator of the Sost gene, which encodes sclerostin. Vinculin interacts with Mef2c and vinculin loss enhances Mef2c nuclear translocation and binding to the Sost enhancer ECR5 to promote sclerostin production in osteocytes. Deleting Sost expression reverses the osteopenic phenotypes caused by vinculin loss in mice. We demonstrate that estrogen is a major regulator of vinculin expression in osteocytes and that more importantly vinculin loss mediates estrogen deficiency induction of bone loss in mice. Thus, we demonstrate a novel mechanism through which vinculin inhibits the Mef2c-driven sclerostin expression in osteocytes to promote bone formation. . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Introduction The adult skeleton is a dynamic tissue that undergoes constant bone remodeling, a process during which the osteoclast-mediated bone resorption is closely coupled with the osteoblast-mediated bone formation (Compston, McClung, & Leslie, 2019; X. Feng & McDonald, 2011). Impairment in the bone remodeling process results in osteoporosis characterized with low bone mass and bone fracture (Einhorn & Gerstenfeld, 2015; Wawrzyniak & Balawender, 2022). Understanding the mechanisms behind bone remodeling will advance bone biology research and identify new targets for treating metabolic bone diseases (Wong, Chin, Suhaimi, Ahmad, & Ima-Nirwana, 2016). The adult skeleton is a dynamic tissue that undergoes constant bone remodeling, a process during which the osteoclast-mediated bone resorption is closely coupled with the osteoblast-mediated bone formation (Compston, McClung, & Leslie, 2019; X. Feng & McDonald, 2011). Impairment in the bone remodeling process results in osteoporosis characterized with low bone mass and bone fracture (Einhorn & Gerstenfeld, 2015; Wawrzyniak & Balawender, 2022). Understanding the mechanisms behind bone remodeling will advance bone biology research and identify new targets for treating metabolic bone diseases (Wong, Chin, Suhaimi, Ahmad, & Ima-Nirwana, 2016). The adult skeleton is a dynamic tissue that undergoes constant bone remodeling, a process during which the osteoclast-mediated bone resorption is closely coupled with the osteoblast-mediated bone formation (Compston, McClung, & Leslie, 2019; X. Feng & McDonald, 2011). Impairment in the bone remodeling process results in osteoporosis characterized with low bone mass and bone fracture (Einhorn & The focal adhesion (FA), which consists of integrins, extracellular matrix (ECM), cytoskeleton, kindlin-2, talin, vinculin and other proteins, mediates communication between cells and their environment and plays a central role in regulation of the cell-ECM adhesion, migration, differentiation, survival and mechanotransduction (Calderwood, Campbell, & Critchley, 2013; Larjava, Plow, & Wu, 2008; Ma, Qin, Wu, & Plow, 2008; Montanez et al., 2008; Qin, Liu, Cao, & Xiao, 2020; Qin, Yang, Yi, Cao, & Xiao, 2021; Ussar, Wang, Linder, Fässler, & Moser, 2006; H. Xu, Cao, & Xiao, 2016). Abnormalities in expression and activation of the FA proteins are involved in the pathogenesis and metastasis of cancers (Guo & Wu, 2019, 2020; Lin et al., 2017; Theodosiou et al., 2016; Xue, Xue, Wan, Li, & Shi, 2020; Zhan & Zhang, 2018). More recent studies reveal that FA proteins are critical for control of formation and organs and tissues, including skeleton (Cao et al., 2020; S. Chen et al., 2022; Fu . Introduction CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint 2016; Y. Wang et al., 2019; C. Wu et al., 2015; X. Wu, Cao, & Xiao, 2021; X. Wu et al., 2022), heart (Liang, Sun, & Chen, 2009; Qi et al., 2019; Zhang et al., 2016), 1980; Geiger, 1979). Vinculin is critical for the FA formation and maintenance. Cells overexpressing vinculin assemble large FAs (Janssen et al., 2006; Rodríguez Fernández, Geiger, Salomon, & Ben-Ze'ev, 1993), whereas vinculin-deficient cells form smaller and fewer FAs (Peng, Maiers, Choudhury, Craig, & DeMali, 2012; W. . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Gao et al., 2017). However, the function of vinculin in bone has not been explored. In this study, we demonstrate that mice lacking vinculin in the dentin matrix protein 1 (Dmp1)-positive cells (i.e., osteocytes and mature osteoblasts) display a severe bone loss with impaired bone formation, fail to properly respond to mechanical loading, and do not show further bone loss on estrogen deficiency. Vinculin interacts with Mef2c and vinculin loss increases Mef2c nuclear translocation and binding to the Sost enhancer ECR5 to promote sclerostin production in osteocytes and thereby inhibit bone formation. Results Vinculin is downregulated in osteocytes in human osteoporotic bones and Vinculin is downregulated in osteocytes in human osteoporotic bones and vinculin loss impairs osteocyte adhesion and spreading. vinculin loss impairs osteocyte adhesion and spreading. As an initial attempt to explore the potential involvement of alteration in expression of FA protein vinculin in the pathogenesis of osteoporosis, we collected human bone tissue samples from young (from 29 to 32 years old) and aged individuals (from 78 to 88 years old) and performed immunofluorescence (IF) staining of these bone sections to determine the expression level of vinculin protein. The results showed that osteocytes embedded in the trabecular bone matrix in the young bone samples expressed a high level of vinculin protein, which was drastically decreased in the aged bones (Fig. 1a, b). To gain insights into the function of vinculin in osteocytes, we utilized the CRISPR-Cas9 technology to delete the Vcl gene, which encodes vinculin, in MLO-Y4 osteocyte-like cells. We found that MLO-Y4 cells with deletion of two . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint alleles of the Vcl gene did not grow and die in culture (data not shown). We therefore knocked down (KD) vinculin expression by deleting one allele of the Vcl gene in MLO-Y4 cells. Note: vinculin KD did not markedly affect the expression levels of other FA proteins, such as integrinb1, kindlin-2, talin and pinch1 (Fig. 1c, d), as measured by IF staining and western blotting analyses. Vinculin KD greatly altered the distribution and orientation of filamentous actin (Fig. 1e) and impaired cell spreading in MLO-Y4 cells (Fig. 1f). Deleting vinculin expression in Dmp1-expressing cells causes a low bone mass in mice. To investigate potential role of vinculin in bone, we deleted its expression in the dentin matrix protein 1 (Dmp1)-expressing cells (primarily osteocytes and mature osteoblasts) by breeding the floxed Vcl mice (Vclfl/fl) with the 10-kb mouse Dmp1-Cre transgenic mice (Dmp1-Cre; Vclfl/fl, referred as cKO hereafter). The results from qRT-PCR and western blotting analyses showed that vinculin mRNA and protein expression was significantly reduced in cKO cortical bones compared to that in control bones (Fig. 2a, b). Micro-computed tomography (µCT) analysis of distal femurs from 3- and 14-mo-old male control and cKO mice showed that vinculin loss caused a severe osteopenia at both ages. Vinculin loss significantly decreased the bone mineral density (BMD) (Fig. 2c, d) and bone volume fraction (BV/TV) (Fig. 2c, e) without affecting the cortical thickness (Ct.Th) (Fig. 2f). Consistent with results from µCT analyses, results from H/E staining of tibial sections showed much less . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint trabecular bone mass in cKO mice than that in control mice (Fig. 2g). Similar reductions in BMD (Fig. 2h, i) and BV/TV (Fig. 2h, j) were observed in 3-mo-old male cKO spine (L4-5) compared to those in control mice (Fig. 2h-j). Note: vinculin loss did not affect the bone mass in skull (Fig. 2k). trabecular bone mass in cKO mice than that in control mice (Fig. 2g). Similar Vinculin loss mainly impairs bone formation without markedly impacting bone To investigate mechanism through which vinculin loss causes a low bone mass, we determined the osteoblast and osteoclast formation and function in control and cKO long bones. Results from the double calcein labeling experiments showed that the mineralization apposition rate (MAR) and bone formation rate (BFR) in the femur metaphyseal cancellous bones from 3-mo-old male cKO mice were significantly decreased compared to those in control mice (Fig. 3a-c). The serum level of the procollagen type 1 amino-terminal propeptide (P1NP), a marker of in vivo bone formation(D'Oronzo, Brown, & Coleman, 2017), was significantly lower in cKO mice than that in control mice (Fig. 3d). To determine the effects of vinculin loss on the osteoid production and mineralization, we performed the von Kossa staining of femur sections of control and dKO mice and found that the osteoid volume/tissue volume (OV/TV) and mineralized bone volume/tissue volume (mBV/TV) were decreased in cKO mice relative to those in control mice (Fig. 3e-g). We next performed the colony forming unit-fibroblast (CFU-F) assay and colony forming performed the colony forming unit-fibroblast (CFU-F) assay and colony forming performed the colony forming unit-fibroblast (CFU-F) assay and colony forming . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint unit-osteoblast (CFU-OB) assay. The results showed that the number of CFU-OB, but not that of CFU-F, was reduced in cKO group compared to that in control group (Fig. 3h, i). We further measured the osteoclast formation and bone-resorbing activity in control and cKO mice. The serum levels of collagen type I cross-linked C-telopeptide (CTX), degradation products from type I collagen during in vivo osteoclastic bone resorption(D'Oronzo et al., 2017), were not significantly different between the two genotypes (Fig. 3j). Vinculin loss mainly impairs bone formation without markedly impacting bone Results from TRAP staining of tibial sections showed that the osteoclast surface/bone surface (Oc.S/BS) and osteoclast number/bone perimeter (Oc.Nb/BPm) in both primary and secondary cancellous bones were not markedly altered in cKO mice relative those in control mice (Fig. 3k-o). 3k-o). Vinculin loss increases, while vinculin overexpression decreases, sclerostin expression without affecting the level of Mef2c protein in osteocytes. Sclerostin is encoded by Sost and mainly secreted by osteocytes. Sclerostin decreases osteoblast and bone formation via inhibiting the Wnt/b-catenin signaling. Sclerostin loss or pharmacological neutralization greatly increases bone formation and bone mass (Reid & Billington, 2022). Because the osteoblast and bone formation was severely impaired by vinculin loss in the cKO mice, as demonstrated above, we next determined whether vinculin loss increased sclerostin production in mice. Results from by IHC, RT-qPCR and western blotting analyses revealed that the expression . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint levels of sclerostin mRNA and protein were strikingly increased in cKO versus control osteocytes and bones (Fig. 4a-e). It should be noted that vinculin loss did not markedly alter the level of Mef2c protein in bone extracts (Fig. 4d, e), a major transcriptional regulator of the Sost gene. In contrast, overexpression of vinculin decreased the level of sclerostin in MLO-Y4 cells (Fig. 4f, g). Vinculin interacts with Mef2c and vinculin loss enhances Mef2c nuclear translocation and binding to the Sost enhancer ECR5 in osteocytes. Vinculin interacts with Mef2c and vinculin loss enhances Mef2c nuclear translocation and binding to the Sost enhancer ECR5 in osteocytes. We found that siRNA knockdown (KD) of Mef2c in MLO-Y4 cells reversed the sclerostin upregulation caused by vinculin loss (Fig. 4h, i). Furthermore, vinculin KD decreased the level of cytoplasmic Mef2c and, in the meantime, increased that of its nuclear protein in MLO-Y4 cells, which were reversed by vinculin overexpression (Fig. 4j, k). IF staining revealed that vinculin and Mef2c colocalized in MLO-Y4 cells and that vinculin KD increased Mef2c nuclear translocation in these cells, which was reversed by vinculin overexpression (Fig. 4l). Results from co-immunoprecipitation (Co-IP) experiments demonstrated interactions of endogenous or overexpressed vinculin and Mef2c proteins in MLO-Y4 cells (Fig. 4m-o). Results from ChIP assay using the MLO-Y4 cells revealed that vinculin KD dramatically increased the binding of Mef2c to the Sost enhancer ECR5 (Fig. 4p). Consistent with the fact that sclerostin is a potent inhibitor of the Wnt/b-catenin pathway, the level of active b-catenin, but not that of its total protein, was dramatically reduced in cKO BMSC cultures relative to that in control BMSC dramatically reduced in cKO BMSC cultures relative to that in control BMSC . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint cultures (Fig. 4q). . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Deleting Sost expression in Dmp1-expressing cells reverses the osteopenia induced by vinculin loss. Deleting Sost expression in Dmp1-expressing cells reverses the osteopenia induced by vinculin loss. Above results suggest that the sclerostin upregulation by vinculin loss may play a role in causing the bone loss in cKO mice. To determine if this is the case, we next determined the effects of Sost deletion in Dmp1-expressing cells on the osteopenic phenotypes caused by vinculin loss in mice. We bred the Dmp1-Cre; Vclfl/fl (cKO) mice with Sostfl/fl mice and generated Dmp1-Cre; Vclfl/fl; Sostfl/fl and Dmp1-Cre; Sostfl/fl mice. We performed µCT analyses of the femurs of the indicated groups (Fig. 5a). As expected, Sost loss increased the BMD, BV/TV and Ct.Th (Fig. 5b-d). Importantly, Sost deletion largely reversed the osteopenia of cKO mice (Fig. 5b, c). H/E staining of the tibial sections revealed that Sost ablation reversed the low bone mass in vinculin-deficient mice (Fig. 5e). Sost inactivation similarly reversed the osteopenic phenotypes in spine (L4-L5) in vinculin cKO mice (Fig. 5f-h). Because it is known that sclerostin reduces bone formation by inhibiting Wnt/b-catenin pathway, we measured the bone-forming activity of osteoblasts in vivo by performing the double calcein labeling experiments. As expected, we observed significant increases in the MAR and BFR after Sost inactivation (Fig. 5i-k). Importantly, deleting Sost expression largely restored the impairment in bone formation in cKO mice (Fig. 5i-k). Results from the TRAP staining of tibial sections showed no marked differences in osteoclast formation between the control and cKO mice with and . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint without Sost deletion (Fig. 5l-p). Vinculin loss impairs the anabolic responses of skeleton to mechanical loading It is now widely believed that osteocytes embedded in the mineralizing matrix are the major mechanosensors of bone (Lewis, 2021; Qin et al., 2020). We next examined whether vinculin is involved in the bone mechanotransduction by performing the tibial loading experiments in control and cKO mice (Qin et al., 2022). Results from µCT analyses showed that 2 weeks’ mechanical loading caused significant increases in the BMD, BV/TV and Ct.Th in control tibiae, which were essentially abolished in cKO tibiae (Fig. 6a-d). Results from H/E staining of the tibial sections showed that mechanical loading markedly increased the trabecular volume in control but not cKO mice (Fig. 6e). Mechanical loading significantly increased the values of MAR and BFR in control but not cKO tibiae (Fig. 6f-h). Finally, tibial loading decreased the Oc.Nb/BPm, but not the OC.N/BPm, in control mice, which was lost in cKO mice (Fig. 6i-m). Estrogen loss reduces vinculin expression in osteocytes and ovariectomy no longer causes bone loss in vinculin-deficient mice. Estrogen loss reduces vinculin expression in osteocytes and ovariectomy no longer causes bone loss in vinculin-deficient mice. We next determined vinculin expression in osteocytes in mice with ovariectomy (OVX), which mimics the postmenopausal osteoporosis in humans. Surprisingly, we found that the expression level of vinculin protein was strikingly decreased in . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint osteocytes embedded in the bone matrix in OVX mice (Fig. 7a, b). We next osteocytes embedded in the bone matrix in OVX mice (Fig. 7a, b). We next determined whether estrogen can directly regulate vinculin expression in cultured osteocytes and found that estrogen increased the level of vinculin protein in MLO-Y4 cells in a dose-dependent manner (Fig. 7c, d). In contrast, fulvestrant, an estrogen receptor antagonist, decreased the level of vinculin protein in MLO-Y4 cells (Fig. 7c, e). We next compared the effects of OVX on reduction of bone mass in control and vinculin cKO mice. To this end, 3-month-old control and vinculin cKO female mice were subjected to sham or OVX surgery, as we previously described (Fu et al., 2020). At two months after surgery, the bone mass was reduced in control mice, which is expected. Shockingly, the OVX-induced trabecular bone loss was dramatically reduced (BV/TV) or completely abolished (BMD) in cKO mice (Fig. 7f-i). While OVX did not markedly impact the MAR and BFR in both control and cKO mice (Fig. 7k-m), it caused dramatic increases in the OC.S/BS and OC.N/BPm in control mice, which were lost in vinculin cKO mice (Fig. 7n-r). Discussion We summarize the main findings of the present study as follows. First, the expression of FA protein vinculin is drastically reduced in osteocytes in patients with age-related osteoporosis and in mice with estrogen deficiency. Second, deleting vinculin in Dmp1-expressing cells, i.e., primarily osteocytes and mature osteoblasts, causes a severe bone loss in both young and aged mice. Third, vinculin deletion impairs the bone mechanotransduction in mice. Fourth, vinculin expression in osteocytes is . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint critically involved in estrogen control of bone mass in mice. Finally, vinculin regulates osteocyte adhesion and inhibits sclerostin expression to promote bone formation. critically involved in estrogen control of bone mass in mice. Finally, vinculin regulates osteocyte adhesion and inhibits sclerostin expression to promote bone formation. In this study, we demonstrate that vinculin increases bone mass and BMD by primarily promoting bone formation. Thus, vinculin loss in osteocytes and mature osteoblasts dramatically decreased the values of serum P1NP, BFR, MAR, OV/TV and mBV/TV, all osteoblastic parameters. These impairments lead to reduced bone formation and severe osteopenia. Of note, vinculin loss does not markedly alter osteoclast formation (OC.S/BS and OC.N/BPm) and bone resorption (serum CTX-1). This result on osteoclast formation is similar to that in mice lacking the other FA proteins pinch1/2 in Dmp1-expressing cells (Y. Wang et al., 2019), but in contrast to those in mice with deletion of FA protein kindlin-2 in the same cell type, which displayed increased osteoclast formation and bone resorption in part due to enhanced Rankl production in osteocytes (Cao et al., 2020). The reason(s) for this discrepancy are not clear. Our findings from this study strongly suggest that vinculin inhibits sclerostin expression in osteocytes and mature osteoblasts to promote the osteoblast-mediated bone formation. Our in vitro and in vivo results demonstrate that vinculin-deficient osteocytes produce a large amount of sclerostin protein, which inhibits binding of Wnt ligands to the LRP5/6 receptors and, thereby, the Wnt/b-catenin signaling. The latter is a major player in control of the bone mass accrual in vertebrates. Consistently, vinculin loss reduces the level of active b-catenin protein and CFU-OB formation in . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint bone marrows and bone formation in mice. Of particular significance, deleting Sost expression in Dmp1-expressing cells essentially reverses the low bone mass caused by vinculin loss. Thus, we provide important genetic evidence that FA protein vinculin plays a critical role in promoting bone formation by facilitating the Wnt/b-catenin signaling in osteoblastic cells. critically involved in estrogen control of bone mass in mice. Finally, vinculin regulates osteocyte adhesion and inhibits sclerostin expression to promote bone formation. At the molecular level, we provide intriguing evidence that vinculin loss promotes Sost expression through, at least in part, Mef2c, a major transcriptional regulator of the Sost gene (Collette et al., 2012; Kramer, Baertschi, Halleux, Keller, & Kneissel, 2012). Importantly, upregulation of sclerostin expression induced by vinculin loss is largely reversed by Mef2c KD in osteocytes. While vinculin loss does not alter the expression level of total Mef2c protein in osteocytes, it increases the Mef2c nuclear translocation and binding to the Sost enhancer ECR5. It is known that Mef2c binding to this enhancer is critical for Sost expression in osteocytes (Leupin et al., 2007). Our results suggest that binding of vinculin to Mef2c prevents the Mef2c nuclear translocation by retaining it in the cytoplasm. While estrogen deficiency causes the postmenopausal osteoporosis, its mechanism(s) remain incompletely understood. We demonstrate that OVX mice express an extremely low level of vinculin protein in osteocytes in bone. Of particular significance, mice lacking vinculin in osteocytes are resistant to OVX-induced bone loss. We find that estrogen directly increases vinculin expression in osteocytes. While estrogen deficiency causes the postmenopausal osteoporosis, its mechanism(s) remain incompletely understood. We demonstrate that OVX mice express an extremely low level of vinculin protein in osteocytes in bone. Of particular significance, mice lacking vinculin in osteocytes are resistant to OVX-induced bone loss. We find that estrogen directly increases vinculin expression in osteocytes. Collectively, these results suggest that estrogen signaling favors bone formation by in part inducing vinculin expression in osteocytes. This knowledge improves our Collectively, these results suggest that estrogen signaling favors bone formation by in part inducing vinculin expression in osteocytes. This knowledge improves our . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint understanding of the molecular mechanism(s) underlying the postmenopausal osteoporosis. understanding of the molecular mechanism(s) underlying the postmenopausal osteoporosis. Mechanical force is the most potent anabolic stimulus for bone formation. Mechanical force is the most potent anabolic stimulus for bone formation. Osteocytes, the most abundant ed cells embedded in the mineralizing matrix in bone, are now believed to be the major sensor and mediator of mechanotransduction in bone (Qin et al., 2020). In this study, we demonstrate that vinculin expression in osteocytes is essential for skeletal response to mechanical loading to increase bone formation. It should be noted that loss of other FA proteins Kindlin-2 or pinch in osteocytes caused a similar defect in the anabolic effects of mechanical loading on bone in mice (Qin, Fu, et al., 2021; Y. Wang et al., 2019). Collectively, these results suggest a critical role of the FA signaling pathway in mediation of the mechanotransduction in bone. Notably, previous studies demonstrate that mechanical force promotes vinculin activation through conformational changes and a loss of tension causes vinculin to be rapidly inactivated (Carisey et al., 2013). Finally, we propose a working model regarding how FA protein vinculin expression in osteocytes embedded in the bone matrix controls bone formation (Fig. 8). In young and adult animals, vinculin is highly expressed in osteocytes where it, probably together other FA proteins, such as talin and actin, forms a complex with Mef2c in the cytoplasm. Complex formation prevents the nuclear translocation of Mef2c, leading to reduced expression and production of sclerostin and, thereby, increased bone formation. In contrast, in the presence of vinculin deficiency in osteocytes, which is related to aging and estrogen deficiency, the nuclear translocation . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint of Mef2c and its binding to the Sost enhancer ECR5 are enhanced, thus stimulating Sost expression and inhibiting bone formation. understanding of the molecular mechanism(s) underlying the postmenopausal osteoporosis. In summary, in this study, we demonstrate that vinculin plays an important role in control of bone formation and may be a useful target for the prevention and treatment of aging and estrogen deficiency induced osteoporosis. Tissue samples Human cancellous tissues and their corresponding adjacent normal controls were collected from the Shenzhen Hospital of Guangzhou University of Chinese Medicine. Written informed consent was obtained from all patients. The study has been approved by the Shenzhen Hospital of Guangzhou University of Chinese Medicine, China (NO. GZYLL(KY)-2022-027). Specimens were collected and stored in formaldehyde after surgery. Animal studies Dmp1-Cre mice were generously provided by Dr. Jian Q Feng (Baylor College of Dentistry) (J. Q. Feng et al., 2003). Vcl fl/fl mice were purchased from the Jackson Laboratory. The experimental animals used current studies were obtained using a 2-step breeding strategy. Homozygous Vcl fl/fl mice were first crossed with Dmp1-Cre transgenic mice to generate Dmp1-Cre; Vcl fl/+ mice. These offspring were then crossed with Vcl fl/fl to generate Dmp1-Cre; Vcl fl/fl mice. The generation of the Dmp1-Cre; Vcl fl/fl; Sost fl/fl mice was as follow: Dmp1-Cre; Vcl fl/fl mice were first crossed with Sostfl/fl mice to generate Dmp1-Cre; Vcl fl/+; Sost fl/+ mice. These offspring were then intercrossed with Vcl fl/fl; Sost fl/fl mice to generate the Dmp1-Cre; Vcl fl/fl; Sost fl/fl mice and other genotypes. In vivo tibial loading experiments were performed as previously described (Qin, Fu, et al., 2021). All animal experiments in this study were approved by the Institutional Animal Care and Use Committees (IACUC) of the Southern University of Science and Technology. . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Micro-computerized tomography (µCT) analysis Fixed non-demineralized femur, tibia, spine or skull were used for µCT analysis in the Experimental Animal Center of Southern University of Science and Technology using a Bruker µCT (SkyScan 1176 Micro-CT, Bruker MicroCT, Kontich, Belgium) following the standards of techniques and terminology recommended by the American Society for Bone and Mineral Research (ASBMR) (Bouxsein et al., 2010). BMSC culture Primary bone marrow stromal cells (BMSC) were isolated from femurs of 3-month-old male mice as previously described (Yan, Gao, Yao, Ling, & Xiao, 2022). Briefly, bone marrow cells were cultured on 60-mm cell culture dishes in a-MEM (Hyclone, USA) containing 15% FBS. After 48 h, the non-adherent cells were removed. On the seventh day, the cells trypsinized for subsequent experiments. Colony forming unit-fibroblast (CFU-F) assay and colony forming unit-osteoblast (CFU-OB) assay were performed as we previously described (Lei et al., 2020). Histological evaluation and bone histomorphometry For histology, bone tissues were fixed in 4% paraformaldehyde (PFA) at 4oC for 24 h, decalcified in 10% EDTA (pH 7.4) for 21 d, and embedded in paraffin after dehydration. Bone sections were used for hematoxylin and eosin (H/E) and tartrate-resistant acid phosphatase (TRAP) staining using our standard protocols (Y. Wang et al., 2019; C. Wu et al., 2015). . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Immunohistochemistry (IHC) and immunofluorescence (IF) staining For IHC staining, 5-µm sections were stained with antibodies or control IgG using the EnVision+System-HRP (DAB) kit (Dako North America Inc, Carpinteria, CA, USA) as previously described (Cao et al., 2020). IF staining of bone sections and MLO-Y4 cells was performed as we previously described (Zhu et al., 2020). Western blot analysis Western blot analysis was performed as previously described (Y. Wang et al., 2021). Briefly, whole-cell lysates were prepared in RIPA lysis buffer (Sigma, USA) and aliquots of 15 µg protein were separated by SDS-PAGE and blotted onto a polyvinylidene fluoride (PVDF) membrane (Millipore, MA, USA). Membranes were blocked at room temperature for 15 min in QuickBlock™ Western (Beyotime), Western blot analysis was performed as previously described (Y. Wang et al., 2021). Briefly, whole-cell lysates were prepared in RIPA lysis buffer (Sigma, USA) and aliquots of 15 µg protein were separated by SDS-PAGE and blotted onto a polyvinylidene fluoride (PVDF) membrane (Millipore, MA, USA). Membranes were blocked at room temperature for 15 min in QuickBlock™ Western (Beyotime), followed by an overnight incubation at 4 °C with specific antibodies. After incubation with appropriate HRP-conjugated secondary antibodies (ZSGB-bio), blots were developed using an enhanced chemiluminescence (ECL Kit, BIORAD) and exposed in ChemiDoc XRS chemiluminescence imaging system. Antibodies used in this study are listed in Supplementary Table 2 followed by an overnight incubation at 4 °C with specific antibodies. After incubation with appropriate HRP-conjugated secondary antibodies (ZSGB-bio), blots were developed using an enhanced chemiluminescence (ECL Kit, BIORAD) and exposed in ChemiDoc XRS chemiluminescence imaging system. Antibodies used in this study are listed in Supplementary Table 2 RNA extraction and qRT-PCR analysis RNA isolation and quantitative real-time RT-PCR analysis were performed as we previously described (H. Gao et al., 2019). The specific primers for gene expression analysis were listed in Supplementary Table 1. ELISA assays Serum levels of P1NP were measured using the RatLaps EIA Kit (cat# AC-33F1) according to the manufacturer’s instruction (Immunodiagnostic Systems Limited). Serum levels of CTX, degradation products from type I collagen during osteoclastic bone resorption, were measured using the RatLaps EIA Kit (cat# AC-06F1) according to the manufacturer’s instruction (Immunodiagnostic Systems Limited). . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Co-immunoprecipitation (Co-IP) assay Co-IP assay was performed as previously described (Fu et al., 2020). Briefly, cells were incubated for 10 min at 4 °C in RIPA buffer (Sigma, USA). After a centrifugation at 12,000 × g for 10 min at 4 °C, the supernatant was first incubated with corresponding primary antibody overnight and then with Protein A/G Magnetic Co-IP assay was performed as previously described (Fu et al., 2020). Briefly, cells were incubated for 10 min at 4 °C in RIPA buffer (Sigma, USA). After a . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Beads at room temperature for 1 h. DynaMag™-2 Magnet (Thermo Fisher) was used to collect dynabeads-antigen-antibody complex. The complex was washed with IP buffer three times and resuspended with 60 µl 1× loading buffer and cooked at 95 °C for 5 min, followed by SDS-PAGE and western blotting. Chromatin immunoprecipitation (ChIP) assay ChIP assay was performed using the ChIP Kit (Abcam, ab500) as previously described (X. Wang et al., 2020). Briefly, 1 × 107 cells were collected in lysis buffer and sonicated to generate chromatin samples with average fragment sizes of 100–500 bp. Cell lysates were incubated with the indicated antibodies or IgG overnight at 4°C. Then, the supernatants were mixed with the blocked Protein A/D sepharose beads to collect the antibody–chromatin complexes. After washing 4 times, the immunoprecipitated DNA was eluted and purified for the subsequent qPCR analysis. Statistical Analyses The sample sizes for all experiments conducted in this study were determined based on our previous experience on similar studies. Mice used in this study were randomly grouped. The IF, IHC and histology were conducted and analyzed under double-blind conditions. Statistical analyses were completed using the Prism GraphPad. Two-way ANOVA and unpaired two-tailed Student’s t-test was used as indicated. P < 0.05 was considered statistically significant. . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Data availability All data generated or analysed during this study are included in the manuscript and supporting file; Source Data files have been provided for Figures. . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Acknowledgments The authors acknowledge the assistance of Core Research Facilities of Southern University of Science and Technology. This work was supported, in part, by the National Key Research and Development Program of China Grant (2019YFA0906004), the National Natural Science Foundation of China Grants (82230081, 82250710175, 81991513, 81630066, 81870532, 82004395), the China Postdoctoral Science Foundation (2021M691435) and the Guangdong Provincial Science and Technology Innovation Council Grant (2017B030301018). Author contributions: Study design: GX and YW. Conducting study, data collection and analyses: YW, JH, SL, LQ, DH, PZ and SH. Data interpretation: GX, YW, XZ and DC. 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Xiao, G. (2020). Kindlin-2 modulates MafA and β-catenin expression to regulate β-cell function and mass in mice. Nat Commun, 11(1), 484. doi:10.1038/s41467-019-14186-y . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Figure 1. Vinculin regulates osteocyte adhesion and is downregulated in Figure 1. Vinculin regulates osteocyte adhesion and is downregulated in osteocytes in human osteoporotic bones. a, b Immunofluorescence (IF) staining and hematoxylin and eosin (H/E) staining. Sections of human cancellous samples from young (29-32-yrs-old) and old 78-88-yrs-old) subjects were subjected to H/E and IF staining with a vinculin antibody. Scale bars: 50 µm. Quantitative data (b). Results were expressed as mean ± s.d. N = 3 biologically independent replicates per group, **P < 0.01 versus young, unpaired two-tailed Student’s t test. c Western blot analysis. Protein extracts isolated from MLO-Y4 osteocyte-like cells with and without vinculin knockdown (KD) by CRISPR-Cas9 technology were subjected to western blotting using the indicated antibodies. d IF staining. MLO-Y4 cells with and without vinculin KD were subjected to IF staining using phalloidin or DAPI. e IF staining. MLO-Y4 cells with and without vinculin KD were subjected to IF staining using the indicated antibodies. f Cell adhesion assay. MLO-Y4 cells with and without vinculin KD were seeded in a 96-well plate at a density of 1×105 cells/well. The absorbance was measured at the time points of 0.5h, 1h, 3h, 6h and 12h, respectively. Results were expressed as mean ± s.d., **P < 0.01, ***P < 0.001 versus controls, unpaired two-tailed Student’s t test. two-tailed Student’s t test. Figure 2. Vinculin loss in Dmp1-expressing cells causes severe osteopenia by impairing bone formation in mice. a Real-time RT-PCR (qPCR) analyses. Total RNAs isolated from the indicated tissues of 3 mo-old male control (con) and cKO . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint mice were used for qPCR analysis for expression of Vcl gene, which was normalized to Gapdh mRNA. Results were expressed as mean ± s.d., N = 3 biologically independent replicates per group, **P < 0.01 versus controls, unpaired two-tailed Student’s t test. b Western blot analysis. Figure 1. Vinculin regulates osteocyte adhesion and is downregulated in Protein extracts were isolated from the indicated tissues of the control and cKO mice were subjected to western blotting analysis for vinculin expression. Gapdh was used for loading control. c Three-dimensional (3D) reconstruction from micro-computerized tomography (µCT) scans of distal femurs from male control and cKO mice with the indicated ages. d-f Quantitative analyses of the bone volume/tissue volume (BV/TV), cortical thickness (Ct.Th) and bone mineral density (BMD) of distal femurs from male control and cKO mice with the indicated ages. Results were expressed as mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05, **P < 0.01, ***P < 0.001 versus controls, unpaired two-tailed Student’s t test. g H/E staining of tibial sections of 3-mo-old male control and cKO mice with the indicated ages. h 3D reconstruction from µCT scans of spine (L4, L5) from 3-mo-old male control and cKO mice. i, j Quantitative analyses of the bone volume/tissue volume (BV/TV) and bone mineral density (BMD) of spine from male control and cKO mice. Results were expressed as mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05, **P < 0.01 versus controls, unpaired two-tailed Student’s t test. k 3D reconstruction from µCT scans of skull. . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint affecting the osteoclast formation and bone resorption. a-c Calcein double labeling affecting the osteoclast formation and bone resorption. a-c Calcein double labeling. Representative images of 3-mo-old male control and cKO femur sections (a). Sections of non-demineralized femurs of 3-mo-old male control and cKO mice were used for measurements of the mineral apposition rate (MAR) and bone formation rate (BFR). Quantitative MAR (b) and BFR (c) for the metaphyseal trabecular bones of the two genotypes. Scale bar, 50 µm. Results were expressed as mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05, **P < 0.01 versus controls, unpaired two-tailed Student’s t test. d Serum level of procollagen type 1 amino-terminal propeptide (P1NP). Sera harvested from 3-mo-old male control and cKO mice were subjected to ELISA assay for P1NP. Results were expressed as mean ± s.d., N = 6 biologically independent replicates per group, **P < 0.01 versus controls, unpaired two-tailed Student’s t test. e-g von Kossa staining. Undecalcified sections of femora from 3-mo-old male control and cKO mice were subjected to von Kossa staining (e). Quantitative OV/TV (osteoid volume/tissue volume) (f) and mBV/TV (mineralized bone volume/tissue volume) (g) data for the cancellous bones from distal femora were measured by bone morphometry. Scale bar, 50 µm. Results were expressed as mean ± s.d., N = 5 biologically independent replicates per group, *P < 0.05, **P < 0.01 versus controls, unpaired two-tailed Student’s t test. h Colony forming unit-fibroblast (CFU-F) assays. Bone marrow nucleated cells from 3-mo-old male control and cKO mice were seeded in a 6-well plate with a cell density of 2x106 . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint 14 days, followed by Giemsa staining. i Colony forming unit-osteoblast (CFU-OB) assays. affecting the osteoclast formation and bone resorption. a-c Calcein double labeling Bone marrow nucleated cells from 3-mo-old male control and cKO mice were seeded in a 6-well plate with a cell density of 4x106 per well and cultured in osteoblast differentiation medium (complete a-MEM containing 50 µg/ml L-ascorbic acid and 2.0 mM b-glycerophosphate) for 21 d and media were changed every 48h, followed by alizarin red staining. j Serum level of collagen type I cross-linked C-telopeptide (CTX). Sera collected from 3-mo-old male control and cKO mice were subjected to ELISA assay for CTX. Results were expressed as mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05 versus controls, unpaired two-tailed t test. k-o Tartrate-resistant acid phosphatase (TRAP) staining. Tibial sections of 3-mo-male control and cKO mice were used for TRAP staining (k). Osteoclast surface/bone surface (Oc.S/BS) (l, m) and osteoclast number/bone perimeter (Oc.N/BPm) (n, o) of primary and secondary cancellous bones were measured using Image-Pro Plus 7.0. Scale bar, 50 µm. Results were expressed as mean ± s.d., N = 7 biologically independent replicates per group, *P < 0.05 versus controls, unpaired two-tailed Student’s t test. Figure 4. Vinculin interacts with Mef2c and vinculin knockdown increases Mef2c nuclear translocation and binding to the Sost enhancer ECR5 to promote sclerostin expression in osteocytes. a, b Immunohistochemical (IHC) staining. Tibial sections of 3-mo-old male control and cKO mice were stained with an anti-sclerostin antibody. Quantitative data (b). N = 5 biologically independent Figure 4. Vinculin interacts with Mef2c and vinculin knockdown increases . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint replicates per group, **P < 0.01, versus controls, unpaired two-tailed Student’s t test. c qPCR analyses. Total RNA isolated from cortical bone of 3 mo-old male mice was used for qPCR analysis for expression of Sost gene, which was normalized to Gapdh mRNA. Results were expressed as mean ± s.d., N = 5 biologically independent replicates per group, ***P < 0.001 versus controls, unpaired two-tailed Student’s t test. d, e Western blot analyses. Protein extracts isolated from cortical bones of 3 mo-old male mice were subjected to western blotting using the indicated antibodies. Results were expressed as mean ± s.d., N = 3 biologically independent replicates per group, **P < 0.01 versus controls, unpaired two-tailed Student’s t test. f, g Vinculin overexpression. Protein extracts isolated from MLO-Y4 cells transfected with control or vinculin-expressing plasmid were subjected to western blotting using the indicated antibodies. Results were expressed as mean ± s.d., **P < 0.01, ***P < 0.001 versus veh, unpaired two-tailed Student’s t test. h, i Whole cell extracts from MLO-Y4 cells with and without vinculin or Mef2c siRNA knockdown (KD) were subjected to western blotting using the indicated antibodies. Results were expressed as mean ± s.d., *P < 0.05, **P < 0.01 versus veh, two-way ANOVA. j,k Mef2c nuclear translocation. Cytoplasmic (CE) and nuclear extracts (NE) from MLO-Y4 cells with and without vinculin KD and with and without vinculin overexpression (OE) were subjected to western blotting with the indicated antibody. Quantitative data (k). Results were expressed as mean ± s.d., N = 3 biologically independent replicates per group, **P < 0.01, ***P < 0.001 versus controls, unpaired two-tailed Student’s t test. l Vinculin-Mef2c colocalization. MLO-Y4 cells treated as in h were replicates per group, **P < 0.01, versus controls, unpaired two-tailed Student’s t test. c qPCR analyses. Figure 4. Vinculin interacts with Mef2c and vinculin knockdown increases Total RNA isolated from cortical bone of 3 mo-old male mice was used for qPCR analysis for expression of Sost gene, which was normalized to Gapdh mRNA. Results were expressed as mean ± s.d., N = 5 biologically independent replicates per group, ***P < 0.001 versus controls, unpaired two-tailed Student’s t test. d, e Western blot analyses. Protein extracts isolated from cortical bones of 3 mo-old male mice were subjected to western blotting using the indicated antibodies. Results were expressed as mean ± s.d., N = 3 biologically independent replicates per group, **P < 0.01 versus controls, unpaired two-tailed Student’s t test. f, g Vinculin overexpression. Protein extracts isolated from MLO-Y4 cells transfected with control or vinculin-expressing plasmid were subjected to western blotting using the indicated antibodies. Results were expressed as mean ± s.d., **P < 0.01, ***P < 0.001 versus veh, unpaired two-tailed Student’s t test. h, i Whole cell extracts from MLO-Y4 cells with and without vinculin or Mef2c siRNA knockdown (KD) were subjected to western blotting using the indicated antibodies. Results were expressed as mean ± s.d., *P < 0.05, **P < 0.01 versus veh, two-way ANOVA. j,k Mef2c nuclear translocation. Cytoplasmic (CE) and nuclear extracts (NE) from MLO-Y4 cells with and without vinculin KD and with and without vinculin overexpression (OE) were subjected to western blotting with the indicated antibody. Quantitative data (k). Results were expressed as mean ± s.d., N = 3 biologically independent . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint subjected to IF staining with the indicated antibody. Scale bars: 50 µm. m-o Co-immunoprecipitation (co-IP) assay. Protein extracts from MLO-Y4 cells with and without overexpression of HA-vinculin and Flag-Mef2c were incubated with the indicated antibodies or IgG, and the immunocomplexes were separated by SDS-PAGE, followed by western blotting with the indicated antibodies. p CHIP-qPCR analysis. Figure 4. Vinculin interacts with Mef2c and vinculin knockdown increases It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint (i-m) Tartrate-resistant acid phosphatase (TRAP) staining. Tibial sections of 3-mo-male mice were used for TRAP staining with indicated genotype. (i). Osteoclast surface/bone surface (Oc.S/BS) (j, k) and osteoclast number/bone perimeter (Oc.N/BPm) (l, m) of primary and secondary cancellous bones were measured using Image-Pro Plus 7.0. Scale bar, 50 µm. Results were expressed as mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05 versus controls, unpaired two-tailed Student’s t test. p 3D reconstruction from µCT scans of spine (L4, L5) from 3-mo-old male mice with indicated genotype. q, r Quantitative analyses of bone volume/tissue volume (BV/TV) and bone mineral density (BMD) of spine. Results were expressed as mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05, **P < 0.01, ***P < 0.001 versus controls, unpaired two-tailed Student’s t test. test. Figure 4. Vinculin interacts with Mef2c and vinculin knockdown increases The expression of Sost enhancer ECR5 combined with Mef2c antibody, which was normalized to IgG. Results were expressed as mean ± s.d., *P < 0.05, **P < 0.01 versus control, unpaired two-tailed Student’s t test. q Western blot analyses. Protein extracts isolated from BMSC cultures of 3 mo-old male control and cKO mice were subjected to western blotting using the indicated antibodies. subjected to IF staining with the indicated antibody. Scale bars: 50 µm. m-o Co-immunoprecipitation (co-IP) assay. Protein extracts from MLO-Y4 cells with and without overexpression of HA-vinculin and Flag-Mef2c were incubated with the indicated antibodies or IgG, and the immunocomplexes were separated by SDS-PAGE, followed by western blotting with the indicated antibodies. p CHIP-qPCR analysis. The expression of Sost enhancer ECR5 combined with Mef2c antibody, which was normalized to IgG. Results were expressed as mean ± s.d., *P < 0.05, **P < 0.01 versus control, unpaired two-tailed Student’s t test. q Western blot analyses. Protein extracts isolated from BMSC cultures of 3 mo-old male control and cKO mice were subjected to western blotting using the indicated antibodies. CHIP-qPCR analysis. The expression of Sost enhancer ECR5 combined with Mef2c antibody, which was normalized to IgG. Results were expressed as mean ± s.d., *P < 0.05, **P < 0.01 versus control, unpaired two-tailed Student’s t test. q Western blot analyses. Protein extracts isolated from BMSC cultures of 3 mo-old male control and cKO mice were subjected to western blotting using the indicated antibodies. Figure 5. Deleting sclerostin in Dmp1-expressing cells reverses the osteopenia induced by vinculin loss. a 3D reconstruction from µCT scans of tibia from 3-mo-old male control and cKO mice treated with or without tibial loading experiment. Scale bar, 250 µm. b H/E staining of tibial sections of 3-mo-old control and cKO mice were treated with or without tibial loading experiment. Scale bar, 200 µm. c-e Quantitative analyses of BV/TV Ct.Th and BMD. Results were expressed as mean ± s.d., N = 7 biologically independent replicates per group, *P < 0.05, **P < 0.01, ***P < 0.001 versus controls, unpaired two-tailed Student’s t test. f-h Calcein double labeling. Representative images of femur sections (f). Sections were used for measurements of mineral apposition rate (MAR). Quantitative MAR data for metaphyseal trabecular bones (g) and bone formation rate (BFR) (h). Scale bar, 50 µm. . CC-BY 4.0 International license perpetuity. Figure 6. Vinculin deletion reduces mechanical loading-stimulated bone formation in mice. a 3D reconstruction from µCT scans of tibiae from 3-mo-old male control and cKO mice treated with or without tibia loading experiment. Scale bar, 100 µm. b H/E staining of tibial sections of 4-mo-old control and cKO mice were treated with or without tibia loading experiment. Scale bar, 200 μm. c-e Quantitative analyses of BV/TV, Ct.Th and BMD. Results were expressed as mean ± s.d., N = 7 biologically independent replicates per group, *P < 0.05, **P < 0.01 versus controls, two-way ANOVA. f-h Calcein double labeling. Representative images of tibial sections (f). Sections were used for measurements of MAR and BFR for metaphyseal . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint trabecular bones. Scale bar, 50 µm. Results were expressed as mean ± s.d., N = 5 biologically independent replicates per group, *P < 0.05, **P < 0.01 versus controls, two-way ANOVA. i-m TRAP staining. Tibial sections of 4-mo-male control and cKO mice were used for TRAP staining (i). Oc.S/BS) (j, k) and Oc.N/BPm (l, m) of primary and secondary cancellous bones were measured using Image-Pro Plus 7.0. Scale bar, 50 μm. Results were expressed as mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05 versus controls, two-way ANOVA. Figure 7. Estrogen controls vinculin expression in osteocytes and vinculin cKO mice are resistant to OVX-induced bone loss. a, b IF staining. Tibial sections of sham and OVX mice with an anti-vinculin antibody, Scale bars: 50 µm. Qauntitative data (b). N = 6 biologically independent replicates per group, **P < 0.01, versus controls, two-way ANOVA. c-d Western blot analysis. MLO-Y4 cells were treated with increasing concentration of estrogen or fulvestrant (an estrogen receptor antagonist) for 24 h. Gapdh was used as a loading control. Quantitative data from three biologically independent replicates. Figure 6. Vinculin deletion reduces mechanical loading-stimulated bone ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint Supplementary Table 1: Mouse real-time RT-PCR (qPCR) primers Name 5’ primer 3’ primer Vcl GCTTCAGTCAGACCCATACTCG AGGTAAGCAGTAGGTCAGATGT Gapdh CAGTGCCAGCCTCGTCCCGTAG A CTGCAAATGGCAGCCCTGGTGAC Sost AGCCTTCAGGAATGATGCCAC CTTTGGCGTCATAGGGATGGT Supplementary Table 2: Antibody information Antibody Company Catalog # Application/Dilution Mef2c Proteintech 10056-1-AP WB (1:2000) IF (1:200) talin-1 Proteintech 14168-1-AP WB (1:1000) IF (1:200) vinculin Proteintech 66305-1-Ig WB (1:1000) IF (1:200) active b-catenin CST 8814S WB (1:2000) b-catenin CST 9562S WB (1:1000) lamin b1 CST 13435s WB (1:1000) Flag-Tag CST 14793S WB (1:1000) HA-Tag CST 3724S WB (1:1000) pinch1 Abcam ab108609 WB (1:1000), IF (1:200) b1 integrin Abcam ab95623 WB (1:1000), IF (1:200) sclerostin Abcam Ab63097 WB (1:1000), IHC (1:200) phalloidin-488 Invitrogen™ A12379 IF (1:500) tubulin ZSGB-BIO TA-10 WB (1:1000) Gapdh ZSGB-BIO TA-08 WB (1:1000) Figure 6. Vinculin deletion reduces mechanical loading-stimulated bone Results were expressed as mean ± s.d., *P < 0.05 versus control. f 3D reconstruction from µCT scans of femurs from 5-mo-old control and cKO female mice performed with sham or OVX surgeries. Scale bar, 250 µm. g-i Quantitative analyses of the BV/TV, Ct.Th and BMD. Results were expressed as mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05, **P < 0.01 versus controls, two-way ANOVA. g H/E staining of tibial sections. Scale bar, 200 μm. k-m Calcein double labeling. Representative images of 3-mo-old male femur . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint sections (k). Sections of non-demineralized femurs were used for measurements of MAR and BFR for the metaphyseal trabecular bones. Scale bar, 50 µm. Results were expressed as mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05 versus controls, two-way ANOVA. n-r TRAP staining. Tibial sections of 3-mo-male control and cKO mice were used for TRAP staining (n). Oc.S/BS (o, p) and Oc.N/BPm (q, r) of primary (o, q) and secondary (p, r) cancellous bones were measured using Image-Pro Plus 7.0. Scale bar, 50 µm. Results were expressed as mean ± s.d., N = 6 biologically independent replicates per group, *P < 0.05, **P < 0.01 versus controls, two-way ANOVA. . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. ; https://doi.org/10.1101/2022.11.09.515817 doi: bioRxiv preprint . CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 10, 2022. Supplementary Table 1: Mouse real-time RT-PCR (qPCR) primers Name 5’ primer 3’ primer Vcl GCTTCAGTCAGACCCATACTCG AGGTAAGCAGTAGGTCAGATGT Gapdh CAGTGCCAGCCTCGTCCCGTAG A CTGCAAATGGCAGCCCTGGTGAC Sost AGCCTTCAGGAATGATGCCAC CTTTGGCGTCATAGGGATGGT Supplementary Table 1: Mouse real-time RT-PCR (qPCR) primers Name 5’ primer 3’ primer Vcl GCTTCAGTCAGACCCATACTCG AGGTAAGCAGTAGGTCAGATGT Gapdh CAGTGCCAGCCTCGTCCCGTAG A CTGCAAATGGCAGCCCTGGTGAC Sost AGCCTTCAGGAATGATGCCAC CTTTGGCGTCATAGGGATGGT Supplementary Table 2: Antibody information Antibody Company Catalog # Application/Dilution Mef2c Proteintech 10056-1-AP WB (1:2000) IF (1:200) talin-1 Proteintech 14168-1-AP WB (1:1000) IF (1:200) vinculin Proteintech 66305-1-Ig WB (1:1000) IF (1:200) active b-catenin CST 8814S WB (1:2000) b-catenin CST 9562S WB (1:1000) lamin b1 CST 13435s WB (1:1000) Flag-Tag CST 14793S WB (1:1000) HA-Tag CST 3724S WB (1:1000) pinch1 Abcam ab108609 WB (1:1000), IF (1:200) b1 integrin Abcam ab95623 WB (1:1000), IF (1:200) sclerostin Abcam Ab63097 WB (1:1000), IHC (1:200) phalloidin-488 Invitrogen™ A12379 IF (1:500) tubulin ZSGB-BIO TA-10 WB (1:1000) Gapdh ZSGB-BIO TA-08 WB (1:1000) Figure 1 vinculin DAPI Merged H&E MLO-Y4(WT) KD-1 KD-2 talin intergrin β1 Phalloidin DAPI Merged KD-2 KD-1 MLO-Y4(WT) vinculin/DAPI Aged Aged Young Young a c b d e f vinculin talin integrin β1 Gapdh pinch1 con KD-1 KD-2 ** ** *** ** NS NS 100kD pinch1 310kD 75kD 35kD 45kD MLO-Y4(WT) KD-1 KD-2 talin intergrin β1 vinculin/DAPI d pinch1 vinculin DAPI Merged H&E Aged Aged Young Young a d d a KD-2 Aged b c b e vinculin talin integrin β1 Gapdh pinch1 con KD-1 KD-2 ** 100kD 310kD 75kD 35kD 45kD Phalloidin DAPI Merged KD-2 KD-1 MLO-Y4(WT) e Phalloidin DAPI Merged MLO-Y4(WT) e c e e f ** *** ** NS NS f ** *** ** NS NS f Figure 2 3m/male 14m/male con cKO con cKO con cKO a b e 14m 3m con cKO g h i k con cKO f ** *** ** *** ** ** NS NS Vinculin Gapdh Heart Liver Spleen Lung Kidney con cKO con cKO con cKO con cKO con cKO con cKO *** NS NS NS NS Cortical bone j con cKO L5 L4 c d Figure 2 100kD 55kD 40kD 130kD a b Vinculin Gapdh Heart Liver Spleen Lung Kidney con cKO con cKO con cKO con cKO con cKO con cKO *** NS NS NS NS Cortical bone Figure 100kD 55kD 40kD 130kD b a 3m/male 14m/male con cKO con cKO e 14m 3m g h i k f ** *** ** *** ** ** NS NS Vinculin Gapdh con cKO con cKO con cKO con cKO con cKO con cKO *** NS NS NS NS j con cKO L5 L4 c d 100kD 55kD 40kD 130kD 3m/male 14m/male con cKO con cKO e i f ** *** ** *** NS NS j con cKO c d 14m/male con cKO e f ** *** con cKO d d c 3m/male f f e e i f ** *** NS NS j con cKO i ** j con cKO 14m 3m con cKO g h i k con cKO ** ** j L5 L4 h 14m 3m g h con cKO L5 L4 g k cKO cKO ** O d Figure 3 Figure 3 Figure 3 14m 3m con cKO a b c ** ** ** ** ** con cKO con cKO e f ** * NS cKO con cKO con CFU-F CFU-OB 3m-con 3m-cKO 14m-con 14m-cKO Primary cancellous Secondary cancellous Primary cancellous Secondary cancellous k l m o NS NS NS NS NS NS NS NS n con cKO d g h i j Figure 3 14m 3m con cKO a b c ** ** ** ** ** con cKO con cKO e f ** * NS cKO con cKO con CFU-F CFU-OB d g h i j g b c ** ** ** ** ** con cKO e d g b d 14m 3m con cKO a a e con cKO con cKO e f ** * NS cKO con FU-F CFU-OB g i j con cKO e f ** g * g f g 14m cKO con CFU-F h cKO NS j i j l l l m o NS NS NS NS n con cKO k 3m-con 3m-cKO 14m-con 14m-cKO Secondary cancellous Primary cancellous k m o n Secondary cancellous o NS NS sclerostin Gapdh con cKO Mef2c vinculin sclerostin Gapdh con Vcl-OE a b c d f g IHC: sclerostin e Con Vcl-OE ** *** ** ** *** NS con cKO vinculin Mef2c sclerostin Gapdh WT si-NC WT si-Mef2c KD-1 si-NC KD-1 si-Mef2c KD-2 si-NC KD-2 si-Mef2c h i ******** NS NS ** **** ** *** NS j vinculin Mef2c tubulin lamin b1 WT CE WT NE KD-1 CE KD-1 NE KD-2 CE KD-2 NE KD-1CE KD-1 NE KD-2 CE Vcl-OE KD-2 NE *** ** ** ** ** NS l Merged DAPI Mef2c vinculin WT KD-1 KD-2 KD-1+Vcl OE KD-2+Vcl OE k input IgG Mef2c IP: Mef2c IB: Mef2c IB: vinculin Flag Flag-Mef2c HA-Vcl + + - - + + + + - - + + + - + - + + + - + - + + Input IP(Flag) IP(HA) Input IB:HA Flag Flag-Mef2c HA-Vcl IB:HA n o p ** * Figure 4 m NS NS NS 75kD 25kD 45kD 140kD 100kD 35kD 25kD 170kD 100kD 70kD 25kD 25kD 70kD 70kD 70kD 70kD 55kD 70kD 100kD 100kD 130kD 100kD 130kD 130kD Figure 4 sclerostin Gapdh con cKO Mef2c b c d f g e ** *** Figure 4 75kD 25kD 45kD b IHC: sclerostin d c a Con Vcl-OE ** *** D D f vinculin sclerostin Gapdh con Vcl-OE f g e C V ** ** *** NS 140kD 100kD 35kD 25kD e g sclerostin Gapdh *** NS con cKO vinculin Mef2c sclerostin Gapdh WT si-NC WT si-Mef2c KD-1 si-NC KD-1 si-Mef2c KD-2 si-NC KD-2 si-Mef2c h i ******** NS NS ** **** ** *** NS j vinculin Mef2c tubulin lamin b1 WT CE WT NE KD-1 CE KD-1 NE KD-2 CE KD-2 NE KD-1CE KD-1 NE KD-2 CE Vcl-O KD-2 *** ** ** ** ** NS l Merged DAPI Mef2c vinculin WT KD-1 KD-2 KD-1+Vcl OE KD-2+Vcl OE k input IgG Mef2c IP: Mef2c IB: Mef2c IB: vinculin Flag Flag-Mef2c HA-Vcl + + - - + + + + - - + + + - + - + + + - + - + + Input IP(Flag) IP(HA) Input IB:HA IB:Flag Flag Flag-Mef2c HA-Vcl IB:HA IB:Flag n o p ** * con cKO active β-catenin β-catenin Gapdh q m NS NS NS 35kD 25kD 170kD 100kD 70kD 25kD 25kD 70kD 100kD 100kD 130kD 70kD 55kD 100kD 130kD 70kD 55kD 75kD 75kD 45kD 130kD i ******** NS NS ** **** ** *** NS j vinculin Mef2c tubulin lamin b1 WT CE WT NE KD-1 CE KD-1 NE KD-2 CE KD-2 NE KD-1CE KD-1 NE KD-2 CE Vcl-OE KD-2 NE 70kD 70kD 70kD 70kD 55kD vinculin Mef2c sclerostin Gapdh WT si-NC WT si-Mef2c KD-1 si-NC KD-1 si-Mef2c KD-2 si-NC KD-2 si-Mef2c h 170kD 100kD 70kD 25kD 25kD i h l *** ** ** ** ** NS l Merged DAPI Mef2c vinculin WT KD-1 KD-2 KD-1+Vcl OE KD-2+Vcl OE k input IgG Mef2c IP: Mef2c IB: Mef2c IB: vinculin m NS NS NS 25kD 70kD 100kD 130kD l *** ** ** ** ** NS k NS NS NS k Merged DAPI M input IgG Mef2c IP: Mef2c IB: Mef2c IB: vinculin m 70kD 100kD 130kD input IgG Mef2c IP: Mef2c IB: Mef2c IB: vinculin m 70kD 100kD 130kD m Flag Flag-Mef2c HA-Vcl + + - - + + + + - - + + + - + - + + + - + - + + Input IP(Flag) IP(HA) Input IB:HA IB:Flag Flag Flag-Mef2c HA-Vcl IB:HA IB:Flag n o p 100kD 130kD 70kD 55kD 100kD 130kD 70kD 55kD + - + - + + + - + - + + IP(Flag) Input Flag Flag-Mef2c HA-Vcl IB:HA IB:Flag o p 100kD 130kD 70kD 55kD 100kD 130kD 70kD 55kD o n p ** * p con cKO active β-catenin β-catenin Gapdh q 75kD 75kD 45kD con cKO active β-catenin β-catenin Gapdh q 75kD 75kD 45kD q b c d * * * ** NS ** *** *** ** * fl Figure 5 Figure 5 a e b c d * * * ** NS ** ** ** ** *** NS *** * ** ** NS * NS Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/fl Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/fl Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vcl fl/fl Sostfl/fl * ** * ** NS ** ** ** ** ** NS *** i * * * ** NS ** * ** * ** NS ** Primary cancellous Secondary cancellous Primary cancellous Secondary cancellous l p n o m NS NS NS NS NS NS NS NS NS NS NS NS Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/fl Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/fl f g h Figure 5 j k a b * * * ** NS ** *** ** Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/fl Figure 5 b a b Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/fl a Dmp1-Cre d c d ** ** ** *** NS *** * ** ** NS * NS e Dmp1-Cre Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/fl c Dmp1-Cre Vclfl/fl e Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl ** ** ** ** NS *** h f * ** * ** NS ** ** ** ** ** NS *** g h h * ** * ** NS ** g Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vcl fl/fl Sostfl/fl f g Sostfl/fl mp1-Cre Vcl fl/fl Sostfl/fl f Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vcl fl/fl Sostfl/fl Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vcl fl/fl Sostfl/fl * * * ** NS ** * ** * ** NS ** j k j * ** * ** NS ** k Dmp i Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/fl k i p1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/fl Primary cancellous Secondary cancellous l Dmp1-Cre Dmp1-Cre Vcl Dmp1-Cre Sost Dmp1-Cre Vcl Sost Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/ l p n o m NS NS NS NS NS NS m o p p NS NS NS p o NS NS NS l/fl P i Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/fl Dmp1-Cre Dmp1-Cre Vclfl/fl Dmp1-Cre Sostfl/fl Dmp1-Cre Vclfl/fl Sostfl/fl Figure 6 Figure 6 Primary cancellous Secondary cance con cKO sham loading con+sham cKO+sham cKO+loading con+loading Primary cancellous Secondary cancellous con+sham con+loading cKO+sham cKO+loading con+Sham con+loading cKO+sham cKO+loading a e b c d f g h i j k l m sh loa ** * * * NS NS * * * NS NS NS * ** * * NS * NS NS NS NS NS NS b sham loading * * NS b a con+sham con+loading cKO+sham cKO+loading con+Sham con+loading cKO+sham cKO+loading a e b c d * * * NS NS * * * NS a c d * NS * * c d e d * * NS con cKO sham loading f g h ** NS NS * ** * h NS ** * f h g Primary cancellous Secondary cancellous sham loading con+sham cKO+sham cKO+loading con+loading Primary cancellous Secondary cancellous i j k l m * NS * NS NS NS NS NS NS Prim g con+sham cKO+sham cKO+loading con+loading Primary cancellous Secondary cancellous i j l * N i j k j k l m * NS NS NS NS Secondary cancellous m NS NS Secondary cancellous Estrogen Control 10 -10 10 -9 10 -8 10 -7 vinculin Gapdh Fulvestrant Control 10 -9 10 -8 10 -7 10 -6 c b d e ** ** ** 130kD 100kD 40kD 35kD Figure 7 Estrogen Control 10 -10 10 -9 10 -8 10 -7 vinculin Gapdh Fulvestrant Control 10 -9 10 -8 10 -7 10 -6 c 130kD 100kD 40kD 35kD Figure 7 Figure 7 Estrogen Control 10 -10 10 -9 10 -8 10 -7 vinculin Gapdh sham con+Sham con+OVX cKO+Sham cKO+OVX con+OVX con+sham cKO+sham cKO+OVX Fulvestrant Control 10 -9 10 -8 10 -7 10 -6 vinculin DAPI Merged con+Sham con+OVX cKO+sham cKO+OVX Secondary cancellous Primary cancellous a c b f OVX h sham OVX k l n o p q r d g e ** ** ** ** * * ** ** NS ** ** NS NS * * ** ** NS j m NS NS NS NS NS NS NS NS i 130kD 100kD 40kD 35kD Figure 7 sham vinculin DAPI Merged a OVX a a c c d b d e ** ** ** b e f g h sham OVX g ** * * i con+Sham con+OVX cKO+Sham cKO+OVX con+Sham con+OVX cKO+sham cKO+OVX f h sham OVX g ** * * ** ** NS j NS NS i cKO+OVX cKO+OVX h ** ** NS h ** ** NS N i h ** ** NS NS NS i h j i l m NS NS NS NS l k m o p q r ** ** NS o p q r ** ** NS ** ** NS p r ** ** NS Con+OVX Con+Sham cKO+Sham cKO+OVX Secondary cancellous Primary cancellous n p o n q r q r NS * * Primary cancellous r NS NS Secondary cancellous Secondary cancellous Figure 8 Vinculin (+) Bone formation Bone formation Vinculin (+) Vinculin ( ) Bone formation Bone formation Bone formation Bone formation Bone formation
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Un nuevo camino en Santiago, el periférico de Compostela
Informes de la construcción
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UN NUEVO CAMINO EN SANTIAGO, EL PERIFÉRICO DE COMPOSTELA (A NEW ROAD IN SANTIAGO, THE COMPOSTELA RING ROAD) Angel González del Rio Ingeniero Director de las obras de la Demarcación de Carreteras del Estado en Galicia. MOPTMA ESPAÑA Fecha de recepción: 12-VI-95 511-3 RESUMEN SUMMARY Se presentan los planteamientos de planificación, proyecto y obra del nuevo periférico de Santiago recientemente puesto en The article presents the approaches to planning, design and work execution of the new Santiago ring road, recently open for traffic. Las peculiaridades históricas, artísticas, culturales y medioambientales de la ciudad, han exigido desarrollar un proyecto especialmente respetuoso con su entorno humano, urbano y natural. The historical, artistic, cultural and environmental peculiarities of Santiago called for the development of a project that would respect with particular care the city's human, urban and natural surroundings. 1. Aspectos más destacables del marco institucional Las bases fundamentales del Convenio son las siguientes: El 18 de noviembre de 1991 sefirmael Convenio entre el Ministerio de Obras Públicas, Transportes y Medio Ambiente y el Ayuntamiento de Santiago de Compostela. Se trata del punto de partida para un ambicioso plan sectorial y urbanístico que de una forma integrada sienta las bases para un profunda transformación de la ciudad de Santiago de Compostela. a) Ejecución del nuevo periférico de la ciudad en 7 tramos que han de conectar las carreteras nacionales N-550 (La Coruña-Vigo y Tuy), N-634 (Santiago-San Sebastián) y N-525 (Zamora-Orense-Santiago), así como los tres enlaces de la Autopista A-9 con la ciudad. Dentro del período 91-99 en el que se desarrolla la planificación existen dos años clave que enmarcan las actuaciones, los Años Jubilares 93 y 99. Las especiales connotaciones históricas y culturales, el crecimiento que experimenta la ciudad al convertirse en capital de Galicia y el año Santo Jacobeo 1993 conforman referencias obligadas al concertar actuaciones. (c) Consejo Superior de Investigaciones Científicas Licencia Creative Commons 3.0 España (by-nc) b) Desarrollo de acciones de ampliación y remodelación del Aeropuerto de Labacolla. c) Ejecución de la Autovía Santiago-Aeropuerto d) Coordinación entre administraciones para la correcta acomodación de las nuevas infraestructuras al planeamiento urbanístico en vigor. e) Desarrollo del Convenio RENFE-Ayuntamiento, bajo http://informesdelaconstruccion.revistas.csic.es 20 Infonnes de la Construcción, Vol. 47, n° 438, julio/agosto 1995 tutela del MOPTMA, desarrollándose diversas actuaciones de remodelación en las estaciones de Cornes y La Sionlla. f) Actuaciones en materia de rehabilitación de la ciudad histórica y programas medioambientales. g) Tratamientos de borde de las nuevas infraestructuras, al objeto de acomodarlas e integrarlas en el tejido urbano. El 11 de octubre de 1993 se firma un protocolo entre la Secretaría General para las Infraestructuras y el Ayuntamiento de Santiago que desarrollaba este último punto concretando actuaciones urbanísticas de borde urbano que afectaban a distintos barrios de Santiago, que de este modo se integraban al nuevo eje de comunicación y desarrollo que constituye el Periférico de la ciudad. nuevas viviendas, el pabellón deportivo del Sar y los barrios tradicionales de Porto, Poza Real, Rocha Vella, Conxo, Castifíeirifío, Lamas de Abad, Viso, San Lázaro y Amio. Santiago se articula ya, en torno a su periférico. La nueva vía de 10,5 km con 15 enlaces y 700 m de distancia media entre enlaces, que permite a Santiago, por un lado, superar sus límites tradicionales, abriendo nuevos espacios y perspectivas y, por otro, recoge e integra en la ciudad sus barrios periféricos y sus nuevos equipamientos culturales y deportivos. En la figura 1 se detalla el modo en el que se implanta el trazado del periférico en el territorio. Su alineación, formando un gran arco al este de la ciudad, constituye un tercer eje infraestructural, sumándose así a la autopista del Atlántico y al ferrocarril La Coruña-Santiago-Vigo. 2. Antecedentes del periférico Los antecedentes del periférico de Santiago han sido dos básicamente. 1.- La Red Arterial del MOP de 1972 2.- El Plan General de Ordenación Urbana de 1989 La red arterial del MOP planteada en 1972, partía de viarios y planificaciones urbanísticas que difieren sustancialmente de las actuales, con algunos aspectos comunes, como sucedía con el trazado del tramo CornesChoupana (Ronda Sur) que enlaza N-525 y N-550. La encendida polémica que surgió entre el planeamiento sectorial viario y los planes de ordenación de la época, supuso la inviabilidad de la red arterial propuesta entonces. El PGOU de 1989 supuso un nuevo marco urbanístico para Santiago, contemplándose como sistemas generales de comunicación los suelos destinados a albergar el nuevo periférico Fig. ].- El Periférico de Santiago. 3. ¿Qué es el periférico? El nuevo periférico de Santiago, es una vía segura de alta capacidad y accesibilidad a la trama urbana, que permite descongestionar los tráficos que afectan al centro histórico de la ciudad y conexionar entre sí las carreteras nacionales N-550, N-634, N-525 y mejorar los accesos de la autopista A-9 en sus distintos enlaces urbanos. El nuevo vial viene a resolver además los graves problemas de accesibilidad que sufrían el polígono industrial del Tambre, en fiíerte proceso expansivo, el nuevo Palacio de Congresos con capacidad para L 500 congresistas instalado en S. Lázaro, el estadio multiusos de S. Lázaro con capacidad para 12.000 espectadores, el centro de acogida de peregrinos ubicado en el Monte del Gozo, el polígono de Fontiñas que alberga un gran centro comercial y 4.000 (c) Consejo Superior de Investigaciones Científicas Licencia Creative Commons 3.0 España (by-nc) % Fig. 2.- Una vista panorámica de los 3 ejes de infraestructuras: A-9, ferrocarril y periférico. http://informesdelaconstruccion.revistas.csic.es 21 Infonnes de la Construcción, Vol. 47, n° 438, julio/agosto 1995 En la figura n° 2 se aprecian estos tres grandes ejes de infraestructuras, que son atravesados por el río Sar en distintos puntos. El periférico, es por otra parte susceptible de ser cerrado completamente por el Oeste como anillo de circunvalación en un futuro próximo, recogiendo las carreteras autonómicas de Noya (salida hacia las playas) y San Comba, si bien, existen suelos de especial protección en el entorno del Monte Pedroso que condicionan las posibles soluciones de trazado. '4 Los seis objetivos del periférico son: 1) Creación de una infraestructura segura y cómoda que mejore la movilidad de Santiago y su entorno para tráficos internos y externos. Pig. J.- Enlace del Polígono Industrial del tambre. 2) Permitir un desarrollo urbano planificado y ordenado. 3) Mejorar la calidad-ambiental del casco Histórico, drenando tráficos hacia la nueva red viaria. 4) Proporcionar conexiones con la malla urbana en los polígonos industriales, barrios tradicionales, nuevas zonas residenciales y equipamientos culturales, deportivos, comerciales y sanitarios. 5) Establecer la conexión de la red planificada con el sistema nacional de carreteras del Estado y Autopistas. De este modo quedaban interconectadas la N-550 (La Coruña, Pontevedra, Vigo y Tuy), N-634 (Oviedo), N-547 (Lugo) y N-525 (Orense), así como los tres enlaces de la A-9 en Santiago. 6) Lograr que la obra respetase el equilibrio ambiental y conseguir unos acabados y calidades acordes con la ciudad en la que se integra. Fig. 4.- Enlace con la A-9 (Norte). 4. El periférico tramo a tramo A modo de rápido viaje de Norte a Sur a través de la nueva infraestructura, pasaremos sobre los cinco tramos puestos en servicio el pasado 31 de enero de 1995 y los dos que actualmente se hallan en ejecución comentando sus aspectos más singulares. ].- Polígono del Tambre-San Lázaro El tramo une el polígono industrial del Tambre y la N-550 con el enlace Santiago Norte de la Autopista A-9 y la N-634 (Oviedo, Lugo). Los aspectos particulares reseñables del tramo son: -Se produjo una afección parcial de los taludes del antiguo vertedero municipal de basuras, motivando especiales (c) Consejo Superior de Investigaciones Científicas Licencia Creative Commons 3.0 España (by-nc) medidas correctoras del impacto visual mediante plantaciones. -Enlace periférico- Pohgono del Tambre. Resuelto mediante un trébol completo. -Especial tratamiento de los fondos de excavación en la zona denominada "Brañas del Sar" (zona inundable en la que nace el río Sar) con sustitución de los dos primeros metros de fango y aportación de piedra sana a efectos de cimentar la nueva infraestructura. -Enlace periférico - A-9 (Norte). Resuelto mediante un diamante con glorieta superior. Esta tipología de enlace ha sido la adoptada con carácter general eatodo el periférico, por las ventajas que presentaba en Guanto a seguridad, sencillez, capacidad y pequeña demanda de suelo frente a otras tipologías. De este modo la movilidad sobre el http://informesdelaconstruccion.revistas.csic.es 22 Infonnes de la Construcción, Vol. 47, n° 438, julio/agosto 1995 periférico no queda interrumpida en los enlaces y los tráficos genuinamente locales se resuelven en laglorieta en un nivel diferente, quedando así jerarquizado el viario. Las estructuras son dos losas postesadas de 24,2 m de longitud y 11,50 m de ancho, cuya planta es una corona circular de 45 m de radio interior. -El barrio de S. Lázaro es atravesado con una rasante deprimida entre muros que evita impactos visuales y de ruidos. El enlace de S. Lázaro, análogo al anterior enlaza con la N-634 (Oviedo), N-547 (Lugo) y el aeropuerto internacional de Labacolla. Fig. 6.- Detalle de los muros ilustrados con motivos Jacobeos. - Se ha tenido especial atención en el cuidado de la reposición del Camino de Santiago (Camino Francés) en su paso por S. Lázaro, disponiendo aceras y acabados de muros con pizarra de Santiago, que dignifican tan insigne itinerario. -En los distintos muros ejecutados buscamos lograr una gran calidad constructiva y estética, compatible con la rapidez de ejecución. Diseñamos así, sobre la base de los muros prefabricados texturizados, un sencillo elemento que es la tradicional concha del peregrino, buscando que el usuario del periférico tuviera la sensación inequívoca de hallarse en Compostela. Además, dicho símbolo, que sirve para señalizar los distintos Caminos hacia Santiago, cumple esta misma misión específica sobre los alzados de los muros del periférico, indicando al usuario como acceder a la universal plaza del Obradoiro 2. - San Lázaro-Fontiñas Sur El tramo une N-634 y N-550 (Avda. de Lugo), proporcionando accesibilidad a los nuevos equipamientos culturales y deportivos de la ciudad, así como al polígono residencial de Fontiñas. Se podrían destacar como aspectos más interesantes del tramo, los siguientes: -En cuanto al medio físico y su geología, la traza se asienta en las inmediaciones del cauce del río Sar, con predominio en el sustrato rocoso de esquistos, anfibolitas y suelos limoarcillosos, procedentes de la alteración de dicho substrato. Una constante del tramo fue la gran heterogeneidad del material, pasándose de zonas rocosas a zonas arcillosas sin material de tránsito. Dicha heterogeneidad se puso de manifiesto al acometer la cimentación de la estructura del enlace del estadio de fútbol de la S.D. Compostela, donde el estribo Sur se ejecutaba con cimentación directa y el estribo Norte con cimentación indirecta, mediante pilotes in situ de 1,50 m y 20 m de profundidad, quedando la cimentación de las pilas intermedias en cotas aproximadamente interpoladas entre ambos valores. ''-^50 -Dicho enlace, proporciona acceso al estadio de la S.D. Compostela (S. Lázaro), al nuevo Palacio de Congresos con capacidad para más de 1.500 personas y al vial que comunica con el recinto del Monte del Gozo, donde se ubica el centro de acogida de peregrinos. Fig. 5.- Enlace de San Lázaro. (c) Consejo Superior de Investigaciones Científicas Licencia Creative Commons 3.0 España (by-nc) En este caso, el tronco del periférico pasa sobre la glorieta inferior, uniéndose a ella mediante un dimnante completo, construyéndose una losa postesada de tres vanos y 80 m de luz total, ejecutándose los dos tableros separados para http://informesdelaconstruccion.revistas.csic.es 23 Infonnes de la Construcción, Vol. 47, n° 438, julio/agosto 1995 Fig. 7.- Tramo San Lázaro-Fontiñas Sur. realizar, posteriormente, la unión de ambos para que tengan un comportamiento resistente solidario. En el acceso al Monte del Gozo se ejecutó una estructura mixta formada por un cajón metálico de acero corten y losa superior en un solo vano de 40 m que salva el río Sar y el Ferrocarril. -Las arcillas de la traza en este tramo tenían una elevada plasticidad, lo cual, unido alrigorclimatológico de Santiago, ha impedido su puesta en obra. -El enlace de Pontifias, sobre el que D. Pernando da Cunha Rivas, Ingeniero Autor del Proyecto, ha escrito un artículo específico dentro de este número especial dedicado a Santiago, es una bella, diáfana yfiíncionalrealización, que resuelve con elegancia, en un exiguo espacio entre el ferrocarril y el propio polígono ,el acceso a Pontifias, donde se ubican en simbiosis urbana usos residenciales (4.000 viviendas), administrativos (nuevos juzgados y dependencias de la Xunta), deportivos (nuevo pabellón deportivo y piscinas del Sar) y comerciales (Área Central). Fig. 8.- Enlace multiusos de San Lázaro. (c) Consejo Superior de Investigaciones Científicas Licencia Creative Commons 3.0 España (by-nc) Por su ubicación, permeabilidad visual y solución constructiva, el enlace de Pontifias se convierte en uno de los elementos singulares del periférico. Su permeabilidad transversal fue condicionante básico de disefio al efecto de no introducir labarrera visual que hubiera supuesto ejecutar muros y terraplenes entre las zonas de^ar (donde se halla la joya románica de la Colegiata de Sar) y Pontifias. La http://informesdelaconstruccion.revistas.csic.es 24 Informes de la Construcción, Vol. 47, n° 438, julio/agosto 1995 estructura de la glorieta superior es una losa pretensada con planta de corona circular de 18,25 m de radio en el eje y 11,40 m de anchura transversal. El ramai permeabilizado, es una losa pretensada de 117 m de longitud total y 7,10 m de anchura. Los pilares en V, dispuestos perimetralmente, contribuyen decisivamente al airoso resultado de la estructura. -La construcción de las nuevas piscinas y pabellón del Sar a las que habíamos de proporcionar acceso, unido a la barrera urbanística que suponía el terraplén existente del ferrocarril La Coruña-Santiago-Vigo en la zona de Sar, hizo que nos decantásemos por la solución de construir un paso inferior de hormigón armado por empuje oleodinámico de grandes dimensiones ( 15 m de gálibo horizontal, 5 m de gálibo vertical y 24 m de longitud, para salvar el terraplén RENFE). El empuje lo proporcionaron 24 gatos de 200 t, con un esfuerzo máximo de empuje de 3.2301 y el peso propio de la estructura (2.430 t). Fue necesario sobredimensionar la potencia máxima de empuje para repartir mejor las cargas y aliviar los esfuerzos en el muro de reacción, a efectos de no correr riesgos de rotura del sistema de tuberías existentes de pluviales y saneamiento de Fontiñas, que estaban bajo el cajón, quedando así, desafectadas. Se procedió al empuje del cajón, vaciando simultáneamente el terraplén de la vía, no siendo preciso alterar los tráficos ferroviarios en ningún momento. POUGONO DE Fig. 10.- Cajón empujado bajo FFCC. La Coruña-Vigo. ,^^^^# FOirriÑAS Fig. 11.- Enlace avda. de Lugo. -Finalizaba este tramo con el enlace con la N-550 en su tramo urbano conocido como avda. de Lugo. El periférico enlaza así con la antigua ronda, cuya sección transversal también se remodela y ensancha . Fig, 9.- Enlace de Fontiñas. (c) Consejo Superior de Investigaciones Científicas Licencia Creative Commons 3.0 España (by-nc) El enlace de la avda. de Lugo, se realiza deprimiendo entre muros el tronco del periférico, quedando la glorieta en el plano superior, coincidente con la rasante existente de la antigua circunvalación. La estructura es^na losa postesada, con planta de semi-corona circular apoyada en tres estribos. http://informesdelaconstruccion.revistas.csic.es 25 Informes de la Construcción, Vol. 47, n° 438, julio/agosto 1995 3.-Ampliaciónde laAvda. de Lugo (Fontiñas Sur-Cornes) Se trata del único tramo del periférico, en el que se aprovechael tramo existente, ampliándosey reordenándose la sección transversal, dotada de tres carriles por sentido, con aparcamientos y amplias aceras. Actualmente se halla en fase de ejecución, estando prevista su puesta en servicio en Otoño de 1996. Incluye como obras singulares: -Resolver la afección del talud de Bellvis, sobre el que se halla el Seminario Menor de Santiago ,mediante la técnica del ''talud claveteado", con bulones de 4-5 m, gunitado y revestimiento. Fig. 13.- Glorieta de Conxo. -Ejecutar en voladizo parte de la calzada y acera en el entorno de la estación de ferrocarril de Cornes. -Glorieta en Conxo para conectar dicho barrio con el periférico. -Construcción de un nuevo enlace en Sar que permitirá efectuar un by-pass entre tráficos N-5 25/N-5 5 O desafectando la glorieta de Cornes, que es el punto con mayor carga de tráfico de Santiago (IMD=45.000), ejecutando un cajón empujado bajo el haz de vías. -Se construyen dos importantes permeabilizaciones en el Pajonal y Torrente resueltas con losas postesadas de 125 m y 140 m, donde el PGOU desarrollará fiituros viales y zonas verdes. 4. - Comes - Choupana Finaliza el tramo en el nudo de La Choupana, resuelto mediante un diamante con glorieta superior. Su amplio Este tramo del periférico es prácticamente idéntico al que ya recogía el estudio de la Red Arterial de 1972 del MOP. Enlaza la N-525 (Zamora-Orense-Vigo) y la N-550 (Pontevedra), atravesando el tradicional barrio de Conxo. Sus nudos y aspectos más destacables son: -Nueva glorieta de Cornes que recoge los tráficos de la antigua N-525 y la c/ Romero Donallo, actual salida hacia la Universidad, Noya y playas. Hay que significar que la Xunta de Galicia está desarrollando el proyecto La RochaVidán, nuevo tramo del periférico que permitirá enlazar la N-550 (Pontevedra) con la C-543 (Noya). -Nuevo enlace con el tramo del periférico CornesCastifíeiriño que constituirá la nueva salida hacia Orense (N-525). Fig. 12.- Glorieta de Comes. (c) Consejo Superior de Investigaciones Científicas Licencia Creative Commons 3.0 España (by-nc) Fig. 14.- Imagen virtual del Enlace de la Choupana (arriba). Enlace de la Choupana (abajo). http://informesdelaconstruccion.revistas.csic.es 26 Momies de la Constnicción, Vol. 47, n° 438, julio/agosto 1995 campo visual hizo que estudiásemos muy especialmente el diseño de este enlace, realizando distintas imágenes virtuales que nos permitieron optimizar la solución. En este nudo queda prevista con un paso inferior la futura conexión con la carretera autonómica C-543 a Noya. -Fue tratada especificamente la reposición del itinerario peatonal relativo al Camino Portugués hacia Santiago. 5.- Choupana - A-9 Este tramo es una adaptación de la sección tipo de la antigua carretera de 2 carriles N-550, a la nueva del periférico. Las singularidades más destacadas del tramo son las siguientes: -Se ha ampliado el antiguo Puente de la Rocha en la N-550 (Pontevedra), que salva una pronunciada vaguada de unos 260 m sobre el río Sar. Es una obra singular dentro del periférico, que ha precisado idear un original sistema constructivo para poder ampliar la sección transversal, desde 10 m a 22 m, sin afectar el tráfico del acceso desde Pontevedra y Vigo a Santiago (IMD=22.000). En un articulo especifico dentro de esta misma revista, D. José Antonio Barbosa Ayúcar, Ingeniero proyectista y Jefe de Obra de Dragados, explica detalladamente la génesis y desarrollo de la técnica aplicada en esta obra, realizada con elementos prefabricados (dinteles, soportes y vigas). 6.- Castiñeiriño-Comes -Supone el desarrollo del nuevo acceso de laN-525 (OrenseSantiago) a Compostela, totalmente en variante. -En el nudo de Cornes se dispone un paso inferior para los vehículos que saldrán hacia Orense. -Posteriormente, para salvar las vías del tren y la vaguada existente entre Cornes y el Monte do Xeixo, proyectamos un gran viaducto de 450 m, que salvaba la vaguada y las vías del ferrocarril Santiago-Vigo y Santiago-Orense, y que se bifurcan en este punto, con gran esviaje respecto al trazado del nuevo vial. La estructura se rechaza en 15 vanos isostáticos de 30 m de longitud, con vigas artesa y cimentaciones directas, generalmente. -Finalmente, el tramo llega al Castiñeiriño, barrio tradicional de Santiago que se salva con un paso inferior, para evitar impactos visuales y de ruidos en el barrio, resolviéndose en la glorieta superior los tráficos urbanos. -Se construyeron también nuevas conexiones con los barrios de Rocha Vella y Porto, mejorando el control de dichos accesos. Fig. 16.- Virtualización del Enlace de Castiñeiriño (N-525). Fig. 15.- El Puente de la Rocha, tras la colocación de dinteles. (c) Consejo Superior de Investigaciones Científicas Licencia Creative Commons 3.0 España (by-nc) Fig. 17.- Tramo Castiñeiriño -A-9. http://informesdelaconstruccion.revistas.csic.es 27 Infonnes de la Construcción, Vol. 47, n° 438, julio/agosto 1995 7. - Castiñeiriño-A -9 Tramo que concluye el nuevo vial de acceso a Santiago de laN-525 (Orense - Santiago). Este tramo, continuación de la Variante Cornes-Castiñeiriño, supuso la readaptación de la antigua N-525 a la nueva sección del periférico, resolviendo el control de accesos. Las peculiaridades del tramo ñieron: -Generar un enlace en trompeta con el núcleo de Lamas de Abad y centros escolares de la zona. -Disponer una nueva conexión con la A-9 (enlace N-525). -Mejorar el control de accesos, generando vías de servicio. -Ampliación del puente sobre el ff.cc. Santiago-Orense, adaptándolo a los gálibos prescritos por RENFE. 5. Aspectos generales -La cifra de inversión final del periférico se sitúa en 10.000 millones, de los cuales 7.000 millones corresponden a la ejecución de la infraestructura ( 700 millones/km), 2.000 millones para expropiación (200 millones/km), 1.000 millones para los servicios afectados ( 100 millones/km). -La sección tipo del periférico es uniforme, incluyendo firme drenante, barrera rápida y luminarias con báculos dobles de 9 y 12 m, con lámparas de VASP de 25 OW. En glorietas hemos preferido la solución de iluminar con torres de iluminación únicas de gran altura, centradas en la glorieta frente a la iluminación perimetral, para facilitar la percepción nocturna de los nudos. -El capítulo de expropiaciones ha sido especialmente dificultoso, afectando a 90 edificaciones (70 viviendas y 20 naves y talleres) y a 1.500 fincas, estando precedido de intensos trabajos y de reuniones con los afectados, para intentar resolver los problemas de sustitución de viviendas, reclamaciones legales y económicas, coordinando los plazos de ocupación de fincas y edificaciones, además de los programas de trabajo de las distintas obras. A modo de ejemplo, destacaría la solución adoptada de forma conjunta para el modo de realojo que ñie adoptado en el tramo Cornes-Choupana, donde los afectados por la expropiación de sus casas actuaron con promotores de las nuevas viviendas de sustitución, y que ñieron construidas en una pieza de suelo urbanizable programado del barrio de Conxo. Los expropiados consiguieron el suelo a través de la firma de un convenio urbanístico que contemplaba la permuta de superficies, en fiínción de las calificaciones urbanísticas del PGOU. -Los servicios afectados por el periférico han sido repuestos de acuerdo con las secciones y demandas estimadas en el año horizonte del PGOU. Se han enterrado las líneas para evitar impactos visuales y se han creado galerías de servicios en los tramos en que se reordenaban y ampliaban las secciones existentes. -De los 7 tramos, cuatro de ellos son variantes, con control total de accesos, y 3 tramos, readaptaciones de la sección transversal ,en las que se han reordenado y restringido los accesos. -Las características geométricas son homogéneas en planta y alzado con R = 350 m y pendiente máxima del 5%, salvo la rampafinal de subida del Polígono del Tambre, que tiene un 6%. -Se ha cuidado especialmente la corrección de impa tos ambientales con plantaciones, hidrosiembras y pantallas arbóreas, especialmente útiles en un clima como el de Santiago, y tratamientos específicos de jardinería en cada enlace o glorieta, siempre con instalaciones de riegos por aspersión. Q^y-c^:^-Cí,Q'^. SECCIÓN TIPO "•,V;V/-VtVo--:-r.Cv.\Cv.\C J^"* A- Capa de rodadura drenante B- Capa intermedia S-20 C- Base asfáltica G-25 D- Zaiiorra artificial Fig. 18.- Sección tipo del Periférico. (c) Consejo Superior de Investigaciones Científicas Licencia Creative Commons 3.0 España (by-nc) ^*\' X, ^ ^ ^ ^ p Fig. 19.- Viviendas de Conxo. http://informesdelaconstruccion.revistas.csic.es 28 Informes de la Construcción, Vol. 47, n° 438, julio/agosto 1995 -Todos los trazados en planta y alzado fueron almacenados en el ordenador de la Demarcación de Carreteras de Galicia del MOPTMA, permitiéndonos realizar ajustes, definir con precisión y agilidad detalles, y lograr una adecuada coordinación entre tramos. 6. Conclusiones El recorrido a través del nuevo periférico de Santiago de Compostela nos ha mostrado una solución de red arterial urbana singular, que ha tratado de plantearse en consonancia con la propia singularidad de la ciudad. Los nuevos viales constituyen un nuevo camino en Santiago, que resolviendo los problemas específicos de accesibilidad de los barrios periféricos de la ciudad y los nuevos equipamientos urbanos, vienen también a ahviar las fuertes tensiones creadas por el tráfico dentro del casco histórico. Me gustaría significar el alto grado de colaboración entre instituciones que se ha alcanzado en Santiago, que ha hecho posible, en muy corto espacio de tiempo, desarrollar todos los estudios previos, proyectos de trazado, construcción y ejecución de las obras. Quisiera agradecer al gran equipo humano que ha trabajado en el periférico, en el que se han integrado la Demarcación de Carreteras de Galicia del MOPTMA, el Ayuntamiento de Santiago de Compostela y las empresas constructoras y consultoras adjudicatarias de los distintos tramos, por el generoso esfuerzo y la gran ilusión depositada al servicio de la obra. Publicación del Instituto Eduardo Torroja - CSIC INSTITUTO DE CIENCIAS DE LA CONSTRUCCIÓN EDUARDO TORROJA La revista MATERIALES DE CONSTRUCCIÓN, con periodicidad trimestral y dedicada con exclusividad a la investigación científica y técnica *de la construcción y sus materiales, está editada por el INSTITUTO EDUARDO TORROJA, Centro dependiente del Consejo Superior de Investigaciones Científicas. Constituye, desde hace cuarenta y cinco años, un eficaz vehículo de transmisión de nuevos conocimientos científicos y técnicos en el campo de los materiales de construcción y de otros temas relacionados con los mismos. Prestigiosos científicos y técnicos de todo el mundo colaboran en su publicación; no obstante, MATERIALES ha pretendido tener siempre una especial incidencia en el mundo investigador y técnico en el ámbito internacional y, muy especialmente, en los países de habla hispana. M lATERÜ^LES DE C ONSTRXJCCION I C S I C l CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS Conviene resaltar, una vez más, la importancia que tiene el desarrollo de los materiales de construcción considerados tradicionales: el cemento y el hormigón, no sólo desde el punto de vista técnico sino por la importancia social y económica que conlleva ese desarrollo. Como muestra, se pueden recordar unas recientes declaraciones del doctor Schartz, del Instituto Nacional de Normalización de Estados Unidos, en las que decía: "La investigación del iiormigón supone un enorme potencial de mejora en ese campo. Lo que se haya de invertir en los próximos veinticinco años, puede depender de una pequeña inversión en el quinquenio inmediato." La indudable interrelación de disciplinas y ámbitos ha aconsejado ampliar la línea editorial de MATERIALES a otros campos del conocimiento que no estaban suficientemente recogidos. Por lo cual nuestra Revista incluye con mayor frecuencia artículos de investigación —e incluso de divulgación—, temas cuya importancia está siendo objeto de una atención prioritaria tanto por las autoridades científicas de nuestro país, como por los propios responsables de la política investigadora europea. Un ejemplo destacado son los estudios sobre Restauración y Conservación del Patrimonio Histórico y, en general, del Patrimonio Arquitectónico y de la incidencia del medio ambiente en el comportamiento de los materiales, tanto tradicionales como no tradicionales. Algunos de estos artículos se publican en versión española e inglesa. (c) Consejo Superior de Investigaciones Científicas Licencia Creative Commons 3.0 España (by-nc) http://informesdelaconstruccion.revistas.csic.es
https://openalex.org/W3198975419
https://zenodo.org/record/5783070/files/fqab032.pdf
English
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A data-driven approach to studying changing vocabularies in historical newspaper collections
Digital scholarship in the humanities
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cc-by
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DigitalScholarshipintheHumanities,Vol.36,Supplement2,2021. V C TheAuthor(s)2021.PublishedbyOxfordUniversityPressonbehalfofEADH. ThisisanOpenAccessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. doi:10.1093/llc/fqab032 E-mail: use state-of-the-art word embeddings to describe how this process is reflected in the written use of four different languages: Dutch, English, Swedish, and Finnish. Earlier work has focused on words and concepts relating to nationhood, pointing out the gen- eral trajectories of word use and the increased levels of vagueness of ‘nation’ as a concept (Kemila¨inen, 1964; A data-driven approach to studying changing vocabularies in historical newspaper collections ata-driven approach to studying nging vocabularies in historical wspaper collections ............................................................................................................................................. Simon Hengchen Spra˚kbanken Text, University of Gothenburg, Sweden and iguano- don.ai, Belgium Ruben Ros Centre for Contemporary and Digital History (C2DH), University of Luxembourg, Luxembourg Jani Marjanen and Mikko Tolonen Helsinki Computational History Group, University of Helsinki, Finland ...................................................................................................................................... Abstract Nation andnationhoodare amongthe mostfrequentlystudiedconcepts in the fieldof intellectualhistory.Atthesametime,theword‘nation’anditshistoricalusagearevery vague. The aim in this article was to develop a data-driven method using dependency parsing and neural word embeddings to clarify some of the vagueness in the evolution of this concept. To this end, we propose the following two-step method. First, using linguistic processing, we create a large set of words pertaining to the topic of nation. Second,wetraindiachronicwordembeddingsandusethemtoquantifythestrengthof the semantic similarity between these words and thereby create meaningful clusters, which are then aligned diachronically. To illustrate the robustness of the study across languages, time spans, as well as large datasets, we apply it to the entirety of five historical newspaper archives in Dutch, Swedish, Finnish, and English. To our know- ledge, thus far there have been no large-scale comparative studies of this kind that purport to grasp long-term developments in as many as four different languages in a data-driven way. A particular strength of the method we describe in this article is that, by design, it is not limited to the study of nationhood, but rather expands beyond it to other research questions and is reusable in different contexts. ............................................................................................................................................ Ruben Ros Centre for Contemporary and Digital History (C2DH), University of Luxembourg, Luxembourg Abstract Nation andnationhoodare amongthe mostfrequentlystudiedconcepts in the fieldof intellectualhistory.Atthesametime,theword‘nation’anditshistoricalusagearevery vague. The aim in this article was to develop a data-driven method using dependency parsing and neural word embeddings to clarify some of the vagueness in the evolution of this concept. To this end, we propose the following two-step method. First, using linguistic processing, we create a large set of words pertaining to the topic of nation. Second,wetraindiachronicwordembeddingsandusethemtoquantifythestrengthof the semantic similarity between these words and thereby create meaningful clusters, which are then aligned diachronically. To illustrate the robustness of the study across languages, time spans, as well as large datasets, we apply it to the entirety of five historical newspaper archives in Dutch, Swedish, Finnish, and English. To our know- ledge, thus far there have been no large-scale comparative studies of this kind that purport to grasp long-term developments in as many as four different languages in a data-driven way. A particular strength of the method we describe in this article is that, by design, it is not limited to the study of nationhood, but rather expands beyond it to other research questions and is reusable in different contexts. Correspondence: Simon Hengchen, University of Gothenburg, Gothenburg, Sweden. E il 1 Introduction One of the benefits of our case is that the words nation and national exist in all four languages as cognates or, in the case of Finnish, as neologisms in the 19th century. The historical trans- latability makes it ideal for comparative study in that it highlights both similarities as well as differences be- tween the languages in question. y The linguistic change relating to ‘national’ consists of a gradual growth in frequency and an expansion in language domains over time. Setting up a method- ology that grasps this development over a long period of time, does so in different languages, is statistically robust and does so in a data-driven way, will pave the way for further historical study that could challenge and complement earlier qualitative accounts of na- tion-building. We point out that hypotheses devel- oped in earlier studies based on limited source corpora have referred to nations and a shift in focus from the economy to culture and politics (Viroli, 1995; Ihalainen, 2007; Nurmiainen, 2009; Marjanen, 2013). We further propose that a data-driven cluster- ing of the vocabulary relating to national allows for a more fine-grained image of the expansion of the na- tional imaginary. We show signs of change in the lan- guage of nationhood that could perhaps be described as processes of culturalization, de-economization, and institutionalization, which should be evaluated more closely in historical research. What this means is that, over the course of the research period, terminology related to culture and political institutions became more commonly labelled as something national (as in national literature or national party), whereas eco- nomic terminology became proportionately less dom- inant in the discourse. Many studies on semantic change of particular words or concepts over long periods of time tend to focus on changes in words that shift between two dis- tinct senses (Recchia et al., 2017; Tahmasebi et al., 2018). The case of national that we chose for this study is different in that it relates to historical processes that are of interest to historians in particular, but it also provides a challenging case for the use of computa- tional methods as it is not about detecting polysemy, but rather about grasping a vague term and its increas- ing importance in political discourse over time (on vagueness, see Geeraerts, 1993). 1 Introduction There has been extensive research on the process in which nation-states become pivotal units for inter- national politics and crucial categories of belonging for individuals (O¨ zkırımlı, 2000; Anderson, 2006; Smith, 2013, 2008). Our aim in this article was to S. Hengchen et al. domains, and that historical actors seem to have cared a lot about which uses were correct. The vagueness of key terms for navigating society is inherently tied to the complexity of the data required to detect shifts in language use. Historical data have developed in con- junction with societal processes and events (every- thing from growing wealth to war and censorship practices to changing fashions), and therefore form non-standard data units in terms of computation (Ma¨kela¨ et al., 2020). More importantly, develop- ments in the data, in our case, newspapers, are part of the process in which the terminological changes took place. This means that these newspapers cannot be used just to study changes, as the changes in them also need to be factored into the interpretation of the analyses. Gschnitzer et al., 1978). Word embeddings are com- monly used in natural language processing (NLP), but their application in historical research is still at the experimental stage. There have been many robust attempts at evaluation in state-of-the-art research using embeddings, but in the case of historical data, the evaluation has to be against historical research. It therefore remains difficult to determine what the real object of the modelling is and if the results are trans- ferable to other languages, different corpora, or time spans. Gschnitzer et al., 1978). Word embeddings are com- monly used in natural language processing (NLP), but their application in historical research is still at the experimental stage. There have been many robust attempts at evaluation in state-of-the-art research using embeddings, but in the case of historical data, the evaluation has to be against historical research. It therefore remains difficult to determine what the real object of the modelling is and if the results are trans- ferable to other languages, different corpora, or time spans. Our large-scale comparative perspective demon- strates changes in the development of nationhood with greater clarity than before in focusing on the term ‘national’ and using words associated with it to analyse domains that were increasingly being concep- tualized as national. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 1 Introduction This also holds for most of the key terms of interest in understanding political, social, and cultural transformation in the modern period. Words such as state, nation, ideology, culture, gender, and racism have been extensively researched as pivotal terms that have been contested in past debates and whose changing meanings have been indicative of historical transformation, but have also been the cause of change in the past (see e.g. Koselleck, 1972–1997; Ball et al. 1989). Although many of these words are polysemous, the aspect that makes them interesting politically and culturally is that they are also vague, at least in one of their senses, that they are used in rather different language Our method is particularly suited to analysing complex historical keywords that are usually at the heart of studying the history of political and social thought. The development of methods and the concrete plots we devise in this study relate to the ii110 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 i110 A data-driven approach to study changing vocabularies All of the above-mentioned studies, in one way or another, concern long-term trends in the meanings and uses of the words ‘nation’, ‘national’, and ‘nation- alism’. However, apart from in a few isolated cases of resorting to relative frequencies, the use of quantita- tive methods to trace long-term developments in this vocabulary is almost completely non-existent. The one exception is Van den Bos and Giffard’s study, which focuses on key junctures in Dutch history and the language of nation (van den Bos and Giffard, 2016). The present study takes a step forward and a step backward. On the one hand, it engages in earlier claims about changes in word use being part of the process in which past expectations and experiences about nationhood were articulated (Koselleck, 1972, 2011), which on the other hand leads to claims that an over-arching study of the language of national could, in a general way, describe the process through which the national perspective became dominant in how people saw the world (Anderson, 2006). Although interpretations such as these already exist, they all rely on examples of particular texts rather than any kind of data-driven analysis, which means that they may be detailed in terms of individual examples, but they are not even close to capturing the whole story. 1 Introduction vocabulary revolving around the adjective national, but the aim here is not primarily to make a historical argument about nation building. We rather purport to identify ways of using computation to analyse his- torical trends in past conceptualizations of the world in a more nuanced way than key-word searches, rela- tive frequencies, or topic models have made possible. Ultimately, the methods used to address historically informed questions need some level of tailoring to the data and the type of questions asked. However, given that the bulk of large-scale diachronic text data sets provide possibilities for the study of language in rela- tion to historical processes, there are good possibilities of reuse in other research cases. This goes hand- in-hand with open science and the envisioning of research data as an ecosystem (Lahti et al., 2019). 2.1 Language and nationalism Nationalism is a widely studied phenomenon and the role of semantic and lexical change has been noted in literature that provides overviews of the topic (see, in particular, Leersen, 2006, p. 15; Burke, 2013; Gilbert, 2018), but the bulk of the literature on nationalism has still been surprisingly indifferent towards the language of nationhood. This disinterest in the long-term changes in language relating to nationhood means that the analytical distinctions relating to nation-states and their emergence has been prioritized at the ex- pense of enhancing understanding of the historical experience of nationhood. Methods for tracing this kind of change are not a perfect match for the historical questions posed in earlier research (Hengchen et al., 2021). It is clear that earlier abstract claims about the shift in focus in the language of nationhood remain too broad to be captured in a meaningful way by methods for tracing semantic change in that they capture many different and partly conflicting signals from the data. Human interpretation has tended to filter them out, and quan- titative methods for assessing shifting vocabulary ne- cessarily have to find a good way of balancing detailed view and a result that is interpretable for human readers. There are good arguments for claiming that modelling may in some cases be less transparent and cannot capture the same things as qualitative interpretation (Biernacki, 2014), but in terms of understanding the evolving language of nationhood, the aspect of modelling and quantification has been completely missing. Studies focusing on language tend to reflect an interest in the differences and similarities between pat- riotism and nationalism (Cunningham, 1989; Dietz, 1989; Viroli, 1995; Hont, 2005, pp. 447–528; Schierle, 2009). Another strongly related strand concerns the link between nation and fatherland in particular European languages (Kemila¨inen, 1964; de Bertier de Sauvigny, 1970; Godechot, 1971; Gschnitzer et al., 1978; Frautschi, 1993; Van Sas, 1999; Brenner, 2013). A few studies have also paid attention to na- tionalism as an ism in political discourse (Gschnitzer et al., 1978; Ba¨renbrinker and Jakubowski, 1995; Freeden, 2009, pp. 204–224; Kettunen, 2018; Kurunma¨ki and Marjanen, 2018). 2.2 Evolving vocabularies 2.3 Representing meaning in time As noted above, previous attempts at studying an evolving discourse diachronically made use of com- putational methods and large corpora. More recent approaches lean on NLP. In this section, we discuss the state-of-the-art and illustrate why studying a specific theme over time is not trivial. Topic modelling is extensively discussed and is sometimes used in the humanities (Fridlund and Brauer, 2013; Viola and Verheul, 2019). Although the soft clustering method is most commonly used synchronically for exploratory research, there are also dynamic topic models (DTMs) that take time as a variable and allow the extraction of topics across time slices. DTMs (Blei and Lafferty 2006) divide the data into discrete time slices and infer topics across them to capture topics evolving over time. A different approach, Topics over Time (Wang and McCallum 2006), treats time as a continuous variable and the data are not discretized. Although both approaches are promising, their major drawback is that the topic models do not allow for a topic to be defined a priori: they allow an exploratory look at the data, but there is no easy way to ensure that a certain topic will be found. The challenge in analysing vocabulary is to ‘strike a balance between an adaptive strategy that responds to changes in vocabulary, and a more conservative ap- proach that keeps the vocabulary stable’ (Kenter et al., 2015). The vocabulary must maintain a minimal de- gree of stability in order for it to be historically rele- vant and meaningful, but at the same time, it should solve the problem of different words relating to the same concept over time (onomasiology). Rather than considering a predefined group of words over time, distributional methods allow for a more data-driven approach. Recent scholarship in history has used word embeddings to identify seman- tically related words and to follow their development over time. This requires an initial set of seed terms that is subsequently expanded by selecting similar words (Kenter et al., 2015; Recchia et al., 2017). Another approach is to identify a vocabulary based on features of single words such as ‘isms’ (Pivovarova et al., 2019, Marjanen et al., 2020), or sequences of words (n- grams). The latter approach constructs a vocabulary based on words that are directly preceded (Wevers, 2017; Van Eijnatten and Ros, 2019) or modified (Hill et al., 2018) by a common adjective, and subse- quently focuses on the temporal changes. 2.2 Evolving vocabularies The traditional focus in conceptual history has been on specific keywords such as ‘democracy’, ‘liberalism’, Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 ii111 S. Hengchen et al. and ‘nation’, but only to a limited degree has there been any systematic analysis of semantic and lexical fields related to these keywords. The concentration on words has led to extensive discussions about their exact relationship with concepts (Steinmetz, 2012; Bolla et al., 2019; La¨hteenma¨ki and Kaukua, 2019; Bolla et al., 2020). Although we do not assume that we can grasp the conceptual level behind words as such, we take a pragmatic approach and use distribu- tional1 methods to study changing vocabulary. These methods allow us to broaden the scope from words to groups of words (that are in some way related to con- cepts) through time. We are still intent on using words as proxies and thus remaining on the level of words and language use, because that will enable us to cap- ture at least some of the personal experiences of his- torical actors. When they sought to express certain concepts, they chose particular words that reflected their own positions and thus left a trace of their experiences in the data. Moreover, focusing on words allows for the relatively easy tallying of their occurrences. insights into conceptual and distributional change that would go unnoticed were the focus only on spe- cific keywords. Our method builds on such previous work, and in delegating the choice of ‘seed terms’ to nouns modified by a specific adjective allows for a more data-driven approach, while at the same time retaining some ‘topical control’ and harnessing se- mantic information from word embeddings. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 3 Methodology As we point out above, studying the changing vocabu- lary of a concept is no easy task. Doing so in a way that informs research in the humanities in a data-driven way adds a layer of complexity: if a certain, specific theme is to be studied it has to be defined a priori, and operational choices must be made5 that might bias any quantitative method applied to the resulting sub- set of the data. Our methodological contribution is an approach that follows the fine line between having a precise research question and making use—in a data- driven way—of all the data available. It is a two-step approach, which we illustrate below in a case study on the changing vocabulary of nationhood in four coun- tries and four languages. Thus, there have been robust attempts to evaluate and sometimes compare systems, but it remains dif- ficult to determine what is actually being modelled, and whether the performances are transferable to other languages, different corpora, or dissimilar time spans. In short, it is arduous to determine whether NLP systems can be applied as-is to humanities data. Indeed, as McGillivray et al. (2019) remark, for example, despite being promising with regard to English, SCAN (Frermann and Lapata, 2016) per- forms poorly on an Ancient Greek corpus with sparse data and extended time bins, and the performance of an updated model (Perrone et al., 2019) does benefit from additional information such as literary genre. To illustrate that the method is robust enough to tackle different data, languages, and periods, we carry it out on Dutch, Finnish, Swedish, and British news- paper data. The newspapers stem from different sour- ces and countries and are available in different formats. Massive digitized newspaper collections are increasingly used to address historical questions through mining textual data.6 The material, as well as the pre-processing steps, is laid out below, and the distribution of the data is available in Figs 1 and 2. The Dutch data are the Delpher open newspaper archive (Royal Dutch Library, 2017) for the period 1618 until 1876 included. 2.3 Representing meaning in time all time bins) to create vector representations, and more recently contextual- ized word embeddings (which have token vectors and not type vectors2) have been applied to diachronic corpora. example)4 and through how researchers can process it electronically (missing, incomplete, or wrong meta- data, varying OCR quality, etc.) (Piotrowski, 2012). Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 2.3 Representing meaning in time This leads to the quantification of conceptual extension, and gives Another field in which meaning is studied compu- tationally across time is that of lexical semantic change, which is particularly suited for conceptual change in that it focuses on words and not general themes (Kutuzov et al., 2018; Tahmasebi et al., 2018; Tang, 2018). To study meaning change, computation- al methods proceed in two steps: first, they distribu- tionally model meaning in different time bins (subsequent temporal slices of the data at hand). Second, the focus is to detect, for any word w, whether the signal between time bins changes in a significant way. In recent years, even laws of semantic change have been proposed (Dubossarsky et al., 2015; Hamilton et al., 2016) and then disproved ii112 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 A data-driven approach to study changing vocabularies (Dubossarsky et al., 2017). Some methods have been under rigorous evaluation (Dubossarsky et al., 2019; Schlechtweg et al., 2019, 2020; Shoemark et al., 2019). At the same time, new methods and paradigms aimed at diachronically modelling semantic information are being developed further: DTMs specifically targeting words (Frermann and Lapata, 2016; Perrone et al., 2019) use bag-of-words to draw sense distributions for certain target words over time, dynamic, and con- tinuous word embeddings (Bamler and Mandt, 2017; Rosenfeld and Erk, 2018; Rudolph and Blei, 2018; Yao et al., 2018; Dubossarsky et al., 2019; Gillani and Levy, 2019) differ from static embeddings in that they use the entirety of the data (i.e. all time bins) to create vector representations, and more recently contextual- ized word embeddings (which have token vectors and not type vectors2) have been applied to diachronic corpora. (Dubossarsky et al., 2017). Some methods have been under rigorous evaluation (Dubossarsky et al., 2019; Schlechtweg et al., 2019, 2020; Shoemark et al., 2019). At the same time, new methods and paradigms aimed at diachronically modelling semantic information are being developed further: DTMs specifically targeting words (Frermann and Lapata, 2016; Perrone et al., 2019) use bag-of-words to draw sense distributions for certain target words over time, dynamic, and con- tinuous word embeddings (Bamler and Mandt, 2017; Rosenfeld and Erk, 2018; Rudolph and Blei, 2018; Yao et al., 2018; Dubossarsky et al., 2019; Gillani and Levy, 2019) differ from static embeddings in that they use the entirety of the data (i.e. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 3 Methodology This archive is said to con- tain all newspapers for that period.7 For the years 1877–1899 included, currently only available through the API, we queried the API for every item of the ‘artikel’ type (‘article’, the Dutch data have article seg- mentation and further differentiates between adver- tisements and articles) category containing the determiner de (‘the’) at least once. Although this does not guarantee a 100% recall, de is so frequent that we are confident the extreme majority of articles of the necessary length for our tasks are retrieved. For anything pre-1877, we discarded pages that had any- thing other than exclusively ‘nl’ or ‘NL’ as language tags in the metadata. Articles from colonial newspa- pers were systematically removed. This is motivated As anyone who works with historical material is aware, language changes over time. To avoid anach- ronisms, one has to make sure that texts are under- stood in their own context, rather than through a contemporary lens. Although historians have been trained to do this, as the above paragraph shows, cur- rent NLP methods might not be completely fit for the task. Additionally, NLP usually focuses on relatively straightforward cases,3 and it is unclear whether or not the signal picked up by computational models is use- ful for humanities research, given that the changes in meaning being studied may well not be as obvious (Hengchen et al., 2021). Finally, the computational processing of humanities data notoriously poses spe- cific challenges both by its nature (evolving grammar and orthography, uneven size of data across time, for ii113 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 S. Hengchen et al. Fig. 1. Distribution of data size over time in token counts for FI, NL, and SV g Downloaded from https://academic.oup.com/dsh/article/36/Supplement by the fact that only the Dutch dataset has an extensive coverage of colonial newspapers, and including them would have complicated our comparisons with the other countries in our study. The newspapers from Finland comprise two language corpora: we used the entirety of the Finnish Sub-corpus of the Newspaper and Periodical Corpus of the National Library of Finland (National Library of Finland, 2011a) for articles in Finnish, and the corresponding Swedish Sub-corpus of the Newspaper and Periodical Corpus of the National Library of Finland (National Library of Finland, 2011b).8 Swedish newspapers are available in Fig. 1. 3 Methodology Distribution of data size over time in token counts for FI, NL, and SV Fig. 2. Distribution of data size over time in token counts for GB Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 ii114 Downloaded from https://academic.oup.com/dsh/article/36/Supplement_2/ii109/6421793 by Bibliotheque nationale de France user on 15 December 2021 Fig. 1. Distribution of data size over time in token counts for FI, NL, and SV Fig. 1. Distribution of data size over time in token counts for FI, NL, and SV by the fact that only the Dutch dataset has an extensive coverage of colonial newspapers, and including them would have complicated our comparisons with the other countries in our study. The newspapers from Finland comprise two language corpora: we used the and Periodical Corpus of the National Library of Finland (National Library of Finland, 2011a) for articles in Finnish, and the corresponding Swedish Sub-corpus of the Newspaper and Periodical Corpus of the National Library of Finland (National Library of Fig. 2. Distribution of data size over time in token counts for GB ment_2/ii109/6421793 by Bibliotheque nationale de France user on 15 December 2021 Fig. 2. Distribution of data size over time in token counts for GB nt_2/ii109/6421793 by Bibliotheque nationale de France user on 15 Fig. 2. Distribution of data size over time in token counts for GB and Periodical Corpus of the National Library of Finland (National Library of Finland, 2011a) for articles in Finnish, and the corresponding Swedish Sub-corpus of the Newspaper and Periodical Corpus of the National Library of Finland (National Library of Finland, 2011b).8 Swedish newspapers are available in by the fact that only the Dutch dataset has an extensive coverage of colonial newspapers, and including them would have complicated our comparisons with the other countries in our study. The newspapers from Finland comprise two language corpora: we used the entirety of the Finnish Sub-corpus of the Newspaper Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 ii114 A data-driven approach to study changing vocabularies the Kubhist 2 corpus digitized by the Royal Library of Sweden, processed with the Sparv pipeline (Borin et al., 2016), and made available online9 by Spra˚kbanken through Korp (Borin et al, 2012). 3 Methodology Finally, the British data consist of the British Library Newspapers covering especially the 19th century,10 the 17th and 18th Century Nichols collection,11 and the 17th and 18th Century Burney collection.12 nationality’ as it is a noun in its own right,16 and the Finnish kansalliskirjasto ‘national library’ became kan- sallinen þ kirjasto. Only modified nouns are kept. For newspapers in Finnish and in Swedish from Finland, we used linguistic information made available by the language bank of Finland,17 and similarly for news- papers in Swedish published in Sweden we used in- formation made available by the language bank of Sweden18—both sets of data were produced by differ- ent versions of the same pipeline, Sparv (Borin et al., 2016). Dutch and English datasets were dependency- parsed using spaCy 2 (Honnibal and Montani, 2017). The large models were chosen for both languages. Unfortunately, no assessment of the quality of the dependency parsing is available for Finnish and Swedish.19 The changes in corpus size over time bins poses a problem for any computational text-mining task. Our approach creates intermediate data points in separate time bins of 20 years,13 and it is only the aggregate information that is compared over time. As such, common pitfalls related to aspects such as limited vocabularies or the representativity of the data do not necessarily apply, as we spell out in our evaluation. The absolute counts of nouns modified by ‘nation- al’ are displayed in Fig. 3. The relative frequencies show a similar pattern. A further issue is that our data (historical news- papers) are not only data in which we study changing language: the change in corpus size and the growing importance of newspapers as a medium are parts of the historical process in which the language of nation- hood has also changed. Growing amounts of news- papers created a different habitat in which the vocabulary of national could flourish; hence, there is no reasonable way of even trying to achieve a balance with the corpus used for the purpose of computation. Rather understanding changes in the corpus and the development of the public sphere in general is a form of corpus control, which is essential in terms of under- standing the changing vocabulary of nationhood (Marjanen et al., 2019; Tolonen et al., 2019). Because the meaning of ‘national’ changes over time, it is possible that other adjectives referred to what we now classify as national. 3 Methodology To evaluate the ‘cen- trality’ of the adjective in the different time periods, therefore, we aggregated all other adjectives that modified the nouns modified by national. For ex- ample, in Dutch, this resulted in adjectives such as ‘public’, ‘Dutch’, ‘royal’, and ‘foreign’. The frequen- cies of these ‘competing’ adjectives were lower in all decades, however, as well as in the overall time frame. This shows that the adjective ‘national’ was indeed the most commonly used to modify these nouns. The ‘competing’ adjectives sometimes perform a supple- mentary function but, as we will reveal, the discourse of national had a clear role of its own in all languages. 3.1 Extracting nationhood First, using dependency parsing,14 we utilized the method proposed by Hill et al. (2018) and extracted all the nouns modified by the adjective at hand, in our case ‘national’.15 With regard to the other languages we extracted nouns modified by nationaal and natio- nale in Dutch, nationella, nationell, and national in Swedish, and kansallinen in Finnish. Obviously, dif- ferent languages have different properties. We resorted to splitting the Finnish and Swedish com- pound nouns starting with kansallis- and national-, respectively, while making sure they were genuine compounds, removed the ‘national’, and added the remaining part to our tally. As an example, Swedish nationalbiblioteket ‘the national library’ became natio- nell þ biblioteket, but we discarded nationaliteten ‘the Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 ii11 3.2 From words to concepts Second, to allow the semantic clustering of all nouns relating to the concept of ‘nation’, we trained dia- chronic word embeddings on the entirety of the full text. Given that there was no conclusive way of deter- mining what type of embedding was best for our data and that word embeddings are still poorly understood, and since we argue that dynamic and continuous word embeddings models cannot reliably be used here on account of the extremely uneven distribution of the data, we experimented with two fairly old archi- tectures, CBOW and SGNS (Mikolov et al., 2013a,b), which have been studied more thoroughly.20 For the ii115 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 S. Hengchen et al. Fig. 3. Absolute counts of nouns modified by ‘national’ over time in Dutch, Finnish, Swedish from Finland, and Swedish from Sweden. Relative frequencies, not plotted, show a similar pattern Fig. 3. Absolute counts of nouns modified by ‘national’ over time in Dutch, Finnish, Swedish from Finland, and Swedish from Sweden. Relative frequencies, not plotted, show a similar pattern previous work based on the same data (Hengchen et al., 2019; Pivovarova et al., 2019; Marjanen et al., 2020). These models are referred to later in this article as UPDATE. At the same time, we independently trained word embeddings for all time bins, which we then aligned post hoc as proposed by Kulkarni et al. (2015). The spaces were aligned by means of orthog- onal Procrustes analysis, as first done by Hamilton et al. (2016).22 We refer to these models later in this article as ALIGN. Aside from the frequency threshold, which we raised due to the enormous number of types23 in our corpora, we used the default (hyper)- parameters.24 We are releasing the models along with this article.25 same reason, we created diachronic word embeddings using the two most frequently applied methods, post hoc alignment and incremental updating (described in detail below). We chose to train mod- els on double decades for three reasons: first, 20 years roughly corresponds to a ‘generation’ in historical sociolinguistics (Sa¨ily, 2016); second, we needed a certain number of nouns related to the nation for the clustering to make sense, and bins of 20 years allow enough to be gathered, especially in the earlier periods; third, and somewhat echoing the second reason, it allowed us to have relatively stable models for the earlier periods. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 3.2 From words to concepts produces results that are useful for downstream tasks and analyses such as the study of a concept across large time scales. Word embedding models are commonly evaluated using for example word analogies or word similarities. It should be pointed out that these evaluations are carried out on present-day data for which ground truth exists. To take but one example, Pennington et al. (2014) used the analogy task in Mikolov et al. (2013a) as well as the word similarities available in WordSim-353 (Finkelstein et al., 2002). However, ground truth is not available for our data. Were we to find enough annotators30 to create ground truth and evaluate our embeddings, creating such ground truth would entail creating an unreasonable amount,31 given that we are training different models on different time bins.32 This is well beyond the scope of this project. Finally, as Chiu et al. (2016) point out, there is no guarantee that intrinsic evaluations of word embeddings such as described above indicate better performance in downstream tasks. Instead, we rely on recent conclusions reported by Hill and Hengchen (2019), who point out that, on historical, OCRed, relatively dirty data (i.e. texts with an F-score of 0.75 compared with their corresponding keyed-in ground truth) does not severely impact the perform- ance of vector space models. g g As can be inferred from the previous subsections, the main strength of our approach is that it allows researchers to rely on hypotheses stemming from his- torical research while being data-driven. To a certain extent, we used the entirety of the data available (for English, upwards of 50 billion words) while guiding the process—the only interference, which we admit is crucial and requires domain expertise, was choosing a key adjective on which to focus. The final product, fine-grained on a one-year basis, is refined enough to be analysed in broad strokes as well as to lead to deeper dives into specific periods. Through the use of the entirety of the data, and time-specific meaning representations of words, the method avoids the com- mon trap of teleology. Unfortunately, an inherent weakness to type embeddings is that polysemous words have a single representation in vector space, ‘ironing out’ the polysemy. 3.2 From words to concepts For each time bin, we trained two types of word embeddings using gensim (Reh˚urek and Sojka, 2010), a Python library for vector space modelling. Because separately trained vector spaces cannot be compared directly, we used two different methods to make the spaces comparable, and thus to ensure a sound dia- chronic approach. On the one hand, we followed Kim et al. (2014) and initialized the vector space for time bin t1 with the space from t0,21 and updated the vec- tors by continuing the training. This differs slightly from the original approach in setting the learning- rate value of t1 to that of the end of the previous model (in this case, t0). The aim was to prevent the models from diverging too rapidly, as successfully reported in Once the word embeddings were trained, we built, for each time bin, a similarity matrix between all the nouns extracted above. In other words, we queried the word-embedding models for a degree of ‘semantic similarity’26 between all words at hand and stored those relations in a table. Semantic clusters can then be created. We used two hard clustering algorithms, which we describe briefly below. We created the semantic clusters using k-means clus- tering (MacQueen, 1967) and affinity propagation (Frey and Dueck, 2007). The aim in k-means is to group similar data points together. Its main limitation, in our ii116 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 A data-driven approach to study changing vocabularies case, is that the number of clusters needs to be decided a priori. Our second clustering algorithm, affinity propa- gation, has the advantage of finding the number of clusters automatically: it splits the data into exemplars and instances, exemplars being representative tokens of their instances, the non-exemplar tokens in the same cluster. As Pivovarova et al. (2019) point out, ‘Affinity Propagation has been previously used for several NLP tasks, including collocation clustering into semantically related classes (Kutuzov et al., 2017) and unsupervised word sense induction (Alagic et al., 2018)’. Given that, just as in the above-cited article, we lacked a gold stand- ard, we used standard hyperparameters27 as available in the scikit-learn package (Pedregosa et al., 2011). The main weakness of affinity propagation remains the computational and memory costs: its O(n2)28 cost is limiting in larger datasets. 3.2 From words to concepts This is problematic in that some words might have a certain meaning in the context of the topic at hand that is not the main sense of the word, leading to bad clusters.29 Following this, we performed a manual evaluation on certain words to make sure that the models output semantically similar words. The models for all lan- guages except Swedish output words that were deemed correct.33 As a result, we retrained the Swedish word embeddings after performing some data alteration: we only kept sentences that were at least ten tokens long and for which the Sparv process- ing pipeline could find at least 50% of lemmas. Our manual checking confirmed that the word similarities for all languages and models post-1700 (where available) seemed meaningful, and that OCR errors were indeed captured and deemed similar.34 Similarly, all clusters—either with k-means or affinity propagation—were meaningful, as illustrated in the example in Fig. 4. Plotting clusters and their evolution across time—clusters are given weight through a fre- quency count of their members—showed the expected signal. For example, Fig. 435 shows the 1860–1880 situation in Finnish-language Finnish newspapers. The 1863 peak for the legislative cluster Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 4 Evaluation The method proposed in this article can be evaluated from two perspectives. First, intrinsically, we show that choices made in the preparation of the data and in the creation of the intermediate, aggregate data are reliable and produce sound output. Second, through a case study in four languages, we show that the method ii117 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 S. Hengchen et al. Fig. 4. Finnish-language clusters for 1860–1880 Downloaded from https://academic.oup.com/dsh/article/36/Supple Downloaded from https://academic.oup.com/dsh/article/36/Supplement_2/ii109/6421793 by Bibliotheque nationale de France user on 15 December 2021 Downloaded from https://academic.oup.com/dsh/article/36/Supplement_2/ii109/6421793 by Bibliotheque nationale de France user on 15 Fig. 4. Finnish-language clusters for 1860–1880 knowledge of the period. In English, for instance, we show (in Fig. 5) how affinity propagation produces only one cluster from the time bins from the 18th century, indicating that the language of national was tied to issues related to the military and the economy (debt in particular). Earlier research focusing on the history of economic thought has pointed this out (Hont, 2005), but perhaps because of the focus on the economy, the point has not been widely accepted in the literature. Our analysis on the totality of the material does point to a dominance of economic and military discourse in the period when conceptu- alizing things as national started to become more common. As expected, we also show that the era of the French revolution heralded a period of gestation in which national themes were associated with political and, to a certain extent, sentiment-related themes. This entailed a clear expansion of the conceptualiza- tion of what could be perceived as national. This pro- cess continued and, consequently, affinity propagation provides many more distinct clusters for the early 19th century. (hallitus, hallituksen, puolueen, hallitns, sota)36 stems from content about the 1863–1864 session of the Diet of Finland,37 the legislative assembly of the Grand Duchy of Finland. The red cluster exploding in 1871 (kokous—kokouksen—kokouksessa—kokoukselle— kokoukseen)38 stems largely from texts relating to the Franco-Prussian War. As we are proposing a method for which there is no gold standard and to which the notion of ‘absolute truth’ cannot be applied, the only way to determine whether the approach serves a purpose is to establish its usefulness.39 The second, extrinsic, part of our evaluation is described in the next section. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 5 Findings Harnessing word embeddings to cluster words is a powerful and useful tool when matched with the right kind of research questions. In the case of the expand- ing discourse of ‘national’, for example, our clustering proves the expansion of the vocabulary of nationhood. This does not as such challenge existing historiog- raphy, but clusters based on affinity propagation in- dicate this change in all four languages such that the clusters make sense to a reader with historical The clustering for Swedish, Finnish, and Dutch follows a similar pattern, but there are some differ- ences in the timing and contents. In Finnish, for in- stance, the word kansallinen (as a translation of the ii118 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 A data-driven approach to study changing vocabularies Downloaded from https://academic.oup.com/dsh/article/36/Supplement_2/ii109/6421793 by Bibliotheque nationale de France user on 15 Decem Fig. 5. Sankey chart of British clusters, 1740–1820 Downloaded from https://academic.oup.com/dsh/article/36/Supplement_2/ii109/6421793 by Bibliotheque nationale de France user on 15 December 2021 Fig. 5. Sankey chart of British clusters, 1740–1820 Fig. 5. Sankey chart of British clusters, 1740–1820 national) did not become really frequent before the 1850s (depending on the threshold), so naturally the development is different with a much quicker expan- sion of the vocabulary as established notions of na- tionhood readily translated into Finnish from Swedish, German, and English. As such, this suggests that the findings resonate with historical knowledge of the period and could therefore be used to further ex- plore national peculiarities with regard to the vocabu- lary of nationhood. signals in the data than a human reader could. We may now begin to examine in a data-driven way how different types of attitudes to nationhood emerge over time and in different places and languages. Our distributional methods based on affinity propagation performed well in tracing general devel- opment with regard to nationhood, but also point towards more detailed findings that could be eval- uated from the perspective of historical change. As such, we come much further from the use of key- word searches, simple plots of relative frequency, or even topic models in providing methods for diachron- ic change that relates to theories of long-term histor- ical change. It should also be possible to use the method in analyses of other themes such as (the changing vocabularies) of secularization, moderniza- tion, and the process of civilization. 5 Findings One way of looking at the cluster differences in the case of national is to pay attention to the nature of the clusters and not only to the linked individual words. Although focusing on the 19th century, such an ap- proach results in a clear division between sentiment- based (feeling, spirit, pride, prejudice) and object- based (bank, schools, council, government) nouns related to nationhood. When studying nationalism, this is a crucial division as they direct our attention to the growth of discourses relating to identity and affinity on the one hand and state institutions on the other. As such, they channel attention to the hypotheses about culturalization and institutionaliza- tion mentioned in Section 1. The aim in this article was not to make a full-fledged historical argument; however, it is enough to observe that, in the study of nationalism, the clusters produced through affinity propagation are perhaps more precise than what a historian reading texts would consider relevant themes, but at the same time, more detailed clusters could be thematically grouped and would seem to capture a greater level of (sometimes conflicting) Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 References Alagic, D., Snajder, J., and Pado´, S. (2018). Leveraging lex- ical substitutes for unsupervised Word sense induction. In Proceedings of the AAAI Conference on Artificial Intelligence (vol. 32, No. 1). Anderson, B. (2006). Imagined Communities: Reflections on the Origin and Spread of Nationalism. London: Verso. Antoniak, M. and Mimno, D. (2018). Evaluating the stabil- ity of embedding-based word similarities. Transactions of the Association for Computational Linguistics, 6: 107–19. Ball, T., Farr, J., and Hanson, R. L. (1989). Political innov- ation and conceptual change. Cambridge: Cambridge University Press. Funding Word embeddings, which are also at the core of the method in this article, have recently gained popularity in NLP, but their successful use in histor- ical studies is not so evident. Although there have been robust attempts to evaluate and sometimes compare NLP methods, it remains difficult to deter- mine what is actually modelled in different cases, and whether the performances are transferable to other languages, different corpora, or dissimilar time spans. In semantically clustering, all nouns relating to the word ‘national’, we trained diachron- ic word embeddings on the entirety of the full-text historical newspaper corpora at our disposal in Dutch, Swedish, Finnish, and English. We used both k-means and affinity propagation clustering, of which the latter seems to provide results that are more intuitive to a domain expert. Given that there is no safe way of determining what type of embed- ding best suits our purpose, and that no dynamic and continuous word-embedding models could be reliably used due to the extremely uneven distribu- tion of the data, we experimented with two relatively old architectures (CBOW and SGNS). This turned out to be a good, pragmatic choice: our manual evaluation showed that the models output seman- tically similar words and that the clustering lends itself to historical interpretation. As evaluation in the sense of using a gold standard is not possible, further evaluation of the method is to conduct more case studies that would allow deeper interpretations of changing vocabularies related to historical processes. This work was supported by the European Union’s Horizon 2020 research and innovation programme under grant 770299 (NewsEye), and computational resources were provided by CSC—IT Center for Science Ltd. S.H. is currently funded by the project Towards Computational Lexical Semantic Change Detection supported by the Swedish Research Council (2019–2022; dnr 2018-01184). Acknowledgements The authors are grateful to many people for the constructive discussions that led to this article. In par- ticular, and in no particular order: Melvin Wevers, Lidia Pivovarova, Elaine Zosa, Steven Claeyssens, Nina Tahmasebi, Sara Budts, Dominik Schlechtweg, Haim Dubossarsky, Joris van Eijnatten, Eetu Ma¨kela¨, Krister Linde´n, Gale Cengage, our reviewers, and the Helsinki Computational History (COMHIS) group. 6 Conclusion The aim in this article was to develop a data-driven method using word embeddings to examine how na- tion-states became central units for international pol- itics in the 19th century Europe. The study relied on large digitized newspaper datasets in four different languages. To our knowledge, such a large-scale com- parative study that grasps long-term development in as many as four languages and is statistically robust has not been attempted before. A major strength of this article is that by design, it is not limited to the study of nationhood but extends beyond it to different ii119 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 S. 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Association for Computational Linguistics, Florence, Italy, pp. 56–66. Marjanen, J. Author Contributions (2013).Den ekonomiska patriotismens uppga˚ng och fall: Finska husha˚llningssa¨llskapet i europeisk, svensk ochfinskkontext1720–1840.Helsinki:Helsinginyliopisto. Marjanen, J., Kurunma¨ki, J., Pivovarova, L., and Zosa, E. (2020). The expansion of isms, 1820–1917: Data-driven analysis of political language in digitized newspaper col- lections. Journal of Data Mining and Digital Humanities 10.46298/jdmdh.6159. Piotrowski, M.(2012). Naturallanguageprocessing forhis- torical texts. Synthesis Lectures on Human Language Technologies, 5: 1–157. ii123 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 S. Hengchen et al. Barcelona, Spain: Association for Computational Linguistics. Pivovarova, L., Marjanen, J., and Zosa, E. (2019). Word clus- tering for historical newspapers analysis. RANLP 2019 3. Recchia, G., Jones, E., Nulty, P., Regan, J., and de Bolla, P. (2017). Tracing shifting conceptual vocabularies through time. In Knowledge Engineering and Knowledge Management. Cham: Springer International Publishing, pp. 19–28 (https://doi.org/10.1007/978-3-319-58694-6_2). Shoemark, P., Ferdousi Liza, F., Nguyen, D., Hale, S. A., and McGillivray, B. (2019). Room to glo: a systematic comparison of semantic change detection approaches with word embeddings. In Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing. Barcelona, Spain: Association for Computational Linguistics. Reh˚urek, R. and Sojka, P. (2010). Software framework for topic modelling with large corpora. In Proceedings of the LREC 2010 Workshop on New Challenges for NLP Frameworks. ELRA, Valletta, Malta, pp. 45–50. Smith, A. (2013). Nations and Nationalism in a Global Era. New York: Wiley. Smith, A. (2008). The Ethnic Origins of Nations, 17 edn [reprint]. Malden: Blackwell. Rosenfeld, A. and Erk, K. (2018). Deep neural models of semantic shift. In Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Vol. 1 (Long Papers), New Orleans, Louisiana, pp. 474–84. Steinmetz, W. (2012). Some thoughts on a history of twen- tieth-century german basic concepts. Contributions to the History of Concepts, 7: 87–100. van Strien, D., Beelen, K., Ardanuy, M. C., Hosseini, K., McGillivray, B., and Colavizza, G. (2020). Assessing the impact of OCR quality on downstream NLP tasks. In ICAART (1), Valletta, Malta, pp. 484–96. Royal Dutch Library. (2017). Delpher open krantenarchief (1.0) CC BY 4.0 (text corpus). Royal Dutch Library. Rudolph, M. R. and Blei, D. M. (2018). Dynamic embed- dingsforlanguageevolution.InWWW2018.ACM,Lyon, France, pp. 1003–1011. Tahmasebi, N., Borin, L., and Jatowt, A. (2018). Survey of computational approaches to lexical semantic change. CoRR abs/1811.06278. Sa¨ily, T. (2016). Sociolinguistic variation in morphological productivity in eighteenth-century English. Corpus Linguistics and Linguistic Theory, 12: 129–151. Tang, X. (2018). Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 Author Contributions The complete list of newspapers is available at https://www.kielipankki.fi/wp-con tent/uploads/klk-lehdet-fi.pdf for Finnish, and at https:// www.kielipankki.fi/wp-content/uploads/klk-lehdet-sv.pdf for Swedish. Both links last accessed 4 November 2019. 8 We made use of text files created from the original XMLs by Prof. Eetu Ma¨kela¨, whom we thank. The complete list of newspapers is available at https://www.kielipankki.fi/wp-con tent/uploads/klk-lehdet-fi.pdf for Finnish, and at https:// www.kielipankki.fi/wp-content/uploads/klk-lehdet-sv.pdf for Swedish. Both links last accessed 4 November 2019. Author Contributions Survey paper: a state-of-the-art of semantic change computation. National Language English, 24: 649–76. Schierle, I. (2009). Patriotism and Emotions: Love of the Fatherland in Catherinian Russia. Ab Imperio, 3: 65–93. Tolonen, M., Lahti, L., Roivainen, H., and Marjanen, J. (2019). A quantitative approach to book-printing in Sweden and Finland, 1640–1828. Historical Methods: A JournalofQuantitativeandInterdisciplinaryHistory,52:57–78. Schlechtweg,D.,Ha¨tty,A.,DelTredici,M.,andSchulteim Walde, S. (2019). A wind of change: detecting and eval- uating lexical semantic change across times and domains. In Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics. Association for Computational Linguistics, Florence, Italy, pp. 732–746. VanSas,N.(1999).Vaderland:eengeschiedenisvandevijftiende eeuw tot 1940 (Reeks Nederlandse begripsgeschiedenis). Amsterdam, The Netherlands: Amsterdam University Press. Viola, L. and Verheul, J. (2019). Mining ethnicity: Discourse-driven topic modelling of immigrant discourses in the USA, 1898–1920. Digital Scholarship in the Humanities, 35(4): 921–43 (https://doi.org/10.1093/llc/fqz068). Schlechtweg, D. and Schulte im Walde, S. (2018). Comparing annotation frameworks for lexical semantic change. In Proceedings of the Workshop on Automatic Detection of Language Change 2018, Gothenburg, Sweden. Viroli, M. (1995). For Love of Country: An Essay on Patriotism and Nationalism. Oxford: Clarendon Press. Schlechtweg, D., Schulte im Walde, S., and Eckmann, S. (2018). Diachronic usage relatedness (DURel): A frame- work for the annotation of lexical semantic change. In Proceedings of NAACL-HLT, New Orleans, Louisiana, pp. 169–174. Wang, X., and McCallum, A. (2006). Topics over time: a non-Markovcontinuous-timemodeloftopicaltrends.In In Proceedings of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Philadelphia, Pennsylvania, pp. 424–433. Schlechtweg, D., McGillivray, B., Hengchen, S., Dubossarsky, H., and Tahmasebi, N. (2020). SemEval-2020 Task 1: unsupervised lexical semantic change detection. In Proceedings of the 14th International Workshop on Semantic Evaluation. Wevers, M. J. H. F. (2017). Consuming America: A Data-Driven Analysis of the United States as a Reference Culture in Dutch Public Discourse on Consumer Goods, 1890–1990. Utrecht, The Netherlands: Utrecht University. ii124 Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 4 A data-driven approach to study changing vocabularies Yao, Z., Sun, Y., Ding, W., Rao, N., and Xiong, H. (2018). Dynamicwordembeddingsforevolvingsemanticdiscov- ery. In Proceedings of the Eleventh ACM International Conference on Web Search and Data Mining, WSDM’18. ACM, Marina Del Rey, California, pp. 673–681 (https:// doi.org/10.1145/3159652.3159703) 7 https://www.delpher.nl/nl/platform/pages/helpitems? title¼dataþinþdelpher, last accessed 4 November 2019. 8 We made use of text files created from the original XMLs by Prof. Eetu Ma¨kela¨, whom we thank. Notes 9 To the best of our knowledge, there is no official data release for this public data. We retrieved the files starting with ‘kubhist2’ on https://spraakbanken.gu.se/lb/resur ser/meningsmangder/ (last accessed 1 November 2019) and, with the help of a Spra˚kbanken researcher, made sure that the data downloaded were the entirety of the corpus. S.H. was still affiliated with the University of Helsinki at that time. 9 To the best of our knowledge, there is no official data release for this public data. We retrieved the files starting with ‘kubhist2’ on https://spraakbanken.gu.se/lb/resur ser/meningsmangder/ (last accessed 1 November 2019) and, with the help of a Spra˚kbanken researcher, made sure that the data downloaded were the entirety of the corpus. S.H. was still affiliated with the University of Helsinki at that time. 1 The distributional hypothesis (Harris, 1954), popularised by the sentence ‘a word is characterized by the company it keeps’ (Firth, 1957) is the idea that words that occur in the same contexts tend to have similar meanings. 1 The distributional hypothesis (Harris, 1954), popularised by the sentence ‘a word is characterized by the company it keeps’ (Firth, 1957) is the idea that words that occur in the same contexts tend to have similar meanings. 2 A type is a class, whereas a token is an instance of that class. In the case of textual corpora, a type is a word, whereas ‘tokens’ denote all instances of that word. As an example, ‘to be or not to be’ contains four types (‘to’, ‘be’, ‘or’, and ‘not’) and six tokens. In the case of embeddings, a type-vector is a vector representation for all instances of a word (and thus conflates poly- semy), whereas a token-vector has a distinct vector representation for all occurrences of all tokens in the vocabulary. 10 https://www.gale.com/intl/primary-sources/british-li brary-newspapers (last accessed 1 November 2019). 11 https://www.gale.com/intl/c/17th-and-18th-century-nich ols-newspapers-collection(lastaccessed1November2019). 12 https://www.gale.com/intl/c/17th-and-18th-century- burney-newspapers-collection (last accessed 1 November 2019). Gale’s British Library Newspapers collection is large, but it is not comprehensive in the same sense as the National Library of Finland’s news- paper coverage, which has certain omissions of individ- ual issues and even newspaper titles but still be considered a full run of newspapers. The nineteenth- century coverage of the British newspaper collection is more local and regional, missing some of the central- London-based newspapers in particular. 12 https://www.gale.com/intl/c/17th-and-18th-century- burney-newspapers-collection (last accessed 1 November 2019). Notes Gale’s British Library Newspapers collection is large, but it is not comprehensive in the same sense as the National Library of Finland’s news- paper coverage, which has certain omissions of individ- ual issues and even newspaper titles but still be considered a full run of newspapers. The nineteenth- century coverage of the British newspaper collection is more local and regional, missing some of the central- London-based newspapers in particular. 3 Some examples from the NLP literature are: ‘gay’ (cheer- ful -> homosexual), ‘tweet’ (bird noise -> twitter post), and ‘broadcast’ (to sow seeds -> to transmit TV/radio). 4 Nonetheless, initiatives to tackle this very problem at the intersection of NLP and DH are being set up. For example, the International Workshop on Computational Approaches to Historical Language Change 2019 (https://language change.org/events/2019-acl-lcworkshop/, last accessed 3 November 2019) was an NLP workshop specifically aiming to be ‘an outlet for disseminating cutting-edge research on topics concerning language change’, to ‘bring together do- main experts across disciplines’, and to ‘raise fundamental theoreticalandmethodologicalchallenges’.Anotherexample is the SemEval 2020 Task 1 on Unsupervised Lexical Semantic Change Detection (https://competitions.codalab. org/competitions/20948, last accessed 3 November 2019), which uses unbalanced (except for English) historical data. 4 Nonetheless, initiatives to tackle this very problem at the intersection of NLP and DH are being set up. For example, the International Workshop on Computational Approaches to Historical Language Change 2019 (https://language change.org/events/2019-acl-lcworkshop/, last accessed 3 November 2019) was an NLP workshop specifically aiming to be ‘an outlet for disseminating cutting-edge research on topics concerning language change’, to ‘bring together do- main experts across disciplines’, and to ‘raise fundamental theoreticalandmethodologicalchallenges’.Anotherexample is the SemEval 2020 Task 1 on Unsupervised Lexical Semantic Change Detection (https://competitions.codalab. org/competitions/20948, last accessed 3 November 2019), which uses unbalanced (except for English) historical data. 13 We clarify the reasons behind the choice of this size in the next section. 13 We clarify the reasons behind the choice of this size in the next section. 14 In NLP, dependency parsing is the task of extracting syntactic relations between words in a sentence. For a gentle introduction to dependency grammar and de- pendency parsing, we recommend Nivre (2005). 14 In NLP, dependency parsing is the task of extracting syntactic relations between words in a sentence. For a gentle introduction to dependency grammar and de- pendency parsing, we recommend Nivre (2005). Notes 15 For the sake of clarity and unless we refer to a specific instance in another language, we use English words in the remainder of this article. 15 For the sake of clarity and unless we refer to a specific instance in another language, we use English words in the remainder of this article. 5 Such choices include: deciding on a (set of) word(s) to follow, ‘reading tea leaves’ (Chang et al., 2009) in a topic model, etc. We discuss the a priori definition of a topic in the following section. 16 In this precise case, nationaliteten is the singulardefinite form of nationalitet. 16 In this precise case, nationaliteten is the singulardefinite form of nationalitet. 16 In this precise case, nationaliteten is the singulardefinite form of nationalitet. 17 Kielipankki/Spra˚kbanken, https://www.kielipankki.fi/ language-bank/ (last accessed 26 October 2019). 17 Kielipankki/Spra˚kbanken, https://www.kielipankki.fi/ language-bank/ (last accessed 26 October 2019). 18 Spra˚kbanken, https://spraakbanken.gu.se/en (last accessed 18 November 2020). 18 Spra˚kbanken, https://spraakbanken.gu.se/en (last accessed 18 November 2020). 6 For recent examples and further discussion , see for in- stance Brandtzæg et al.(20182); Buntinx et al.(2017); and van den Bos and Giffard (2016). For a discussion on the role of the digitization of newspapers in historical re- search see Cordell (2016 102) and Milligan (2013). 19 We did not carry out a systematic, large-scale evalu- ation of the results of dependency parsing on English or Dutch, as this is well beyond the scope of this paper. 19 We did not carry out a systematic, large-scale evalu- ation of the results of dependency parsing on English or Dutch, as this is well beyond the scope of this paper. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 ii125 ii125 S. Hengchen et al. A manual evaluation of the results for all time bins indicates relatively high precision (i.e. output is made up of nouns), but we have no information regarding recall. For more on dependency parsing on (historical, OCRed) newspapers, see van Strien et al. (2020). A manual evaluation of the results for all time bins indicates relatively high precision (i.e. output is made up of nouns), but we have no information regarding recall. For more on dependency parsing on (historical, OCRed) newspapers, see van Strien et al. (2020). Notes 30 In general, between three and five annotators are needed to be able to calculate satisfactory inter-annotator agree- ment.SeeSchlechtwegetal.(2018,2020)andSchlechtweg and im Walde (2018) for a discussion on creating anno- tated ground-truth in diachronic corpora, and particular- ly on how domain experts (in that case, historical linguists) have better agreement scores—reinforcing our intuition that domain experts are needed. 20 See for example: Antoniak and Mimno (2018) and Mimno and Thompson (2017). 21 And thus t2 with t1, and t3 with t2, etc. 22 We used the code provided by Ryan Heuser, whom we thank. A copy is available at: https://gist.github.com/faus tusdotbe/5a87007aaccc1342608c049af83fc5d2.Asthecode effectively deletes vectors that are not in all time bins, we made sure our nation-related nouns were not deleted. 31 Additionally, we echo similar work (Hengchen and Tahmasebi, 2021) in stating that diachronic word embedding models finetuned on one task are not ne- cessarily perfect for other tasks. 32 Even if the OCR tool used is the same across all time bins, there is still variation in the input data (fonts, columns, etc.), forcing us to be thorough, and to evalu- ate all models. 23 As an extreme example: the 1880–1900 time bin of British newspaperscontains16,853,339,700tokensfor664,897,852 (lower-cased) types. Dropping tokens with a frequency below100forthetwodecadesleavesuswith2,043,844types (0.3% of the original), while still retaining 15,661,451,873 tokens(92.9% oftheoriginal).Todrivethepointhome:the enormous number of types is attributable to OCR errors. 33 A more thorough analysis should be conducted, but it seemed that the model could not abstract from the structure of definites and indefinites: for example, brev ‘letter’ and brevet ‘the letter’ were deemed less similar than brevet and gardet ‘the guard’—two tokens that share nothing apart from their suffix. Note: this observation was made on the first version of the corpus (Kubhist), the final embeddings used and released were trained on the larger, more recent version (Kubhist 2). 24 For both strategies and all languages, tokens were lower cased and the (hyper)parameters were as follows: con- tinuous bag-of-words (CBOW) for UPDATE and skip- gram with negative sampling (SGNS) for ALIGN, epochs ¼ 5, window ¼ 5, min_count ¼ 100, negative ¼ 5 (for SGNS), alpha ¼ 0.025 (for ALIGN and the first UPDATE model) and sample ¼ 0.001. 34 The reason we do not delve into the difference between clusters created with ALIGN and UPDATE models is that we could not find a meaningful difference. 25 https://zenodo.org/record/3585027 (last accessed 18 November 2020). Notes 26 For words w1 and w2, the similarity score is (w1w2)/ (kw1k kw2k), where w1 and w2 are, respectively, the L2- normalised vectors for w1 and w2 and k  k denotes the Euclidean norm. 35 The clusters were created using k-means with eight clusters. Different cluster sizes for the same time bin show the same behaviour. 36 Literally: ‘government’ in the nominative, ‘govern- ment’ in the genitive, ‘political party’ in the genitive, ‘government’ in the nominative with an OCR error, ‘war’ in the nominative. 27 Although the number of clusters cannot be set, the pref- erence hyperparameter (which defines the ‘will’ of an item to be an exemplar) can be tuned. 28 The ‘Big O notation’ is used to describe how calculation time or space requirements grow as the input of a cer- tain algorithm grows. In the case of O(n2), this means that the growth is quadratic: with an input of 10 the requirement is 102 ¼ 100, with an input of 100 the requirement is 1002 ¼ 10,000, etc. 37 Note that even if the original noun (waltiopa¨iva¨t, val- tiopa¨iva¨t, ‘state diet’) is not present as a keyword be- cause it was not modified by ‘national’, the event is still present. 37 Note that even if the original noun (waltiopa¨iva¨t, val- tiopa¨iva¨t, ‘state diet’) is not present as a keyword be- cause it was not modified by ‘national’, the event is still present. 38 Literally ‘meeting/assembly’ in different cases. 38 Literally ‘meeting/assembly’ in different cases. 39 For amore extensive discussion on the notion of ‘fitness for use’, see Boydens (1999). 29 We did not find that to be the case in our case study, and do not expect it to be a large problem. 29 We did not find that to be the case in our case study, and do not expect it to be a large problem. Digital Scholarship in the Humanities, Vol. 36, Supplement 2, 2021 ii126
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https://www.qeios.com/read/36PAZ1/pdf
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Review of: "Is gastrulation the most important time in your life?"
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Qeios, CC-BY 4.0 · Review, July 10, 2023 Qeios ID: 36PAZ1 · https://doi.org/10.32388/36PAZ1 Review of: "Is gastrulation the most important time in your life?" Yi Zheng1 1 Syracuse University Yi Zheng1 1 Syracuse University Potential competing interests: No potential competing interests to declare. Potential competing interests: No potential competing interests to declare. The author briefly summarized the evolvement of our understanding on gastrulation in an interesting way, and discussed neuromesoderm to challenge existing concepts. I agree with the author's perspective that there are still quite some unknown about embryo development. As a matter of fact, based on the studies of pluripotent stem cells, e.g., embryonic stem cells, a equivalent of in vivo epiblast, early cell lineages are still very plastic. The cells sometimes do not have to go through the natural developmental stages to differentiate into certain tissues cells. These cells can even be readily converted back to cell fates of earlier developmental stages. As we conduct more experiments, we may realize that cells, e.g., mesoderm, have more diverse sources than the views in the classical text books. To make this article more comprehensive, the authors could discuss more along this path. Qeios ID: 36PAZ1 · https://doi.org/10.32388/36PAZ1 1/1
https://openalex.org/W4240635492
http://scielo.iics.una.py/pdf/ccv/v8n1/2226-1761-ccv-8-01-5.pdf
Spanish; Castilian
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Prof. Dra. Elizabeth Nuñez Grüner, M.Sc Directora de la Revista “Compendio de Ciencias Veterinarias” doi: 10.18004/compend.cienc.vet.2018.08.01.5-6 DESAFÍOS DE LA INVESTIGACIÓN CIENTÍFICA Y TECNOLÓGICA La Facultad de Ciencias Veterinarias de la Universidad Nacional de Asunción está llamada a asumir de manera impostergable el desafío de imprimir mayor fuerza a la búsqueda de soluciones para la realidad nacional mediante la investigación científica y tecnológica. Los lineamientos en este ámbito deben orientarse a favorecer el logro de los objetivos estratégicos de la visión país 2030, de reducción de la pobreza, promoción del crecimiento económico inclusivo e inserción del país en el mundo. (1) En concordancia con el hecho de que son temas relevantes, el gasto público en este ítem se ha incrementado de 0,06% del PIB en el año 2008 a 0,13% del PIB en el 2015; aun así, continúa siendo la más baja inversión per cápita de la región (Br 1,14%, Ar 0,58%, Uy 0,33%). (2) En el contexto al que se hace referencia, nuestra casa de estudios ha tenido progresos. Entre ellos, se ha creado el Departamento de Investigación Científica y Tecnológica (DICT), definido líneas de investigación, el lanzamiento en el año 2011 de la revista “Compendio de Ciencias Veterinarias”. Así también, la FCV cuenta con Docente Investigador de Dedicación Completa (DIDCom) y una veintena de colegas del plantel docente, que han ingresado como investigadores categorizados del Consejo Nacional de Ciencia y Tecnología (CONACYT), hecho iniciado en el año 2013 y que al 2018 casi ha duplicado el número inicial. Por otro lado, se ha incrementado la calidad y cantidad de publicaciones científicas; que son logros destacables y dan cuenta de un franco avance hacia la internalización del concepto de que si no hay investigación, no hay conocimiento y si no hay conocimiento, no hay progreso. Por tanto, haciendo una pausa y mirando hacia atrás, es un hecho que el camino se ha iniciado y es preciso avanzar hacia la construcción de una comunidad educativa capaz de entregar medidas efectivas y eficaces a la sociedad en materia de generación y transferencia de conocimientos; con una gestión de investigación basada no solo en la interdisciplinariedad y concurrencia temática; sino que también y sobre todo, en dar respuestas a problemas trascendentes de la realidad nacional y regional. Prof. Dra. Elizabeth Nuñez Grüner, M.Sc Directora de la Revista “Compendio de Ciencias Veterinarias” doi: 10.18004/compend.cienc.vet.2018.08.01.5-6 5 ISSN 2226-1761 Compend. cienc. vet. 2018; 08 (01) : 5 - 6 ISSN 2226-1761 Compend. cienc. vet. 2018; 08 (01) : 5 - 6 5 ISSN 2226-1761 Prof. Dra. Elizabeth Nuñez Grüner, M.Sc Directora de la Revista “Compendio de Ciencias Veterinarias” SCIENTIFIC AND TECHNOLOGICAL RESEARCH CHALLENGES Veterinary Sciences Faculty of the National University of Asunción, it´s called to assume, in an urgent way, the challenge of strength the search of solutions for national reality through scientific and technological research. The guidelines, in this area, should be oriented to improve the strategic objectives achievement of the 2030 country vision, poverty reduction, inclusive economic growth promoting and the country's insertion in the world (1). Consistent with the fact that they are relevant issues, public spending on this item has increased from 0.06% of GDP in 2008 to 0.13% of GDP in 2015; even so, it continues to be the lowest investment per capita in the region (Br 1.14%, Ar 0.58%, Uy 0.33%). (2) In the context to which reference are made, our Studies House has made progress. Among them, the Scientific and Technological Research Department (DICT) has been created, defined research lines and the "Veterinary Sciences Compendium" magazine was launched in 2011. Likewise, the FCV has full-time Research Teachers (DIDCom) and about twenty colleagues from the teaching staff, who have entered as categorized researchers of the Science and Technology National Council (CONACYT), a fact that began in 2013 and that 2018 has almost doubled the initial number. On the other hand, quality and quantity of scientific publications have increased; which are remarkable achievements and account for a frank advance towards the internalization of the concept that if there is no research, there is no knowledge and if there is no knowledge, there is no progress. Therefore, by pausing and looking back, it is a fact that the road has begun and it is necessary to move towards the construction of an educational community capable of delivering effective measures to society in terms of knowledge generation and transfer. With a research management based not only on interdisciplinary and thematic concurrence, but also and above of all, in giving answers to transcendental problems of the national and regional reality. 6 ISSN Compend. cienc. vet. 2018; 08 (01) : 5 - 6 Compend. cienc. vet. 2018; 08 (01) : 5 - 6
https://openalex.org/W3158344372
https://iris.unipa.it/bitstream/10447/569585/2/StatisticsInMedicine2021.pdf
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Nowcasting COVID‐19 incidence indicators during the Italian first outbreak
Statistics in medicine
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Correspondence Correspondence Pierfrancesco Alaimo Di Loro, Department of Statistical Sciences, University of Rome “La Sapienza”, Rome, Lazio 00185, Italy. Email: pierfrancesco.alaimodiloro@uniroma1.it K E Y W O R D S 6Department of GEPLI, Libera Universitá Maria Ss Assunta, Rome, Italy COVID-19, growth curves, Richards’ equation, SARS-CoV-2 COVID-19, growth curves, Richards’ equation, SARS-CoV-2 7Department of Mathematics, University of Bergen, Bergen, Norway 8IAC - CNR, Institute of Applied Computing “M. Picone”, Rome, Italy Received: 24 October 2020 Revised: 8 March 2021 Accepted: 8 April 2021 Received: 24 October 2020 Revised: 8 March 2021 Accepted: 8 April 2021 DOI: 10.1002/sim.9004 Revised: 8 March 2021 Accepted: 8 April 2021 Received: 24 October 2020 DOI: 10.1002/sim.9004 R E S E A R C H A R T I C L E Nowcasting COVID-19 incidence indicators during the Italian first outbreak Pierfrancesco Alaimo Di Loro1 Fabio Divino2 Alessio Farcomeni3 Giovanna Jona Lasinio1 Gianfranco Lovison4,5 Antonello Maruotti6,7 Marco Mingione1,8 Pierfrancesco Alaimo Di Loro1 Fabio Divino2 Alessio Farcomeni3 Giovanna Jona Lasinio1 Gianfranco Lovison4,5 Antonello Maruotti6,7 Marco Mingione1,8 1Department of Statistical Sciences, University of Rome “La Sapienza”, Rome, Italy 2Department of Bio-Sciences, University of Molise, Campobasso, Italy 3Department of Economics and Finance, University of Rome “Tor Vergata”, Rome, Italy 4Department of Economics, Management and Statistics, University of Palermo, Palermo, Italy 5Department of Epidemiology and Public Health, Swiss TPH Basel, Basel, Switzerland 6Department of GEPLI, Libera Universitá Maria Ss Assunta, Rome, Italy 7Department of Mathematics, University of Bergen, Bergen, Norway 8IAC - CNR, Institute of Applied Computing “M. Picone”, Rome, Italy Correspondence Pierfrancesco Alaimo Di Loro, Department of Statistical Sciences, University of Rome “La Sapienza”, Rome, Lazio 00185, Italy. Email: pierfrancesco.alaimodiloro@uniroma1.it 1Department of Statistical Sciences, University of Rome “La Sapienza”, Rome, Italy 1Department of Statistical Sciences, University of Rome “La Sapienza”, Rome, Italy A novel parametric regression model is proposed to fit incidence data typically collected during epidemics. The proposal is motivated by real-time monitoring and short-term forecasting of the main epidemiological indicators within the first outbreak of COVID-19 in Italy. Accurate short-term predictions, includ- ing the potential effect of exogenous or external variables are provided. This ensures to accurately predict important characteristics of the epidemic (e.g., peak time and height), allowing for a better allocation of health resources over time. Parameter estimation is carried out in a maximum likelihood framework. All computational details required to reproduce the approach and replicate the results are provided. 2Department of Bio-Sciences, University of Molise, Campobasso, Italy 3Department of Economics and Finance, University of Rome “Tor Vergata”, Rome, Italy 4Department of Economics, Management and Statistics, University of Palermo, Palermo, Italy K E Y W O R D S COVID-19, growth curves, Richards’ equation, SARS-CoV-2 K E Y W O R D S COVID-19, growth curves, Richards’ equation, SARS-CoV-2 © 2021 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd. 2 10% of those infected.3 During the outbreak, it was crucial to set up appropriate data collection and modeling systems quickly. Both were necessary for monitoring, evaluation of policy interventions, and prediction. 10% of those infected.3 During the outbreak, it was crucial to set up appropriate data collection and modeling systems quickly. Both were necessary for monitoring, evaluation of policy interventions, and prediction. Generally speaking, the nature of epidemics’ spread has nearly always followed the same scenario: first, the growth in the number of infected people is (close to) exponential; in a second moment, this growth gradually but consistently slows down as an effect, for instance, of various containment measures. This pattern can cyclically recur until the outbreak is tamed. So far, in order to explain the spread of epidemics and predict their consequences, a number of mathematical and sta- tistical models of different complexity levels have been used. The starting point is often the Verhulst logistic equation,4 which can easily capture both the exponential increase in the number of infected people at the initial stage of the epi- demic development, and the tendency towards a constant value by its ending. In more complex models, people are divided into different groups: (S) the susceptible class, namely those individuals who are capable of contracting the dis- ease and becoming infected; (I) the infected class, namely those individuals who are capable of transmitting the disease to others; (R) the removed class, namely infected individuals who are deceased or have recovered, who are either perma- nently immune or isolated. This group of mathematical models are called SIR (or compartmental) models.5 References include,6-9 and several more. However, whilst being potentially very appropriate to model the dynamics underlying any epidemic, SIR-based models rely on accurate initial estimates of several quantities governing its spreading mechanism (which are unknown). Poor data input on key features of the pandemic can heavily bias these estimates, jeopardizing the reliability of any theory-based forecasting effort. SIR models are microsimulation models and we believe that, gen- erally speaking, they should be used mostly for “scenario evaluation” rather than predicting future outcomes. Indeed, they rely on several speculations and strict theoretical assumptions, not necessarily met by the analyzed data and, espe- cially during the first stage of the outbreak, failed in predicting various COVID-19 related outcomes.10 Such specifics lead the choice of coefficients in the equations defining the SIR model and define its initial conditions. It is well known that even a slight change in those can lead to large differences in the final results. For instance, at the beginning of the epi- demic, early data providing estimates for case fatality rate, infection fatality rate, basic reproductive number, and other key numbers that are essential for the modeling, are often inflated and may cause potentially large overestimation of the epidemic severity. Similar criticism to using compartmental modeling for nowcasting can also be found in Reference 11, and references therein. Hence, we have preferred to follow an alternative approach, which involved direct modeling of the observed counts.12 This encompasses the use of phenomenological models without detailed mechanistic foundations, but which have the advantage of allowing simple calibrations to the empirical reported data. Such approaches are partic- ularly suitable when substantial uncertainty tarnishes the epidemiology of an infectious disease, including the potential contribution of multiple transmission pathways. In these situations, phenomenological models provide a starting point for obtaining early estimates of the transmission potential and short-term forecasts of the epidemic evolution.13 g We propose a parametric regression model for the modeling of incidence indicators (defined in Section 2.1) based on the use of the Richards’ curve (a generalized logistic function) in place of the widely used exponential or polynomial trends. Furthermore, we replace the generally entrenched Gaussian assumption for the distribution of log-counts14,15 by the more appropriate Poisson or Negative Binomial distributions for counts. In this way we avoid the implausible assumptions stemming from the more common alternatives: the former allows the underlying counts to potentially grow indefinitely; the latter neglects the proper specification of dependence between mean and variance under the log-normal distribution. We further propose different ways of including the effect of exogenous information on the response function of counts, in an extended generalized linear model framework. These models have been implemented during the outbreak with the aim of modeling the medium to long term evolution of the epidemic wave. 1 INTRODUCTION Italy has been the first European country to be severely hit by the first epidemic wave due to the spread of the SARS-CoV-2 virus. COVID-19 syndrome emerged in northern Italy in February 2020, with a basic reproduction number R0 between 2.5 and 4.1 In its most severe form, COVID-19 has two challenging characteristics:2 it is highly infectious and, despite having a benign course in the vast majority of patients, it requires hospital admission and even intensive care for about 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. © 2021 The Authors Statistics in Medicine published by John Wiley & Sons Ltd Italy has been the first European country to be severely hit by the first epidemic wave due to the spread of the SARS-CoV-2 virus. COVID-19 syndrome emerged in northern Italy in February 2020, with a basic reproduction number R0 between 2.5 and 4.1 In its most severe form, COVID-19 has two challenging characteristics:2 it is highly infectious and, despite having a benign course in the vast majority of patients, it requires hospital admission and even intensive care for about wileyonlinelibrary.com/journal/sim Statistics in Medicine. 2021;1–22. 1 ALAIMO DI LORO et al. 2.1 Incidence and prevalence indicators: different mathematical features The epidemiological data provided by CPD can be distinguished into two basic types: 1. incidence indicators (flows) 1. incidence indicators (flows) 2. prevalence indicators (stocks) The use of logistic-based curves is also widely discussed in the literature.16-18 Logistic growth curves can be seen as a flexible formulation for approximating a large variety of growth phenomena, especially in biology and in epidemiology.19-23 In particular, highly flexible parametric models such as Gompertz curves and the unified Richards’ family24 have been proposed in the study of organisms’ growth, for a review see Reference 25. The article is organized as follows: Section 2 gives a detailed description of the Italian situation and provides a brief account of the Italian public data made available daily, with some remarks on limitations and flaws in the data collection process; Section 3 contains a description of our approach to modeling incidence indicators, including remarks on how to obtain standard errors for parameters and predictions performances; Section 4 illustrates results of our approach applied to the incidence indicators recorded during first wave of the Italian outbreak of COVID-19. Finally, results are discussed and commented along with some concluding remarks in Section 5. The methods discussed in this article have also been implemented in a Shiny app, publicly available at https:// statgroup19.shinyapps.io/StatGroup19-Eng/. in this article have also been implemented in a Shiny app, publicly available at https:// tatGroup19-Eng/. ALAIMO DI LORO et al. 3 2 AVAILABLE DATA AND THEIR LIMITATIONS The Italian Civil Protection Department (CPD), starting from February 24th, 2020, has been gathering data at the regional level every day and making these public in a GitHub repository. During most of the Italian epidemic, data were com- mented by the department head in an official press release at about 6 pm. The daily updated data are currently stored at https://github.com/pcm-dpc/COVID-19. For public health service purposes, Italy is divided into 21 regions. There are 19 administrative regions, plus two autonomous provinces (Trento and Bolzano) that form the administrative region of Trentino-Alto-Adige. In the sequel, we focus on modeling the indicators aggregated at the national level. Nevertheless, the supplementary material contains graphical and quantitative performances of our model on the 21 single regions. 2.1.1 Incidence indicators (B) F I G U R E 1 Time series the Italian daily incidence indicators: daily positives, A an daily deceased, B (B) F I G U R E 1 Time series of the Italian daily incidence indicators: daily positives, A and daily deceased, B F I G U R E 1 Time series of the Italian daily incidence indicators: daily positives, A and daily deceased, B (A) (B) (B) F I G U R E 2 Time serie the Italian cumulative incide indicators: cumulative positiv A and cumulative deceased, B (B) (A) F I G U R E 2 Time series of the Italian cumulative incidence indicators: cumulative positives, A and cumulative deceased, B F I G U R E 2 Time series of the Italian cumulative incidence indicators: cumulative positives, A and cumulative deceased, B (A) (B) By their nature of cumulative counts, these data series are necessarily monotonically nondecreasing (see Figure 2 for the positives and deceased example). By their nature of cumulative counts, these data series are necessarily monotonically nondecreasing (see Figure 2 for the positives and deceased example). 2.1.1 Incidence indicators Incidence indicators measure the number of individuals with a particular condition, related with the epidemic, recorded during a given period. They can be referred to different time periods; in particular, in the CPD dataset, daily incidence counts are available for the following indicators: • positives, which are subclassified into two subconditions: – hospitalized (either in regular wards or in ICU) – isolated-at-home • deceased • recovered/discharged • recovered/discharged These indicators can be considered, by analogy with the terminology used in econometrics, as flow data, quantifying the daily input (positives) and output (deceased and recovered/discharged) of the system. The time series of daily positives and daily deceased aggregated at the national level are shown in Figure 1. From the viewpoint of the following modeling effort, one important feature of these indicators is that they can be referred to longer time intervals, simply cumulating them over time. The most interesting cumulative incidence indicators are those referring to the whole history of the pan- demic, computed from a conventional date of “beginning of the pandemic” (typically, the day the systematic recording of daily positives began) to the current day: • cumulative positives • cumulative deceased • cumulative recovered/discharged In particular, given Y 0 = 0, we can build the whole series of cumulative counts conditionally on the value of the cumulative indicator at time (t −1), and the incidence indicators at time t, for each t = 1, … , T: Y c t = Y c t−1 + It, where Y c t represents the cumulative indicator and It represents the inputs in the system, for example: cumulative positives at time t are the cumulative positives at time (t −1) plus the daily positives at day t. 4 ALAIMO DI LORO et al. (A) (B) F I G U R E 1 Time series of the Italian daily incidence indicators: daily positives, A and daily deceased, B (A) (B) F I G U R E 2 Time series of the Italian cumulative incidence indicators: cumulative positives, A and cumulative deceased, B By their nature of cumulative counts, these data series are necessarily monotonically nondecreasing (see Figure 2 for the positives and deceased example). 4 (A) ALAIMO DI LORO et al. 2.1.2 Prevalence indicators Prevalence indicators measure the number of individuals with a particular condition, related with the epidemic, at a given instant in time (or at a given short interval of time, eg, a day). They are typically obtained from simple algebra from other indicators; in particular, in the CPD dataset, the following indicators are available daily: • current positives; • current intensive care units (ICU) occupancy. These indicators result from the balance between total inputs and outputs of the system, for example: current positives are the difference between cumulative positives and cumulative deceased plus recovered/discharged. Again, by analogy with the terminology used in econometrics, they can be considered as stock data. In particular, given Y 0 = 0, we can build the whole series conditionally on the value of the prevalence indicator at time (t −1), and the incidence indicators at time t, for each t = 1, … , T: Y p t = Y p t−1 + It −Ot, ALAIMO DI LORO et al. 5 F I G U R E 3 Time series of Italian daily prevalence indicators: current positive, A and ICU occupancy, B (A) (B) where Y p t represents the prevalence indicator, It represents the inputs in the system and Ot represents the outputs, for example: current positives at time t are the current positives at time (t −1) plus the daily positives at day t and minus the sum of deceased and discharged recovered at day t. However, given the different delay in reporting the various information by the regional agencies, there exists a relevant temporal misalignment among all the quantities reported at the daily scale. Therefore, the simultaneous consideration of all these flows may be significantly flawed and we rather prefer modeling the indicators individually. Two important features of these indicators are that: 5 (B) ALAIMO DI LORO et al. 2.1.2 Prevalence indicators by their own nature, these indicators are not monotone, since they can increase or decrease as a result of different trends of the component series. Typically, we expect the series of current positives and ICU occupancy to increase in the rising phase of an epidemic, reach a peak and then decrease to a lower asymptote (see Figure 3), although more complex patterns due to resurgence of the epidemic are also plausible. Prevalence indicators are characterized by a strong and tangled dependence structure which is cumbersome to simplify into a manageable and useful statistical model on the short run. For this reason, the focus of this work concerns only incidence indicators. Our model proposal, from a strictly mathe- matical point of view, could potentially applied also on prevalence indicators. However, from the statistical point of view, the modeling assumptions which are assumed to hold (with good approximation) considering the incidence indicators, are likely to be strongly violated by prevalence indicators and the resulting outcome cannot be considered reliable. A brief discussion about some possible approaches for the analysis of prevalence indicators is given in Section 5. 2.1.2 Prevalence indicators 5 Time series of evalence rent positive, upancy, B (A) F I G U R E 3 Time series of Italian daily prevalence indicators: current positive, A and ICU occupancy, B F I G U R E 3 Time series of Italian daily prevalence indicators: current positive, A and ICU occupancy, B (B) (A) where Y p t represents the prevalence indicator, It represents the inputs in the system and Ot represents the outputs, for example: current positives at time t are the current positives at time (t −1) plus the daily positives at day t and minus the sum of deceased and discharged recovered at day t. However, given the different delay in reporting the various information by the regional agencies, there exists a relevant temporal misalignment among all the quantities reported at the daily scale. Therefore, the simultaneous consideration of all these flows may be significantly flawed and we rather prefer modeling the indicators individually. Two important features of these indicators are that: where Y p t represents the prevalence indicator, It represents the inputs in the system and Ot represents the outputs, for example: current positives at time t are the current positives at time (t −1) plus the daily positives at day t and minus the sum of deceased and discharged recovered at day t. However, given the different delay in reporting the various information by the regional agencies, there exists a relevant temporal misalignment among all the quantities reported at the daily scale. Therefore, the simultaneous consideration of all these flows may be significantly flawed and we rather prefer modeling the indicators individually. Two important features of these indicators are that: 1. given their stock nature, they cannot be aggregated (eg,: it does not make sense to compute “cumulative current positives”); 1. given their stock nature, they cannot be aggregated (eg,: it does not make sense to compute “cumulative current positives”); 2. by their own nature, these indicators are not monotone, since they can increase or decrease as a result of different trends of the component series. Typically, we expect the series of current positives and ICU occupancy to increase in the rising phase of an epidemic, reach a peak and then decrease to a lower asymptote (see Figure 3), although more complex patterns due to resurgence of the epidemic are also plausible. 2. could be even weeks before. Positive status is also counted on the day that test results are received, with swabs being processed from one day to weeks after symptoms’ onset. No distinction between actively symptomatic and asymptomatic patients was made. Swabs and positive cases are not time-aligned. For example, in countries like Singapore (https://www.moh.gov.sg/ covid-19), daily data include information on total swabs tested, total unique persons swabbed as well as total swabs per 1 000 000 total population and total unique persons swabbed per 1 000 000 total population. In Italy, up to April 19th, 2020, only the total number of daily swabs is available, and no linkage between swabs and tested individuals was kept in the data repository. Hence, it is impossible to make statistically sound use of swabs’ count to model the whole first pandemic wave. Finally, it is crucial to recall that people diagnosed with COVID-19 disease are only a small fraction of the people infected by the virus. Moreover, since the tracking was highly symptoms driven, especially in the first phase of the out- break, the detected number of positives cases can provide only a partial estimate of the true incidence of COVID-19 in the Italian population. Eventually, we expect this detected fraction to vary wildly over space and time. In our opinion, the most reliable indicator is the count of ICU occupancy. The reason is that the Italian Society for Emergency Care issued national guidelines (that did not change substantially during the epidemic) for testing patients with a suspected infection by SARS-CoV-2, who also had top priority for swab access and reporting; and ICU admissions can be expected to depend on the proportion of infected population susceptible to severe infection, rather than on the regional strategy for testing and contact tracing. However, while probably reliable, this indicator also presents some draw- backs. First of all, it provides only a partial snapshot of the epidemic’s current stage, which concerns the most severe cases of the disease. The latter is a critical issue, especially in the COVID-19 case, which is known to present severe symptoms only in a small percentage of the currently affected individuals. Second, this snapshot is affected by a constant delay (ie, the time between catching the disease and manifesting severe symptoms). As mentioned in Section 2.1.2, its daily vari- ation is obtained as a combination of new incoming patients (+) and the deceased or recovered ones (-), whose effects blend and are hard to disentangle. As a consequence, incidence indicators, such as daily positives and daily deceased, while being measured with some error and even more delay in the case of deaths, still represent the critical indicators for timely and appropriate monitoring of the pandemic. 3 MODEL SPECIFICATION The time series of any of the observed indicators, denoted by z = {zt}T t=t0, is modeled separately and considered as the realization of the stochastic process Z = {Zt}T t=t0. The idea behind this article is to model any of the mentioned indicators through a Generalized Model with a response function E[Zt] = 𝜇(t) = g−1(t; 𝜽), where g(⋅) is a known link function and 𝜽is a parameter vector, that is appropriate for the specific mathematical features of the epidemic process. This must be coupled with a response distribution f(Zt; 𝛉) coherent with the domain of such indicators, which are counts and therefore Natural numbers. 2.2 Data issues COVID-19 public Italian data present several issues that severely affect their quality. The information has been gathered and reported at a regional level, and each regional healthcare organization has a different transmission and data collection system*. Measurement errors, and errors in data entry, are expected to be often present. Delays in reporting has been, sometimes, substantial. Some patients were transferred (eg, from Lombardia to Puglia, and even to Germany) without notification, and they were counted as hospital patients of the receiving region (or not at all when sent abroad) and posi- tive cases of the region of residence. Most importantly, counts were updated on the notification day rather than aligned to a more appropriate date. For example, death is counted on the day of the reporting, not on the day of the outcome, which *see https://www.epiprev.it/materiali/2020/EP2-3/112_edit1.pdf for further details. ALAIMO DI LORO et al. 3.1 Response function for incidence indicators F I G U R E 4 Example of Richards’ curve, A and derivative of the Richards’ curve, B 0.0 0.3 0.6 λ 0.9 0 1 2 3 4 5 t (A) t F I G U R E 4 Example of Richards’ curve, A and derivative of the Richards’ curve, B F I G U R E 4 Example of Richards’ curve, A and derivative of the Richards’ curve, B (B) can be expressed as: can be expressed as: E[Y c t ] = g−1(t; 𝜸) = 𝜆𝜸(t) = b + r (1 + 10h(p−t))s . (1) E[Y c t ] = g−1(t; 𝜸) = 𝜆𝜸(t) = b + r (1 + 10h(p−t))s . (1) b ∈R+ represents a lower asymptote and r > 0 is the distance between the upper and the lower asymptote, hence b + r would be the final epidemic size; h is known as the hill, and represents the infection/growth rate; p ∈R represents a lag-phase of the trajectory and determines the peak position (it tells when the curve growth speed slows down); s ∈R is an asymmetry parameter regulating differences in the behavior of the ascending and descending phase of the outbreak. In our context, since cumulative incidences are always monotone increasing indicators, it is reasonable to assume h, s > 0 †. An extensive review of the Richards’ curve and other logistic growth models, together with discussion on the proper interpretation of the parameters, is given in Reference 24. An extensive review of the Richards’ curve and other logistic growth models, together with discussion on the proper interpretation of the parameters, is given in Reference 24. An Extended Generalized Linear Model with (1) as response function seems to be a natural choice for modeling time series of cumulative counts, whose monotonically nondecreasing average behaves as the Richards’ curve. Unfortunately, there is a significant drawback to this choice. As it will be better clarified in Section 3.2, a very useful working assumption would be that all these counts were stochastically independent, given their mean function 𝜆𝜸(t). However, we cannot consider this assumption as realistic in the case of cumulative counts, since the constraint on the domain of definition on subsequent counts (ie, yc t ≥yc 𝜏, ∀𝜏< t) is not guaranteed to be satisfied. †Conversely, we may assume h, s < 0 3.1 Response function for incidence indicators Let us denote by {yc t}T t=0 the time-series of cumulative incidence indicators since the start of the epidemic (t0 = 0, first day of systematic data recording). Visual inspection of these indicators in Figure 2 suggests that their expected values follow a logistic-type growth curve. Different example of logistic curves have been proposed in the literature, all representing solutions to specific differential equations that model the spread of epidemics.26-28 Differently from the more standard exponential models, these are able to describe the slowdown of the outbreak associated with a decaying transmission rate just after the number of cases approaches its inflection point. They have been already widely used to describe the evolution of the COVID-19 pandemic in different states during its early to medium stage.29,30 Here, for all the incidence indicators, we consider the Generalized Logistic Function, also known as Richards’ curve (see Figure 4 as an example), as response function for the mean of the process.31 This curve was widely used to describe various biological processes,32 but has been recently adapted also in epidemiology for real-time prediction of outbreak of diseases.33-35 The specialty of the Richards’ curve lies in its ability to describe a great variety of growing processes, endowed with strong flexibility, that includes as special cases the standard logistic growth curve,36 the Gompertz growth curve37 and others. It can be expressed in different forms.38-41 One of its most general formulation depends on the vector of five parameters 𝜸⊤= [b, r, h, p, s] and ALAIMO DI LORO et al. 7 F I G U R E 4 Example of Richards’ curve, A and derivative of the Richards’ curve, B 0.0 0.3 0.6 λ λ 0.9 0 1 2 3 4 5 t (A) (B) t 0.00 0.02 0.04 0.06 0 1 2 3 4 5 t t ~ can be expressed as: E[Y c t ] = g−1(t; 𝜸) = 𝜆𝜸(t) = b + r (1 + 10h(p−t))s . (1) 7 λ (B) 0.00 0.02 0.04 0.06 0 1 2 3 4 5 t t ~ ALAIMO DI LORO et al. 8 ALAIMO DI LORO et al. In addition, we may also consider adding a kink effect/baseline 𝛼to the first differences ̃𝜆𝜸(⋅), which is to say assuming the following functional form for the mean of the daily counts: ̃𝜇𝜽(t) = 𝛼+ ̃𝜆𝜸(t), 𝛼≥0, (2) ̃𝜇𝜽(t) = 𝛼+ ̃𝜆𝜸(t), 𝛼≥0, (2) ̃𝜇𝜽(t) = 𝛼+ ̃𝜆𝜸(t), 𝛼≥0, (2) where 𝜽= (𝛼, 𝜸). This would correspond to the following mean function for the cumulative counts: orrespond to the following mean function for the cumulative counts: 𝜇𝜽(t) = 𝛼⋅(t −1) + 𝜆𝜸(t). 𝜇𝜽(t) = 𝛼⋅(t −1) + 𝜆𝜸(t). In practice, the parameter 𝛼includes the possibility of having a strictly positive baseline rate, which can be interpreted as the endemic steady state incidence rate. This is in line with the current perspective that SARS-CoV-2 might not be completely eradicated within the next few years.42 On the other hand, the first differences of the Richards’ curve ̃𝜆𝜸(t) are (by construction) forced to decrease asymptotically to the value of 0. However, this asymptotic result is not necessarily observed in real data. In particular, Figure 1 highlights that both time-series do not attain the 0 value, but settle to a low, constant level. This situation may, potentially, continue indefinitely: new cases will be found as long as people will be tested. Consequently, the model without a baseline lacks the ability to catch this tail and, because of the curve parametric form, this may indirectly affect the fit on the whole series. In practice, the parameter 𝛼includes the possibility of having a strictly positive baseline rate, which can be interpreted as the endemic steady state incidence rate. This is in line with the current perspective that SARS-CoV-2 might not be completely eradicated within the next few years.42 On the other hand, the first differences of the Richards’ curve ̃𝜆𝜸(t) are (by construction) forced to decrease asymptotically to the value of 0. However, this asymptotic result is not necessarily observed in real data. In particular, Figure 1 highlights that both time-series do not attain the 0 value, but settle to a low, constant level. This situation may, potentially, continue indefinitely: new cases will be found as long as people will be tested. Consequently, the model without a baseline lacks the ability to catch this tail and, because of the curve parametric form, this may indirectly affect the fit on the whole series. 8 In the first instance, one solution would be to fit the model, including the kink effect 𝛼. Afterward, if it is estimated not to be sensibly different from 0, the model without 𝛼can be fitted again to stabilize the estimation procedure and decrease the uncertainty on the other parameters. 3.2 Response distribution for incidence indicators Before introducing the distributions for the daily incidence counts, we must make some assumptions about the time dependence structure. In particular, we assume that given the mean function ̃𝜇𝜽(t), the daily incidence counts Y t are stochastically independent from the previous cumulative counts: Yt⊥Y c 𝜏∀𝜏< t. We denote this hypothesis of indepen- dence by HI. We also assume the value of the first cumulative count Y c 0 = yc 0 to be known and fixed. Exploiting HI, we can express the joint density of all the subsequent cumulative counts conditional on Y c 0 = yc 0 as the product of the univariate densities of the corresponding daily counts {Yt}T t=1. The equivalence follows from the following conditional argument: fY c 1, … ,Y c T(yc 1, … , yc T|yc 0; 𝜃) = T ∏ t=1 fY c t (yc t|yc 0, … , yc t−1; 𝜃) = T ∏ t=1 fY c t (yt + yc t−1|yc 0, … , yc t−1; 𝜃) = = T ∏ t=1 fYt(yt|yc 0, … , yc t−1; 𝜃) HI= T ∏ t=1 fYt(yt|𝜃), where the second identity is justified in the light of Y c t = Yt + Y c t−1, t = 1, … , T, which is true by definition. From a practical point of view, this also implies a first-order Markov property for the cumulative counts: where the second identity is justified in the light of Y c t = Yt + Y c t−1, t = 1, … , T, which is true by definition. From a practical point of view, this also implies a first-order Markov property for the cumulative counts: Y c t |Y c t−1⊥Y c 1, … , Y c t−2, t = 1, … , T Y c t |Y c t−1⊥Y c 1, … , Y c t−2, t = 1, … , T and mutual independence between the daily counts: and mutual independence between the daily counts: Yt⊥Y𝜏, ∀t, 𝜏, t ≠𝜏. We remark that although these independence structure is just an approximation in the present case, this kind of approach has provided valid inference for all the available Italian incidence indicators. We remark that although these independence structure is just an approximation in the present case, this kind of approach has provided valid inference for all the available Italian incidence indicators. 3.1 Response function for incidence indicators On the other hand, the stochastic independence assumption sounds more reasonable, albeit not necessarily true, for the daily incidence counts {yt}T t=1, that is, the addenda of the cumulative counts excluding the starting point y0, which can be defined as: yc t = t∑ 𝜏=0 y𝜏 ⇒ yt = yc t −yc t−1, t = 1, … , T, where y0 = 0 by definition. where y0 = 0 by definition. y0 y Using Equation (1), and exploiting the additive properties of the expected value, we have: Using Equation (1), and exploiting the additive properties of the expected value, we have: ̃𝜇(t) = E[Yt] = E[Y c t ] −E[Y c t−1] = 𝜆𝜸(t) −𝜆𝜸(t −1) = = r ⋅[(1 + 10h(p−t))−s −(1 + 10h[p−(t−1)])−s] = ̃𝜆𝜸(t) which, in particular, does not depend on the baseline b. Therefore, we shall adopt an extended Generalized Model with response function given by the first differences of the Richards’ curve ̃𝝀𝜸= { ̃𝜆𝜸(t)}T t=1 to model the daily expected values 𝝁= {𝜇(t)}T t=1 of the observed incidence counts y = {yt}T t=1 (see example in Figure 4). which, in particular, does not depend on the baseline b. Therefore, we shall adopt an extended Generalized Model with response function given by the first differences of the Richards’ curve ̃𝝀𝜸= { ̃𝜆𝜸(t)}T t=1 to model the daily expected values 𝝁= {𝜇(t)}T t=1 of the observed incidence counts y = {yt}T t=1 (see example in Figure 4). †Conversely, we may assume h, s < 0 3.2.1 Poisson distribution or of daily incidence counts, y = {y1, … , yt}, is composed of independent Poisson realizations Let us assume that the vector of daily incidence counts, y = {y1, … , yt}, is composed of independent Poisson realizations with expected value ̃𝜇𝜽(t): Yt|𝜽∼Pois( ̃𝜇𝜽(t)), t = 1, … , T. Hence, the likelihood can be written as: Hence, the likelihood can be written as: Hence, the likelihood can be written as: (𝜽|y) = T ∏ t=1 Pois(yt| ̃𝜇𝜽(t)) ∝ ∝̃𝜇𝜽(t) ∑T t=1yt ⋅exp { − T ∑ t=1 ̃𝜇𝜽(t) } and the log-likelihood is given by: l(𝜃|y) = log (𝜽|y) ∝ T ∑ t=1 yt log( ̃𝜇𝜽(t)) − T ∑ t=1 ̃𝜇𝜽(t). (𝜽|y) = T ∏ t=1 Pois(yt| ̃𝜇𝜽(t)) ∝ ∝̃𝜇𝜽(t) ∑T t=1yt ⋅exp { − T ∑ t=1 ̃𝜇𝜽(t) } and the log-likelihood is given by: and the log-likelihood is given by: l(𝜃|y) = log (𝜽|y) ∝ T ∑ t=1 yt log( ̃𝜇𝜽(t)) − T ∑ t=1 ̃𝜇𝜽(t). Remark that, under the assumption of Poisson distribution and the baseline 𝛼= 0 (ie, ̃𝜇(𝛼,𝜸) = ̃𝜆𝜸(⋅)), we can exploit the well-known Poisson’s additive property ‡ to conclude that each cumulative count Y c t is still marginally distributed according to a Poisson, parameterized by the original Richards’ curve function 𝜆𝜸(⋅): Y c t |𝜸∼Pois ( t∑ 𝜏=1 ̃𝜆𝜸(𝜏) ) = Pois(𝜆𝜸(t)). 3.2 Response distribution for incidence indicators For communication purposes, it can be of interest to report the results of analyses and predictions in terms of cumu- lative, rather than daily, incidence indicators. Clearly, it is possible to model and predict the daily incidence indicators and, from these estimates and predictions, obtain the relevant cumulative incidence indicators. ALAIMO DI LORO et al. 9 3.3 Response function depending on covariates The trend of any of the considered indicators may also depend on additional exogenous information, which we may assume to be known a priori either because it is immutable (ie, the day of the week), or because policymakers fixed it (daily number of tested cases/swabs set by the government). For instance: one might want to correct for possible weekly seasonality, which is known to affect the daily positives series since many laboratories are closed during the weekend and cannot evaluate swabs. The latter can be used to disentangle the underlying trend of the epidemic from the obvious positive correlation between tested cases and daily positives. In general, we may want to include the effect of any set of k time-varying covariates XT×(k+1) = [x(t)]T t=1 in the Richards’ framework through the usual linear predictor 𝜂(X) = X𝜷, where 𝜷is a k + 1-dimensional vector of real valued parameters (including intercept). Let us denote the mean function of the considered indicator as ̃𝜇𝜃(t) = E[Yt], where 𝜽= (𝛼, 𝜸, 𝜷). In order to respect the positivity of the mean parameter (which is necessary both in the Poisson and in the Negative Binomial case), we consider the link function g(⋅) = log(⋅), so that the effect on the mean is expressed as: 𝜇𝜷(X) = exp{𝜂(X)} = exp{X𝜷}. Considering a single time point t, we would get the following functional form: Considering a single time point t, we would get the following functional form: 𝜇𝜷(x(t)) = exp{x(t)𝜷}. The mean term of our model shall take into account both the effect of the covariates through 𝜇𝜷(⋅) and the temporal behavior induced by the Richards’ curve 𝜆𝜸(⋅). As a matter of fact, these two components may be combined in different ways. We considered two alternative specifications denoted in the sequel as: additive and multiplicative. 3.3.1 Additive inclusion of covariates The inclusion of an additive effect of covariates implies that the effect of every covariate is constant through-out the pandemic, notwithstanding the current contagion level: for instance, one may think that an increase of daily tested cases will always produce the same increase of daily daily positives. If that is the case, we may just express the baseline parameter 𝛼at each time-point t as the linked linear combination of covariates 𝜇𝜷(x(t)) = exp{x(t)𝜷}, which would produce the following mean function: ̃𝜇𝜃(t) = 𝜇𝜷(x(t)) + ̃𝜆𝜸(t). On the whole vector of observations, this can be expressed as ̃𝝁𝜽= 𝜇𝜷(X) + ̃𝝀𝜸. 10 The Negative Binomial does not satisfy the same additive property as the Poisson, hence we cannot draw the same conclusion reached in the Poisson case about the marginal distribution of the cumulative count Y c t when 𝛼= 0. In gen- eral, the cumulative count in the NB case will follow the distribution stemming from the sum of independent Negative Binomial r.v. with common dispersion parameter 𝜈but different means ̃𝝁= { ̃𝜆𝜸(t)}T t=1. 3.2.2 Negative Binomial distribution When counts are overdispersed the Poisson distribution is not a suitable choice. We can model the observed daily inci- dence counts y = {y1, … , yt} as independent realizations from a Negative Binomial with mean ̃𝜆𝜸(t) and dispersion parameter 𝜈∈R+: Yt|𝜽∼NB( ̃𝜇𝜽(t), 𝜈), t = 1, … , T. Hence, the likelihood can be written as: Hence, the likelihood can be written as: (𝜽, 𝜈|d) = T ∏ t=1 NB(yt| ̃𝜇𝜽(t), 𝜈) ∝ ∝ T ∏ t=1 [Γ(𝜈+ yt) Γ(𝜈) ( 𝜈 𝜈+ ̃𝜇𝜽(t) )𝜈( ̃𝜇𝜽(t) 𝜈+ ̃𝜇𝜽(t) )yt] (𝜽, 𝜈|d) = T ∏ t=1 NB(yt| ̃𝜇𝜽(t), 𝜈) ∝ ∝ T ∏ t=1 [Γ(𝜈+ yt) Γ(𝜈) ( 𝜈 𝜈+ ̃𝜇𝜽(t) )𝜈( ̃𝜇𝜽(t) 𝜈+ ̃𝜇𝜽(t) )yt] and the log-likelihood is: l(𝜃, 𝜈|y) = log (𝜽, 𝜈|y) ∝ T ∑ t=1 log (Γ(𝜈+ yt) Γ(𝜈) ) + 𝜈 T ∑ t=1 log ( 𝜈 𝜈+ ̃𝜇𝜽(t) ) T ( ) (𝜽, 𝜈|d) = T ∏ t=1 NB(yt| ̃𝜇𝜽(t), 𝜈) ∝ ∝ T ∏ t=1 [Γ(𝜈+ yt) Γ(𝜈) ( 𝜈 𝜈+ ̃𝜇𝜽(t) )𝜈( ̃𝜇𝜽(t) 𝜈+ ̃𝜇𝜽(t) )yt] and the log-likelihood is: l(𝜃, 𝜈|y) = log (𝜽, 𝜈|y) ∝ T ∑ t=1 log (Γ(𝜈+ yt) Γ(𝜈) ) + 𝜈 T ∑ t=1 log ( 𝜈 𝜈+ ̃𝜇𝜽(t) ) + T ∑ t=1 yt log ( ̃𝜇𝜽(t) ̃𝜇𝜽(t) + 𝜈 ) . ‡the sum of independent Poissons is still a Poisson with parameter the sum of the parameters ‡the sum of independent Poissons is still a Poisson with parameter the sum of the parameters 10 ALAIMO DI LORO et al. 3.3.2 Multiplicative inclusion of covariates The inclusion of a multiplicative effect of covariates would imply that the more serious the pandemic situation, the more severe the impact of any covariate on the indicators’ daily rate. p y y First, let us recall that in Section 2.1.1 we computed the first differences of the Richards’ curve function as: ̃𝜆𝜸(t) = r ⋅[(1 + 10h(p−t))−s −(1 + 10h[p−(t−1)])−s] = r ⋅̃𝜆𝜸,−r(t). On the log-scale, it would return the more familiar: log( ̃𝜆𝜸(t)) = log(r) + log( ̃𝜆𝜸,−r(t)). (3) (3) (3) log( ̃𝜆𝜸(t)) = log(r) + log( ̃𝜆𝜸,−r(t)). ALAIMO DI LORO et al. 11 From Equation (3), it comes natural the idea of expressing log(r) at each time-point t as the linear combination of covariates 𝜂(x(t)) as in a Generalized Poisson model with log link function. Indeed this provides a multiplicative effect of the covariates, where the parameter r can be expressed as 𝜇𝜷(⋅) in the following way: r𝜷(x(t)) = 𝜇𝜷(x(t)) = exp{x(t)𝜷}. (4) r𝜷(x(t)) = 𝜇𝜷(x(t)) = exp{x(t)𝜷}. (4) (4) r𝜷(x(t)) = 𝜇𝜷(x(t)) = exp{x(t)𝜷}. Note that the constant r is still present and included in Equation (4) through the intercept 𝛽0. Therefore, the mean at time t is expressed as: ̃𝜇𝜃(t) = 𝛼+ r𝜷(x(t)) ⋅̃𝜆𝜸,−r(t). Considering the whole vector of observations, we would have the following vector of means ̃𝝁𝜽= 𝜶+ r𝜷(X) ⋅̃𝝀𝜸,−r, where 𝜶= 𝛼⋅1T. Considering the whole vector of observations, we would have the following vector of means ̃𝝁𝜽= 𝜶+ r𝜷(X) ⋅̃𝝀𝜸,−r, where 𝜶= 𝛼⋅1T. 3.4 Model estimation Parameters can be estimated by maximizing the log-likelihood l(𝜽|y), where 𝜽in this case includes all the parameters the likelihood depends on (eg, includes 𝜈in the Negative Binomial case). This optimization problem does not have an analytical solution, and numerical maximization must be used. To improve computation, we derived analytical expres- sions for the gradient and Hessian of the two possible log-likelihoods (ie, Poisson or Negative Binomial counts), making Fisher-scoring iteration very fast. The expressions are reported in the supplementary material. Given the nonsmooth shape of the objective function, we are at risk of being trapped by local maxima of the log-likelihood, depending on the initial conditions. Therefore, in order to strengthen the optimization procedure, a multistart procedure based on a combination of genetic and gradient descent algorithms has been used.43,44 Once an approximate point of maximum ̂𝜽has been obtained, we could theoretically obtain an estimate of the asymp- totic variance-covariance matrix of the estimated parameters through inverse of the negative log-likelihood Hessian in ̂𝜽 (which corresponds to the Observed Fisher Information): ̂V𝜽= −H(l(̂𝜽|y))−1, where H denotes the Hessian matrix. Nevertheless, we may want to account for the potential misspecification of our model potentially arising from the independence assumption HI in Section 3.2. Therefore, we resort to a robust approach for estimating the standard errors and covariance structure associated with the parameter vector 𝜽. In particular, we consider the Huber Sandwich Estimator of the variance-covariance matrix,45,46 that can be computed as: where H denotes the Hessian matrix. Nevertheless, we may want to account for the potential misspecification of our model potentially arising from the independence assumption HI in Section 3.2. Therefore, we resort to a robust approach for estimating the standard errors and covariance structure associated with the parameter vector 𝜽. In particular, we consider the Huber Sandwich Estimator of the variance-covariance matrix,45,46 that can be computed as: ̂V R 𝜽= (−H(l(̂𝜽|y))−1)∇l(̂𝜽|y)∇l(̂𝜽|y)⊤(−H(l(̂𝜽|y))−1), ̂V R 𝜽= (−H(l(̂𝜽|y))−1)∇l(̂𝜽|y)∇l(̂𝜽|y)⊤(−H(l(̂𝜽|y))−1), ̂V R 𝜽= (−H(l(̂𝜽|y))−1)∇l(̂𝜽|y)∇l(̂𝜽|y)⊤(−H(l(̂𝜽|y))−1), where ∇l(̂𝜽|y) represents the gradient of the log-likelihood in the point of maximum. Interval estimates for the parameters are directly derived through the asymptotic distribution of the Maximum Likelihood Estimator, with the corresponding robust covariance matrix ̂𝜽∼(𝜽, ̂V R 𝜽). A similar theoretical result for predictions is not as straightforward. Therefore, these are derived through a parametric double bootstrap procedure,47-49 which accounts for both the uncertainty of parameter estimation and the randomness of the observations. In practice, resampled trajectories {Yi}B i=1 are obtained by simulating B sets of parameters from their asymptotic distribution and computing B mean functions trajectories {𝜇𝜽i(t)}B i=1. An artificial time series of counts is then simulated for each of the B trajectories and 95% confidence intervals are obtained by computing the pointwise 2.5% and 97.5% quantiles. The dispersion parameter 𝜈, being a poorly identifi- able nuisance parameter of no impact on the mean curve behavior, has been excluded from the bootstrapping procedure and kept fixed at its estimated value ̂𝜈. Diagnostic check on the model has been performed through the Pearson residuals and the Deviance residuals. Computation of the former is trivial, where we recall their definition as: ̂𝜌t = yt −̂yt ̂ Var[Yt] , t = 1, … , T. ALAIMO DI LORO et al. 12 and Negative Binomial assumptions we have: Under the Poisson and Negative Binomial assumptions we have: Under the Poisson and Negative Binomial assumptions we have: ̂ VarPoi[Yt] = 𝜇̂𝜽(t), ̂ VarNB[Yt] = 𝜇̂𝜽(t) + 𝜇̂𝜽(t)2 ̂𝜈 , (5) (5) (5) respectively. The Deviance Residuals are instead defined as the individual contributions of each observation to the Deviance of the model, that is, the discrepancy between the proposed model and the full model (perfect fit) fits in terms of log-likelihood: ̂dt = 2 ⋅[log(f(yt|̂𝜽s) −log(f(yt|̂𝜽)], where f(⋅|⋅) is the chosen distribution function and ̂𝜽s is the parameter vector of the saturated model. For the Poisson and Negative Binomial this can be computed as: where f(⋅|⋅) is the chosen distribution function and ̂𝜽s is the parameter vector of the saturated model. ̂V R 𝜽= (−H(l(̂𝜽|y))−1)∇l(̂𝜽|y)∇l(̂𝜽|y)⊤(−H(l(̂𝜽|y))−1), For the Poisson and Negative Binomial this can be computed as: ̂d Poi t = sgn(yt −𝜇̂𝜽(t)) ⋅ √ 2yt log ( yt 𝜇̂𝜽 ) −(yt −𝜇̂𝜽(t)), ̂d NB t = sgn(yt −𝜇̂𝜽(t)) ⋅ √ 2 [ yt log ( yt 𝜇̂𝜽(t) ) −(yt + 𝜈) ⋅log ( yt + 𝜈 𝜇̂𝜽(t) + 𝜈 )] , respectively.50 If the model correctly describes the variability in the data, then both the Pearson residuals and the Deviance residuals are expected to be Normally distributed and independent, with the latter being generally more robust to outliers. 3.5 Validation Fitting performances are further evaluated through numerical metrics such as the pseudo-R2 and coverage of the 95% prediction intervals: R2 = 1 −MSE 𝜎2 y = 1 − ∑T t=1 (yt −̂yt)2 ∑T t=1 (yt −y)2 , Cov95% = 1 T ⋅ T ∑ t=1 I(̂yl t;̂yu t )(yt), where MSE is the Mean Squared Error, y = 1 T ∑T t=1 yt and I(⋅) denotes the indicator function over the set . where MSE is the Mean Squared Error, y = 1 T ∑T t=1 yt and I(⋅) denotes the indicator function over the set . 4 NOWCASTING THE ITALIAN OUTBREAK OF COVID-19 For the sake of brevity, here we present results referred to the proposed Richards’ growth model only for daily positives aggregated at the national level. Further results of the model performances for daily deceased are included in the supple- mentary material. We only present results obtained adopting the Negative Binomial distribution because of the substantial overdispersion present at all levels for these indicators (spatially and temporally heterogeneous data collection process, varying containment measures, and so on). We first show the fitted curve for each indicator, and compare its shape with the observed time series. We also calculate the residuals and check if model assumptions under the proposed framework hold. According to the results drawn from the residual analysis, we modify the empirical setting, keeping the theoretical one fixed, to better capture specific data features. Later on, we show the performance for two fundamental issues: (i) predicting the epidemic trend in advance and (ii) predicting the date of the peak of the epidemic. 3.6 Step-ahead predictions We test our model’s ability to predict the evolution of the epidemic (at least its first wave) from the short to the medium term. Indeed, while the choice of a rigid parametric form for the mean function is penalizing in terms of flexibility and fitting ability, it allows for extrapolation outside the observed domain and is supposed to provide robust forecasts (at least in the short/medium term). Therefore, using the best model for the two indicators (ie, baseline + week-day additive effect), we calculated the out-of-sample root mean squared prediction error (RMSPE) for: • different fitting windows t = 1, … , ̃t; • different forecast horizons, say K ∈{1, 5, 10, 15}. We recall that, given the fitting window set 1, … , ̃t: RMSPẼt,K = √ √ √ √1 K K ∑ j=1 (ỹt+j −̂ỹt+j)2. 13 ALAIMO DI LORO et al. 13 Index Model without baseline Model with baseline log-likelihood −1081.4 −982.8 AIC 2152.7 1953.6 BIC 2162.3 1965 AICc 2137.8 1935.7 13 TA B L E 1 Log-likelihood, AIC, BIC, and AICc for the model without baseline and the model with baseline, on daily positives TA B L E 2 Parameters’ points estimates and 95% confidence intervals for the model with baseline on daily positives TA B L E 2 Parameters’ points estimates and 95% confidence intervals for the model with baseline on daily positives Parameter Point estimate 95% Interval 𝛼 173.17 (103.2, 290.54) r 222.95 × 103 (220.56 × 103, 225.36 × 103) h 0.0288 (0.0285, 0.0291) p −31.18 (−32.75, −29.62) s 72.54 (48.29, 96.79) 𝜈 18.73 (17.77, 19.73) 4.1 Model on daily positives 14 (B) Cumulative 0K 50K 100K 150K 200K 250K 01−Mar 01−Apr 01−May 01−Jun 01−Jul 01−Aug µt F I G U R E 5 Bootstrapped trajectories corresponding to the Huber Sandwich covariance matrix in the point of maximum for the model with baseline on daily positives viceversa). Finally, 𝜈is an overdispersion parameter and does not present any evident communicable interpretation. The larger it is and the lower the overdispersion, according to the formula in Equation (5). viceversa). Finally, 𝜈is an overdispersion parameter and does not present any evident communicable interpretation. The larger it is and the lower the overdispersion, according to the formula in Equation (5). We here want to stress the fact that the uncertainty characterizing some of the parameters (like s) is not alarming. In particular, variations of s at values distant from 1 have very little effect on the curve shape. Furthermore, the parameter vector presents a covariance structure that highlights how different combination of parameters can yield similar curves. Indeed, simulating M = 5000 set of parameters from the Normal distribution with variance corresponding to the covari- ance underlying the Huber Sandwich covariance matrix, we get the set of difference and cumulative curves represented in Figure 5. g We can also directly obtain point predictions {̂yt}T t=1 as: point predictions {̂yt}T t=1 as: We can also directly obtain point predictions {̂yt}T t=1 as: (6) ̂yt = 𝜇̂𝜽(t), t = 1, … , T, (6) and prediction intervals {(̂yl t; ̂yu t )}T t=1 through the same set of bootstrapped trajectories, whose statistical validity relies on the asymptotic properties introduced in Section 3.4. Figure 6 shows the model fit on the whole available time series of counts: the former on the daily series, the latter on the cumulative one. We can see how the estimated curve does catch the observed general behavior, providing a smooth approximation only marginally influenced by extreme values. Our model produces an R2 = 0.941 and coverage Cov95% = 0.945, meaning that the percentage of observed daily counts falling inside the estimated bounds is perfectly coherent with the specified confidence level. Looking at Figure 6, we notice how daily counts boundaries get smaller as time passes, due to the implicit relationship between mean and variance that characterizes count distributions. At the same time, the opposite happens to the bounds on the cumulative counts. 4.1 Model on daily positives To decide whether or not to include the kink effect, we fitted the model with and without the baseline 𝛼and compared the two fits in terms of log-likelihood, AIC, BIC, and corrected AIC (AICc). The values are presented in Table 1 and pro- vide clear evidence in favor of the model with baseline (ie, with mean 𝜇𝜽(⋅) as in Equation (2)). Parameters’ estimates of the model ̂𝜽and the respective 95% confidence intervals are shown in Table 2, where the baseline 𝛼is estimated to be ̂𝛼= 173.17, with interval (103.2, 290.54), which confirms that the baseline is estimated to be significantly different from 0, and it should be included in the model. As explained in Section 3.1, this parameter represents the long-term endemic incidence rate that may (possibly indefinitely) follow the end of the main outbreaks. This obviously would hold exactly with constant social interactions, containment measures, control of cases, and so on. Hence, in the considered time hori- zon, we expect this endemic level to be of ≈173 daily positives per day. When the baseline is included, the parameter r does not indicate anymore the final epidemic size, but only the final outbreak size. This is the number of positive cases due to the uncontrolled outbreak, additional to what would have been observed in the steady endemic state. This amount is estimated to be ≈222 950, an amount that would have been reached in ≈1288 days at the endemic state level. The parame- ters h, p, and s do not have an easily quantifiable and absolute interpretation, but are useful for comparison. As explained in Section 3.1, the first indicates how fast the infection spreads, the second how soon it starts descending (lag-phase) and the last asymmetries between the ascending and descending phase (s < 1 the ascending is slower than the descending and 14 ALAIMO DI LORO et al. 0K 2K 4K 01−Mar 01−Apr 01−May 01−Ju (A) First differences (B) Cumulative n 01−Jul 01−Aug µt 0K 50K 100K 150K 200K 250K 01−Mar 01−Apr 01−May 01−Jun 01−Jul 01−Aug µt F I G U R E 5 Bootstrapped trajectories corresponding to the Huber Sandwich covariance matrix in the point of maximum for the model with baseline on daily positives ALAIMO DI LORO et al. 4.1 Model on daily positives The latter is not surprising: indeed, they are built marginally on all the epidemic’s possible scenarios. Therefore, they give us a clear sight of what we could have currently observed, keeping into account and aggregating the uncertainty at each stage of the epidemic. We performed a diagnostic check on both the Pearson and the Deviance residuals. The plots in Figure 7 show the Deviance residuals behavior: histogram (A), including the P-value from the Shapiro test; Normal qq-plot (B); autocorrelation plot (C); plot of the residuals vs fitted values (D). The first two check the (approximated) Normality assumption on the residuals, while the second two control for the correlation of the residuals (among them and with the observed values). 4.1.1 Weekly seasonality The diagnostic check on both type of residuals showed that the Normality assumption is not rejected, but the correla- tion plot manifests undesirable patterns (see Figure 7). In particular, the autocorrelation between errors is larger at lag 7 ALAIMO DI LORO et al. 15 F I G U R E 6 Observed (black dots) and fitted values (gray solid lines) with 95% confidence intervals (gray dashed lines) for the model with baseline on daily positives (A) (B) F I G U R E 7 Deviance residuals for the model with baseline on daily positives (A) (B) (C) (D) (and multiples of this). We can interpret this outcome as the presence of an intense weekly seasonality (especially dur- ing/after the weekend). This suggests people would rather not come forward for testing on the weekend or, alternatively, ALAIMO DI LORO et al. 15 (B) (A) (A) (B) F I G U R E 7 Deviance residuals for the model with baseline on daily positives (A) (B) (C) (D) (and multiples of this). We can interpret this outcome as the presence of an intense weekly seasonality (especially dur- ing/after the weekend). This suggests people would rather not come forward for testing on the weekend or, alternatively, the system has less capacity at the weekend, meaning it is more challenging to get a test. Undeniably, viruses work 7 days a week. Looking at the low numbers during/after the weekend might give you a false sense of reassurance. This is because it seems cases are down, and therefore elimination of the virus is possible. But, unlike our population, viruses do work on weekends. This may be adjusted by simply adding a weekday effect in our model as a covariate, using the approach in Section 3.3. Such effect may be included either in an additive or a multiplicative fashion. At first, we considered effects for each day of the week, taking Monday as a corner point. Preliminary results showed that not all week-days present a significant deviation from the common mean. On the other hand, the distribution of the Deviance residuals ̂dt of the stan- dard model aggregated by week-day (see Figure 8) shows that an evident overestimation pattern (ie, negative deviations) is taking place on Monday and Tuesday. 4.1.1 Weekly seasonality −2 0 2 Monday Tuesday Wednesday Thursday Friday Saturday Sunday d^ F I G U R E 8 Deviance residuals distribution aggregated by day of the week for daily positives Index Additive effect Multiplicative effect log-likelihood −971.74 −974.1 AIC 1929.48 1934.3 AICc 1942.67 1947.5 BIC 1908.60 1913.4 TA B L E 3 Log-likelihood, AIC, BIC, and AICc for the models with baseline including additive or multiplicative week-day effect on daily positives (A) (B) F I G U R E 9 Observed (black dots) and fitted values (gray solid lines) with 95% confidence intervals (gray dashed lines) for the model with baseline and week-day additive effect, estimated on the daily positives may suffer from week seasonality. The additive option is chosen over its alternative because of its lower/improved AIC, BIC, and AICc score (see Table 3). The resulting fit of the model with week seasonality on the observed data are shown in Figure 9, where, on the left, we show the fitted curve and the 95% confidence intervals; on the right, we can observe the fit on the cumulative indicator. Estimated parameters are shown in Table 4 This model estimates the baseline to be at e ̂𝛽0 = 192 48 on Wednesday to 16 ALAIMO DI LORO et al. −2 0 2 Monday Tuesday Wednesday Thursday Friday Saturday Sunday d^ F I G U R E 8 Deviance residuals distribution aggregated by day of the week for daily positives Index Additive effect Multiplicative effect log-likelihood −971.74 −974.1 TA B L E 3 Log-likelihood, AIC, BIC, and AICc for the models with baseline including additive or multiplicative week-day effect on daily positives 16 −2 0 2 Monday Tuesday Wednesday Thursday Friday Saturday Sunday d^ ALAIMO DI LORO et al. 4.1.1 Weekly seasonality 16 F I G U R E 8 Deviance residuals distribution aggregated by day of the week for daily positives F I G U R E 8 Deviance residuals distribution aggregated by day of the week for daily positives TA B L E 3 Log-likelihood, AIC, BIC, and AICc for the models with baseline including additive or multiplicative week-day effect on daily positives Index Additive effect Multiplicative effect log-likelihood −971.74 −974.1 AIC 1929.48 1934.3 AICc 1942.67 1947.5 BIC 1908.60 1913.4 (A) (B) F I G U R E 9 Observed (black dots) and fitted values (gray solid lines) with 95% confidence intervals (gray dashed lines) for the model with baseline and week-day additive effect, estimated on the daily positives may suffer from week seasonality. The additive option is chosen over its alternative because of its lower/improved AIC, BIC, and AICc score (see Table 3). (B) F I G U R E 9 Observed (black dots) and fitted values (gray solid lines) with 95% confidence intervals (gray dashed lines) for the model with baseline and week-day additive effect, estimated on the daily positives (A) (A) (B) may suffer from week seasonality. The additive option is chosen over its alternative because of its lower/improved AIC, BIC, and AICc score (see Table 3). h l i fi f h d l i h k li h b d d h i i h h l f may suffer from week seasonality. The additive option is chosen over its alternative because of its lower/improved AIC, BIC, and AICc score (see Table 3). The resulting fit of the model with week seasonality on the observed data are shown in Figure 9, where, on the left, we show the fitted curve and the 95% confidence intervals; on the right, we can observe the fit on the cumulative indicator. ̂ Estimated parameters are shown in Table 4. This model estimates the baseline to be at e ̂𝛽0 = 192.48 on Wednesday to Sunday and at e ̂𝛽0+ ̂𝛽wd = 121.51 on Mondays and Tuesdays. Deriving the corresponding 95% intervals, these two baselines result significantly different from the estimate of the overall baseline ̂𝛼in the model without covariates. 4.1.1 Weekly seasonality (A) (B) F I G U R E 7 Deviance residuals for the model with baseline on daily positives F I G U R E 7 Deviance residuals for the model with baseline on daily positives (B) (A) (A) (B) (D) (C) (C) (D) (and multiples of this). We can interpret this outcome as the presence of an intense weekly seasonality (especially dur- ing/after the weekend). This suggests people would rather not come forward for testing on the weekend or, alternatively, the system has less capacity at the weekend, meaning it is more challenging to get a test. Undeniably, viruses work 7 days a week. Looking at the low numbers during/after the weekend might give you a false sense of reassurance. This is because it seems cases are down, and therefore elimination of the virus is possible. But, unlike our population, viruses do work on weekends. This may be adjusted by simply adding a weekday effect in our model as a covariate, using the approach in Section 3.3. Such effect may be included either in an additive or a multiplicative fashion. At first, we considered effects for each day of the week, taking Monday as a corner point. Preliminary results showed that not all week-days present a significant deviation from the common mean. On the other hand, the distribution of the Deviance residuals ̂dt of the stan- dard model aggregated by week-day (see Figure 8) shows that an evident overestimation pattern (ie, negative deviations) is taking place on Monday and Tuesday. f Therefore, in the sequel, we will present only results obtained with the dichotomous variable that is equal to 1 when- ever the week-day is Monday or Tuesday (0 vice versa). Note that lower tests effort during the weekend shows in the data on Monday and Tuesday, since daily reports involve mostly results received the day before, with swabs therefore dating back 48 hours on the day of publication. This confirms that working with daily data require special care as the cases reporting 16 ALAIMO DI LORO et al. 4.1.1 Weekly seasonality The diagnostic check of the Pearson’s and Deviance residuals showed that adherence to Gaussianity improved and the correlation pattern at lag 7 is still present but mitigated (see Figure 10 for the Deviance F I G U R E 10 Deviance residuals for the model with baseline and week-day additive effect estimated on daily positives (A) (B) (A) (D) (C) (C) (D) covariates, denoting less overdispersion with respect to the equivariance hypothesis. This is completely reasonable since the week-day effect is able to explain some of the previously unaccounted heterogeneity. In terms of model validation, the inclusion of this effect improves sensibly the R2 (0.956), while the average cover- age Cov95% is constant (0.950). The diagnostic check of the Pearson’s and Deviance residuals showed that adherence to Gaussianity improved and the correlation pattern at lag 7 is still present but mitigated (see Figure 10 for the Deviance residuals). 4.1.1 Weekly seasonality The estimates of the outbreak size ̂r and of the infection rate ̂h of the two models are in agreement, while the point estimates of the asymmetry parameter ̂s are different but both large and mutually included in the corresponding 95% intervals. This is reasonable since we would not expect the outbreak size, rate and symmetry to vary after accounting for week-day het- erogeneity. On the other hand, the new estimate ̂p of p detects a shorter lag-phase and hence a slightly faster approach to the descending phase. Finally, the estimate of the dispersion parameter ̂𝜈is slightly larger than in the model without ALAIMO DI LORO et al. 17 ALAIMO DI LORO et al. 17 TA B L E 4 Parameters’ point estimates and 95% confidence intervals for the additive model on daily positives Parameter Point estimate 95% Interval 𝛽0 5.26 (5.18, 5.34) 𝛽wd −0.46 (−0.53, −0.38) r 224.57 × 103 (224.13 × 103, 225.01 × 103) h 0.0289 (0.0287, 0.0291) p −23.26 (−29.64, −16.88) s 44.42 (−35.67, 124.51) 𝜈 22.01 (21.35, 22.70) F I G U R E 10 Deviance residuals for the model with baseline and week-day additive effect estimated on daily positives (A) (B) (C) (D) TA B L E 4 Parameters’ point estimates and 95% confidence intervals for the additive model on daily positives Parameter Point estimate 95% Interval 𝛽0 5.26 (5.18, 5.34) 𝛽wd −0.46 (−0.53, −0.38) r 224.57 × 103 (224.13 × 103, 225.01 × 103) h 0.0289 (0.0287, 0.0291) p −23.26 (−29.64, −16.88) s 44.42 (−35.67, 124.51) 𝜈 22.01 (21.35, 22.70) s 44.42 (−35.67, 124.51) 𝜈 22.01 (21.35, 22.70) F I G U R E 10 Deviance residuals for the model with baseline and week-day additive effect estimated on daily positives (A) (B) (C) (D) covariates, denoting less overdispersion with respect to the equivariance hypothesis. This is completely reasonable since the week-day effect is able to explain some of the previously unaccounted heterogeneity. In terms of model validation, the inclusion of this effect improves sensibly the R2 (0.956), while the average cover- age Cov95% is constant (0.950). 4.1.2 Prediction of future cases and of the peak date For the latter empirical model, the RMSPEs for each steps-ahead are presented in Figure 11. Results match the expecta- tions as: (i) the error decreases with the length of the fitting window; (ii) the error trend is more stable on larger testing windows (10-15 steps ahead vs 1-5 steps ahead); (iii) larger errors are made around the day of the peak. It can be seen nevertheless that predictions are always reasonable at these time horizons. This is a good point for our theoretical frame- work, as it can be used as a guidance tool to plan nonpharmaceutical-interventions due to its capability to predict future scenarios with reasonable accuracy. Of course, with more detailed data and including confounding factors, the accuracy may be further improved. Unfortunately, the aggregated available data do not contain important information which may strongly improve the prediction, for example, stratifications of cases by age, gender, comorbidities, and so on. Finally, we evaluate the model’s ability to predict the date of the peak. The approximate dates and heights of the peak have important epidemiological implications. This becomes possible under the assumption that sensible modifications ALAIMO DI LORO et al. 18 18 ALAIMO DI LORO et al. 4.1.2 Prediction of future cases and of the peak date kk k k k k k k k k k kk k k k k k k k k k k k k k kk k kk kk k kkk k k k k k k k k k kk kk k k k k k kk k k k k kk k k k kkkk k kkk k k kk kkk kkkkkkkkkkkkkk k kkk k kkkkkkkkk 0 500 1000 1500 01−Apr 01−May 01−Jun 01−Jul RMSPE 1 step−ahead k kkk k k k k k k k k k k k k k k k k k k k kkkkk kkkkkkkk kkkkk k kkkkkk kkkkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk 0 500 1000 1500 01−Apr 01−May 01−Jun 01−Jul RMSPE 5 step−ahead kk k k k k kk k k k kk k k k k kk kk k k kkkkkkkk kkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk 0 500 1000 1500 01−Apr 01−May 01−Jun 01−Jul RMSPE 10 step−ahead kkk k k k k k k k k kkk k k k k kk k k k kkk kkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk 0 500 1000 1500 01−Apr 01−May 01−Jun 01−Jul RMSPE 15 step−ahead F I G U R E 11 Root mean squared prediction error for daily positives at different steps-ahead (A) (B) (C) (D) F I G U R E 12 Estimation of the date of the peak for daily positives at different steps-before of the adopted epidemiological strategies do not emerge. However, if exogenous events, for example, efficient treatments or vaccines, arise at a certain point in time, our framework allows to include it to predict the peak, in a similar manner as we did for the week seasonality effect. To do so, we estimate the model without covariates, using all available data until K ∈{15, 10, 5, 3, 2, 1} days before the observed peak. For the sake of conciseness, we only report results for K ∈{10, 5, 2, 1} as shown in Figure 12. When s = 1, the peak ̂t is directly expressed by the parameter p. 4.1.2 Prediction of future cases and of the peak date When s ≠1, after some algebra it can be seen that the peak can still be computed analytically as: k kkk k k k k k k k k k k k k k k k k k k k kkkkk kkkkkkkk kkkkk k kkkkkk kkkkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk 0 500 1000 1500 01−Apr 01−May 01−Jun 01−Jul RMSPE 5 step−ahead F I G U R E 11 Root mean squared prediction error for daily positives at different steps-ahead kk k k k k k k k k k kk k k k k k k k k k k k k k kk k kk kk k kkk k k k k k k k k k kk kk k k k k k kk k k k k kk k k k kkkk k kkk k k kk kkk kkkkkkkkkkkkkk k kkk k kkkkkkkkk 0 500 1000 1500 01−Apr 01−May 01−Jun 01−Jul RMSPE 1 step−ahead kkk k k k k k k k k kkk k k k k kk k k k kkk kkkkkkkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk 0 500 1000 1500 01−Apr 01−May 01−Jun 01−Jul RMSPE 15 step−ahead kk k k k k kk k k k kk k k k k kk kk k k kkkkkkkk kkkkkkkkkk kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk 0 500 1000 1500 01−Apr 01−May 01−Jun 01−Jul RMSPE 10 step−ahead RMSPE RMSPE (B) (A) F I G U R E 12 Estimation of the date of the peak for daily positives at different steps-before F I G U R E 12 Estimation of the date of the peak for daily positives at different steps-before (A) (B) (D) (C) (C) (D) of the adopted epidemiological strategies do not emerge. However, if exogenous events, for example, efficient treatments or vaccines, arise at a certain point in time, our framework allows to include it to predict the peak, in a similar manner as we did for the week seasonality effect. To do so, we estimate the model without covariates, using all available data until K ∈{15, 10, 5, 3, 2, 1} days before the observed peak. For the sake of conciseness, we only report results for K ∈{10, 5, 2, 1} as shown in Figure 12. of the adopted epidemiological strategies do not emerge. 4.1.2 Prediction of future cases and of the peak date The dashed gray vertical lines represent the bounds of the confidence interval and the predicted date of the peak (confidence area is shaded with the same gray). The solid vertical black line represents the “true” date of the peak (ie, obtained via smoothing of the observed counts through nonparametric polynomial approximations). The observed time-series is represented through point and lines, where the black section is referred to the training window while the gray section is referred to the testing (out-of-sample) window. Confidence intervals are obtained through the same bootstrap procedure introduced in Section 3.4. The dashed gray vertical lines represent the bounds of the confidence interval and the predicted date of the peak (confidence area is shaded with the same gray). The solid vertical black line represents the “true” date of the peak (ie, obtained via smoothing of the observed counts through nonparametric polynomial approximations). The observed time-series is represented through point and lines, where the black section is referred to the training window while the gray section is referred to the testing (out-of-sample) window. As expected, as we approach the real date of the peak, we predict it more accurately. Point predictions are very accu- rate since 5 days before the actual peak. At the same time, interval bounds get tighter and tighter as the fitting interval approached the day of the peak and, in general, the day of the peak is always included in such bounds (see Table 5 for exact numerical evaluation). All the aforementioned results have been calculated also for the national aggregated daily deceased. Exposition and discussion of these results, which are in fact very similar to the daily positivesones, are included in the supplementary material. Here, we just want to highlight how the peak is accurately predicted with a shorter delay and generally smaller uncertainty for the daily deceased than for the daily positives (see Table 5). This is probably related to the more regular behavior of the series, due to a likely more homogeneous collection process of the records. Finally, we here want to stress the point that we are introducing a framework with the highly desirable goal to formu- late a model which would predict an evolution curve. 4.1.2 Prediction of future cases and of the peak date To be more precise, a great variety of epidemiological models have been proposed in the literature, but most standard versions of SIR-like models typically yield an increase before the peak that is quite similar to the decrease after the peak. The proposed framework, based on more complex evolution dynamics, is robust enough to be fitted successfully on the (poor quality) available data while explaining and forecasting different increasing and decreasing behavior before and after the peak. We emphasize that such increase-decrease quantitative behaviors appear to satisfactorily conform to reality. 4.1.2 Prediction of future cases and of the peak date However, if exogenous events, for example, efficient treatments or vaccines, arise at a certain point in time, our framework allows to include it to predict the peak, in a similar manner as we did for the week seasonality effect. To do so, we estimate the model without covariates, using all available data until K ∈{15, 10, 5, 3, 2, 1} days before the observed peak. For the sake of conciseness, we only report results for K ∈{10, 5, 2, 1} as shown in Figure 12. When s = 1, the peak ̂t is directly expressed by the parameter p. When s ≠1, after some algebra it can be seen that the peak can still be computed analytically as: ̂t ̂𝜸= ̂p + log10(̂s) ̂h . ALAIMO DI LORO et al. 19 TA B L E 5 Delay (days) in point estimation of the peak 10 5 2 1 Days before Delay Width Delay Width Delay Width Delay Width daily deceased −1 37 –3 25 –4 22 –3 21 daily positives 20 106 17 69 1 37 2 37 Confidence intervals are obtained through the same bootstrap procedure introduced in Section 3.4. The dashed gray vertical lines represent the bounds of the confidence interval and the predicted date of the peak (confidence area is shaded with the same gray). The solid vertical black line represents the “true” date of the peak (ie, obtained via smoothing of the observed counts through nonparametric polynomial approximations). The observed time-series is represented through point and lines, where the black section is referred to the training window while the gray section is referred to the testing (out-of-sample) window. As expected, as we approach the real date of the peak, we predict it more accurately. Point predictions are very accu- rate since 5 days before the actual peak. At the same time, interval bounds get tighter and tighter as the fitting interval ALAIMO DI LORO et al. 19 TA B L E 5 Delay (days) in point estimation of the peak 10 5 2 1 Days before Delay Width Delay Width Delay Width Delay Width daily deceased −1 37 –3 25 –4 22 –3 21 daily positives 20 106 17 69 1 37 2 37 TA B L E 5 Delay (days) in point estimation of the peak Confidence intervals are obtained through the same bootstrap procedure introduced in Section 3.4. ORCID Pierfrancesco Alaimo Di Loro https://orcid.org/0000-0002-6075-3659 Alessio Farcomeni https://orcid.org/0000-0002-7104-5826 Giovanna Jona Lasinio https://orcid.org/0000-0001-8912-5018 Gianfranco Lovison https://orcid.org/0000-0003-3861-8204 Antonello Maruotti https://orcid.org/0000-0001-8377-9950 h // id / Pierfrancesco Alaimo Di Loro https://orcid.org/0000-0002-6075-3659 Alessio Farcomeni https://orcid.org/0000-0002-7104-5826 Giovanna Jona Lasinio https://orcid.org/0000-0001-8912-5018 Gianfranco Lovison https://orcid.org/0000-0003-3861-8204 Antonello Maruotti https://orcid.org/0000-0001-8377-9950 Marco Mingione https://orcid.org/0000-0002-5662-3499 20 20 A limitation of our approach is that logistic growth curves are constrained so that only one wave at a time can be successfully modeled. This implies that initial (and possibly final) dates shall be set by the user to identify a wave. This is rather simple empirically (eg, the initial date can be the last day with zero incidence, and the final date can be the first day with incidence above (or under) a prespecified threshold). On the other hand, multiple waves could be modeled by modification of our nonlinear model as a weighted average of multiple Richards’ curves (one for each wave), in which weights of the noncurrent wave are forced to decay to zero with the distance from the wave-specific peak. We leave this as grounds for further work. A Bayesian approach will also be experimented in order to overcome possible issues with the asymptotic properties of the maximum likelihood estimator. Notably, implementation of the no-U-turn sampler algorithm for the estimation of nonlinear models might be a valid working solution. In addition, a Bayesian approach may also be used to include spatial dependence into the modeling framework and also to relax the first-order Markov assumption for taking into account more complex temporal dependence. In particular, the latter may be key in order to adapt the introduced Richards’ curve model for the nowcasting of prevalence indicators, for example, current positives and current intensive care units occupancy. Indeed, any modeling effort shall account for the strong temporal dependence between subsequent counts stemming from the fact that daily counts at time t potentially include units which are in stock since times 𝜏< t. Furthermore, as specified in Section 2.1.2, prevalence indicators are nonmonotonic and their value is the result of the combination of the incidence components building up each of those. These two last issues may be addressed by adapting the Richards’ response function to accommodate nonmonotonicity and/or by hierarchically specifying a model for the prevalence indicators through the combination of models for their incidence components. A successful attempt in accurately nowcasting the ICU occupancy is given in Reference 51. SOFTWARE Software in the form of R code, together with a sample input dataset and complete documentation is available on request from the corresponding author. DATA AVAILABILITY STATEMENT The data that support the findings of this study are openly available in “Protezione Civile Italiana GitHub Repository” at https://github.com/pcm-dpc/COVID-19. 20 ALAIMO DI LORO et al. 5 DISCUSSION AND FURTHER WORK We presented an approach to modeling and prediction of epidemic indicators that has proven useful during the first outbreak of COVID-19 in Italy. The model has been validated on publicly available data, and has proved flexible enough to adapt to different indicators. It is important to underline up front that the available data are clearly biased. Incidence depends on testing and trac- ing efforts, whose indications have varied wildly over time and space. Comparability of indicators over time and space might in part be achieved by including the daily number of swabs as a predictor, which anyway would make predictions cumbersome. Different definitions of COVID-19 related death make it also very hard to compare mortality across coun- tries. This problem does not apply to our data, that refer only to Italy. However, while this definition has been constant over time in Italy, it shall be remarked that also deaths might be underestimated, with the degree of undercount positively associated with incidence. Correcting for this bias is not trivial, and would require corrections based on individual-level data and/or reliable statistics about excess mortality. Summarizing the results, we would like to emphasize that the proposed Richards’ curve model describes properly the growth in the number of COVID-19 daily positives and daily deceased, despite its simplicity. Indeed, it is able to reflect properly the trend of the daily incidence indicators; and also allows for the straightforward inclusion of exogenous infor- mation. Basic covariates such as the week-day effect proved to sensibly enhance model fitting and prediction accuracy. While we have illustrated results at the national level, the model can be used also at the regional/local level (perhaps including specific local effects). The resulting fits are included in the supplementary material. The maximum likelihood approach so far considered is rather stable, as long as reasonable starting values are found to initialize the algorithm. 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Farcomeni A, Maruotti A, Divino F, Jona-Lasinio G, Lovison G. An ensemble approach to short-term forecast of COVID-19 intensive care occupancy in Italian regions. Biom J. 2020;63:503-513. SUPPORTING INFORMATION y p p pp ( ) 50. Svetliza CF, Paula GA. Diagnostics in nonlinear negative binomial models. Commun Stat Theory Methods. 2003;32(6):1227-1250. 51 Farcomeni A Maruotti A Divino F Jona-Lasinio G Lovison G An ensemble approach to short-term forecast of COVID-19 intensive care 9. o . ayes a e e ce a d t e pa a et c bootst ap. nn ppl Stat. 0 ;6( ): 97 . 50. Svetliza CF, Paula GA. Diagnostics in nonlinear negative binomial models. Commun Stat Theory Methods. 2003;32(6):1227-1250. 51. Farcomeni A, Maruotti A, Divino F, Jona-Lasinio G, Lovison G. An ensemble approach to short-term forecast of COVID-19 intensive care occupancy in Italian regions. Biom J. 2020;63:503-513. 51. Farcomeni A, Maruotti A, Divino F, Jona-Lasinio G, Lovison G. An ensemble approach to short-term forecast of COVID-19 intensive care occupancy in Italian regions. Biom J. 2020;63:503-513. SUPPORTING INFORMATION How to cite this article: Alaimo Di Loro P, Divino F, Farcomeni A, et al. Nowcasting COVID-19 incidence indicators during the Italian first outbreak. Statistics in Medicine. 2021;1–22. https://doi.org/10.1002/sim.9004
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Analysis of the Influence of the Board of Directors, Company Size, Management Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat (BPR)
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ANALYSIS OF THE INFLUENCE OF THE BOARD OF DIRECTORS, COMPANY SIZE, MANAGEMENT OWNERSHIP, AND KAP AUDIT ON THE FINANCIAL PERFORMANCE OF BANK PERKREDITAN RAKYAT (BPR) This type of research is associative research. In this study, the population of rural banks located in the Bekasi area was used. The data obtained is based on financial reports that have been published on the website of the Financial Services Authority (www.ojk.go.id) for the period 2018-2021. The data obtained from the results of the study were analyzed using multiple linear regression analysis models using the Eview 10 software program. The results showed that the KAP audit variable had a significant influence on the return on assets of rural banks in the Bekasi area. This is because the resulting p-value is smaller than 0.05. Then the firm size variable significantly affects non-performing loans with a negative relationship direction. The KAP audit variable was also proven to have a significant effect on non-performing loans with a similar direction, namely negative. Both are able to affect non- performing loans because the p-value obtained is smaller than 0.05. Simultaneously also found the effect of the board of directors, company size, managerial ownership, and KAP audits on the return on assets or non-performing loans of BPRs in the Bekasi area for the 2018-2021 period. KEYWORDS Board of Directors, Company Size, Managerial Ownership, KAP Audit, Return on Assets, Non Performing Loan This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International This study aims to analyze the effects of the board of directors, firm size, managerial ownership, and audit of KAP (Public Accounting Firm) audit on the financial performance of Bank Perkreditan Rakyat (BPR). This type of research is associative research. In this study, the population of rural banks located in the Bekasi area was used. The data obtained is based on financial reports that have been published on the website of the Financial Services Authority (www.ojk.go.id) for the period 2018-2021. The data obtained from the results of the study were analyzed using multiple linear regression analysis models using the Eview 10 software program. The results showed that the KAP audit variable had a significant influence on the return on assets of rural banks in the Bekasi area. This is because the resulting p-value is smaller than 0.05. Then the firm size variable significantly affects non-performing loans with a negative relationship direction. The KAP audit variable was also proven to have a significant effect on non-performing loans with a similar direction, namely negative. ANALYSIS OF THE INFLUENCE OF THE BOARD OF DIRECTORS, COMPANY SIZE, MANAGEMENT OWNERSHIP, AND KAP AUDIT ON THE FINANCIAL PERFORMANCE OF BANK PERKREDITAN RAKYAT (BPR) How to cite: Riwandari Juniasti. (2022). Analysis of the Influence of the Board of Directors, Company Size, Management Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat (BPR). Journal Eduvest. Vol 2(2): 397-405 E-ISSN: 2775-3727 Published by: https://greenpublisher.id/ Riwandari Juniasti Universitas Kristen Indonesia Email: Riwandari.juniasti@uki.ac.id ARTICLE INFO ABSTRACT Received: January, 26th 2022 Revised: February, 17th 2022 Approved: February, 18th 2022 This study aims to analyze the effects of the board of directors, firm size, managerial ownership, and audit of KAP (Public Accounting Firm) audit on the financial performance of Bank Perkreditan Rakyat (BPR). This type of research is associative research. In this study, the population of rural banks located in the Bekasi area was used. The data obtained is based on financial reports that have been published on the website of the Financial Services Authority (www.ojk.go.id) for the period 2018-2021. The data obtained from the results of the study were analyzed using multiple linear regression analysis models using the Eview 10 software program. The results showed that the KAP audit variable had a significant influence on the return on assets of rural banks in the Bekasi area. This is because the resulting p-value is smaller than 0.05. Then the firm size variable significantly affects non-performing loans with a negative relationship direction. The KAP audit variable was also proven to have a significant effect on non-performing loans with a similar direction, namely negative. Both are able to affect non- performing loans because the p-value obtained is smaller than 0.05. Simultaneously also found the effect of the board of directors, company size, managerial ownership, and KAP audits on the return on assets or non-performing loans of BPRs in the Bekasi area for the 2018-2021 period. KEYWORDS Board of Directors, Company Size, Managerial Ownership, KAP Audit, Return on Assets, Non Performing Loan This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International How to cite: Riwandari Juniasti. (2022). Analysis of the Influence of the Board of Directors, Company Size, Management Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat (BPR). Journal Eduvest. Vol 2(2): 397-405 E-ISSN: 2775-3727 Published by: https://greenpublisher.id/ Received: January, 26th 2022 Revised: February, 17th 2022 Approved: February, 18th 2022 This study aims to analyze the effects of the board of directors, firm size, managerial ownership, and audit of KAP (Public Accounting Firm) audit on the financial performance of Bank Perkreditan Rakyat (BPR). Eduvest – Journal of Universal Studies Volume 2 Number 2, February 2022 p- ISSN 2775-3735 e-ISSN 2775-3727 Eduvest – Journal of Universal Studies Volume 2 Number 2, February 2022 p- ISSN 2775-3735 e-ISSN 2775-3727 ANALYSIS OF THE INFLUENCE OF THE BOARD OF DIRECTORS, COMPANY SIZE, MANAGEMENT OWNERSHIP, AND KAP AUDIT ON THE FINANCIAL PERFORMANCE OF BANK PERKREDITAN RAKYAT (BPR) INTRODUCTION In this era of free competition, banks must be good at reading opportunities and taking advantage of them in order to survive. Various methods are used by banks to increase market share and profits (Indiatsy, Mucheru, Mandere, Bichanga, & Gongera, 2014). One way that can be done to improve banking performance is through the implementation of Good Corporate Governance (GCG) (Napitupulu, Primiana, Nidar, Effendy, & Puspitasari, 2020). The The factor that underlies the company implementing GCG is due to the agency theory which assumes a conflict of interest between the executive (agent) and the shareholders (principal) and other stakeholders, where the company's management does not act in the interests of shareholders but prioritizes the interests of shareholders (Jahja, Mohammed, Lokman, & Mohamed, 2020). himself. In such conditions, GCG is present. The implementation of GCG is expected to increase supervision over management to encourage effective decision making, prevent opportunistic actions that are not in line with the interests of the company, and reduce information asymmetry between executives and company stakeholders. Thus, GCG is expected to be able to create conducive conditions and a solid foundation for a good Rural Bank (BPR) operation (Manor & Desiana, 2018). Rural Banks (BPR) are banks that carry out conventional business activities which in their activities do not provide services in payment traffic as referred to in the Law concerning banking (Financial Services Authority Number 4/POJK.03/2015). y Based on the Financial Services Authority Regulation Number 4/POJK.03/2015 concerning the Implementation of Governance for Rural Banks, it is stated that Governance is the governance of BPRs that apply the principles of transparency, accountability, and responsibility independence (independency), and fairness (fairness). BPRs are required to implement Good Corporate Governance in each of their business activities at all levels or levels of the organization (Harjanto, 2019). One of them is implementing regulations regarding the number of directors based on core capital, a BPR with a core capital of at least 50 billion must have at least 3 (three) directors and a BPR with a core capital of less than 50 billion must have at least 2 (two) members of the board of directors. . Even for share ownership alone, the directors, either individually or jointly, are prohibited from owning shares of more than 25%. ANALYSIS OF THE INFLUENCE OF THE BOARD OF DIRECTORS, COMPANY SIZE, MANAGEMENT OWNERSHIP, AND KAP AUDIT ON THE FINANCIAL PERFORMANCE OF BANK PERKREDITAN RAKYAT (BPR) Both are able to affect non- performing loans because the p-value obtained is smaller than 0.05. Simultaneously also found the effect of the board of directors, company size, managerial ownership, and KAP audits on the return on assets or non-performing loans of BPRs in the Bekasi area for the 2018-2021 period. Analysis of the Influence of the Board of Directors, Company Size, Management Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat (BPR) 398 Eduvest – Journal of Universal Studies Volume 2 Number 2, February 2022 companies. On the other hand, board size in non-family firms has no systematic relationship with firm performance (Saidat, Silva, & Seaman, 2019). companies. On the other hand, board size in non-family firms has no systematic relationship with firm performance (Saidat, Silva, & Seaman, 2019). The financial report is an information product produced by the company, and is a very important instrument related to the condition of the company (Lev, 2018). Therefore, every policy and decision taken in the process of preparing financial statements will greatly influence the assessment of the company's performance (Lev, 2018). According to POJK No. 4/POJK.03/2015 concerning Implementation of BPR Governance Article 76, RBs are required to send reports on the implementation of governance to the Financial Services Authority, the BPR Association in this case Perbarindo, and to 1 (one) media office or economic and financial magazine. Based on the data from Perbarindo, the names of 32 BPRs in the Bekasi area were taken which sent reports on their governance implementation as well as the published financial reports of BPRs for the first quarter of 2019 - until the second quarter of 2021 in the Bekasi area from the website of the Financial Services Authority. By nature, banks are no different from other commodity companies or service companies. In this case, the bank produces output in the form of credit and input in the form of public savings funds (Bvirindi, 2021). Thus, banks can bridge the interests of the owners of funds with those who need funds or are called carrying out the intermediation function (Disemadi, 2019). The banking industry has a very important role in economic development. The history of the Indonesian economy shows that the Indonesian economy moves in tandem with the banking industry (Rizvi, Narayan, Sakti, & Syarifuddin, 2020). The Indonesian economy is a bank-based economy, an economy that depends on the existence of banks as a source of financing. Therefore, efforts to strengthen a healthy, efficient and beneficial banking system for the economy are the key to success in maintaining the sustainability of national economic development (Zhang, Shi, Zhang, & Xiao, 2019). Examines the relationship between the GCG index and five financial performance measures (Suhadak, Rahayu, & Handayani, 2019). Partially, no statistically significant relationship was found. Simultaneously, however, statistically significant relationships emerged in both directions for most financial performance measures. Eduvest – Journal of Universal Studies Volume 2 Number 2, February 2022 Then Mahrani & Soewarno (2018) tested the effect of Good Corporate Governance and Corporate Social Responsibility on the company's financial performance, from the results of testing and analysis of the GCG and CSR mechanisms that had a positive effect on financial performance and earnings management. Based on the study of thought above, the researcher is interested in raising the title "Analysis of the Influence of the Board of Directors, Company Size, Managerial Ownership, KAP Audit on the Financial Performance of BPRs in the Bekasi Region for the 2018-2021 period”. INTRODUCTION OJK also regulates the implementation of an external audit function, in this case BPRs are required to appoint a Public Accountant and a Public Accounting Firm to conduct an annual audit. BPRs are required to implement Good Corporate Governance in each of their business activities at all levels or levels of the organization (Endah, Tarjo, & Musyarofah, 2020). The implementation of Good Corporate Governance in financial institutions is important to do in order to further foster trust in the community and improve banking performance and progress (Olannye & Anuku, 2014). The problem of Good Corporate Governance and corporate ownership structure is not new, especially public companies which are usually owned by many shareholders (Jiang & Kim, 2020). Several studies have tested the effect of GCG on the company's financial performance. Sa'diyah (2020) examines the Effect of Good Corporate Governance on the Financial Performance of Islamic Commercial Banks in Indonesia, finding that corporate governance proxied by the Board of Commissioners, Independent Board of Commissioners, Board of Directors and Sharia Supervisory Board has no effect on financial performance. Saidat et al. (2018) also in his research examining the relationship between GCG and the financial performance of companies in Jordan, found that board size has a negative relationship with the performance of family (BPR) 398 Eduvest – Journal of Universal Studies Volume 2 Number 2, February 2022 RESEARCH METHOD This research is an associative type, where the research uses four independent variables, namely (board of directors, company size, managerial ownership, and KAP audit) and two dependent variables (return on assets and non-performing loans). This type of data collection uses secondary data obtained from quarterly BPR financial reports published by the Financial Services Authority (www.ojk.go.id) for the period March 2018 - June 2021 from a BPR in the Bekasi area who sends a report on the implementation of its governance to the http://eduvest.greenvest.co.id 399 Riwandari Juniasti BPR Association, in this case Perbarindo. The data analysis method used in this study is simple regression analysis with assistance program Eviews 10. The following will explain the operational definition of each variable. Table 1 Operationalization of Research Variables Kind of Variable Variable Name Parameter Scala Independent Board of Directors Variable Name Dummy = complete 1, incomplete 0 Company Size Board of Directors Ln (Total Assets) Managerial ownership Company Size Dummy = There is 1, there is not 0 KAP Audit managerial ownership Dummy = KAP audit 1, no KAP audit 0 Dependent Financial performance Return on Asset (ROA) Non Performing Loan (NPL) Source: Research Results (2021) Classic assumption test One of the classic assumptions used in this research is the normality test. Where in this study there are two dependent variables, so that the results of the normality test are presented as follows: Table 2 Normality Test Model 1 Variabel Dependen Jarque-Bera Probability Return on Asset 66570.87 0.000000 ource: Data Processing Results with Eviews version 10 (2021) The results of the normality test of model 1 obtained a Jarque-Bera value of 66570.87 with a probability value of 0.000000 which is smaller than a significant level of 0.05, so it is stated that the data in this study is not normally distributed. Because the results of the normality test in model 1 are not normally distributed, the data is regressed using the eviews application and using the Newey-West HAC test. Where this method is one way of dealing with data that are not normally distributed or data variants are not homogeneous. For the results of the second model normality test as follows: Table 3 Normality Test Model 2 Variabel Dependen Jarque-Bera Probability Non Performing Loan 331.9191 0.000000 Source: Data Processing Results with Eviews version 10 (2021) Furthermore, the results of the normality test of model 2 show that the Jarque- Bera value is 331.9191 with a probability value of 0.000000 which is smaller than the 0.05 significant level, so it can be concluded that the data in this study is not normally Analysis of the Influence of the Board of Directors, Company Size, Management Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat (BPR) 400 Analysis of the Influence of the Board of Directors, Company Size, Management Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat (BPR) 400 400 Eduvest – Journal of Universal Studies Volume 2 Number 2, February 2022 distributed. Because the results of the normality test in model 2 are not normally distributed either, the data is regressed using the eviews application and the Newey-West HAC test. Multiple Linear Regression Test Because the data in model 1 and model 2 are not normally distributed, the data analysis in this study used multiple linear regression analysis with the Newey-West HAC test. The results of the Newey-West HAC test with multiple linear regression are presented in table 4 below. Table 4 Newey-West Model 1 . HAC Test Results Variable Coefficient Std. Error t-Statistic Prob. C 10.95765 2.558122 4.283475 0.0000 BOARD OF DIRECTORS -1.050886 1.902787 -0.552288 0.5810 SIZE 5.93E-09 3.49E-09 1.700895 0.0897 KEPMAN -0.795014 0.952309 -0.834827 0.4043 AUDIT -6.910605 2.472688 -2.794774 0.0054 Source: Data Processing Results with Eviews version 10 (2021) Table 4 Newey-West Model 1 . HAC Test Results Based on the results of the regression model 1 output that has been carried out in this study, a regression equation model can be made as follows: ROA_Y1 = 10.95765 – 1.050886DIREKSI + 5.93 SIZE – 0.795014KEPMAN – 6.910605 + ε Table 5 Newey-West Model 2 . HAC Test Results Variable Coefficient Std. Error t-Statistic Prob. C 21.54757 3.052198 7.059691 0.0000 BOARD OF DIRECTORS -3.417810 1.823933 -1.873868 0.0616 SIZE -2.17E-08 4.73E-09 -4.301113 0.0000 KEPMAN -1.108887 1.480745 -0.748871 0.4543 AUDIT -7.087053 2.627483 -2.697278 0.0073 Source: Data Processing Results with Eviews version 10 (2021) Based on the results of the regression model 2 output that has been carried out in this study, a regression equation model can be made as follows: Based on the results of the regression model 2 output that has been carried out in this study, a regression equation model can be made as follows: NPL_Y2 = 21.54757– 3.417810DIREKSI - 2.17SIZE – 1.108887KEPMAN – 7.087053AUDIT + ε Hypothesis testing y, g q NPL_Y2 = 21.54757– 3.417810DIREKSI - 2.17SIZE – 1.108887KEPMAN – 7.087053AUDIT + ε Hypothesis testing Hypothesis testing is a testing procedure that will result in a decision, namely the decision to accept or reject the hypothesis in a study. Hypothesis testing in this study uses partial hypothesis testing (t test), coefficient of determination test (R2), and F test. t test (Partial Hypothesis Testing) Statistical t test is used to determine the effect of an independent variable individually in explaining the variation of the dependent variable (Ghozali, 2013). Criteria for acceptance and rejection of the hypothesis are based on the significance value of p-value. If the p-value (significance) > 0.05, the research hypothesis is rejected. http://eduvest.greenvest.co.id 401 Riwandari Juniasti If the p-value (significance) <0.05, the research hypothesis is accepted. Based on the results of testing the partial hypothesis (t test) in the previous table, it can be concluded: Based on the results of testing the partial hypothesis (t test) in the previous tabl it can be concluded: 1. Influence of the Board of Directors on Financial Performance Return on Assets Based on the table, the beta coefficient value for the model 1 board of directors variable is -1.050886 with a negative relationship direction, the p-value of model 1 is 0.5810 > 0.05. Thus it can be concluded that the board of directors has no effect on the return on assets of the BPR. Based on the table, the beta coefficient value for the model 1 board of directors variable is -1.050886 with a negative relationship direction, the p-value of model 1 is 0.5810 > 0.05. Thus it can be concluded that the board of directors has no effect on the return on assets of the BPR. 2. The Effect of Firm Size on Financial Performance Return on Assets Based on the table, the beta coefficient value of the model 1 firm size variable is 5.93 and the p-value of model 1 is 0.0897 > 0.05. Thus it can be concluded that the size of the company has no effect on the return on assets at BPR. Based on the table, the beta coefficient value of the model 1 firm size variable is 5.93 and the p-value of model 1 is 0.0897 > 0.05. Thus it can be concluded that the size of the company has no effect on the return on assets at BPR. 3. The Effect of Managerial Ownership on Financial Performance Return on Assets Based on the table, the beta coefficient value of the managerial ownership variable model 1 is -0.795014 with a negative relationship direction, the p-value of model 1 is 0.4043 > 0.05, in this model the p-value is greater than 0.05 so that concluded that managerial ownership has no effect on return on assets at BPR. Based on the table, the beta coefficient value of the managerial ownership variable model 1 is -0.795014 with a negative relationship direction, the p-value of model 1 is 0.4043 > 0.05, in this model the p-value is greater than 0.05 so that concluded that managerial ownership has no effect on return on assets at BPR. 4. Coefficient of Determination Test Coefficient of Determination Test The coefficient of determination (R2) test explains the percentage of total variation in the dependent variable which is explained together. R2 describes the measure of conformity (goodness of fit), namely the extent to which the sample regression line matches the existing data. The criterion is that the higher the value of R2 (R2 is close to 1), the better the regression line of the sample. The results of the coefficient of determination in this study are as follows: Table 6. Coefficient of Determination Test Results (R2) R-Squared Model 1 0.031170 (3,11%) Model 2 0.133453 (13,34%) Source: Data Processing Results with Eviews version 10 (2021) Table 6. Coefficient of Determination Test Results (R2) Based on Table 6 above, it is known that the results of the coefficient of determination test of the two models in this study will be explained below. 1. The R-square value in model 1 is 0.031170, this indicates that 3.11% of the variables of the board of directors, firm size, managerial ownership, and audit firm are influenced by the return on assets variable, while the remaining 96.89% is influenced by other variables. outside of the research. 2. The R-square value in model 2 is 0.133453 this shows that 13.34% of the board of directors variables, company size, managerial ownership, and KAP audit are influenced by non-performing loans, while the remaining 86.66% is influenced by other variables. outside of the research. F test (simultaneous hypothesis testing) Riwandari Juniasti The Effect of KAP Audit on Financial Performance Return on Assets 4. The Effect of KAP Audit on Financial Performance Return on Assets Based on the table, the beta coefficient value of the audit variable KAP model 1 is - 6.910605 with a negative relationship direction, the p-value of model 1 is 0.0054 <0.05. The KAP audit variable model 1 has a p-value that is smaller than 0.05, which means that the fourth hypothesis is accepted. 5. Influence of the Board of Directors on the Financial Performance of Non-Performing Loans Based on the table, the beta coefficient value for the board of directors variable model 2 is -3.417810 with a negative relationship direction, the p-value of model 2 is 0.0616 > 0.05. Thus it can be concluded that the board of directors has no effect on non-performing loans at BPR. 6. The Effect of Firm Size on the Financial Performance of Non-Performing Loans 6. The Effect of Firm Size on the Financial Performance of Non-Performing Loans Based on the table, the beta coefficient value of the model 2 firm size variable is -2.17 with a negative relationship direction, the p-value of model 2 is 0.0000 <0.05. Thus, it can be concluded that company size has effect on non-performing loans at BPR. 7. The Effect of Managerial Ownership on the Financial Performance of Non-Performing Loans Based on the table, the beta coefficient value of the managerial ownership variable model 2 is -1.108887 with a negative relationship direction, the p-value of model 2 is 0.4543 > 0.05. Thus, it can be concluded that managerial ownership has no effect on non- performing loans at BPR. 8. The Effect of KAP Audits on the Financial Performance of Non-Performing Loans Based on the table, the beta coefficient value of the audit variable KAP model 2 is - 7.087053 with a negative relationship direction, the p-value of model 2 is 0.0073 <0.05. The p-value obtained is smaller than 0.05, so it can be concluded that the KAP audit has effect on non-performing loans at BPR. 402 Eduvest – Journal of Universal Studies Volume 2 Number 2, February 2022 CONCLUSION This study aims to determine the effect of the board of directors, firm size, managerial ownership, and KAP audit on return on assets and non-performing loans at BPR. Based on the explanation above, it is concluded that it is proven that in model 1 only KAP audits have a significant influence on return on assets. Meanwhile, for model 2, firm size and KAP variables have a significant negative effect on non-performing loans. Simultaneously the board of directors, company size, managerial ownership, and KAP audits are able to have an influence on both the return on assets and non-performing loans of BPR Bekasi area for the 2018-2021 period. F test (simultaneous hypothesis testing) F test (simultaneous hypothesis testing) The F test (simultaneous test) is used to test whether together all independent variables have a significant effect on the dependent variable. The results of the F test are presented in the following table: Table 7 F-test F-statistic Prob (F-statistic) Model 1 3.5551/12 0.007206 Model 2 17.01758 0.000000 Source: Data Processing Results with Eviews version 10 (2021) Referring to the table above, the significant value of p-value for model 1 is 0.007 < 0.05, with a statistical F value of 3.555 > 2.625. This means that the variables of the board of directors, company size, managerial ownership, and KAP audit together have a significant influence on the return on assets of BPR. Then the p-value of model 2 is 0.000 <0.05, with a statistical F value of 17.017 > 2.625. Thus, the variables of the board of directors, firm size, managerial ownership, and KAP audit together have a significant influence on non-performing loans in rural banks. Then the p-value of model 2 is 0.000 <0.05, with a statistical F value of 17.017 > 2.625. Thus, the variables of the board of directors, firm size, managerial ownership, and KAP di h h i ifi i fl f i l i l b k 2.625. Thus, the variables of the board of directors, firm size, managerial ownership, and KAP audit together have a significant influence on non-performing loans in rural banks. 403 http://eduvest.greenvest.co.id REFERENCES Bvirindi, Tinashe C. (2021). Banking. In A Practical Guide to Financial Services (pp. 39–64). Routledge. Disemadi, Hari Sutra. (2019). Risk Management In The Provision Of People’s Business Credit As Implementation Of Prudential Principles. Diponegoro Law Review, 4(2), 194–208. Endah, Nur, Tarjo, Tarjo, & Musyarofah, Siti. (2020). The Implementation Of Good Corporate Governance And Efforts To Prevent Fraud In Banking Companies. Jurnal Reviu Akuntansi Dan Keuangan, 10(1), 136–149. Harjanto, Nung. (2019). Developing Stronger Indonesian Rural Banks. Review of Integrative Business and Economics Research, 8, 313–324. Indiatsy, Christopher Masinde, Mucheru, Stephen Mwangi, Mandere, Evans Nyamboga, Bichanga, Julius Miroga, & Gongera, Enock George. (2014). The application of Porter’s five forces model on organization performance: A case of cooperative bank of Kenya Ltd. Jahja, Junino, Mohammed, Nor Farizal, Lokman, Norziana, & Mohamed, Norazida. (2020). Corporate governance, managerial diversion, and Indonesian state-owned enterprises: a literature review. International Journal of Financial Research, 11(5), 510–517. Jiang, Fuxiu, & Kim, Kenneth A. (2020). Corporate governance in China: A survey. Review of Finance, 24(4), 733–772. Lev, Baruch. (2018). The deteriorating usefulness of financial report information and how to reverse it. Accounting and Business Research, 48(5), 465–493. Manor, Usman, & Desiana, Putri Mega. (2018). Work-Life Balance, Motivation and Personality of MSE Owners on Firm Performance in Greater Jakarta. Pertanika Journal of Social Sciences and Humanities, 26, 127–138. Napitupulu, Sotarduga, Primiana, Ina, NIDAR, Sulaeman R., Effendy, Nury, & Puspitasari, Devy Mawarnie. (2020). The effect of management capabilities in implementing good corporate governance: A study from indonesia banking sector. The Journal of Asian Finance, Economics and Business, 7(1), 159–165. Olannye, A. Peter, & Anuku, David. (2014). Corporate governance and organizational performance in the Nigerian banking industry. Journal of Emerging Trends in Economics and Management Sciences, 5(6), 525–531. Rizvi, Syed Aun R., Narayan, Paresh Kumar, Sakti, Ali, & Syarifuddin, Ferry. (2020). Role of Islamic banks in Indonesian banking industry: an empirical exploration. Pacific-Basin Finance Journal, 62, 101117. Analysis of the Influence of the Board of Directors, Company Size, Management Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat (BPR) 404 Analysis of the Influence of the Board of Directors, Company Size, Management Ownership, and Kap Audit on the Financial Performance of Bank Perkreditan Rakyat (BPR) 404 404 Eduvest – Journal of Universal Studies Volume 2 Number 2, February 2022 Eduvest – Journal of Universal Studies Volume 2 Number 2, February 2022 Saidat, Zaid, Silva, Mauricio, & Seaman, Claire. (2019). Saidat, Zaid, Silva, Mauricio, & Seaman, Claire. (2019). The relationship between corporate governance and financial performance: Evidence from Jordanian family and nonfamily firms. Journal of Family Business Management. f y f g Zhang, Tong, Shi, Xunpeng, Zhang, Dayong, & Xiao, Junji. (2019). Socio-economic development and electricity access in developing economies: A long-run model averaging approach. Energy Policy, 132, 223–231. Saidat, Zaid, Silva, Mauricio, & Seaman, Claire. (2019). The relationship between corporate governance and financial performance: Evidence from Jordanian family and nonfamily firms. Journal of Family Business Management. Suhadak, Suhadak, Rahayu, Sri Mangesti, & Handayani, Siti Ragil. (2019). GCG, financial architecture on stock return, financial performance and corporate value. International Journal of Productivity and Performance Management. Zhang, Tong, Shi, Xunpeng, Zhang, Dayong, & Xiao, Junji. (2019). Socio-economic development and electricity access in developing economies: A long-run model averaging approach. Energy Policy, 132, 223–231. REFERENCES The relationship between corporate governance and financial performance: Evidence from Jordanian family and nonfamily firms. Journal of Family Business Management. y f y g Suhadak, Suhadak, Rahayu, Sri Mangesti, & Handayani, Siti Ragil. (2019). GCG, financial architecture on stock return, financial performance and corporate value. International Journal of Productivity and Performance Management. y Suhadak, Suhadak, Rahayu, Sri Mangesti, & Handayani, Siti Ragil. (2019). GCG, financial architecture on stock return, financial performance and corporate value. International Journal of Productivity and Performance Management. Zhang, Tong, Shi, Xunpeng, Zhang, Dayong, & Xiao, Junji. (2019). Socio-economic development and electricity access in developing economies: A long-run model averaging approach. Energy Policy, 132, 223–231. Zhang, Tong, Shi, Xunpeng, Zhang, Dayong, & Xiao, Junji. (2019). Socio-economic development and electricity access in developing economies: A long-run model averaging approach. Energy Policy, 132, 223–231. 405 http://eduvest.greenvest.co.id
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Intervenções temporárias no espaço público da cidade de Natal - RN
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Intervenções temporárias no espaço público da cidade de Natal - RN: O caso do movimento Eco Praça Manuela Carvalhoa e Ruth Ataídeb a Universidade Federal do Rio Grande do Norte, Departamento de Arquitetura e Urbanismo, Programa d Pós-Graduação em Arquitetura e Urbanismo, Natal, Rio Grande do Norte, Brasil. E-mail: contatomcarquiteta@gmail.com Manuela Carvalhoa e Ruth Ataídeb a Universidade Federal do Rio Grande do Norte, Departamento de Arquitetura e Urbanismo, Programa de Pós-Graduação em Arquitetura e Urbanismo, Natal, Rio Grande do Norte, Brasil. E-mail: contatomcarquiteta@gmail.com Manuela Carvalhoa e Ruth Ataídeb a Universidade Federal do Rio Grande do Norte, Departamento de Arquitetura e Urbanismo, Programa de Pós-Graduação em Arquitetura e Urbanismo, Natal, Rio Grande do Norte, Brasil. E-mail: contatomcarquiteta@gmail.com b Universidade Federal do Rio Grande do Norte, Departamento de Arquitetura e Urbanismo (DARQ), Programa de Pós-Graduação em Arquitetura e Urbanismo (PPGAU), Natal, Rio Grande do Norte, Brasil. E-mail: rataide_58@hotmail.com Submetido em 20 de março de 2019. Aceito em 30 de julho de 2019. Resumo. A atual conformação das cidades e o marcante distanciamento das pessoas do espaço público têm proporcionado o aparecimento de movimentos sociais de naturezas diversas que reivindicam novas formas de uso e apropriação do espaço. Nesse contexto, o movimento Eco Praça surge em Natal-RN como um projeto de intervenções temporárias que se fundamenta na mobilização social, estimulando o uso de praças subutilizadas, promovendo a transformação no seu uso e apropriação pelos moradores da cidade. Este artigo, que resulta de uma pesquisa exploratória, analisa esses processos e a significância deste movimento enquanto uma ação de resistência no âmbito local com ênfase na morfologia das praças e na percepção dos agentes envolvidos direta e indiretamente. Palavras-chave. apropriação do espaço público, territórios alternativos, resistência, lugar, Eco Praça. Revista de MorfologiaUrbana (2019) 7(1): e00051 Introdução Ainda, analisou-se a natureza do movimento enquanto ação transformadora desses espaços e a rua em relação com a percepção das pessoas envolvidas. O resultado desse processo é um espaço fragmentado, individualista e sem identidade, marcado pela privatização dos espaços públicos, pela ausência de corpos na cidade e por uma cultura do espetáculo, que padroniza pensamentos, comportamentos e ações das pessoas, gerando uma nova lógica da dinâmica urbana (Olivi, 2012, p. 04). O ato de ocupar, ressignificar, recriar novos lugares na cidade, passa a emergir como resistência e reinventa, através de diversas práticas efêmeras, os espaços da cidade. No caso do presente estudo são destacadas as intervenções temporárias expressas no Movimento “Eco Praça” como formas de apropriação que surgem de maneira despretensiosa, muitas vezes pouco organizadas, mas que tentam transformar a vida pública por meio de práticas simples, as quais visam dar uma maior dimensão à necessidade de viver e reposicionar as práticas coletivas na cidade. Introdução privados, maquiados e vendidos pelo consumo, entre tantas outras ações que modificam o espaço na contemporaneidade. O espaço urbano é um laboratório de experiências e de construção de identidades. Apropriar-se dele é reaproximar os corpos da rua, buscar novas formas de manifestação, ao mesmo tempo que pensa em como transformar e criar/recriar lugares coletivamente. No contexto atual, o uso lúdico dos espaços pelos movimentos temporários de resistência, assim como a ocupação de áreas subutilizadas com o estímulo ao retorno das pessoas às ruas, constituem ações que interferem e alteram o tratamento dos nossos espaços públicos, na medida em que evidenciam alguns problemas enfrentados pela sociedade contemporânea. Assim, a ocupação de espaços públicos abandonados, de praças, parques e canteiros, ou mesmo de resíduos do espaço privado da cidade formal, torna-se significante ao promoverem alterações na sua dinâmica espacial e formas de utilização, assim como de outras alternativas para se viver a cidade. Nesse sentido, o movimento “Eco Praça” – objeto de estudo deste trabalho e caracterizado aqui como um tipo de intervenção temporária – merece destaque por se tratar de uma ação requalificadora e transformadora na cidade de Natal-RN, que ao ocupar diversas praças subutilizadas, promoveu, ainda que temporariamente, a apropriação e a ressignificação desses espaços pela população. Tais problemas se materializam nas cidades por meio das ações que privilegiam os interesses individuais em detrimento dos coletivos, por exemplo, na produção de grandes escalas de planejamento, na priorização do transporte motorizado, na transformação do público em espaços O propósito do estudo foi compreender essas ações temporárias como geradoras de novas Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 2 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN práticas coletivas e a sua relação com o restabelecimento das condições de vitalidade e urbanidade nos espaços ocupados e em seus respectivos entornos. Com isso, buscou-se analisar não apenas o espaço físico contido nos limites das praças, mas também o processo de apropriação dessas pelas pessoas e a significância do movimento enquanto ação de resistência no contexto da cidade de Natal. As considerações da pesquisa tiveram como enfoque principal a forma como essas praças eram utilizadas – durante e depois das intervenções –, assim como a relação do existente (espaço físico e inserção dele nos repectivos entornos com as ocupações). Morfologia, intervenções temporárias e a criação de novos lugares na cidade O espaço público surge como palco principal das representações socias, culturais e políticas, respondendo assim aos discursos dos agentes públicos e da sociedade em geral. As configurações morfológicas dele refletem e influenciam o modo como os indivíduos e grupos sociais usam a cidade, as suas relações com o cotidiano, a cultura e os costumes. Essa cidade, lida através do corpo e dos seus usos manifestos nos lugares, adquire significado e torna-se o principal palco de estudo dessas experiências. Tais intervenções são definidas como temporárias por não promoverem necessariamente ações de longo prazo ou tampouco se organizarem em torno de um cronograma rígido. Movidas por novos conceitos, como o urbanismo tático1 e o placemaking2, essas ações buscam, por meio de iniciativas simples de ocupação do espaço público, promover transformações no cotidiano das pessoas que observam e também interagem com elas. Em geral, essas práticas permitem que se possa apreciar e compreender a cidade de forma lúdica, entendida pela corpografia3 e significada pelo uso e pela criação de lugares. A partir dessa compreensão, notam-se as diferentes formas de transformação dos espaços das cidades, muitos desprovidos de vitalidade e complexidades sociais, seja pelas relações mais fluidas e individualistas, resultantes de um modelo funcionalista de planejamento urbano, ou por transformações inevitáveis, que surgem devido às estruturas sociais/políticas emergentes. Nesse sentido, os espaços públicos são os mais afetados, tranparecendo na subutilização dele e no seu distanciamento, a necessidade de constante apropriação e ocupação por parte das pessoas. Para Adriana Sansão Fontes (2013, p. 36), as intervenções temporárias são basicamente ações intencionais que buscam transformar o espaço de forma efêmera, sem necessariamente manter uma temporalidade. São em sua maioria pequenas, particulares em relação aos locais utilizados, subversivas, pois não seguem um padrão único, e interativas por estimularem a socialização. A autora classifica essas ações na forma de apropriações espontâneas, intervenções de arte pública e festas locais, mas, Para Adriana Sansão Fontes (2013, p. 36), as intervenções temporárias são basicamente ações intencionais que buscam transformar o espaço de forma efêmera, sem necessariamente manter uma temporalidade. São em sua maioria pequenas, particulares em relação aos locais utilizados, subversivas, pois não seguem um padrão único, e interativas por estimularem a socialização. Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Morfologia, intervenções temporárias e a criação de novos lugares na cidade A autora classifica essas ações na forma de apropriações espontâneas, intervenções de arte pública e festas locais, mas, principalmente, as caracteriza com a marca principal da intencionalidade transformadora, na medida em que rompem com o cotidiano, transitando sempre entre os usos comuns da cidade e os grandes eventos. Alessandra Olivi (2012, p. 4) considera que o atual modelo de produção do espaço urbano sob os moldes capitalistas se apropria dos lugares da vida e dos seus significados, e ameaça a capacidade de identificação pessoal e cultural. Isso prejudicará drasticamente a vida urbana e a reprodução das múltiplas identidades que a compõem. Para a autora: principalmente, as caracteriza com a marca principal da intencionalidade transformadora, na medida em que rompem com o cotidiano, transitando sempre entre os usos comuns da cidade e os grandes eventos. Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 3 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN Essas ações fortificam as relações já propostas nos espaços e fomentam, por meio das ações lúdicas e corpóreas, a criação de novos lugares. Para Vicente Del Rio (1990), o lugar corresponde ao conjunto de elementos que conformam o nosso ambiente mais imediato: “São muito fortes, e empiricamente verificáveis, as sensações de pertencer, de proteção, de territorialidade, de domínio” (Del Rio, 1990, p. 88). permanece geralmente subentendida, ainda que sempre recebendo um forte e explícito viés de funcionalidade: lugares seriam aqueles espaços urbanos cuidadosamente localizados, quantificados e definidos, destinados basicamente ao desempenho de funções de cunho social. Ou seja: espaços nos quais as pessoas iriam se encontrar e realizar seus contatos sociais, esperando-se que, nesse exercício, fossem sociabilizar comunitariamente em seus relacionamentos interpessoais. Lugares, numa visão como essa, não seriam mais do que áreas funcionais destinadas ao exercício da sociabilização, isto é, áreas destinadas a funcionar como espaços de convívio (Castello, 2006, p. 80). Segundo esse autor, a psicologia ambiental permite compreender o lugar a partir da comparação dele com o espaço e esse tem em suas dimensões uma espacialidade física; enquanto o lugar está mais presente como uma dimensão psicológica, o espaço “é mensurável, o lugar é holístico” (Del Rio, 2003, p. 14). Morfologia, intervenções temporárias e a criação de novos lugares na cidade alimentação, locais de entretenimento, complexos esportivos, complexos híbridos, cinemas multiplex, museus, bibliotecas” (Castello, 2006, p. 78). alimentação, locais de entretenimento, complexos esportivos, complexos híbridos, cinemas multiplex, museus, bibliotecas” (Castello, 2006, p. 78). que se exprimem no uso, no acidental: “É o espaço passível de ser sentido, pensado, apropriado e vivido através do corpo” (Carlos, 2007, p. 17). Assim, afirma a autora: Anteriormente, Marc Augé (1994) definiu esses espaços como “não-lugares”. Caracterizados como espaços criados como/pela mercadoria, eles unificam e simplificam a vida, a arquitetura, os desejos e as relações dentro de si. Para esse autor, aeroportos, shoppings centers, grandes obras viárias, conveniências e fast foods, passam a reproduzir em suas estruturas características que os padronizam mesmo que em locais diferentes do globo; a cultura de massas passa a ser disseminada de acordo com moldes estéticos e consumistas, que buscam, acima de tudo, alienar as relações e disseminar novas necessidades às pessoas. Nesse mesmo ritmo, as cidades se modificam, na indústria, na publicidade, comércio, turismo, tornando-se uma alegoria de signos (Augé, 1994, p. 73). O lugar é produto das relações humanas, entre homem e natureza, tecido por relações sociais que se realizam no plano do vivido, o que garante a construção de uma rede de significados e sentidos que são tecidos pela história e cultura civilizadora produzindo a identidade, posto que é aí que o homem se reconhece porque é o lugar da vida. Cada sujeito se situa num espaço concreto e real onde se reconhece ou se perde, usufrui e modifica, posto que o lugar tem usos e sentidos em si (Carlos, 1996, p. 29). Para Carlos (2007), o lugar não nos propõe o entendimento enquanto parte associada do espaço, mas como parte do processo de reprodução da vida. Assim, o lugar abre a perspectiva para se pensar o viver e o habitar, o uso e o consumo, os processos de apropriação do espaço (Carlos, 2007, p. 14). O autor destaca que os não-lugares se apresentam na multiplicação de referências imaginárias, nas acelerações dos meios de transporte e nas mudanças de escala, e são produtos da supermodernidade. Nessa perspectiva, eles seriam essas instalações necessárias ao trânsito rápido – viadutos, pontes, túneis; os grandes centros comerciais; e até mesmo áreas criadas para abrigar pessoas, instalações efêmeras que podem ser replicadas em qualquer lugar. Morfologia, intervenções temporárias e a criação de novos lugares na cidade Del Rio destaca ainda que a partir dos estudos do psicólogo ambiental David Canter, o lugar pode ser definido por três dimensões: as atividades que ocorrem nele, as concepções desse ambiente construído e seus atributos físicos, como mostra o diagrama: Já durante o pós-modernismo, segundo Castello (2006), o tema do lugar passa a enquandrar-se em um enfoque mais fenomenológico, conceituando “lugar de modo a considerá-lo como algo mais do que uma mera localização espacial” (Castello, 2006, p. 82). Com isso: Figura 1. Diagrama de Venn indica o conceito de lugar pelas suas intersecções (fonte: produzido pelas autoras a partir de Del Rio, 2003). O peso fenomenológico que o conceito encerra vê-se consideravelmente aumentado: lugar é consagrado como conceito urbano de natureza fenomenológica. A cidade, percebida por suas características de produção de bens e serviços é, também, percebida por suas características de produção de experiências humanas. Experiências que se processam em uma rede de lugares: lugares que se preocupam com humanismo e com a concretização do espaço existencial [...] A compreensão de lugar como fenômeno passa vigorosamente a pressionar com cada vez maior intensidade as ponderações da intelectualidade arquitetônico- urbanística da época (Castello, 2006, p. 83). Figura 1. Diagrama de Venn indica o conceito de lugar pelas suas intersecções (fonte: produzido pelas autoras a partir de Del Rio, 2003). Na mesma concepção urbanística de Del Rio (1990), Lineu Castello (2006) destaca dois momentos em que a noção de lugar ganha destaque no século XX: no modernismo e nas teorias arquitetônicas-urbanísticas pós- modernas. Para o autor, durante o modernismo, o conceito de lugar foi visto com certo desinteresse: Ao tratar do lugar como parte da experiência humana em um campo de estudo mais ligado à geografia urbana, Ana Fani Alessandri Carlos (2007) admite o lugar como a base da reprodução da vida, que pode ser identificado pelo conjunto – habitante, identidade e lugar. Esse lugar surge pelas relações que os indivíduos mantêm com os espaços habitados O conceito de lugar não chega a ser expresso de maneira clara no Modernismo. A expressão lugar Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Intervenções temporárias no espaço público da cidade de Natal - RN 4 / 13 alimentação, locais de entretenimento, complexos esportivos, complexos híbridos, cinemas multiplex, museus, bibliotecas” (Castello, 2006, p. 78). Morfologia, intervenções temporárias e a criação de novos lugares na cidade Ou ainda, o não-lugar pode vir a se tornar um lugar à medida que é apropriado, que ganha significado: “O lugar e o não-lugar são, antes, polaridades fugidias: o primeiro nunca é completamente apagado e o segundo nunca se realiza totalmente” (Augé, 1994, p. 74). Pensando nisso, o uso de um espaço em determinado intervalo de tempo – mesmo que curto e pontual – por ações dotadas de significado e identidade, transmitem e criam lugares, sendo eles efêmeros ou não. Essa improvisação colide diretamente com a lógica racional de produção e utilização do espaço, reproduzindo um cotidiano marcado pela presença nas ruas, convívios reais e trocas simultâneas de experiências. A importância de se discutir os conceitos de lugar e não-lugar dentro do contexto da cidade contemporânea está na compreensão da atividade temporária como resistência e marco na criação de novos lugares, ou, simplesmente, da modificação dos não- lugares, garantindo a esses uma nova identidade específica. Para isso, cabe relacionar essas ações à novas formas de reinventar o “lugar” e de ressignificar a memória coletiva da cidade. Entende-se, à vista disso, que as intervenções temporárias recriam e reestabelecem as condições necessárias à geração de novos lugares da cidade, proporcionando aos espaços subutilizados um novo caráter identitário – mesmo que temporariamente – e dotando-os de um significado comum às pessoas que dele partilham. O uso efêmero garante um ecoar de possibilidades cotidianas que podem ser usadas coletivamente, recorrendo às soluções simples como a utilização alternativa de mobiliários, o uso artístico das calçadas ou simplesmente o encontro grupal em um determinado local da cidade. É nessa criação de novos lugares na cidade que as intervenções temporárias ganham corpo e podem ser tratadas como efetivadoras e promotoras do direito à cidade, aos espaços públicos e à vida coletiva. O lugar passa a ser resistente a um modelo de cidade fragmentada, hierarquizada e excludente, que nega as experiências da vida cotidiana e as vende a partir das necessidades do capital. Portanto, as intervenções temporárias aparecem aqui como formas apropriadas de ocupação de espaços residuais na cidade, assim como de não-lugares, que, realçando o valor da arte, da cultura, da música, ou dos simples encontros e derivas casuais, são capazes de agitar e recriar lugares, fomentar novas relações e promover diversas práticas colaborativas, contribuindo para o espaço da cidade. Morfologia, intervenções temporárias e a criação de novos lugares na cidade Segundo o autor: Nesse mesmo sentido, Eugenio Queiroga (2012) traz o lugar enquanto “lugar público”, como aquele espaço que se situa como o local que é apropriado pelo coletivo, mesmo não se trata de um espaço público propriamente dito; podendo, portanto, combinar espaços públicos e privados. Para o autor, o lugar público nos permite compreender as relações entre a vida pública e os espaços da cidade, e ainda pode se prestar à esfera pública ou privada, tendo assim um caráter dual em sua atuação. Para ele: “Todo lugar público é, ainda que esporadicamente, um subespaço da esfera pública, mas nem todas as ações da esfera pública se manifestam nos espaços públicos” (Queiroga, 2012, p. 216). Se um lugar pode se definir como identitário, relacional e histórico, um espaço que não pode se definir nem como identitário, nem como relacional, nem como histórico definirá um não-lugar. A hipótese aqui defendida é a de que a supermodernidade é produtora de não-lugares, isto é, de espaços que não são em si lugares antropológicos e que, contrariamente à modernidade baudelairiana, não integram os lugares antigos: estes, repertoriados, classificados e promovidos a ‘lugares de memória’, ocupam aí um lugar circunscrito e específico (Augé, 1994, p. 73). Para tanto, cabe aqui mencionar que na cidade contemporânea tem surgido diversos novos lugares – sejam públicos ou privados – que se concretizam perante às necessidades das novas informações, dos fluxos e, principalmente, do capital. A partir disso, Castello (2006, p. 78) denota esses novos espaços como “lugares geneticamente modificados”. Esses novos lugares se apresentam sobre diversas conformações: “nos shopping malls, cenários históricos revitalizados, praças de O não-lugar não possui relações/trocas sociais, identidade e não transmite, portanto, a história de um grupo, de uma sociedade. Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 5 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN medianeiras abandonadas. A sua flexibilidade, diversidade – de público, de organização, de efeitos – e a fluidez com que acontecem, potencializam tais realizações e transgridem a formalidade estrutural do espaço público, ao lidar diretamente com as regras impostas pela cidade. Logo, o não-lugar se relaciona com o lugar, na medida que sempre existe uma relação entre os dois: um só existe sobre a forma do outro; o não-lugar existe sob a perspectiva da ausência do lugar. Morfologia, intervenções temporárias e a criação de novos lugares na cidade Essas ações traduzem então uma forma de apropriação dos espaços públicos, que remodelam a vida urbana a partir das necessidades de diferentes pessoas e grupos diversos. Aproximação: O Movimento “Eco Praça” na cidade de Natal - RN Aproximação: O Movimento “Eco Praça” na cidade de Natal - RN Como discutido, os Movimentos temporários diversos têm surgido nas grandes cidades como forma de resistência, para confrontar os padrões individualistas de vivência do espaço, as pressões do capital na mercantilização da cidade e um modelo de planejamento que segrega e exclui a vida pública. Nesse contexto, tem surgido nos últimos anos na cidade de Natal - RN, movimentos temporários diversos, representados por ocupações efêmeras materializadas na arte, na cultura e nas práticas de lazer, que retomam os espaços públicos tidos como subutilizados. Assim, essas intervenções resultam de várias motivações, desde a resistência a uma ideia de cidade que segrega a vida pública a um combate a essa nova individualidade presente em nossa sociedade. Por motivos diversos, uns mais pessoais, outros mais coletivos, tais apropriações resultam em feiras livres, projetos de arte em comunidades, ocupação de praças de bairros, vendas ambulantes, festas ao ar livre ou simples grafites em Tais ações, convertem o espaço público em palcos de eventos com expressões artísticas, como a dança e a música, com bazares culturais e outras oportunidades de trocas comerciais; e o mais importante, criam lugares afetivos e ativos que proporcionam Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 6 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN atividades no interior do estado do Rio Grande do Norte, nos municípios de Pedro Avelino e Lajes. Para este artigo, foram destacadas apenas as dez praças, excluindo as demais ocupações (Quadro 1 e Figura 02). atividades no interior do estado do Rio Grande do Norte, nos municípios de Pedro Avelino e Lajes. Para este artigo, foram destacadas apenas as dez praças, excluindo as demais ocupações (Quadro 1 e Figura 02). atividades no interior do estado do Rio Grande do Norte, nos municípios de Pedro Avelino e Lajes. Para este artigo, foram destacadas apenas as dez praças, excluindo as demais ocupações (Quadro 1 e Figura 02). conversas e trocas de experiências. Segundo Alessandra Olivi (2012), esse controle do espaço pelos movimentos sociais adquire relevância particular em um contexto onde a privatização, a homogeneização, a mercantilização e a vigilância do espaço passam a alterar os valores públicos, sociais e políticos. Figura 2. Localização por bairros das praças ocupadas pelo movimento entre 2013 e 2016 (fonte: produzido pelas autoras a partir de Carvalho, 2017). Aproximação: O Movimento “Eco Praça” na cidade de Natal - RN Nesse sentido, o movimento “Eco Praça” em Natal - RN se apresenta como um movimento efêmero de apropriações de praças subutilizadas, que conseguiu alterar, ainda que temporariamente, as suas funções e formas de apropriação de lugar de passagem para espaços de integração e convivência no cotidiano das comunidades onde se inserem. Iniciado em 2013 na Praça dos Eucaliptos, localizada no bairro de Candelária, suas ações tiveram prosseguimento e destaque até o ano de 2016, promovendo a ocupação de dez praças em nove bairros – Candelária, Capim Macio, Potengi, Cidade Alta, Mãe Luiza, Ponta Negra, Neópolis e Petrópolis – do município; um espaço semi-público – a Cidade da Criança; e um espaço privado – a fundação Hélio Galvão, ambos em Natal. Ainda, em outros momentos, realizou Figura 2. Localização por bairros das praças ocupadas pelo movimento entre 2013 e 2016 (fonte: produzido pelas autoras a partir de Carvalho, 2017). Quadro 1. Localização das praças por bairros (fonte: produzido pelas autoras em 2018 a partir de Carvalho, 2017). Bairros x Regiões Administrativas de Natal Praças Bairro Região Praça do Ralf Lagoa Azul Norte Área de Lazer Panatis Potengi Norte Praça André de Albuquerque Cidade Alta Leste Praça 7 de Setembro Cidade Alta Leste Praça Cívica Petrópolis Leste Praça Edgar Borges Mãe Luiza Leste Praça dos Eucaliptos Candelária Sul Parque de Capim Macio Capim Macio Sul Praça Central de Neópolis Neópolis Sul Praça Omar O’Graddy Ponta Negra Sul Praças Praça do Ralf Área de Lazer Panatis Praça André de Albuquerque Praça 7 de Setembro Praça Cívica Praça Edgar Borges Praça dos Eucaliptos Parque de Capim Macio Praça Central de Neópolis Praça Omar O’Graddy nos quais elas se inserem. De acordo com o Anuário Estatístico do município de 2018, publicado pela SEMURB4, Natal se divide em quatro regiões administrativas (Norte, Sul, Leste e Oeste), sendo a Região Norte a maior delas em superfície e em população, envolvendo sete bairros. Neste trabalho, Da configuração morfológica dos espaços: As praças e seus respectivos entornos Ao tratar das dez praças discutidas neste artigo, cabe apresentar algumas notas sobre a configuração espacial e a divisão administrativa do município, assim como uma abordagem geral de alguns dos bairros Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Intervenções temporárias no espaço público da cidade de Natal - RN 7 / 13 redes sociais. Tais realizações ocorriam de forma despretensiosa e se manifestavam em cangas estendidas, pequenas vendas, rodas de conversas e apresentações musicais pontuais. Para Adriana Sansão Fontes (2013), essas ações eventuais de poetização e reconquista da cidade se intensificaram nos últimos anos, muitas vezes motivadas pelas redes sociais, movidas por uma causa comum de usar a cidade, e buscam nas estratégias de intervenções temporárias reestabelecer um elo com o cotidiano e com a vida coletiva. devido ao recorte da ocorrência das ocupações, foram analisadas dez praças localizadas nas regiões Norte, Sul e Leste, em nove bairros da cidade. Para entender a inserção do movimento nessas regiões, cabe evidenciar alguns aspectos urbanísticos, especialmente os referentes à oferta de serviços e equipamentos coletivos. A Região Norte possui 55 equipamentos desportivos (quadras, estádios, campos de futebol) e 62 praças; a Região Sul possui 34 equipamentos e 87 praças; a Região Leste 16 equipamentos e 74 praças; e a Região Oeste, 18 equipamentos e 31 praças. Com isso, nota-se que a Região Oeste – única a não possuir intervenção em suas praças – é a mais carente de equipamentos de lazer públicos (SEMURB, 2018, p. 152). Com o avanço das experiências, as ocupações foram se ampliando e agregando novos participantes de diferentes tribos e idades, estimulando o surgimento de novas demandas e evidenciando a necessidade de estruturação do movimento, como o apoio do poder público e o patrocínio de empresas privadas. As ações se converteram em grandes encontros marcados por práticas esportivas, apresentações culturais e musicais, hortas urbanas, conversas e discussões sobre temas atuais, barracas gastronômicas e bazares de diferentes estilos; tendo como principais atores: os organizadores do movimento, expositores e apoios, moradores do entorno das praças analisadas e os participantes. Da configuração morfológica dos espaços: As praças e seus respectivos entornos Ainda com relação às atividades instaladas e à infraestrutura, os bairros de Candelária, Capim Macio e Ponta Negra (Região Sul) são predominantemente residenciais, com uma grande diversidade de serviços e comércios localizadas nas avenidas principais, e seus moradores, em sua maioria, se inserem nos extratos de média e alta renda, residindo em casas e apartamentos de médio e alto padrão. Enquanto os bairros de Mãe Luiza (região Leste), Potengi e Lagoa Azul (Lagoa Azul) concentram uma população de pouca renda (até três salários mínimos) e que vivem, em sua maioria, em condições de precariedade urbanística e de moradia (Semurb, 2018). Mesmo estruturado em ações pontuais, o movimento “Eco Praça” reafirma a necessidade de reocupar a cidade através do corpo, do uso do espaço público e da coletividade transcrita nessas apropriações. Mesmo estruturado em ações pontuais, o movimento “Eco Praça” reafirma a necessidade de reocupar a cidade através do corpo, do uso do espaço público e da coletividade transcrita nessas apropriações. Essas intervenções, tornam-se revolucionárias por criarem uma nova consciência sobre como ocupar os largos, parques, praças, de maneira simples e despretensiosa; proporcionando através de diversos atrativos um novo sentido de lugar a esses espaços. Nesse sentido, também se encontra o olhar de David Harvey (2012), quando afirma que Essas intervenções, tornam-se revolucionárias por criarem uma nova consciência sobre como ocupar os largos, parques, praças, de maneira simples e despretensiosa; proporcionando através de diversos atrativos um novo sentido de lugar a esses espaços. Nesse sentido, também se encontra o olhar de David Harvey (2012), quando afirma que Com relação às praças escolhidas pelo movimento “Eco Praça”, cabe destacar: 44,44% das praças utilizadas estão localizadas em conjuntos habitacionais que deram origem ou impulsionaram a ocupação do solo dos respectivos bairros (Candelária, Lagoa Azul, Potengi, Ponta Negra e Neópolis), e muitas delas são espaços centrais em seus bairros, lugares mais legíveis e de maior movimentação de pessoas, moradores ou passantes. Constatado esse cenário, foi possível analisar a forma como o movimento enxerga a escolha e a ocupação dos espaços para a realização das suas atividades e a importância dessas escolhas para o sucesso das suas intervenções. [...] as táticas das ocupações consistem em tomar um espaço público central […] e convertê-lo em um espaço político de iguais, um lugar de discussão aberta e debate sobre o que esse poder está fazendo e as melhores formas de se opor ao seu alcance. Da configuração morfológica dos espaços: As praças e seus respectivos entornos Essa tática […] mostra como o poder coletivo de corpos no espaço público continua sendo o instrumento mais efetivo de oposição quando o acesso a Como referido, as intervenções do movimento “Eco Praça” se caracterizavam inicialmente como ocupações simples, organizadas por poucas pessoas por meio das Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Intervenções temporárias no espaço público da cidade de Natal - RN 8 / 13 todos os outros meios está bloqueado (Harvey, 2012, p.64). quais se agruparam em três níveis para uma melhor caracterização dos espaços ocupados: 1. configuracionais, onde se analisa o entorno imediato e os elementos constituintes das praças a partir de uma classificação tipológica; Nesses novos movimentos, o ato de reocupar passa a ser uma luta constante por espaços mais dignos e uma melhor qualidade da vida urbana, seja ela proporcionada por uma infraestrutura mais eficiente, por maiores atrativos – música, arte, feiras ao ar livre –, assim como novas possibilidades de encontros, marcados por uma maior corporeidade na cidade, tudo isso acontecendo de maneira simples. Diante disso, torna-se relevante compreender as ações realizadas pelo movimento “Eco Praça” na busca da relação dessas práticas com o restabelecimento das condições de vitalidade – mesmo que temporárias – nos locais ocupados, como também o seu real significado para a população natalense e seus visitantes. ç p g 2. perceptivos, destacando o significado e a legibilidade; 3. físicos e paisagísticos, com atenção especial para os equipamentos urbanos, o plano de suporte, a segurança e a arborização. Ao tomar como referência a estrutura metodológica proposta por Panerai (2006), a análise configuracional foi estruturada para enfatizar a relação com a cidade e os padrões de ocupação do entorno imediato (levando em consideração as quadras mais próximas à praça) com destaque para os usos e atividades e a intensidade construtiva dada pelo gabarito. Essa análise dos padrões de ocupação também procura realçar as relações entre a arquitetura do entorno e a rua, destacando os graus de acessibilidade e integração (aberturas, fechamentos) nos termos definidos por Ferdinando Rodrigues (2005). A classificação das tipologias das praças teve como referência Robba e Macedo (2002), levando em consideração uma análise mais paisagística, e Rodrigues (2005) ao analisar de forma mais geométrica. Percursos metodológicos e resultados prévios Métodos e técnicas aplicados à pesquisa Buscou-se com este artigo demonstrar como as intervenções temporárias realizadas pelo Movimento “Eco Praça”, na cidade de Natal, durante o período de 2014 à 2016, tiveram um impacto significativo no uso e na apropriação das praças utilizadas pelas ações, assim como nos seus entornos, recorrendo-se a uma análise morfológica e perceptiva. Quanto à percepção, utilizou-se os conceitos de visibilidade e legibilidade propostos por Lynch (1990), buscando compreender a imagem dos usuários sobre as praças no contexto da cidade, seja pela sua tipologia, pelo do reconhecimento visual e dos elementos simbólicos no seu entorno. Cabe mencionar que a pesquisa foi estruturada em dois momentos: no primeiro foi realizada uma análise morfológica das praças e seus entornos a partir da observação e da catalogação de atributos físicos; no segundo, foram realizadas entrevistas semiestruturadas com os principais agentes envolvidos. Neste artigo, recortamos apenas a análise morfológica, e para tanto, recorreu- se às contribuições dos seguintes autores: Philippe Panerai (2006), Ferdinando de Moura Rodrigues (2005), Roberto Lobato Corrêa (2004), Robba e Macedo (2002), Kevin Lynch (1990), Jan Gehl (2015) e Jane Jacobs (2014). No estudo dos elementos físicos, considerou- se fatores como: grau de conservação, quantidade e distribuição dos equipamentos urbanos; os desníveis, rampas e acessos; segurança – presença de policiamento e sinais de vandalismo para caracterizar o plano suporte; quantidade de árvores, vegetação predominante, porte predominante, e relevância do sombreamento, sem levar em consideração análises quantitativas mais aprofundadas através dos conceitos de Robba e Macedo (2002). A primeira etapa da análise consistiu na escolha das intervenções a serem analisadas, baseando-se no recorte temporal e nos atores a serem entrevistados. Alguns resultados da análise morfológica A partir desse estudo, tem-se que as praças localizadas na Região Norte (Praça do Ralf e Área de Lazer Panatis) possuem em comum A partir do recorte, demonstrado no quadro A partir do recorte, demonstrado no quadro 1, foram analisados os atributos físicos, aos p , q 1, foram analisados os atributos físicos, aos Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 9 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN Norte e o Tribunal de Justiça do Estado. Norte e o Tribunal de Justiça do Estado. Ainda, trata-se de locais bastante permeáveis, sem cercamentos, desníveis ou barreiras físicas, fato que contribuiu também para esses usos. o fato de estarem em áreas mais degradadas e descuidadas do olhar do poder público. Os dois espaços têm seus equipamentos bastante depredados e necessitados de manutenção, apesar de constatarmos a intensidade do uso e da apropriação do lugar pela população residente no entorno e nos bairros onde se inserem. Figura 3. “Eco Praça” na Área de Lazer Panatis, Região Norte, Natal (fonte: Carvalho, 2017). A Praça do Ralf está localizada no Bairro de Lagoa Azul, mais precisamente no Conjunto Gramoré, entre as Avenidas Guaíra e Tocantina, em uma área predominantemente residencial, de baixo gabarito e de fácil conexão com a cidade, além de estar adequadamente ajustada às necessidades do pedestre e ser totalmente permeável e acessível, física e visualmente. Diferente disso, observou-se que a Área de Lazer Panatis5 (figura 3) tem seu único acesso público em uma importante avenida coletora da cidade – Av. João Medeiros Filho6 –, fato que dificulta o acesso livre dos pedestres que circulam na sua outra margem, além de possuir um cercamento e ter seu horário de funcionamento limitado. Essas reflexões inferem em como o movimento tratou essas intervenções e as relações estabelecidas entre os ocupantes dessas áreas, as ações temporárias e os novos participantes, levados por essas realizações a participarem da ocupação. As Praças André de Albuquerque, 7 de Setembro e Cívica ou Pedro Velho, localizadas na Região Leste, destacam-se pelo valor simbólico e patrimonial, principalmente por serem berço e palco das principais manifestações políticas e sociais ocorridas na cidade desde a sua fundação. Alguns resultados da análise morfológica Além disso, evidenciam-se nos seus entornos a presença marcante de edificações de valor patrimonial, grandes instituições governamentais, e a abundância de atividades de comércio e serviços, o que contribuiu para um fácil acesso dos participantes, resultando em ocupações de grande impacto organizadas pelo movimento. Figura 3. “Eco Praça” na Área de Lazer Panatis, Região Norte, Natal (fonte: Carvalho, 2017). Igualmente localizada na Região Leste, a Praça Edgar Borges traz características diferentes das mencionadas anteriormente, por se tratar de uma área mais periférica e de menos visibilidade dentro da cidade, ao se encontrar em um bairro residencial socialmente vulnerável socioeconomicamente (Mãe Luiza), e localizado em uma área de acesso mais restrito (sobre um morro). Apesar disso, em uma visão micro, o seu espaço físico é bastante permeável, de fácil reconhecimento no bairro por estar situada em sua área central, próxima à Igreja Católica Nossa Senhora da Conceição e ao Centro Sócio Pastoral local. Igualmente localizada na Região Leste, a Praça Edgar Borges traz características diferentes das mencionadas anteriormente, por se tratar de uma área mais periférica e de menos visibilidade dentro da cidade, ao se encontrar em um bairro residencial socialmente vulnerável Igualmente localizada na Região Leste, a Praça Edgar Borges traz características diferentes das mencionadas anteriormente, por se tratar de uma área mais periférica e de menos visibilidade dentro da cidade, ao se encontrar em um bairro residencial socialmente vulnerável socioeconomicamente (Mãe Luiza), e localizado em uma área de acesso mais restrito (sobre um morro). Apesar disso, em uma visão micro, o seu espaço físico é bastante permeável, de fácil reconhecimento no bairro por estar situada em sua área central, próxima à Igreja Católica Nossa Senhora da Conceição e ao Centro Sócio Pastoral local. socioeconomicamente (Mãe Luiza), e localizado em uma área de acesso mais restrito (sobre um morro). Apesar disso, em uma visão micro, o seu espaço físico é bastante permeável, de fácil reconhecimento no bairro por estar situada em sua área central, próxima à Igreja Católica Nossa Senhora da Conceição e ao Centro Sócio Pastoral local. Alguns resultados da análise morfológica A visibilidade e o reconhecimento desses espaços dentro da cidade favoreceram ocupações mais bem-sucedidas, principalmente devido à facilidade de acesso a esses – seja por meio do transporte coletivo ou mesmo individual – e por estarem localizadas em áreas centrais, com muito movimento e próximos de diversas atividades institucionais, como a prefeitura de Natal, a Assembleia Legislativa do Rio Grande do A visibilidade e o reconhecimento desses espaços dentro da cidade favoreceram ocupações mais bem-sucedidas, principalmente devido à facilidade de acesso a esses – seja por meio do transporte coletivo ou mesmo individual – e por estarem localizadas em áreas centrais, com muito movimento e próximos de diversas atividades institucionais, como a prefeitura de Natal, a Assembleia Legislativa do Rio Grande do No seu entorno, nota-se a predominância de edificações de uso comercial, de um pavimento e com fachadas de grande Rede Lusófona de Morfologia Urbana ISSN 2182-7214 a de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Intervenções temporárias no espaço público da cidade de Natal - RN 10 / 13 O Parque de Capim Macio foi o segundo espaço mais utilizado pelo movimento “Eco Praça”, tendo um total de seis ocupações realizadas entre os anos de 2014 à 2016. Todas as ocupações tiveram uma temática de apropriação: primavera, permanência e sustentabilidade criativa. Acredita-se que essa popularidade na escolha do Parque como palco ao movimento se deu, principalmente, devido a sua localização privilegiada e a existência de outros grupos ativos que já realizavam ações na praça. permeabilidade em relação ao espaço público. A praça não possui policiamento e apresenta sinais de vandalismo, assim como equipamentos depredados, mas, apesar disso, os moradores entrevistados afirmam que a área é tranquila e bastante frequentada em todos os horários. Contudo, durante a ocupação pelo Movimento “Eco Praça”, foi observada a pouca presença de participantes externos – de outros lugares da cidade, em comparação a uma participação destacada dos moradores do bairro. Na Região Sul, a Praça dos Eucaliptos, localizada no bairro de Candelária, foi o espaço mais utilizado pelo movimento para suas intervenções, tendo sido ocupada sete vezes em três anos. Ao longo das análises e conversas com participantes e com a própria organização, notou-se que o fato se deu principalmente pela localização e a proximidade de moradia do organizador, mas também pelas características físicas e ambientais da praça. Alguns resultados da análise morfológica A Praça dos Eucaliptos (figura 4) se destaca pela sua centralidade, pela proximidade com vias estruturantes e instituições de destaque (Avenidas Salgado Filho e Prudente de Morais e Universidade Federal), pela grande área sombreada proporcionada pelos eucaliptos durante quase todo o dia, além do fácil acesso no interior do bairro e entre esse e a cidade. Figura 4. “Eco Praça” na Praça dos Eucaliptos, Candelária, Natal (fonte: Carvalho, 2017). A escolha dessa praça para diversos eventos do movimento reafirma a importância geográfica, física e simbólica adotada na escolha do espaço a ser ocupado, o que demonstra certa exclusão de áreas mais periféricas e de difícil acesso. Apesar disso, é de suma importância apresentar a ocupação dessas praças como momentos de reapropriação, os quais, mesmo temporários, fomentaram discussões, encontros e outras ações, desencadeadas pelo movimento inicial da “Eco Praça”. Figura 4. “Eco Praça” na Praça dos Eucaliptos, Candelária, Natal (fonte: Carvalho, 2017). Considerações finais Ainda na Região Sul, o Parque de Capim Macio, a Praça de Neópolis e a Praça Anjo Azul, estão situados em bairros de classe média e de localização geográfica favorável no contexto da cidade. Os bairros de Capim Macio, Neópolis e Ponta Negra, destacam-se pela proximidade com avenidas principais da cidade – Avenida Roberto Freire, Salgado Filho e Ayrton Senna – e se constituem como importantes áreas residenciais, de serviço e comércio variados. Com as análises físicas, o contato com moradores dos entornos das praças e entrevistas realizadas com a organização, concluiu-se que em algumas situações, como o Parque de Capim Macio e a Praça Edgar Borges, a escolha do local pelo movimento foi motivada a pedidos de outros grupos atuantes nesses espaços. No Parque, o Grupo Amigos de Capim Macio, que já atuava com ações recorrentes no bairro, convidou a organização do “Eco Praça” a se mobilizarem Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-72 Intervenções temporárias no espaço público da cidade de Natal - RN 11 / 13 11 / 13 para as suas realizações. Pode-se afirmar que cada praça e seu entorno reagiu de maneira diferente às ações da “Eco Praça”. juntos; enquanto na Praça Edgar Borges, a ocupação foi realizada a pedidos da própria comunidade de Mãe Luiza por meio do seu Centro Sócio Pastoral. A partir disso, entende-se como necessária a importância de uma articulação constante entre os diversos movimentos sociais atuantes na cidade, seja por meio de parcerias, apoio ou reconhecimento. Conclui-se ainda a constante necessidade de apropriação do espaço público, de forma efêmera ou não, de modo a reestabelecer as condições necessárias à democratização da cidade. Isso promoverá novos padrões de urbanidade e vitalidade e reconhecerá as conformidades existentes nesses espaços. A Praça Central de Neópolis e a Praça Omar O’Graddy (Praça Anjo Azul) em Ponta Negra, diferentes do Parque de Capim Macio, não se localizam em áreas com fluxo intenso de carros e pessoas, mesmo estando em áreas de centralidade nos seus bairros. As praças são bastante permeáveis visualmente e de fácil reconhecimento para quem não conhece os bairros; em Neópolis, seu maior uso ocorre pela manhã e final da tarde, principalmente por moradores do entorno; a praça Anjo Azul possui um uso menos frequente e se encontra mais depredada. Considerações finais Portanto, entende-se que apesar do Movimento “Eco Praça” não ter obtido grandes transformações físicas nos espaços ao longo das suas ações, a sua significância se rebate no legado que é transmitido através da reinvenção de novos lugares na cidade. Assim como na criação de novos potenciais para o estabelecimento de novas relações de ação pessoa-ambiente e da promoção de uma memória coletiva movida por essas novas formas de resistir. A Praça Central de Neópolis reúne significativa quantidade de equipamentos de esporte e lazer (quadras, academia, bancos), em sua maioria com problemas de manutenção. Tal situação, associada à iluminação precária, contribui para a sua subutilização, principalmente à noite. No caso da praça Anjo Azul, verifica-se a inexistência de equipamentos e a total ausência de manutenção, visto que o espaço se encontrava coberto de vegetação e lixo, o que contribui também para o seu pouco uso. Notas João Medeiros Filho, Paulistana e Acaraú, no bairro Potengi, na Região Norte de Natal. Possui uma área de 29.222 m² distribuída em pista de cooper, quadras, parques, pista de skate e áreas verdes. Fonte: Carvalho, 2017. experimenta, mesmo que involuntariamente (Carvalho, 2017, p. 28). 4 O Anuário Natal 2017-2018 publicado pela Secretaria de Meio Ambiente e Urbanismo de Natal (SEMURB) apresenta informações gerais e específicas do Município referente aos aspectos sociais, demográficos, territoriais, econômicos, de infraestrutura, de serviços públicos e culturais. Disponível em: < 6 A Avenida Doutor João Medeiros Filho é a maior e mais importante via da Região Norte de Natal, tendo seu início no bairro da Redinha e fim no bairro de Igapó. https://www.natal.rn.gov.br/bvn/publicacoes/anua rio_2016.pdf >. Acesso em: jun. 2018. Jacobs, J. (2014) Morte e vida de grandes cidades. São Paulo: Martins Fontes. 3ª ed. Jacobs, J. (2014) Morte e vida de grandes cidades. São Paulo: Martins Fontes. 3ª ed. Notas 1 De acordo com o Tactical Urbanism Guide, o urbanismo tático se refere a uma abordagem urbana, organizacional e/ou liderada pelo cidadão para construção do sentimento de vizinhança usando intervenções de curto prazo, de baixo custo e escaláveis. Essas ações podem vir através de um parklet, uma pequena praça, pinturas no chão, grafitagem; e são catalisadores temporárias que buscam interferir no espaço urbano para demonstrar, através de soluções simples, como ele poderia ser utilizado de uma forma melhor. Disponível em: É importante destacar que a pouca iluminação no turno da noite, a degradação dos equipamentos das praças, assim como sinais de vandalismo, foram os indícios mais apontados pelos entrevistados como fatos agravantes da subutilização desses espaços. Nota-se o descaso do município enquanto gestor e mantenedor do espaço público, fato que tem contribuído para a estigmatização, estranhamento e medo em relação ao uso da cidade. <http://tacticalurbanismguide.com/about/>. Acesso em: 15 Jun. 2018. 2 Placemaking é um processo de planejamento, criação e gestão de espaços públicos totalmente voltado para as pessoas, visando transformar ‘espaços’ e pontos de encontro em uma comunidade – ruas, calçadas, parques, edifícios e outros espaços públicos – em ‘lugares’, que eles estimulem maiores interações entre as pessoas e promovam comunidades mais saudáveis e felizes. Disponível em: http://www.placemaking.org.br/home/o-que-e- placemaking/. Acesso em: 15 Jun. 2018. Por fim, conclui-se como a forma urbana das praças, assim como a relação com seus respectivos entornos, admitindo sua visibilidade e localização dentro da cidade, influenciaram a forma como as intervenções ocorreram – bem-sucedidas ou não. Admite- se que a diferença principal entre as ações – desde a quantidade de pessoas envolvidas, o número de atividades, a duração das ações – está intimamente ligada ao espaço escolhido 3 Segundo Fabiana Dultra Britto e Paola Berenstein Jacques (2008), a corpografia seria a memória urbana no corpo, onde esse surge como um conjunto de condições interativas que expressa assim a sua corporalidade na forma da corpografia urbana. Essa corpografia é uma cartografia corporal, onde a experiência urbana se inscreve no próprio corpo daquele que a Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Intervenções temporárias no espaço público da cidade de Natal - RN 12 / 13 12 / 13 5 A Área de Lazer do Panatis é um complexo de cultura e lazer localizado entre as avenidas Dr. Referências Augé, M. (1994) Não-lugares. Introdução a uma antropologia da supermodernidade. 5 ed. São Paulo: Papirus. 111p. Lynch, K. (1990) A imagem da cidade. São Paulo: Martins Fontes. 280 p. Olivi, A. (2012) La política de los lugares: prácticas de resistência en la ciudad contemporânea. In: Jornada Sobre capital y território III, Sevilla. Disponível em: http://ayp.unia.es/dmdocuments/scyt3_com09.pdf . Acesso em: 15 jun. 2017. Carlos, A. F. A. (2007) O lugar no/do mundo. São Paulo: FFLCH. 85p. Carvalho, M. C. R. (2017) Práticas de resistência através de intervenções temporárias na cidade de Natal: o caso da Eco Praça. Trabalho de Conclusão de Curso (Arquitetura e Urbanismo) – Departamento de Arquitetura e Urbanismo, UFRN, Natal – RN. Panerai, P. (2006). Análise Urbana. Brasília: Editora Universidade de Brasília. 198 pg. Castello, L. (2006) O lugar geneticamente modificado. Arqtexto (UFRGS), v. 9, p. 76-91, 2006. Queiroga, E. (2012) Dimensões públicas do espaço contemporâneo: resistências e transformações de territórios, paisagens e lugares urbanos brasileiros. 284 p. Tese (Livre docência em Arquitetura e Urbanismo) – Faculdade de Arquitetura e Urbanismo, Universidade de São Paulo, São Paulo, 2012. Del Rio, V. (2003) Construindo o nosso lugar: Intersecções entre o mundo interior e o ambiente. Cadernos do Proarq. 7(7), 03-19. Disponível em: http://cadernos.proarq.fau.ufrj.br/public/docs/cade rnosproarq07.pdf. Acesso em 07 de julho de 2019. Robba, F. e Macedo, S.S. (2002) Praças brasileiras. São Paulo: Edusp/ Imprensa Oficial do Estado [Coleção Quapá]. Del Rio, V. (1990) Introdução ao desenho urbano no processo de planejamento. São Paulo: Pini. Rodrigues, F. M. (2005) Forma, imagem e significado em estruturas urbanas centrais. Centro da cidade de Niterói. Projeto de Reestruturação Urbana. Niterói: EdUFF / ProEditores. Fontes, A. S. (2013) Intervenções temporárias, marcas permanentes. Apropriações, arte e festa na cidade contemporânea. 1. ed. Rio de Janeiro: Casa da Palavra. v. 1. 398 pg. SEMURB. Prefeitura Municipal. Secretaria de Meio Ambiente e Urbanismo. Anuário de Natal 2017. Natal, RN, 2018. Disponível em: < https://www.natal.rn.gov.br/semurb/paginas/ctd- 102.html>. Acesso em: 15 jun. 2017. Gehl, J. (2015) Cidade Para as Pessoas. São Paulo: Editora Perspectiva. 3 ed. Harvey, D. (et al.). (2012) Occupy: movimentos de protestos que tomaram as ruas. São Paulo: Editora Boitempo. 64 p. Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-72 13 / 13 Intervenções temporárias no espaço público da cidade de Natal - RN Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Temporary interventions in the public space of the city of Natal - RN: The case of the Eco Praça movement Temporary interventions in the public space of the city of Natal - RN: The case of the Eco Praça movement Abstract. The current conformation of cities and the marked distancing of people from public space have provided the appearance of social movements of different natures that claim new forms of use and appropriation of space. In this context, the Eco Plaza raça movement appears in Natal-RN as a temporary intervention project that is based on social mobilization, stimulating the use of underutilized squares, promoting the transformation in its use and appropriation by the city's residents. This article, which results from an exploratory research, analyzes these processes and the significance of this movement as an action of resistance at the local level with an emphasis on the morphology of the squares and the perception of the agents involved directly and indirectly. Keywords: appropriation of public space, alternative territories, resistance, place, Eco Praça. Editor responsável pela submissão: Vinicius M. Netto Licenciado sob uma licença Creative Commons. Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-7214 Revista de MorfologiaUrbana (2019) 7(1): e00051 Revista de MorfologiaUrbana (2019) 7(1): e00051 Rede Lusófona de Morfologia Urbana ISSN 2182-72
https://openalex.org/W3138686972
https://docusalut.com/bitstream/20.500.13003/18509/1/sensors-2021-21-02237.pdf
English
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Camera-Based Monitoring of Neck Movements for Cervical Rehabilitation Mobile Applications
Sensors
2,021
cc-by
9,882
  Citation: Salinas-Bueno, I.; Roig-Maimó, M.F.; Martínez-Bueso, P.; San-Sebastián-Fernández, K.; Varona, J.; Mas-Sansó, R. Camera-Based Monitoring of Neck Movements for Cervical Rehabilitation Mobile Applications. Sensors 2021, 21, 2237. https:// doi.org/10.3390/s21062237 Keywords: camera-based; inertial sensors; neck; cervical rehabilitation; serious game; head-tracker; therapeutic exercise Received: 30 January 2021 Accepted: 19 March 2021 Published: 23 March 2021 Camera-Based Monitoring of Neck Movements for Cervical Rehabilitation Mobile Applications https:// doi.org/10.3390/s21062237 Academic Editor: Bert Arnrich Received: 30 January 2021 Accepted: 19 March 2021 Published: 23 March 2021   Citation: Salinas-Bueno, I.; Roig-Maimó, M.F.; Martínez-Bueso, P.; San-Sebastián-Fernández, K.; Varona, J.; Mas-Sansó, R. Camera-Based Monitoring of Neck Movements for Cervical Rehabilitation Mobile Applications. Sensors 2021, 21, 2237. https:// doi.org/10.3390/s21062237 Academic Editor: Bert Arnrich Received: 30 January 2021 Accepted: 19 March 2021 Published: 23 March 2021 sensors sensors Camera-Based Monitoring of Neck Movements for Cervical Rehabilitation Mobile Applications 1, Maria Francesca Roig-Maimó 2,*, Pau Martínez-Bueso 1, Katia San-Sebastián-Fernández 3, amon Mas-Sansó 2 Iosune Salinas-Bueno 1, Maria Francesca Roig-Maimó 2,*, Pau Martínez-Bueso 1, Katia San-Sebastián-Fernández 3, Javier Varona 2 and Ramon Mas-Sansó 2 1 Department of Nursing and Physiotherapy, University of the Balearic Islands, Health Research Institute of the Balearic Islands (IdISBa), 07122 Palma, Spain; iosune.salinas@uib.es (I.S.-B.); paz.martinez@uib.es (P.M.-B.) 1 Department of Nursing and Physiotherapy, University of the Balearic Islands, Health Research Institute of the Balearic Islands (IdISBa), 07122 Palma, Spain; iosune.salinas@uib.es (I.S.-B.); paz.martinez@uib.es (P.M.-B.) 2 Department of Mathematics and Computer Science, University of the Balearic Islands, 07122 Palma, Spain; xavi.varona@uib.es (J.V.); ramon.mas@uib.es (R.M.-S.) Balearic Islands (IdISBa), 07122 Palma, Spain; iosune.salinas@uib.es (I.S.-B.); paz.martinez@uib.es (P.M.-B.) 2 Department of Mathematics and Computer Science, University of the Balearic Islands, 07122 Palma, Spain; xavi.varona@uib.es (J.V.); ramon.mas@uib.es (R.M.-S.) 3 Department of Nursing and Physiotherapy, University of the Balearic Islands, 07122 Palma, Spain; katia.sansebastian@uib.es 3 Department of Nursing and Physiotherapy, University of the Balearic Islands, 07122 Palma, Spain; katia sansebastian@uib es * Correspondence: xisca.roig@uib.es Abstract: Vision-based interfaces are used for monitoring human motion. In particular, camera-based head-trackers interpret the movement of the user’s head for interacting with devices. Neck pain is one of the most important musculoskeletal conditions in prevalence and years lived with disability. A common treatment is therapeutic exercise, which requires high motivation and adherence to treatment. In this work, we conduct an exploratory experiment to validate the use of a non-invasive camera-based head-tracker monitoring neck movements. We do it by means of an exergame for performing the rehabilitation exercises using a mobile device. The experiments performed in order to explore its feasibility were: (1) validate neck’s range of motion (ROM) that the camera-based head-tracker was able to detect; (2) ensure safety application in terms of neck ROM solicitation by the mobile application. Results not only confirmed safety, in terms of ROM requirements for different preset patient profiles, according with the safety parameters previously established, but also determined the effectiveness of the camera-based head-tracker to monitor the neck movements for rehabilitation purposes.   Citation: Salinas-Bueno, I.; Roig-Maimó, M.F.; Martínez-Bueso, P.; San-Sebastián-Fernández, K.; Varona, J.; Mas-Sansó, R. Camera-Based Monitoring of Neck Movements for Cervical Rehabilitation Mobile Applications. Sensors 2021, 21, 2237. 1. Introduction Camera-based interfaces provide a hands-free approach to interact with devices. Therefore, they have a straight application in assistive tools for motor-impaired users [1] but also for rehabilitation purposes [2]. Specifically, head-trackers vision-based interfaces, a camera-based approach that tracks the motion of the head, could be used for neck rehabilitation purposes as they demand the movement of the neck joints to interact with the device. 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. Neck pain is one of the most important musculoskeletal conditions in prevalence and years lived with disability, as it becomes chronic in 30–50% of cases [3,4]. The common treatment of neck pain includes conservative and pharmacological interventions. Con- servative treatments often include therapeutic exercise, with the aim of improve mobility, pain, function and quality of life [5–7]. Therapeutic exercise, usually supervised by a phys- iotherapist, includes mobility, strengthening, endurance and motor control exercises [5,7,8]. The long-term beneficial effect is achieved by performing the therapeutic exercise constantly and over time, which requires high motivation and adherence to treatment, especially when it is done at home. The adherence to the treatment will therefore be essential for the maintenance of the effects [5]. One potential way to increase adherence is by means of an exergame, that is, a serious game that aims at physical exercise (in our case, neck 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/sensors Sensors 2021, 21, 2237. https://doi.org/10.3390/s21062237 Sensors 2021, 21, 2237 2 of 15 therapeutic exercise) while entertaining the user. The exergame allows therapeutic exercise performance with assets of motivation, supervision and feedback, which are key factors of adherence [9,10]. With that aim, we started the design and development of a specific mobile application that monitors and analyses the fulfilment of neck therapeutic exercises at home (or else- where). The application includes an exergame individually adapted to the user capabilities at any time of the rehabilitation process. By means of a camera-based head-tracker, user head motion is detected, and used to interact with the exergame application in order to monitor that users perform correctly the neck movements. 1. Introduction The use of the camera has the advantage that it is not invasive, and the user can move comfortably without external limitations. In addition, the fact that it is a mobile application allows doing the therapeutic exercise, with supervision and feedback, available everywhere, anytime, and to anyone. This paper presents the validation experiments performed in order to (1) explore the feasibility of using the head-tracker interface for neck rehabilitation purposes, in the sense of the range of motion (ROM) that the head-tracker was able to detect and (2) determine the safety of the application, as an exploratory safety experiment, in terms of neck ROM solicitation by the mobile application. 1.1. State-of-the-Art It has been proved in the literature that introducing gamification to therapeutic ex- ercise in rehabilitation increases its effectiveness and adherence [11–14]. In this sense, serious exergames have been explored for different rehabilitation purposes, both using commercial games and devices in a rehabilitation context [15] or designing specific serious exergames for health and rehabilitation purposes, under more specific and clinical criteria design [11–14]. Serious exergames have proved to be effective in different neurological and musculoskeletal diseases [12,16,17]. In recent years, several virtual reality (VR) (immersive and non-immersive) serious games for rehabilitation have been developed [16–19]. If they were specifically aimed to a body part, they needed to attach a wearable sensor to the part of the body, as happened in the work of De Oliveira et al. [17], Rechy-Ramirez et al. [20] or interact with a full body camera detection [21]. With the aim of using serious gam- ing with smartphones or mobile devices, with integrated sensors on the mobile phone, Baranyi et al. [16,22] are developing a serious game system for post-stroke rehabilitation. Regarding specifically neck region, Mihajlovic et al. [23] developed a virtual reality serious game, but in order to create the immersion on VR a headset needed to be used by the patient. As for neck movements detection with mobile devices, there have been some authors that have developed neck exercise systems with sensors integrated in mobile devices, i.e., with camera-based head tracking. Lawanont et al. [24,25] developed a neck movement image detection integrated in the smartphone sensors. It was able to calculate neck flexion, so it fulfilled the purpose of monitoring head posture while using smartphones. Yet, it did not detect or monitor other directions of movement. Thus, the issue of detecting all directions on neck movements with no sensors on the user, and to use them as an interaction for a serious exergame for neck rehabilitation with a mobile device remains to explore. 1.2. Camera-Based Head Tracking One common sensor on smartphones and tablets is the front-facing camera, that can be used to perform the user’s head tracking. Such camera-based head-trackers provide a way to interact with these devices through the movements of the head. Using a vision- based head-tracker has several advantages. Mainly, it does not require any calibration or additional hardware, apart from the components already built in mobile devices. It also has the additional advantage that it is not invasive, i.e., the user can comfortably move without the burden imposed by wires or markers. The only requirement is that the main structures of the face (eyes and nose) have to be fully visible by the front-facing camera. We have previously developed a camera-based head-tracker for mobile devices [26] that automatically detects and tracks the position of the user’s nose. To track the nose, Sensors 2021, 21, 2237 3 of 15 the system extracts facial features of its surrounding region, and returns the average of all these features as the nose point. As this region is never occluded by facial hair or glasses, it can be continuously tracked despite the orientation of the user’s head when he or she is looking at the screen. We direct the reader to Roig-Maimó et al. [26] for a technical description of the head-tracker interface. Previous work validated the head-tracker’s viability as a pointing device in target- selection tasks with able-bodied [27] and motor-impaired users [28]. Once the head-tracker interface was validated from the point of view of Human-Computer Interaction, in this work we analyse the feasibility of using it to develop applications for cervical rehabilitation purposes, as it allows the interaction with devices through the movement of the head. 2. Exploratory Experiment: Neck Range of Motion Tracked by the Camera-Based Head-Tracker An exploratory experiment was conducted in order to explore the neck ROM that is effectively tracked by the camera-based head-tracker. With this experiment, we wanted to determine at what extent the head-tracker was able to track the mobility range of the neck, in order to determine if it could be used for ROM rehabilitation purposes. p p The cervical area has a normal maximum mobility of 45◦of flexion, 45◦of extension, 45◦of lateral flexion (each side) and 70◦of rotation (each side) [29]. See Figure 1 in order to observe the movements of the neck joint. Functional mobility, understood as the range of motion used in daily life activities, is 20% to 40% of maximum available cervical ROM [30,31]. Any kind of change in those ROM would alter the functional mobility of the neck and spine, which could alter also the functionality of individuals, causing disability movement [32,33]. Figure 1. Movements of the neck. Seven participants (six females) were recruited from a university campus in Spain. They were staff from the university campus who volunteered for the experiment. Ages ranged from 29 to 48 with a mean of 39.14 years (SD = 6.76). There were no requirements or exclusion criteria on prior experience to participate in the experiment. The experiment was conducted on an Apple iPad Air with a front-facing camera placed in the center on the upper side of the device, in portrait orientation. The software executed the head-tracker interface and showed on the screen the image captured by the front-facing camera with the nose point returned by the head-tracker marked with a blue circle (see Figure 2). An important added value of using the exergame is to enable the user to perform the exercises alone by means of controlling the correct performance. Therefore, it is very important to consider the system’s feedback to inform the user and to help him or her to control the performance. In this sense, it is necessary to explore the neck range of motion (ROM) that could be effectively tracked by the camera-based head-tracker, as a feasibility indicator for neck rehabilitation purposes. Figure 1. Movements of the neck. Figure 1. Movements of the neck. Seven participants (six females) were recruited from a university campus in Spain. They were staff from the university campus who volunteered for the experiment. Ages ranged from 29 to 48 with a mean of 39.14 years (SD = 6.76). 2. Exploratory Experiment: Neck Range of Motion Tracked by the Camera-Based Head-Tracker There were no requirements or exclusion criteria on prior experience to participate in the experiment. Seven participants (six females) were recruited from a university campus in Spain. They were staff from the university campus who volunteered for the experiment. Ages ranged from 29 to 48 with a mean of 39.14 years (SD = 6.76). There were no requirements or exclusion criteria on prior experience to participate in the experiment. p p p p p The experiment was conducted on an Apple iPad Air with a front-facing camera placed in the center on the upper side of the device, in portrait orientation. The software executed the head-tracker interface and showed on the screen the image captured by the front-facing camera with the nose point returned by the head-tracker marked with a blue circle (see Figure 2). The experiment was conducted on an Apple iPad Air with a front-facing camera placed in the center on the upper side of the device, in portrait orientation. The software executed the head-tracker interface and showed on the screen the image captured by the front-facing camera with the nose point returned by the head-tracker marked with a blue circle (see Figure 2). An important added value of using the exergame is to enable the user to perform the exercises alone by means of controlling the correct performance. Therefore, it is very important to consider the system’s feedback to inform the user and to help him or her to control the performance. In this sense, it is necessary to explore the neck range of motion (ROM) that could be effectively tracked by the camera-based head-tracker, as a feasibility indicator for neck rehabilitation purposes. 4 of 15 Sensors 2021, 21, 2237 Figure 2. Screenshot of the experiment software with annotations on an Apple iPad Air (device in portrait orientation). Figure 2. Screenshot of the experiment software with annotations on an Apple iPad Air (device in portrait orientation). Each participant performed the session in an experiment room, seated in upright position, resting their arms on a table. The iPad with the camera-based head-tracker running, was placed in front of their face at approximately 37 cm, a distance equivalent to naturally holding the device by the subject, with the top line of the iPad screen at eye level [34]. 2. Exploratory Experiment: Neck Range of Motion Tracked by the Camera-Based Head-Tracker They were asked to move their head slowly as far as possible in the direction being studied (flexion, extension, right lateral flexion, left lateral flexion, right rotation and left rotation). See Figure 3. At the moment that the head-tracker lost the position of the nose (see Figure 3c), an acoustic alert sounded and the participant was asked to stop the movement. Then, ROM was measured with a goniometer (see Figure 4c), that is a reliable tool for ROM measurement used in standardized clinical examinations [35–37]. It consisted of a stationary arm, a movable arm and a fulcrum or axis, as can be seen in Figure 5. (a) (b) (c) Figure 3. Simulated stages of the experiment procedure for the left rotation movement on the apparatus: (a) participant placed in the initial position with the nose point returned by the head- tracker marked with a blue circle, (b) the participant starts a rotation movement slowly (the nose point returned by the head-tracker is marked with a blue circle), (c) moment when the head-tracker loses the position of the nose (an acoustic alert is triggered) and the participant stops its movement. (c) (a) (b) (a) (b) (c) Figure 3. Simulated stages of the experiment procedure for the left rotation movement on the apparatus: (a) participant placed in the initial position with the nose point returned by the head- tracker marked with a blue circle, (b) the participant starts a rotation movement slowly (the nose point returned by the head-tracker is marked with a blue circle), (c) moment when the head-tracker loses the position of the nose (an acoustic alert is triggered) and the participant stops its movement. Flexion and extension were measured with the axis over the external auditory mea- tus, with the stationary arm parallel to ground and the movement arm in line with the base of nares. Lateral flexion was measured with the axis over spinous process of C7 vertebra, with the stationary arm in line with spinous processes of thoracic vertebrae, so that arm was perpendicular to ground, and the movement arm in line with occipital protuberance. Rotation was measured with the axis located over central aspect of head, with the stationary arm parallel to imaginary line between the two acromial processes, and the movement arm in line with the tip of the nose. All measurements were conducted by an experienced physiotherapist. 2. Exploratory Experiment: Neck Range of Motion Tracked by the Camera-Based Head-Tracker As for rotation, the head-tracker was able to track the nose position up to about 40◦, moment where the nose was no longer visible from the front by the front-facing camera. Figure 6. Mean values of the neck range of motion (ROM) tracked by the head-tracker interface compared to normal maximum mobility. Figure 6. Mean values of the neck range of motion (ROM) tracked by the head-tracker interface compared to normal maximum mobility. Figure 6. Mean values of the neck range of motion (ROM) tracked by the head-tracker interface compared to normal maximum mobility. These results proved that the camera-based head-tracker could track the nose position within functional ROM limits, so it could be useful for the rehabilitation of functional mobility, as well as other parameters of rehabilitation (speed of movement, motor control, oculocervical dissociation) within these ranges. This conclusion led us to the design of a mobile application with an exergame that would aim to rehabilitation of functional movement and motor control. 3. Validation of the Mobile Application for Monitoring the Neck Movements Once it was proved that the camera-based head-tracker was feasible for rehabilitation purposes, in the matter of monitoring functional mobility, the application started to be designed. One of the first steps was to determine its safety, in terms that the software must not require more ROM, rapid or complex movements than patients were able to perform at that moment, as they could cause harm and be counterproductive for patients’ recovery. Therefore, a safety validation was needed. 2. Exploratory Experiment: Neck Range of Motion Tracked by the Camera-Based Head-Tracker Sensors 2021, 21, 2237 5 of 15 (c) (a) (b) (c) Figure 4. Stages of the experiment procedure: (a) participant placed in the initial position, (b) partici- pant once the acoustic alert sounded and the participant stopped the movement, (c) measurement of the neck ROM of the participant using the goniometer. (b) (a) (b) (a) (c) Figure 4. Stages of the experiment procedure: (a) participant placed in the initial position, (b) partici- pant once the acoustic alert sounded and the participant stopped the movement, (c) measurement of the neck ROM of the participant using the goniometer. Figure 5. Dual-arm universal goniometer. Figure 5. Dual-arm universal goniometer. Each movement was repeated three times, and equally measured (see Figure 4). Testing lasted about 15 min per participant. The total number of measures was 7 participants × 6 directions × 3 repetitions = 126. In Table 1, mean and standard deviation values, as well as proportion of normal maximum ROM tracked, are given for each movement direction of the cervical area (flexion, extension, right lateral flexion, left lateral flexion, right rotation, left rotation). s and standard deviation of cervical range of motion measurements, and their relationship with normal Table 1. Mean values and standard deviation of cervical range of motion measurements, and their relationship with normal mobility range. Table 1. Mean values and standard deviation of cervical range of motion measurements, and their relationship with normal mobility range. Movement ROM Detected Normal Maximum ROM % of Maximum ROM Tracked Flexion 29.05◦± 6.25◦ 45◦ 64.55% Extension 22.86◦± 6.63◦ 45◦ 50.79% Right lateral flexion 27.39◦± 4.64◦ 45◦ 60.85% Left lateral flexion 28.10◦± 3.70◦ 45◦ 62.43% Right rotation 39.05◦± 6.25◦ 70◦ 55.78% Left rotation 38.81◦± 6.70◦ 70◦ 55.44% As it is shown in Table 1 and Figure 6, the camera-based head-tracker was able to track the nose position from 50% to 64.5% of the normal maximum cervical mobility ranges. The better detected movements were flexion and lateral flexion, that is, the movements where nose is more visible for the front-facing camera during the user’s movement. Ex- tension implies that nose would be seen in a different position as movement advances, so Sensors 2021, 21, 2237 6 of 15 the head-tracker would lose the nose position at about 23◦of extension. 3.1. Materials and Methods For this first safety experiment we focused on the ROM that the software required, because demanding more movement that a patient was able to perform, or a movement that reproduced pain, was considered a potential source of unsafe situations. We would consider the application as safe, in this sense, if the movements asked for the application and therefore performed by the subject in each direction were within the maximum ROM that a patient was able to achieve with no pain. As it was expected to be safe for different patients with different capabilities, or the same patient at different moments of his or her recovery, it was considered necessary to study safety with different capability profiles. In order to do that, different patient preset profiles were designed. They were designed by experienced physiotherapists, based on general clinical evolution of ROM and neck pain data in actual patients [38,39]: • Profile 1: corresponded to a low cervical mobility person with or without pain associ- ated with movement. • Profile 2: corresponded to a lower-medium cervical mobility person, with less or no pain associated with movement. • Profile 3: corresponded to an upper-medium mobility person and no pain. Sensors 2021, 21, 2237 7 of 15 • Profile 4: was supposed to represent a patient with an advanced recovery situation or a healthy subject, with normal mobility and no pain. • Profile 4: was supposed to represent a patient with an advanced recovery situation or a healthy subject, with normal mobility and no pain. • Profile 4: was supposed to represent a patient with an advanced recovery situation or a healthy subject, with normal mobility and no pain. • Profile 4: was supposed to represent a patient with an advanced recovery situation or a healthy subject, with normal mobility and no pain. Range of motion preset for each profile can be seen in Table 2. Range of motion preset for each profile can be seen in Table 2. Table 2. ROM of the preset profiles. Table 2. ROM of the preset profiles. Profile Flexion Extension Lateral Flexion Rotation Profile 1 20◦ 15◦ 5◦ 25◦ Profile 2 30◦ 20◦ 35◦ 40◦ Profile 3 40◦ 40◦ 45◦ 70◦ Profile 4 45◦ 45◦ 45◦ 70◦ We designed an exergame simulating a dart game with targets to be selected using the movement of the head (see Section 3.1.2 for further description of the game). 3.1. Materials and Methods The configura- tion of target size, target location, order of targets, time of appearance and disappearance of the target, gain of the head-tracker and dwell-time criterion for selection were set differently for each preset profile: • Profile 1: required horizontal, vertical or diagonal simple movements with low ROM, with no speed or time pressure. So, configuration for this profile consisted in offering big, easy targets available all the time, that should be selected in a predetermined order, with a high gain factor and no dwell-time. As an example, to require a simple right rotation movement, three big targets available at the same time, that should be selected left to right, were shown on the screen (see Figure 7a). • Profile 2: the group of exercises included for this profile were those for profile 1 plus exercises with smaller targets, complex movements, and higher speed. These exercises configuration implied more and smaller targets, and a sequential appearance and disappearance of targets, in the preset order of selection, as to introduce a speed factor. As examples of these exercises, Figure 7b shows the location of targets in a simple flexion movement, starting with the upper target, and Figure 7c shows a combined movement: a diagonal. As examples of these exercises, Figure 7b shows the location of targets in a simple flexion movement, starting with the upper target, and Figure 7c shows a combined movement: a diagonal. g • Profile 3: the group of exercises loaded for this profile were those with smaller targets, complex movements, movements at a higher speed and motor control requirements. To do so, targets would appear in a random location, with preset time of appearance and disappearance, and with dwell-time to require steadiness in target selection (see an example exercise in Figure 7d). • Profile 4: the group of exercises loaded for this profile were provided with small targets, complex randomly required movements at a high speed, and motor control requirements. It did not imply more ROM than the previous profiles, as it focused in other parameters (speed, reaction time, motor control). The configuration was similar to profile 3 exercises, but with smaller targets, less time available on screen, less gain factor and more dwell-time on those with motor control requirement. For the application to be considered as safe, it was supposed to solicit movements within the maximum ROM preset for each profile (see Table 2). 3.1.1. Participants A total of 24 asymptomatic participants (12 females) were recruited from staff and postgraduate students from a university campus in Spain. To be included, participants had to be aged 20 to 64. The average age was 34 years (SD = 13.06). They were excluded if they had reported or complained of neck, shoulder, and/or head impairments or had pain in the preceding month. 3.1. Materials and Methods In order to validate that the application induced the user to correctly perform the neck movements for every preset profile, it was required that the performed user neck movements were within 80th percentile of the ROM preset for each movement in the different profiles. 8 of 15 Sensors 2021, 21, 2237 (a) (b) (c) (d) Figure 7. Examples of exercises for every preset profile: (a) dartboards set to induce a simple horizontal movement (rotation) with big targets, (b) dartboards set to induce a simple vertical descending movement (flexion) with small targets, (c) dartboards set in diagonal to induce a combined movement with small targets, and (d) dartboards set randomly. (a) (c) (d) (c) Figure 7. Examples of exercises for every preset profile: (a) dartboards set to induce a simple horizontal movement (rotation) with big targets, (b) dartboards set to induce a simple vertical descending movement (flexion) with small targets, (c) dartboards set in diagonal to induce a combined movement with small targets, and (d) dartboards set randomly. 3.1.2. Apparatus The experiment was conducted on an Apple iPad Mini 4 due to ergonomic reasons related to the device’s weight. All communication with the mobile device was disabled during testing. The software simulated a dart game (see Figure 8 for details). The study involved a simple pointing task where the targets to be selected simulated dartboards of different sizes. User input combined the mobile head-tracker for the pointing action and a dwell-time criterion for selection. 9 of 15 Sensors 2021, 21, 2237 (a) (b) Figure 8. Screenshots of the dart game with two dwell-time criterion: (a) 0-ms dwell-time criterion: the target was selected immediately when the center of the cursor entered inside the target, and (b) 200-ms dwell-time criterion. (a) (b) Figure 8. Screenshots of the dart game with two dwell-time criterion: (a) 0-ms dwell-time criterion: the target was selected immediately when the center of the cursor entered inside the target, and (b) 200-ms dwell-time criterion. The application started with a login form, which was used to determine the patient profile. According to the profile that was established, the application showed different tar- get patterns covering the desired range of motion of the profile (following either horizontal, vertical, diagonal or random paths). The user got a visual feedback of its motion through the movement of a cursor displayed in the dart game. To measure the real-time neck mobility performed by subjects while using the applica- tion, we used wireless ENLAZA inertial sensors (Werium™system [40]). Inertial sensors included an accelerometer, a gyroscope and a magnetometer which sensed linear accelera- tion, the turn rate and an accurate angular monitoring along three reference axis. Inertial sensors are widely used to measure motor activities [41–43]. Specifically, Werium intertial sensors were previously validated for cervical ROM as well as for other joints [44,45]. The sensors are small and lightweight, so they are barely invasive. Their use would allow to record full ROM, as we previously stated that the application itself was not able monitor full ROM. Two sensors were placed on the subject to conduct the real-time measurement, following the location protocol given by the manufacturer. Sensor 1 was placed on the forehead of the subject, fixed with an elastic band (see Figure 9a,c). Sensor 2 was placed on T1-T2 thoracic vertebrae, fixed with double sided fixing tape (see Figure 9b,c). 3.1.3. Procedure The study was conducted according to the guidelines of the Declaration of Helsinki and approved by the Research Ethics Committee of the University of the Balearic Islands (Exp.174CER20). Each experiment was conducted by a collaborator of the research team, with previous training on the procedure. The experiment consisted in performing several games/matches with the exergame, corresponding to different levels of demand of ROM. Sensors 2021, 21, 2237 10 of 15 10 of 15 Informed consent was obtained from all subjects involved in the study. They were instructed to play the exergame, following the application instructions, holding the device still and moving the cursor by moving their head. Subjects were in an experiment room, seated in a chair with their back supported on the backrest, naturally holding the iPad in front of their head (see Figure 10), with their elbows resting on a height-adjustable treatment table. This position (back on the backrest and elbows resting on the table) was designed to maintain a natural position holding a mobile device while controlling possible compensation movements. (a) (b) (c) Figure 9. Placement of the inertial sensors: (a) sensor 1 (b) sensor 2 (c) sensor 1 and sensor 2. (a) (c) (a) (b) (c) Figure 9. Placement of the inertial sensors: (a) sensor 1 (b) sensor 2 (c) sensor 1 and sensor 2. (a) (b) Figure 10. (a) Subject of the experiment playing the exergame in (b) the experiment room. (b) (b) (a) (c) Figure 9. Placement of the inertial sensors: (a) sensor 1 (b) sensor 2 (c) sensor 1 and sensor 2. (b) (a) (a) (b) Figure 10. (a) Subject of the experiment playing the exergame in (b) the experiment room. (a) (b) Figure 10. (a) Subject of the experiment playing the exergame in (b) the experiment room. After sensors were placed, subjects were asked to play the exergame, and to select targets as quickly and accurately as possible. Every subject was asked to play a match with the exergame set for each profile. They were allowed to rest as needed between profiles. Movement in every direction was real-time recorded via the inertial sensors and Werium software. Any incident observed or informed by the subjects was recorded by the collaborator. Testing lasted about 30 min per participant. g p p p The total number of sessions was 24 participants × 4 profiles = 96. 3.1.3. Procedure During every session, the ROM of the subjects reported by the sensors (flexion, extension, lateral flexion, rotation) were recorded. 4. Results and Discussion In this section, results for each preset profile are given for all the movement directions of the cervical area: flexion, extension, right lateral flexion, left lateral flexion, right rotation, left rotation. Outliers were removed using the Interquartile Range (IQR) method. Results showed that recorded mobility was below the 80th percentile of the established maximum at all movements and profiles. Even the maximum movement measured stayed within limits in almost every movement and profile, except for extension. Extension Sensors 2021, 21, 2237 11 of 15 11 of 15 movements in profiles 1 and 2 (see Tables 3 and 4) showed that the maximum recorded exceeded significantly the preset limits at least once. One possible explanation, from the observation and data, suggested that the maximum of extension recorded may be due to moments in which the head-tracker reference was lost, and the manoeuvre done by the subject to recover the nose tracking was doing a movement out of range of the front- face camera and back, that could be an extension movement. Nevertheless, extension movement was within limits at 80th percentile for these profiles. For profiles 3 and 4 (see Tables 5 and 6), the mobile application would not be able to exceed the limits of ROM preset due to the head-tracker limits that were determined in the first experiment. Table 3. ROM results of Profile 1 (After outlier filtering, the analyzed data for the Profile 1 supposed a 98% of the total flexion-extension raw data, a 96% of the total lateral flexion raw data, and a 99% of the total rotation raw data). The cases where the maximum ROM of the subjects reported by the ENLAZA inertial sensors exceeded the preset ROM defined for the profile are marked with an asterisk. Table 3. ROM results of Profile 1 (After outlier filtering, the analyzed data for the Profile 1 supposed a 98% of the total flexion-extension raw data, a 96% of the total lateral flexion raw data, and a 99% of the total rotation raw data). The cases where the maximum ROM of the subjects reported by the ENLAZA inertial sensors exceeded the preset ROM defined for the profile are marked with an asterisk. Table 3. 4. Results and Discussion ROM results of Profile 1 (After outlier filtering, the analyzed data for the Profile 1 supposed a 98% of the total flexion-extension raw data, a 96% of the total lateral flexion raw data, and a 99% of the total rotation raw data). The cases where the maximum ROM of the subjects reported by the ENLAZA inertial sensors exceeded the preset ROM defined for the profile are marked with an asterisk. Movement Mean Standard Deviation Maximum 80th Percentile Preset ROM Flexion 4.39◦ 3.40◦ 19.17◦ 6.91◦ 20◦ Extension 8.15◦ 5.97◦ 26.16◦* 13.15◦ 15◦ Right lateral flexion 2.00◦ 1.62◦ 6.51◦* 3.32◦ 5◦ Left lateral flexion 1.45◦ 1.09◦ 5.49◦* 2.30◦ 5◦ Right rotation 7.03◦ 5.43◦ 23.41◦ 11.60◦ 25◦ Left rotation 5.71◦ 4.21◦ 21.51◦ 9.34◦ 25◦ Table 4. ROM results of Profile 2 (After outlier filtering, the analyzed data for the Profile 2 supposed a 98% of the total flexion-extension raw data, a 97% of the total lateral flexion raw data, and a 98% of the total rotation raw data). The cases where the maximum ROM of the subjects reported by the ENLAZA inertial sensors exceeded the preset ROM defined for the profile are marked with an asterisk. Movement Mean Standard Deviation Maximum 80th Percentile Preset ROM Flexion 9.18◦ 6.84◦ 30.98◦* 14.46◦ 30◦ Extension 7.74◦ 5.77◦ 26.75◦* 12.70◦ 20◦ Right lateral flexion 2.13◦ 1.55◦ 7.10◦ 3.33◦ 35◦ Left lateral flexion 1.78◦ 1.39◦ 6.29◦ 2.85◦ 35◦ Right rotation 6.50◦ 4.92◦ 21.51◦ 10.83◦ 40◦ Left rotation 5.48◦ 4.24◦ 20.00◦ 8.79◦ 40◦ Table 5. ROM results of Profile 3 (After outliers’ filtering, the analyzed data for the Profile 3 supposed a 98% of the total flexion-extension raw data, a 93% of the total lateral flexion raw data, and a 99% of the total rotation raw data). 4. Results and Discussion Movement Mean Standard Deviation Maximum 80th Percentile Preset ROM Flexion 10.16◦ 7.87◦ 33.37◦ 16.96◦ 40◦ Extension 9.01◦ 7.02◦ 30.22◦ 14.78◦ 40◦ Right lateral flexion 2.11◦ 1.81◦ 7.30◦ 3.65◦ 45◦ Left lateral flexion 2.31◦ 1.74◦ 8.00◦ 3.61◦ 45◦ Right rotation 9.00◦ 6.48◦ 29.51◦ 14.67◦ 70◦ Left rotation 6.10◦ 4.96◦ 21.67◦ 10.00◦ 70◦ Movement Mean Standard Deviation Maximum 80th Percentile Preset ROM Flexion 9.18◦ 6.84◦ 30.98◦* 14.46◦ 30◦ Extension 7.74◦ 5.77◦ 26.75◦* 12.70◦ 20◦ Right lateral flexion 2.13◦ 1.55◦ 7.10◦ 3.33◦ 35◦ Left lateral flexion 1.78◦ 1.39◦ 6.29◦ 2.85◦ 35◦ Right rotation 6.50◦ 4.92◦ 21.51◦ 10.83◦ 40◦ Left rotation 5.48◦ 4.24◦ 20.00◦ 8.79◦ 40◦ ts of Profile 3 (After outliers’ filtering, the analyzed data for the Profile 3 supposed a 98% of the total w data, a 93% of the total lateral flexion raw data, and a 99% of the total rotation raw data). Movement Mean Standard Deviation Maximum 80th Percentile Preset ROM Flexion 10.16◦ 7.87◦ 33.37◦ 16.96◦ 40◦ Extension 9.01◦ 7.02◦ 30.22◦ 14.78◦ 40◦ Right lateral flexion 2.11◦ 1.81◦ 7.30◦ 3.65◦ 45◦ Left lateral flexion 2.31◦ 1.74◦ 8.00◦ 3.61◦ 45◦ Right rotation 9.00◦ 6.48◦ 29.51◦ 14.67◦ 70◦ Left rotation 6.10◦ 4.96◦ 21.67◦ 10.00◦ 70◦ Movement Mean Standard Deviation Maximum 80th Percentile 12 of 15 Sensors 2021, 21, 2237 Table 6. ROM results of Profile 4 (After outliers’ filtering, the analyzed data for the Profile 4 supposed a 99% of the total flexion-extension raw data, a 96% of the total lateral flexion raw data, and a 98% of the total rotation raw data). Table 6. ROM results of Profile 4 (After outliers’ filtering, the analyzed data for the Profile 4 supposed a 99% of the total flexion-extension raw data, a 96% of the total lateral flexion raw data, and a 98% of the total rotation raw data). Movement Mean Standard Deviation Maximum 80th Percentile Preset ROM Flexion 7.05◦ 5.16◦ 24.84◦ 11.47◦ 45◦ Extension 8.70◦ 6.16◦ 29.67◦ 14.12◦ 45◦ Right lateral flexion 1.68◦ 1.27◦ 6.15◦ 2.71◦ 45◦ Left lateral flexion 1.96◦ 1.58◦ 6.20◦ 3.39◦ 45◦ Right rotation 6.40◦ 4.80◦ 22.07◦ 10.37◦ 70◦ Left rotation 6.25◦ 4.67◦ 20.70◦ 10.32◦ 70◦ Results not only confirmed safety, in terms of ROM requirements for each profile, according with the safety parameters previously established, but informed also about other aspects. 4. Results and Discussion One of these findings was that the mobile application required similar maximum ROM for the different profiles, with differences in flexion: profiles 1, 2 and 3 showed a slightly increase in mobility demand by the mobile application in flexion. Profile 4 (see Table 6), on the other hand, did not show this increasing tendency. Profile 4 was not preset as to continue this increase tendency, but to focus on other rehabilitation parameters. Thus, it was also expected not to detect an increase of ROM demand for this profile. In addition, one unexpected finding was the virtual absence of lateral flexion for the interaction with the mobile application, observed in every profile. Further work is required to clarify whether it is due to the configuration of the targets on the screen (and so, a mobile application performance finding), or whether it is a phenomenon linked to the interaction with mobile devices in general. All these findings, in addition to the results of the intended evaluation, provided valuable information for future lines of work. Data collected suggested that it would be the combination of different parameters of the mobile application, and not only ROM, what would determine the effectiveness of the exergame as a therapeutic exercise application. In order to work gradually and adapt to the objectives of the rehabilitation and the patient’s situation (functional mobility recovery, motor control, strength, etc.), it would be needed to combine parameters as required speed of movement, dwell-time for target selection, number of targets, moment of appearance or disappearance of the targets, etc. If we want to focus on more ROM demand for the medium and advanced profiles (namely profile 3 and 4), it would be necessary to study the feasibility of working with the gain parameter, so the mobile application would demand more ROM for the same movement in screen. 5. Conclusions In this paper, we present a evaluation study of a camera-based head-tracker mobile application for monitoring neck movements for cervical rehabilitation purposes. Due to the use of the camera, this application has the advantage that it does not need any contact sensor and the user can move freely, without any external limitation. The objective of this paper is to present the technical feasibility and a first safety evaluation of the camera-based head-tracker to monitor the neck movements. First, we explored at what extent the head-tracker was able to monitor the user’s neck movements. On that question, the study found that camera-based head-tracker is able to monitor from the 50% to the 64.5% of the full cervical range of motion. This result proved that a camera-based head-tracker was a feasible tool for cervical rehabilitation purposes, within a functional mobility range of motion. Secondly, an exploratory validation experiment has determined the safety of the designed head-tracker mobile application. We checked that is possible to use the head-tracker for neck movement detection in an exergame for cervical rehabilitation purposes and, that is safe in terms of the required neck range of motion demanded by the exergame for each preset patient profile. At this point, we can conclude that the camera-based exergame did not require more range of motion than the preset profile user was capable to perform. Sensors 2021, 21, 2237 13 of 15 13 of 15 As the objective of this paper was to present the technical feasibility and a first safety study, participants in the presented studies were healthy subjects. In order to continue with the validation of the exergame mobile application using a camera-based head tracker as a sensor, further work needs be conducted, including clinical research studies, with actual patients. In addition, we point out that this research could serve as a base for future studies on the use of camera-based head-trackers for other healthcare purposes, as we proved that is able to monitor the user’s head movements by means of the front-facing camera of a mobile device. Author Contributions: conceptualization, I.S.-B., K.S.-S.-F. and M.F.R.-M.; methodology, I.S.-B., K.S.-S.-F. and R.M.-S.; software, M.F.R.-M. and R.M.-S.; validation, K.S.-S.-F. and I.S.-B.; formal analy- sis, I.S.-B., M.F.R.-M. and R.M.-S.; investigation, I.S.-B., K.S.-S.-F. and P.M.-B.; data curation, M.F.R.-M. and R.M.-S.; writing—original draft preparation, I.S.-B., M.F.R.-M. and R.M.-S.; writing—review and editing, I.S.-B., M.F.R.-M., R.M.-S., P.M.-B. and J.V.; supervision, I.S.-B., M.F.R.-M., R.M.-S. 5. Conclusions and P.M.-B.; project administration, I.S.-B. and J.V. All authors have read and agreed to the published version of the manuscript. Author Contributions: conceptualization, I.S.-B., K.S.-S.-F. and M.F.R.-M.; methodology, I.S.-B., K.S.-S.-F. and R.M.-S.; software, M.F.R.-M. and R.M.-S.; validation, K.S.-S.-F. and I.S.-B.; formal analy- sis, I.S.-B., M.F.R.-M. and R.M.-S.; investigation, I.S.-B., K.S.-S.-F. and P.M.-B.; data curation, M.F.R.-M. and R.M.-S.; writing—original draft preparation, I.S.-B., M.F.R.-M. and R.M.-S.; writing—review and editing, I.S.-B., M.F.R.-M., R.M.-S., P.M.-B. and J.V.; supervision, I.S.-B., M.F.R.-M., R.M.-S. and P.M.-B.; project administration, I.S.-B. and J.V. All authors have read and agreed to the published version of the manuscript. Funding: This research was funded by the Spanish Government with project TIN2016-81143-R (MINECO/AEI/ERDF, EU) and grant number PID2019-104829RA-I00/AEI/10.13039/501100011033. Institutional Review Board Statement: The study was conducted according to the guidelines of the Declaration of Helsinki and approved by the Research Ethics Committee of the University of the Balearic Islands (Exp.174CER20). Informed Consent Statement: Informed consent was obtained from all subjects involved in the study. Informed Consent Statement: Informed consent was obtained from all subjects involved in the study. Data Availability Statement: The data presented in this study are available on request from the corresponding author. The data are not publicly available due to data privacy restrictions. Data Availability Statement: The data presented in this study are available on request from the corresponding author. The data are not publicly available due to data privacy restrictions. Acknowledgments: The authors acknowledge the Ministerio de Economía, Industria y Competitivi- dad (MINECO), the Agencia Estatal de Investigacion (AEI), and the European Regional Development Funds (ERDF) for their support to the project TIN2016-81143-R (MINECO/AEI/ERDF, EU) and the Spanish Government for its support by the Project EXPLainable Artificial INtelligence systems for health and well-beING (EXPLAINING) (PID2019-104829RA-I00/AEI/10.13039/501100011033). We also thank the University of the Balearic Islands, the Department of Nursing and Physiotherapy, and the Department of Mathematics and Computer Science for their support. 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. References 1. Mauri, C.; Granollers i Saltiveri, T.; Lorés Vidal, J.; García, M. 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The Effect of Carbonmonoxide Sources and Meteorologic Changes in Carbonmonoxide Intoxication: A Retrospective Study
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ABSTRACT Objective: Carbon monoxide (CO) poisoning is frequently seen in emergency departments (ED) especially in cold weather. We investigated the relationship of some of the meteorological factors with the sources of CO poisoning. Amaç: Karbonmonoksit (CO) zehirlenmelerine, özellikle soğuk havalarda olmak üzere acil servis birimlerinde sıklıkla karşılaşılır. Çalışmamızda, bazı meteorolojik faktörlerin CO zehirlenmesinin kaynakları ile ilişkisini araştırdık. Yöntem: Retrospektif gözlemsel çalışmamızda, son üç yılda acil servise CO zehirlenmesi ile başvuran 1153 hastayı dahil edildi. Bölgenin atmosferik basıncı, rüzgarın yönü ve hızı, nem düzeyi ve hava sıcaklığı değerleri ve CO zehirlenme tipi karşılaştırıldı. Methods: In this retrospective observational study, we included 1153 patients who were admitted to ED due to CO poisoning in a three years period. Atmospheric pressure, wind direction and speed, humidity level and air temperature of the region at exposure time were compared with CO poisoning type. Bulgular: Hastaların yaş ortalaması 39,5±16,3; kadın cinsiyet %65,7 (n=761) idi. Karbonmonoksit kaynağının kaynağı en sık doğalgaz ısıtıcıları (n=628; %54,4); daha sonra ocak (n=393; %34,1), şofben (n=94; %8,4) ve yangındı (n=38; %3,3). En sık görülen rüzgar yönü kuzey-kuzeydoğu yönü (poyraz) idi. Atmosferik basınç tüm zehirlenme tiplerinde benzerdi. Yangınlarda nem düzeyleri istatistiksel anlamlı düşüktü ve hava sıcaklığı anlamlı yüksekti. Rüzgar hızı yangın tipinde en hızlı ve şofben tipinde en yavaştı. Bulgular: Hastaların yaş ortalaması 39,5±16,3; kadın cinsiyet %65,7 (n=761) idi. Karbonmonoksit kaynağının kaynağı en sık doğalgaz ısıtıcıları (n=628; %54,4); daha sonra ocak (n=393; %34,1), şofben (n=94; %8,4) ve yangındı (n=38; %3,3). En sık görülen rüzgar yönü kuzey-kuzeydoğu yönü (poyraz) idi. Atmosferik basınç tüm zehirlenme tiplerinde benzerdi. Yangınlarda nem düzeyleri istatistiksel anlamlı düşüktü ve hava sıcaklığı anlamlı yüksekti. Rüzgar hızı yangın tipinde en hızlı ve şofben tipinde en yavaştı. Sonuç: Karbonmonoksit zehirlenmeleri ciddi morbidite ve moraliteye neden olabilen acil servis başvuru nedenlerindendir. Başlıca nedeni ev ısıtıcılarıdır. Risk altındaki insanlar CO zehirlenmeleri hakkında ve önemli meteorolojik değişikliklerde ısıtıcaların riskleri hakkında bilgilendirilmelidir. Zehirlenme bulguları görüldüğünde acil servise başvurulmalıdır. A ht K li l At f ik b CO hi l i kl k Results: Mean age of the patients was 39.5±16.3; females were 65.7% (n=761) of the patients. Most frequent source of CO was natural gas heaters (n=628; 54.4%); others were stove (n=393; 34.1%), geyser (n=94; 8.4%) and blaze (n=38; 3.3%). Most frequent direction of the wind was North-North-East (euroclydon). Atmospheric pressure was similar in all of the poisoning types; in blaze, humidity levels was significantly lower, air temperature was significantly higher. ABSTRACT Wind speed was faster in blaze and slowest in geyser type poisoning. Conclusion: Carbon monoxide poisoning is an important cause of emergency visits which can result in serious morbidity or mortality. Main sources are home heating systems. People should be informed about the risks of these heaters and symptoms of CO poisoning and, also in case of important meteorological changes. They should apply to an ED in case of occurrence of intoxication symptoms. Anahtar Kelimeler: Atmosferik basınç, CO zehirlenmesi, sıcaklık, rüzgar, yangın Keywords: Atmospheric pressure, CO intoxication, temperature, wind, humidity Keywords: Atmospheric pressure, CO intoxication, temperature, wind, humidity KARBONMONOKSİT KAYNAKLARININ VE METEOROLOJİK DEĞİŞİKLİKLERİN KARBONMONOKSİT ZEHİRLENMELERİNE ETKİSİ: RETROSPEKTİF ÇALIŞMA Duygu Yılmaz1, Umut Yücel Çavuş2, Sinan Yıldırım3, Bahar Gülcay Çat Bakır4*, Gözde Besi Tetik5, Onur Evren Yılmaz6, Mehtap Kaynakçı Bayram7 1Manisa Turgutlu State Hospital, Department of Emergency Medicine, Manisa, Turkey. 2Ankara Education and Research Hospital, Department of Emergency Medicine, Ankara, Turkey. 3Çanakkale State Hospital, Department of Emergency Medicine, Çanakkale,Turkey. 4Mersin City Education and Research Hospital, Department of Emergency Medicine, Mersin, Turkey. 5Gaziantep Şehitkamil State Hospital, Department of Emergency Medicine, Gaziantep, Turkey. 6Medical Park Hospital, Department of Plastic and Reconstructive Surgery, İzmir, Turkey. 7Kayseri City Education and Research Hospital, Department of Emergency Medicine, Kayseri, Turkey. ÖZ Research Article | Araştırma Makalesi THE EFFECT OF CARBON MONOXIDE SOURCES AND METEOROLOGIC CHANGES IN CARBON MONOXIDE INTOXICATION: A RETROSPECTIVE STUDY THE EFFECT OF CARBON MONOXIDE SOURCES AND METEOROLOGIC CHANGES IN CARBON MONOXIDE INTOXICATION: A RETROSPECTIVE STUDY KARBONMONOKSİT KAYNAKLARININ VE METEOROLOJİK DEĞİŞİKLİKLERİN KARBONMONOKSİT ZEHİRLENMELERİNE ETKİSİ: RETROSPEKTİF ÇALIŞMA Published Online/Online Yayın: 20.02.2020 ● Bu eser, Creative Commons Atıf-Gayri Ticari 4.0 Uluslararası Lisansı ile lisanslanmıştır. Telif Hakkı © 2020 Kocaeli Ü Bu eser, Creative Commons Atıf-Gayri Ticari 4.0 Uluslararası Lisansı ile lisanslanmıştır. Telif Hakkı © 2020 Kocaeli Üniversitesi Tıp Fakültesi Dekanlığı Yılmaz et al., CO Intoxication Due to Meteorologic Changes Results One thousand one hundred fifty-three patients were included the study; females were 65.7% (n=761) of the patients. The mean age of the patients was 39.5±16.3. The mean age of males and females were similar (p=0.676). The most frequent source of CO was natural gas heaters (n=628; 54.4%); others were stove (n=393; 34.1%), geyser (n=94; 8.4%) and blaze (n=38; 3.3%). It is known in the literature that storms and sudden weather changes lead to epidemic CO intoxications.10 To the best of our knowledge the only study that investigated the meteorological parameters like humidity, air pressure and wind speed was Tiekuan Du et al.’s study.11 The most frequent direction of the wind was North- North-East (euroclydon), the second was north winds (Figure 1). In this retrospective study, we investigated the relationship of some of the meteorological factors with the sources of CO poisoning. Figure 1. The relationship of carbon monoxide source and wind direction Statistical Analysis The statistical analyses were performed by SPSS 15.0 for Windows package program. The continuous variables are expressed as mean±SD, categorical variables are expressed as n (%). The normal distribution is determined by histogram and One-Sample Kolmogorov Smirnov test. Comparison of means was evaluated by Mann-Whitney-U test if any of the groups is not normally distributed; if both of the groups are normally distributed, Student’s t-Test is used. p<0.05 is accepted as significant. Introduction demographic data of the patients were obtained from the hospital registration records. Our primary outcome was the frequency of CO sources. Secondary outcomes were the frequency of the wind directions and the most common months of CO poisoning. Carbon monoxide (CO) poisoning is an important public health problem. The emergency visits increase due to CO intoxication caused by use of stove, geyser and other heating devices especially in cold weather. The analysis was performed in Ankara, 870-meter-high above the sea, in the middle of Turkey. The city is located between the northern latitudes of 39° 50´ and 40° 00´and the longitudes of 32° 35´ and 33° 00´. Generally, the continental climate prevails in Ankara. Carbon monoxide was first described by a French chemist de Lassone in 1776.1 Carbon monoxide has more than 210 fold affinity in binding to hemoglobin than oxygen.2 Carbon monoxide combines with hemoglobin to produce carboxyhemoglobin, which is ineffective for delivering oxygen to tissues that finally causes tissue damage.3 The mechanism of CO-induced death is thought to be high affinity binding of CO to hemoglobin and myoglobin, resulting in tissue hypoxia that inhibits cytochrome oxidase synergistically with CO.4 It causes tissue damage in all organs, especially brain, heart and kidney which are very sensitive to hypoxia.5 Cardiac effects, ranging from mild and transitory injury to necrosis and contractile dysfunction has been known in patients with carbon monoxide poisoning.6 The myocardial tissue is highly vulnerable to oxygen deprivation, thus causing a substantial reduction of contractility and cardiac output, which ultimately contribute to the direct worsening injury of CO on cardiomyocytes.7 The most common symptoms of carbon monoxide poisoning are headache, nausea, vomiting, dizziness, fatigue, and a feeling of weakness. Infants may be irritable and malnourished. Neurological symptoms are confusion, disorientation, visual disturbance, syncope and seizure.8 The most important prognostic factor is the exposure duration. Chronic intoxications has worse prognosis.9 The atmospheric pressure, wind direction and speed, humidity level and air temperature of the region at exposition time are recorded from General Directorate of Meteorology. Age and gender of patients, the source of CO, admission time and date are recorded. Discussion The most common reason of CO intoxication in our study was natural gas heaters with 54.4%; the second reason was stove with 34.1%. Natural gas heaters are the most commonly used domestic heating system in our study region; so, the most common cause of CO poisoning was natural gas heaters. Region, ethnic and socio-cultural factors affect the poisoning type.12 Frequency of CO source type varies by location. In some regions, the geyser is the most common cause with a ratio between 68.3% and 77.5%; but in some regions, stove is the most frequent source with a ratio between 85.9% and 89.7%.13-17 Figure 2. The frequency of carbon monoxide poisoning in months In our study, the CO poisoning rate was found to be 74% from December to March, while this rate was found to be between 38.9% and 64.6% in the previous months in our country.14,17-21 The frequency varies, but the main result is a significant increase in CO poisoning in cold weather especially in ice storms.22-24 The Centers for Disease Control and Prevention (CDC) reports also support our results that the CO exposure occurs mostly in winter and at least in July and August.25,26 Figure 2. The frequency of carbon monoxide poisoning in months The mean atmospheric pressure, air temperature, wind speed and humidity levels at exposure time according to the source of CO were expressed in Table 1. The atmospheric pressure was similar in all of the poisoning types; in blaze, humidity levels was significantly lower, air temperature was significantly higher. The wind speed was faster in blaze and slowest in geyser type poisoning. The box-plot graphics of meteorological data according to CO source were given in Figure 3. y g In our study, atmospheric pressure was similar in all types of poisoning. Tiekuan Du et al. reported that air pressure is not associated with CO poisoning, similar to our results. They reported that the only factor affecting CO poisoning is air temperature; CO poisoning frequency increases as temperature decreases.11 This result is partially similar to our study result because we found that the air temperature in CO poisoning associated with the natural gas heater was the lowest. However, the mean temperature was still very low (2.1°±7.1°) compared to winter months. On the other hand, the air temperature was significantly higher at blaze (7.2°±10.0°) but the temperature still indicated cold weather. Methods This retrospective observational study is carried out after local ethical committee approval (Dışkapı Yıldırım Beyazıt Educational and Research Hospital, Approval number: 01/46, Date: 27.02.2012). The study hospital was a third-degree education and research hospital with an annual emergency visit of 250.000 patients. Patients over the age of 18, who were admitted to ED due to stove, natural gas, water heater and smoke-induced CO poisoning with the symptoms of headache, nausea, vomiting, dizziness, syncope, chest pain and dyspnea were investigated in a three year period. Patients diagnosed with CO poisoning were included in the study. Patients with normal carboxyhemoglobin (COHb) levels are excluded. The Figure 1. The relationship of carbon monoxide source and wind direction 2 Yılmaz et al., CO Intoxication Due to Meteorologic Changes Yılmaz et al., CO Intoxication Due to Meteorologic Changes The most common exposure was in January (Figure 2). The visits have significantly decreased after June. Discussion In case of blaze, humidity levels were significantly low and air temperature was significantly higher. Tiekuan Du et al. also investigated other parameters, but they reported that there is no correlation of wind speed and humidity;11 but in our study we showed that wind speed was faster in blaze and slowest in geyser type poisoning. In addition, the humidity level in our study was the highest in geyser type CO poisoning and the lowest in blaze. Table 1. The relationship of carbon monoxide source and meteorological data Table 1. The relationship of carbon monoxide source and meteorological data Carbon monoxide Source Air atmospheric pressure Humidity rate Air temperature Wind speed (mean±SD) (mean±SD) (mean±SD) (mean±SD) Natural gas heater (n=627) 1014±8 80±16 2.1°±7.1° 9.8±8.3 Stove (n=393) 1013±8 81±14 2.9°±6.0° 10.6±8.6 Geyser (n=94) 1014±7 85±14 2.2°±5.8° 7.4±6.8 Blaze (n=38) 1014±5 65±24 7.2°±10.0° 12.1±8.2 Figure 3. The distribution of meteorological data according to carbon monoxide source Table 1. The relationship of carbon monoxide source and meteorological data Carbon monoxide Source Air atmospheric pressure Humidity rate Air temperature Wind speed (mean±SD) (mean±SD) (mean±SD) (mean±SD) Natural gas heater (n=627) 1014±8 80±16 2.1°±7.1° 9.8±8.3 Stove (n=393) 1013±8 81±14 2.9°±6.0° 10.6±8.6 Geyser (n=94) 1014±7 85±14 2.2°±5.8° 7.4±6.8 Blaze (n=38) 1014±5 65±24 7.2°±10.0° 12.1±8.2 Figure 3. The distribution of meteorological data according to carbon monoxide source Figure 3. The distribution of meteorological data according to b id The retrospective nature was a limitation of our study. The main sources of CO poisoning are home heating systems. In case of important meteorological changes, especially at the euroclydon wind direction, people at risk can be informed and warned about the risks. References 17. Uysalol M, Uysalol EP, Saraçoğlu GV, Kayaoğlu S. A retrospective analysis of pediatric patients admitted to the pediatric emergency service for carbon monoxide intoxication. Balkan Medical Journal. 2011;28(3):237-243. doi:10.5174/tutfd.2010.03766.1 1. Cruickshank W. Some observations on different hydrocarbonates and combinations of carbone with oxygen, etc. in reply to some of Dr. Priestley's late objections to the new system of chemistry. Journal of Natural Philosophy, Chemistry and the Arts. 1801;5:1-9. 18. Wilson RC, Saunders PJ, Smith G. An epidemiological study of acute carbon monoxide poisoning in the West Midlands. Occupational and Environmental Medicine. 1998;55(11):723-728. doi:10.1136/oem.55.11.723 2. Phin N. Carbon monoxide poisoning (acute). Clinical Evidence. 2005;13:1732-1743. 2. Phin N. Carbon monoxide poisoning (acute). Clinical Evidence. 2005;13:1732-1743. 3. Tikuisis P, Kane DM, McLellan TM, Buick F, Fairburn SM. Rate of formation of carboxyhemoglobin in exercising humans exposed to carbon monoxide. J Appl Physiol (1985). 1992;72(4):1311-1319. doi:10.1152/jappl.1992. 72.4.1311 19. Ait El Cadi M, Khabbal Y, Idrissi L. Carbon monoxide poisoning in Morocco during 1999-2007. J Forensic Leg Med. 2009;16:385-387. doi:10.1016/j.jflm.2009.01.017 20. Mendoza JA, Hampson NB. Epidemiology of severe carbon monoxide poisoning in children. Undersea&Hyperbaric Medicine: Journal of the Undersea and Hyperbaric Medical Society, Inc. 2006;33:439-446. 4. Cooper CE, Brown GC. The inhibition of mitochondrial cytochrome oxidase by the gases carbon monoxide, nitric oxide, hydrogen cyanide and hydrogen sulfide: chemical mechanism and physiological significance. Journal of Bioenergetics and Biomembranes. 2008;40(5):533-539. doi:10.1007/s10863-008-9166-6 21. Metin S, Yıldız Ş, Çakmak T, Demirbaş Ş. Frequency of carbon monoxide poisoning in Turkey in 2010. TAF Prev Med Bull. 2011;10(5):587-592. doi:10.5455/ pmb.20110417125648 5. Choi IS. Carbon monoxide poisoning: systemic manifestations and complications. Journal of Korean Medical Science. 2001;16(3):253-261. doi:10.3346/ jkms.2001.16.3.253 22. Daley WR, Smith A, Paz-Argandona E, Malilay J, McGeehin M. An outbreak of carbon monoxide poisoning after a major ice storm in Maine. The Journal of Emergency Medicine. 2000;18(1):87-93. doi:10.1016/S0736- 4679(99)00184-5 6. Lippi G, Rastelli G, Meschi T, Borghi L, Cervellin G. Pathophysiology, clinics, diagnosis and treatment of heart involvement in carbon monoxide poisoning. Clinical Biochemistry. 2012;45(16-17):1278-1285. doi:10.1016/ j.clinbiochem.2012.06.004 23. Ghim M, Severance HW. Ice storm-related carbon monoxide poisonings in North Carolina: A reminder. Southern Medical Journal. 2004;97(11):1060-1065. doi:10.1097/01.SMJ.0000144614.38668.60 7. Cervellin G, Comelli I, Rastelli G, Picanza A, Lippi G. Initial blood lactate correlates with carboxyhemoglobin and clinical severity in carbon monoxide poisoned patients. Clinical Biochemistry. 2014;47(18):298-301. doi:10.1016/ j.clinbiochem.2014.09.016 24. Wrenn K, Conners GP. Carbon monoxide poisoning during ice storms: a tale of two cities. The Journal of Emergency Medicine. Financial Disclosure There is no financial disclosure. 16. Akkose Ş, Turkmen N, Bulut M, Akgoz S, Işcimen R, Eren B. An analysis of carbon monoxide poisoning in Bursa, Turkey. East Mediterr Health J. 2010;16:101-106. Compliance with Ethical Standards This retrospective observational study is carried out after local ethical committee approval (Dışkapı Yıldırım Beyazıt Educational and Research Hospital, Approval number: 01/46, Date: 27.02.2012). Figure 3. The distribution of meteorological data according to carbon monoxide source 3 Yılmaz et al., CO Intoxication Due to Meteorologic Changes Medicine. 2010;28(8):928-932. doi:10.1016/ j.ajem.2009.06.019 Medicine. 2010;28(8):928-932. doi:10.1016/ j.ajem.2009.06.019 Conflict of Interest 2010;28(8):928-932. doi:10.1016/ 2010;28(8):928-932. The authors declare that there is no conflict of interest regarding the publication of this article. 12. Baum CR. What's new in pediatric carbon monoxide poisoning? Clin Ped Emerg Med. 2008;9(1):43-46. doi:10.1016/j.cpem.2007.11.002 Author Contribution 13. Keles A, Demircan A, Kurtoglu G. Cabon monoxide poisonig: how many patients do we miss? 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Centers for Disease Control and Prevention (CDC). Carbon monoxide related deaths-United States, 1999-2004. MMWR. Morbidity and Mortality Weekly Report. 2007;56(50):1309-1312. 9. Piantadosi CA. Carbon monoxide poisoning. Undersea& Hyperbaric Medicine: Journal of the Undersea and Hyperbaric Medical Society, Inc. 2004;31(1):167-177. 26. Centers for Disease Control and Prevention (CDC). Nonfatal, unintentional, non fire-related carbon monoxide exposures-United States, 2004-2006. MMWR. Morbidity and Mortality Weekly Report. 2008;57(33):896-899. 10. Henretig FM, Calello DP, Burns MM, O'Donnell KA, Osterhoudt KC. Predictable, preventable, and deadly: Epidemic carbon monoxide poisoning after storms. American Journal of Public Health. 2018;108(10):1320- 1321. doi:10.2105/AJPH.2018.304619 11. Du T, Zhang Y, Wu JS, et al. Domicile-related carbon monoxide poisoning in cold months and its relation with climatic factors. The American Journal of Emergency 4
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Novel Miscanthus hybrids: Modelling productivity on marginal land in Europe using dynamics of canopy development determined by light interception
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Novel Miscanthus hybrids: Modelling productivity on marginal land in Europe using dynamics of canopy development determined by light interception Novel Miscanthus hybrids: Modelling productivity on marginal land in Europe using dynamics of canopy development determined by light interception LJMU Research Online LJMU Research Online Shepherd, A, Awty Carroll, D, Kam, J, Ashman, C, Magenau, E, Martani, E, ‐ Kontek, M, Ferrarini, A, Amaducci, S, Davey, C, Jurišić, V, Petrie, G, Al Hassan, M, Lamy, I, Lewandowski, I, de Maupeou, E, McCalmont, J, Trindade, L, van der Cruijsen, K, van der Pluijm, P, Rowe, R, Lovett, A, Donnison, I, Kiesel, A, Clifton Brown, J and Hastings, A ‐ Shepherd, A, Awty Carroll, D, Kam, J, Ashman, C, Magenau, E, Martani, E, ‐ Kontek, M, Ferrarini, A, Amaducci, S, Davey, C, Jurišić, V, Petrie, G, Al Hassan, M, Lamy, I, Lewandowski, I, de Maupeou, E, McCalmont, J, Trindade, L, van der Cruijsen, K, van der Pluijm, P, Rowe, R, Lovett, A, Donnison, I, Kiesel, A, Clifton Brown, J and Hastings, A ‐ Abstract New biomass crop hybrids for bioeconomic expansion require yield projections to determine their potential for strategic land use planning in the face of global chal- lenges. Our biomass growth simulation incorporates radiation interception and conversion efficiency. Models often use leaf area to predict interception which is demanding to determine accurately, so instead we use low-­cost rapid light in- terception measurements using a simple laboratory-­made line ceptometer and relate the dynamics of canopy closure to thermal time, and to measurements of Novel Miscanthus hybrids: Modelling productivity on marginal land in Europe using dynamics of canopy development determined by light interception Anita Shepherd1   | Danny Awty-­Carroll2   | Jason Kam3  | Chris Ashman2   | Elena Magenau4   | Enrico Martani5  | Mislav Kontek6   | Andrea Ferrarini5   | Stefano Amaducci5  | Chris Davey2  | Vanja Jurišić6  | Gert-­Jan Petrie7  | Mohamad Al Hassan8   | Isabelle Lamy9  | Iris Lewandowski4  | Emmanuel de Maupeou10  | Jon McCalmont1   | Luisa Trindade8   | Kasper van der Cruijsen8  | Philip van der Pluijm10  | Rebecca Rowe11   | Andrew Lovett12  | Iain Donnison2  | Andreas Kiesel4   | John Clifton-­Brown2,13   | Astley Hastings1 Anita Shepherd1   | Danny Awty-­Carroll2   | Jason Kam3  | Chris Ashman2   | Elena Magenau4   | Enrico Martani5  | Mislav Kontek6   | Andrea Ferrarini5   | Stefano Amaducci5  | Chris Davey2  | Vanja Jurišić6  | Gert-­Jan Petrie7  | Mohamad Al Hassan8   | Isabelle Lamy9  | Iris Lewandowski4  | Emmanuel de Maupeou10  | Jon McCalmont1   | Luisa Trindade8   | Kasper van der Cruijsen8  | Philip van der Pluijm10  | Rebecca Rowe11   | Andrew Lovett12  | Iain Donnison2  | Andreas Kiesel4   | John Clifton-­Brown2,13   | Astley Hastings1 Anita Shepherd1   | Danny Awty-­Carroll2   | Jason Kam3  | Chris Ashman2   | Elena Magenau4   | Enrico Martani5  | Mislav Kontek6   | Andrea Ferrarini5   | Stefano Amaducci5  | Chris Davey2  | Vanja Jurišić6  | Gert-­Jan Petrie7  | Mohamad Al Hassan8   | Isabelle Lamy9  | Iris Lewandowski4  | Emmanuel de Maupeou10  | Jon McCalmont1   | Luisa Trindade8   | Kasper van der Cruijsen8  | Philip van der Pluijm10  | Rebecca Rowe11   | Andrew Lovett12  | Iain Donnison2  | Andreas Kiesel4   | John Clifton-­Brown2,13   | Astley Hastings1 1Biological Sciences, University of Aberdeen, Aberdeen, Scotland, UK 2Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK 3Terravesta, Lincoln, UK 5Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Piacenza, Italy 6Department of Ag Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia 8Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands 11NERC Centre for Ecology and Hydrology, Lancaster Environment Centre, Lancaster, UK 12 12School of Environmental Sciences, University of East Anglia, Norwich, UK Article http://researchonline.ljmu.ac.uk/ For more information please contact researchonline@ljmu.ac.uk For more information please contact researchonline@ljmu.ac.uk http://researchonline.ljmu.ac.uk/ Received: 30 November 2022  |  Accepted: 21 December 2022 DOI: 10.1111/gcbb.13029 Received: 30 November 2022  |  Accepted: 21 December 2022 R E S E A R C H A R T I C L E R E S E A R C H A R T I C L E Article Citation (please note it is advisable to refer to the publisher’s version if you intend to cite from this work) Shepherd, A, Awty Carroll, D, Kam, J, Ashman, C, Magenau, E, Martani, E, ‐ Kontek, M, Ferrarini, A, Amaducci, S, Davey, C, Jurišić, V, Petrie, G, Al Hassan, M, Lamy, I, Lewandowski, I, de Maupeou, E, McCalmont, J, Trindade, L, van der Cruijsen, K, van der Pluijm, P, Rowe, R, Lovett, A, Citation (please note it is advisable to refer to the publisher’s version if you intend to cite from this work) Citation (please note it is advisable to refer to the publisher’s version if you intend to cite from this work) Shepherd, A, Awty Carroll, D, Kam, J, Ashman, C, Magenau, E, Martani, E, ‐ Kontek, M, Ferrarini, A, Amaducci, S, Davey, C, Jurišić, V, Petrie, G, Al Hassan, M, Lamy, I, Lewandowski, I, de Maupeou, E, McCalmont, J, Trindade, L, van der Cruijsen, K, van der Pluijm, P, Rowe, R, Lovett, A, Shepherd, A, Awty Carroll, D, Kam, J, Ashman, C, Magenau, E, Martani, E, ‐ Kontek, M, Ferrarini, A, Amaducci, S, Davey, C, Jurišić, V, Petrie, G, Al Hassan, M, Lamy, I, Lewandowski, I, de Maupeou, E, McCalmont, J, Trindade, L, van der Cruijsen, K, van der Pluijm, P, Rowe, R, Lovett, A, LJMU has developed LJMU Research Online for users to access the research output of the University more effectively. 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GCB Bioenergy published by John Wiley & Sons Ltd. 1  |  INTRODUCTION definition of marginal land is different things to different crops and farmers. ‘Less productive’ is a more acceptable term than marginal to growers, not inferring it is their fault (pers. comms. Jason Kam, Terravesta). There is no single definition, but most farms are said to have 10% less pro- ductive (marginal) land area (Clifton-­Brown et al., 2017) which robust miscanthus plants could capitalize on, since plant nutrients are self-­contained in the rhizome and re-­ cycled. This study assumes that the land is the least pro- ductive 10% of land that farmers would be willing to take out of food production to diversify their farms. Lovett et al. (2014) advised that 1.4 million ha of less productive agricultural land of the UK could be used for biomass pro- duction without compromising food production. An acceleration in investment of biomass crops pro- vision and use is required to meet net zero targets. The European Commission and the UK government have set a long-­term goal to develop a low carbon economy by 2050 (Scarlat et al., 2015) where the new bioeconomy's focus is on growth opportunities in bio-­based sectors while considering global challenges (e.g. raw material supply insecurity) and resource and environmental constraints. Scarlat et al. (2015) voiced concerns about competing sec- tors in Europe with bioenergy for land use. This requires solutions to challenges, such as the sustainability of bio- mass raw material and efficiency in biomass use, which could be met using miscanthus for bioenergy. This is be- cause miscanthus is highly sustainable, having a low car- bon footprint, absorbing its nutrients in the rhizome for re-­use and depositing leaf litter to decompose into soil (Shepherd, Clifton-­Brown, et al., 2020). It is also one of the most efficient biomass crops to convert into bioetha- nol (Heaton et al., 2019). Competing sectors with biomass for land use require growing biomass crops without tak- ing away land resources for food. The answer could lie in using marginal lands, lands under-­productive for food production. However, that in itself is a grey area since the Miscanthus is a genus of tropical C4 perennial grasses with origins in Eastern Asia. Selections of naturally occur- ring and synthetic hybrids have sufficient cold tolerance for a wide range of European climates. It is a productive, non-­invasive perennial grass for biomass which is capa- ble of maintaining commercial yields for about 20 years (Anderson et al., 2011). K E Y W O R D S biomass, light absorption, light interception, miscanthus, sacchariflorus, seeded hybrid, simulation, sinensis Funding information Bio-­Based Industries Joint Undertaking, Grant/Award Number: 745012; Biotechnology and Biological Sciences Research Council, Grant/ Award Number: BB/V011553/1; © 2023 The Authors. GCB Bioenergy published by John Wiley & Sons Ltd. |  1 wileyonlinelibrary.com/journal/gcbb GCB Bioenergy. 2023;00:1–18. 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Onlin SHEPHERD et al. Supergen Bioenergy Hub, Engineering and Physical Sciences Research Council, Grant/Award Number: EP/ S000771/1; UK Energy Research Centre, Grant/Award Number: EP/ S029575/1; Aston University, Grant/ Award Number: RG15855 Supergen Bioenergy Hub, Engineering and Physical Sciences Research Council, Grant/Award Number: EP/ S000771/1; UK Energy Research Centre, Grant/Award Number: EP/ S029575/1; Aston University, Grant/ Award Number: RG15855 biomass. We apply the model to project the European biomass potentials of new market-­ready hybrids for 2020–­2030. Field measurements are easier to collect, the calibration is seasonally dynamic and reduces influence of weather variation between field sites. The model obtained is conservative, being calibrated by crops of varying establishment and varying maturity on less productive (marginal) land. This results in conservative projections of miscanthus hybrids for 2020–­2030 based on 10% land use conversion of the least (productive) grassland and arable for farm diversification, which show a European potential of 80.7–­89.7 Mt year−1 biomass, with potential for 1.2–­1.3 EJ year−1 energy and 36.3–­40.3 Mt year−1 car- bon capture, with seeded Miscanthus sacchariflorus × sinensis displaying high- est yield potential. Simulated biomass projections must be viewed in light of the field measurements on less productive land with high soil water deficits. We are attempting to model the results from an ambitious and novel project combin- ing new hybrids across Europe with agronomy which has not been perfected on less productive sites. Nevertheless, at the time of energy sourcing issues, seed-­ propagated miscanthus hybrids for the upscaled provision of bioenergy offer an alternative source of renewable energy. If European countries provide incentives for growers to invest, seeded hybrids can improve product availability and bio- mass yields over the current commercial miscanthus variety. or pesticide in maturity. This results in low field mainte- nance, suitable for busy growers, remote fields and urban neighbours where chemical spraying is not desirable. agricultural land and less productive land, less suitable for food crops (Lewandowski et al., 2016). To understand the potential contribution of Miscanthus to EU targets for do- mestic biomass production, it is critical to be able to model biomass growth under varying environmental conditions on less productive lands. Model development requires high-­quality input data, one such leading experiment is the GRACE project (https://www.grace​-­bbi.eu/) and the only project to provide intensely and frequently measured data on crop performance on less productive land on a transect of field sites across Europe. Even with favourable policies in some European countries, upscaling of miscanthus as a cellulosic peren- nial biomass has been slow. Barriers include uncertainty of yield with poor or slow establishment (Zimmerman et al., 2013), bulkiness for storage and transport and low quality of product for its processing chain (Clifton-­Brown et al., 2017). Poorly established crops are more suscepti- ble to Fusarium and miscanthus blight (Lewandowski et al., 2000). High moisture, ash and silica result in a low quality product for combustion, this can be modified by the timing of senescence and harvest. Earlier flowering times can improve biomass quality by triggering active se- nescence before temperatures fall in autumn with better nutrient remobilization from the shoot to the rhizome and convey cold resistance (Jensen et al.,  2017). Post-­winter harvests improve miscanthus quality criteria for thermal conversion to energy and crop sustainability through re- mobilization of nutrients to the underground rhizome (Jensen et al., 2017). A recent survey of miscanthus grow- ers (Von Hellfeld et al., 2022) showed a major bottleneck to miscanthus uptake was viewed by growers as the cost of logistics, transporting to crop to the processing plant countrywide when the processing plants are in very spe- cific locations. Clifton-­Brown et al. (2017) mention lack of supply chain coordination as a barrier to growth. Growers responses (Von Hellfeld et al., 2022) also mentioned a lack of financial incentives and policies for the perennial bio- mass crop industry. A more reliable crop establishment would avoid unwanted planting gaps, patchiness and yield losses (Hastings et al., 2017), and a shorter time to establishment in cool temperate climates would reach maximum economic harvest faster. 2  |  MATERIALS AND METHODS We use the leading miscanthus growth model, MiscanFor (Hastings, Clifton-­Brown, Wattenbach, Mitchell, & Smith, 2009; Shepherd, Littleton, et al., 2020), a process-­ based model that uses soil properties and meteorological data to predict crop growth through a series of algorithms, running on a daily timestep. The model processes predict the timing of various stages of growth in a mature mis- canthus crop. These are emergence of the shoots, the first leaf, the maximum leaf area, flowering start and stop, the onset of senescence (ripening) and senescence comple- tion. Using calibrations from empirical data the model predicts the rate of leaf expansion, the rate of evapotran- spiration and soil moisture content, rate of photosynthe- sis and rate of leaf fall and senescence. All these rates are modified by air temperature, soil moisture level, nutrient level and solar radiation. For bioenergy, it calculates net power station energy produced and bioenergy carbon capture and storage (BECCS) potential. The model is de- scribed in Hastings, Clifton-­Brown, Wattenbach, Mitchell, and Smith (2009) and Shepherd, Littleton, et al. (2020). A block diagram of the model growth processes is shown in Figure 1 It is hoped the devel- opments in new seed-­propagated miscanthus hybrids and improved agronomic methods can improve establishment, reducing some of the barriers to biomass upscaling. Seed-­ propagated hybrids which can be grown from seed into rhizome plugs for planting at a faster rate than propagat- ing from rhizome to rhizome (Clifton-­Brown et al., 2019). The current commercial miscanthus (Miscanthus × gigan- teus or M × g) is rhizome-­propagated, a slow and land-­ intensive process, which means a delay to growers when they order new crops. One hectare of rhizome plugs cloned has a multiplication rate of 1:20, providing rhizomes for around 20 ha of new plantation, whereas seed-­based hy- brids have multiplication rates of 1:2000 for several hy- brids with multiplication of M. sinensis higher stated at 1:5000–­10,000 (Clifton-­Brown et al., 2019). So how much biomass can those hybrids provide? What is their potential across Europe in terms of biomass, energy and carbon capture and storage (CCS)? We aim to use site measurements from these international field trials to calibrate a biomass crop model to determine the European potential for biomass from these new hybrids, and introduce a novel method in their parameterization for determining biomass. 1  |  INTRODUCTION Miscanthus is a thermally supe- rior biomass crop compared to commonly used maize or wheat straw, it is also a pragmatic solution to farm prob- lems (Shepherd, Clifton-­Brown, et al., 2020). It has a low C footprint (Hastings et al., 2017), requiring no fertilizer SHEPHERD et al. |  3 3 2.1 Databases were obtained and formatted for Europe-­wide spatial simulations. To maximize their contribution to the food resource security element of the European bioeconomy, second-­ generation biomass crops should be grown on lower-­grade Potential land that could be used for the cultivation of biomass crops in Europe was investigated. The Corine land 4  |      FIGURE 1  Schematic of the MiscanFor model. SHEPHERD et al. 4 plant growth during 2020, to provide measurements for parameterizing and calibrating a model and extrapolating the results in space and time period. This work focusses on the seasonal biomass and har- vest potential of three novel miscanthus hybrids plus the current commercial crop M. × giganteus (shortened here to M × g). The novel hybrids are a seed-­propagated M. sinensis × sinensis (shortened here to M. sin × sin), a seed-­ propagated M. sacchariflorus × sinensis (shortened here to seed M. sac × sin, marketed as ‘Aphrodite’) and a clonal M. sacchariflorus × sinensis (shortened here to rhizome M. sac × sin, marketed as ‘Athena’). These hybrids were se- lected for the field trials by the breeders using best infor- mation available at the time of selection. Criteria included (1) evidence of good yield performance traits on a range of sites in UK and EU with contrasting environmental con- ditions; (2) seed production and propagation ability; and (3) diverse morphologies (heights and stem diameters) relative to impacts on harvest logistics and downstream processing operations. FIGURE 1  Schematic of the MiscanFor model. cover map from Copernicus (Buettner, 2014) was used to create a mask of areas unsuitable for the cultivation such as bare rock, or areas that should not be used for cultiva- tion such as forests, wetlands and shrubland. Only arable and pasture classes were considered suitable. In addition, any areas with high carbon soils, typically above 15% or- ganic matter or peatland were considered unsuitable. The field trial involved intensive crop measurements at European sites (Table 1) throughout the growing sea- son of 2020 for crops harvested in March 2021; 2020 was the third year of growth, crops having been planted during 2018. For this simulation work, field measurements were used from the most frequently (two-­weekly) sampled four sites and four hybrids. Further details on the whole field trial can be read in Awty-­Carroll et al. (2022). The soil properties were obtained from the harmonized world soil data base from IIASA (Wieder et al., 2014). 2.1 We only used the dominant soil for each grid block. These soil parameters were used to calculate the wilting point, field capacity and soil carbon to a depth of up to 1 m for each grid pixel. The RCP2.6 future climate scenario from the HADGEM 3 model from the UK Met Office (Martin et al.,  2011) for the period 2020–­2030 in monthly time steps and on a 0.5 degree grid was used as driving climate data. For each hybrid in the field, four replicate blocks were measured. M. sin × sin is planted at double the density (30,000 plants ha−1) of the other hybrids (15,000 plants ha−1) as recommended by its developer Wageningen University. in the UK at Trawsgoed (TWS) near Aberystwyth is nor- mally used for pasture. The shallow stony sandy loam has lead contamination and low water holding capacity. TWS site's low lying position at 72 m asl means that crops ex- perience more temperature extremes than in most of the UK, including more severe late spring and early autumn frosts. TWS has the lowest plant available water (50 mm) of all the field sites. In southern Germany, the field trial was planted at a high-­altitude site (706 m asl) Oberer Lindernhof (OLI) which has a shortened growing sea- son. Over winter, it snows regularly, and temperatures of down to −20°C are reached. OLI has been used for years by cereal breeders to test for overwinter cold tolerance and resistance to late spring and early frosts [e.g. wheat and rye for bioethanol (Rosenberger et al., 2002); durum wheat (Sieber et al., 2014)]. The site in Croatia near Zagreb is limited by local clay soils that have low enzyme activity which suffer from rainfall extremes—­too much in sum- mer and too little in spring (Magenau et al., 2022). The site in Northern Italy near Piacenza (PAC) is the least produc- tive of the sites but continuous arable has compacted and depleted the soil organic carbon (Awty-­Carroll et al., 2022) which can potentially be improved by growing perennials such as Miscanthus. SCH experiences the lowest annual precipitation of the field trial sites, 473 mm. CHV has heavy metals contaminating its soils from surrounding heavy industry, plus copper sulphate fungicide and low soil water retention (Awty-­Carroll et al., 2022). For more detailed mean climate data, see Magenau et al. (2022). Site Lat, Long (decimal deg) Altitude (m asl)* Annual precipitation (mm) Plant available water (mm) Mean temp (degree) Soil texture TWS Trawscoed, Wales 52°24′59.8′′ N, 4°04′02.6′′ W 72 1311 50 10.7 Shallow stony sandy loam OLI Oberer Lindenhof, Germany 48°28′42.1′′ N, 9°18′41.0″ E 706 863 148 8.7 Clay loam ZAG Zagreb, Croatia 45°49′47.9′′ N, 15°58′33.5′′ E 117 891 158 11.7 Clay and silt loam PAC1 Piacenza lowland site, Italy 44°84′50.4′′ N, 9°60′60.7″ E 73 820 166 13.9 Compacted loam PAC2 Piacenza upland site Italy 44°84′50.4′′ N, 9°71′02.4″ E 578 804 140 12.8 Compacted loam SCH Schiphol, Netherlands 52°18′45.2′′ N, 4°39′55.3″ E −4 473 147 10.7 Peat and clay reclaimed land CHV Chanteloup, France 48°58′34.9′′ N, 2°01′57.9″ E 42 537 67 11.9 Sandy loam 2.2  |  Field data, hybrids and site locations The field trial sites (Table 1) chosen for their frequent measurement for modelling are sites nearby Trawscoed (labelled in the text TWS), Oberer Lindenhof (labelled OLI); Zagreb (labelled ZAG); Piacenza lowland site (la- belled PAC); for locations of field sites, see figure 1 in Awty-­Carroll et al. (2022). Further sites used for validation comparison with modelled values were Hoofdoorp near Schiphol airport (labelled SCH), Chanteloup near Paris (labelled CHV) and Piacenza upland site (labelled PAC2). Climate data for modelling at the site level were provided by the WS-­GP 1 weather stations (Delta-­T Devices Ltd), soil data taken from soil core sampling (soil texture and bulk density were used to derive the capillary pressure taken at time-­zero in 2017 using the Campbell method, as defined in Hastings, Clifton-­Brown, Wattenbach, Mitchell, and Smith (2009) which allowed calculation of plant available water), together with the crop measurements. At each site, an automatic weather station (GP1; Delta-­T Devices) measured in field environmental param- eters: hourly solar radiation, rainfall, wind and air tem- perature that determine crop growth processes. The project whose data we are using, aims to develop the technology for upscaling miscanthus production on land with low productivity to avoid competition with the food sector for land use. To achieve this one its work packages includes multi-­location field trials of many mis- canthus hybrids across European sites. Of the 14 hybrids it investigates, four hybrids were selected in this study for intensive growth measurements in four widely distributed locations to create equations for crop modelling. These measurements were scheduled during the third year of Land marginality—­the field trials were performed on less productive/lower-­grade lands (also referred to as mar- ginal lands) that are less suitable for arable food crops. Marginal land is defined (Tóth et al., 2016) as experiencing one or more of environmental stresses (drought, flooding, stoniness, steep slope, exposure to wind and sub-­optimal aspect), low nutrients and/or contaminated soils. The site SHEPHERD et al. |  5 5 2.3.2  |  Seasonal dynamics of light interception (PAR) by the canopy Monsi and Saeki (1953) published the first mathematical model for radiation intercepted by the leaf canopy based on the Beer–­Lambert Law: | in Shepherd, Littleton, et al. (2020) uses the RUE of 2.4 g MJ−1 as a maximum because validation shows this produces realistic modelled versus observed aboveground yield. RUE is reduced by soil water deficit (Clifton-­Brown et al.,  2004) and temperature (Hastings, Clifton-­Brown, Wattenbach, Mitchell, & Smith, 2009). In the MiscanFor model, downregulation via too high or too low tempera- ture is applied to maximum RUE via the temperature vari- ation factor (Farage et al., 2006) because RUE depends on the temperature at leaf formation and the temperature of photosynthesis. Downregulation of RUE via water deficit is applied via coefficients representing the evaporation of rainfall intercepted by leaf and leaf transpiration and evaporation through soil, all limited via water deficit. The process is similar to the one used in SWAT2000 (Neitsch et al., 2005). In the model, these separate coefficients are determined and then combined into a RUE downregula- tion coefficient. and below the leaf canopy. These measures are used to cal- culate the ‘light ratio’, the measured fraction of radiation transmitted though the canopy (i.e. under the canopy and not absorbed by the plant as a portion of radiation above the canopy), and hence 1 − ‘light ratio’ is the fraction of light absorbed, which can replace the term ‘1 − exp (−ext. coeff × LAI)’. Inserting this term into Equation (1) Inserting this term into Equation (1) (3) Plant biomass increase (g)=RUE×(1−}light ratio’) ×cumulative PAR measured (3 Plant biomass increase (g)=RUE×(1−}light ratio’) ×cumulative PAR measured increase (g)=RUE×(1−}light ratio’) (3) ×cumulative PAR measured (3) and rearranging, (4) RUE=plant biomass increase∕ ((1−}light ratio’)×cumulative PAR) (4) and we can measure this over time increments to determine how the RUE changes during the growth period. Plant biomass increase over a time interval (e.g. g dry matter per day) is the product of cumulative radiation in- tercepted by the canopy (e.g. MJ PAR day−1) and the con- version efficiency (RUE, e.g. g MJ−1 PAR): ( Plant biomass increase=RUE×cumulative PAR × fraction of light absorbed (1) Standing crop biomass (for comparison against simu- lated biomass) was determined from a subsampling ap- proach devised and explained fully in Nunn et al. (2017), consisting of fortnightly destructive harvests (known as ‘serial cuts’) of randomly selected shoots per plot (10 for M. sac × sin and 20 shoots for smaller M. sin × sin plants), cut at 10 cm above soil surface. These subsamples were rescaled by multiplying serial dry weight by the ratio of the final 10-­stem weight measurement and the quadrat harvest dry weight taken on the same day. Units were ex- pressed in terms of t ha−1. Because the brown and green leaf biomass and stem biomass were measured separately at each serial cut throughout the season in 2020, canopy dynamics (expansion and senescence) could be identified. The product of a RUEmax and the RUE downregulation coefficient produces the RUE which can be calculated in the field using Equation (1). When changes in crop bio- mass can be detected with sufficient accuracy over short intervals (e.g. weekly or fortnightly), the dynamics of RUE in the field can be related to environmental constraints and plant developmental stages to derive coefficients that can be used for downregulation. 6 2.3.1  |  Maximum radiation use efficiency and its environmental down regulation Miscanthus is a genus of tropical C4 perennial grasses with origins in Eastern Asia. Selections of naturally oc- curring and synthetic hybrids have sufficient cold toler- ance for a wide range of European climates. Radiation use efficiency (RUE) is an estimate of net whole grow- ing season photosynthesis. Field measurements of RUE have been derived multiple times for M × g in ‘largely’ non water limiting temperate conditions in Ireland (Clifton-­ Brown et al., 2000), Wales (Davey, Jones, et al., 2017) and in Netherlands (van der Werf et al., 1992). They average 2.4  g above round dry matter MJ−1 of intercepted pho- tosynthetically active radiation (PAR). Although there are several publications with higher RUE estimates, the MiscanFor model described in Hastings, Clifton-­Brown, Wattenbach, Mitchell, and Smith  (2009) and updated 6 SHEPHERD et al. 2.3.3  |  Seasonal dynamics of aboveground biomass Plant biomass increase=RUE×cumulative PAR × fraction of light absorbed 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Cond each hybrid. The RUE has to be treated the same across all sites of the same hybrid, so the line of best fit is taken for measured values across all field sites for a representative hybrid RUE. applied the model spatially. There are two versions of the MiscanFor model, a single site version and a spatial ver- sion with exactly the same processes but with the capabil- ity to use databases at variable scale and extent. For the spatial model, climate, elevation, soil, land use and land constraint databases were prepared for Europe at 1  km resolution. The crop biomass processes and parameters for the validated site model were input to the spatial model. applied the model spatially. There are two versions of the MiscanFor model, a single site version and a spatial ver- sion with exactly the same processes but with the capabil- ity to use databases at variable scale and extent. For the spatial model, climate, elevation, soil, land use and land constraint databases were prepared for Europe at 1  km resolution. The crop biomass processes and parameters for the validated site model were input to the spatial model. 3.1  |  Method 1 A plot of measured RUE through the season (Figure 2) using the M. sin × sin hybrid is representative of the find- ings for all hybrids. It shows a high variability in 2-­week interval measured RUE between sites and a high standard error between replicates with no statistical significance. Each site's climate which modifies RUE did not produce 2.4 2.4 (2) Radiation below canopy=Radiation above canopy ⋅exp (−ext. coeff×LAI) (2) For each hybrid and each site: The 2020 time series of RUEmeasured (Equation 4) concerning intercepted light for the different hybrids was plotted against simulated RUE (for M × g in the pre-­modified model), which had been downregulated via limitations for soil and leaf water via deficit and photosynthesis via leaf expansion temperature. Leaf area index (LAI) is variable so not easy to mea- sure for calibration, and calculating LAI first in order to then calculate light interception, aggregates uncertainty by having two calculations when one could be used. We replaced the Monsi–­Saeki calculation using a direct mea- surement of light intensity with a line ceptometer (an array of 10 photodiodes spaced along a 1 m stick) above The comparison of RUE from measurement of all sites and simulated RUE allows us to determine the amount of reduction or increase to apply to the simulated RUE for 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for ru |  7 SHEPHERD et al. |  7 2.5.2  |  Method 2b: Logistic light interception-­ degree day relationship The fraction of light interception from top and bottom of the canopy (1 − ‘light ratio’) was plotted against accu- mulated degree day for all field sites, and a logistic curve fitted. The resulting algorithm to determine light intercep- tion from cumulative degree days was used to determine biomass via Equation (1). 2.5  |  Photosynthesis simulation method 2: Replacing LAI with light interception The energy produced by a miscanthus assuming a medium size power plant burning miscanthus bales uses the method of Hastings, Clifton-­Brown, Wattenbach, Mitchell, Stampfl, and Smith (2009). Carbon capture po- tential (CCS) is based on an assumption of 90% efficiency (Albanito et al., 2019) of capture post-­combustion at bio- mass electricity plants. From Equation  (1), biomass increase  =  light intercep- tion × cumulated PAR × RUE. RUE varies with each hybrid as some have more vigour than others. PAR varies for each site, making a comparison of hy- brids difficult, and what we want to do is reduce environ- mental influences to look at the biological operation of the hybrids. In a previous UKRI-­funded project (Shepherd, Littleton, et al.,  2020), the IMAGE IAM which makes socio-­economic decisions had determined land area to locate biomass crops to provide sufficient biomass for car- bon capture schemes to retain global temperature increase under 2°C. IMAGE projected the same global area as con- verting 10% of grassland and 10% of less productive arable land. The industry-­supported field trials we are using are based on less productive arable, so we assume that bio- mass crops would be marketed for such use. The biomass growth calibrations determined from the crop measure- ments on less productive land have been used to produce projections for Europe, taking 10% of each spatial grid square of grassland and arable land use as less productive. We have used this method to produce aggregated European totals rather than using marginal land use databases be- cause the definition of marginal land changes depending on the crop or land use, and because land use databases are based on current/past land use, and we are producing future projections with a proportion of land conversion to biomass determined by a socio-­economic IAM. Moreover, the IAM land area output is related to the RCP 2.6 climate scenario, used in this study, to determine the biomass land area necessary for sufficient BECCS decarbonization to meet the Paris Agreement (United Nations, 2015) limit on global temperature increase under 2°C. The light interception fraction however has the po- tential to work in a simulation common to all hybrids, is dependent on cumulative degree days, and when light interception fraction-­degree days data are plotted, the temperature influence is standardized. This can be useful when you have measurements collected from different cli- mate zones for a single hybrid. 2.5.1  |  Method 2a: Third-­order polynomial light interception-­degree day relationship 2.5.1  |  Method 2a: Third-­order polynomial light interception-­degree day relationship The fraction of intercepted light interception from the top and bottom of the canopy (1 − ‘light ratio’) was plotted against accumulated degree day for all field sites, and a third-­order polynomial curve of the relationship fitted. The resulting algorithm to determine light interception from cumulative degree days was used to determine bio- mass via Equation (1). 2.5.2  |  Method 2b: Logistic light interception-­ degree day relationship 2.6 After satisfactorily validating the MiscanFor model for different sites and years with varying soils and climate, we 8  |      SHEPHERD et al FIGURE 2  Variability of measured radiation use efficiency (RUE, g MJ−1) in M. sin × sin across four field sites (a) TWS: Trawscoed Wales, (b) OLI: Oberer Lindenhof Germany, (c) ZAG: Zagreb Croatia, (d) PAC: Piacenza Italy, and with Std Error bars of four replicates at each field site sampling date. 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Lib SHEPHERD et al. wnloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions ( FIGURE 2  Variability of measured radiation use efficiency (RUE, g MJ−1) in M. sin × sin across four field sites (a) TWS: Trawscoed Wales, (b) OLI: Oberer Lindenhof Germany, (c) ZAG: Zagreb Croatia, (d) PAC: Piacenza Italy, and with Std Error bars of four replicates at each field site sampling date. In a previous project, OPTIMISC, establishment issues were also noted as being problematic for comparative measurement of hybrids (Nunn et al.,  2017). Magenau et al. (2022) also refer to the fact that by the third year at colder locations such as OLI and TWS, the establish- ment of miscanthus takes up to 6 years (citing Christian et al., 2008), while in warmer climates, maximum yields are reached after 2 years (Clifton-­Brown et al., 2000). In Croatia, establishment was hampered by a heavy clay and less productive soil conditions, so that plants in the third year were not fully established. any common relationship for a single hybrid to use extract for modelling and shows that RUE is not static, but dy- namic with climate conditions. Therefore, we conclude that a constant reduction in RUE is not the answer. It was decided to discontinue this method. Ideally, we need a method more based on the drivers of the variability in RUE and the characteristics of the hybrid and reducing the impact of climate. 3.3  |  Method 2b: Logistic fitted light interception curve See the Terms and Conditions URE 3  Field observations with fitted logistic relationship between accumulated light interception and degre g p g p g y p hybrids M. sin × sin (a), M × g (b), seeded M. sac × sin (c), rhizome M. sac × sin (d). Fitted curves are based on all-­site data. In (c) light absorption for the best performing crop at Piacenza is displayed alongside the average-­site data for seeded M. sac × sin due to establishment issues at various sites. Variability of observation in all plots denoted by standard deviation of the four sampled replicates. M × g, Miscanthus × giganteus; M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin, Miscanthus sinensis × sinensis. TABLE 2  Curve fit parameter statistics of observed light interception and fitted logistic values with data aggregated from four measurement sites. Logistic fitted curve Seed M. sin × sin Rh. M × g Seed M. sac × sin Seed M. sac × sin potentiala Rh. M. sac × sin r2 correlation 0.98 0.98 0.93 0.99 0.98 RMSE 12.61 12.98 26.87 2.94 13.89 Mean difference −0.04 −0.02 −0.03 0.003 −0.02 Relative error −5.42 −3.06 −5.46 0.01 −3.46 Maximum error 0.22 0.31 0.40 0.05 0.26 No. of values 44 44 44 12 44 Abbreviations: M × g: Miscanthus × giganteus; M. sac × sin: Miscanthus sacchariflorus × sinensis; M. sin × sin: Miscanthus sinensis × sinensis; Rh.: rhizome; RMSE: root mean square error. aPotential = data from best performing crop at Piacenza only. Logistic fitted curve established as well as other hybrids and shows relatively little variability. relationship using only the data from the best perform- ing crop at PAC. In the light interception plot for seeded M. sac × sin (Figure 3c), observed data and logistic fitted curves based on all-­site data are shown and also the PAC site best performing crop, from which we see a far steeper growth of light interception as the canopy has a more rapid closure with a well-­established crop. We refer to re- sults from the latter as ‘Seed M. sac × sin potential’, statis- tics being included in Table 2 which reflect the consistency Considering such an expensive, measurement inten- sive, international project to determine the potential of new hybrids including seed-­propagated lines, the poor establishment of seeded M. 3.3  |  Method 2b: Logistic fitted light interception curve A third-­order polynomial was fitted to describe the rela- tionship between the radiation intercepted by the canopy and the accumulated degree days across all sites for each hybrid (Supplementary Material S1). Figure  3 plots for each hybrid show the fitted logistic curves for the fraction of light interception from the top and bottom of the canopy against accumulated degree days for data measurements from all field sites. Standard deviation of the four replicate plot measurements at a sin- gle site and in a single sampling have been included for each data point. Seeded hybrid M. sac × sin had the greatest variabil- ity in light interception and growth across field sites (Supplementary Materials S1 and S2c). The widely vary- ing values are due to poor plug plant establishment at some sites and frost damage on the same plot as crops established well with a more rapid canopy closure (Awty-­ Carroll et al., 2022). First-­year overwintering was partic- ularly affected by climate and repeated frosts in Wales UK, which affected the second-­year growth of seeded M. sac × sin hybrids. Field gap filling during establishment prevented compound yield losses. The lowest yielding third-­year site was the Wales UK and the highest in low- land northern Italy. The logistic curves are the best fit (Table 2) and they are also the correct shape for the growth curve starting off with a shallow increase and ending at a plateau. All hy- brids show better fitted curve agreement using a logistic relationship, but the seeded M. sac × sin hybrid had the greatest variance in establishment (reflected in the sta- tistical variability). The other seeded hybrid M. sin × sin |  9 HEPHERD et al. IGURE 3  Field observations with fitted logistic relationship between accumulated light interception and degree days for separate ybrids M. sin × sin (a), M × g (b), seeded M. sac × sin (c), rhizome M. sac × sin (d). Fitted curves are based on all-­site data. In (c) light bsorption for the best performing crop at Piacenza is displayed alongside the average-­site data for seeded M. sac × sin due to establishment 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Li |  9 SHEPHERD et al. wnloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. a rapid rise in growth, they did not occur late enough to delay a high rate of increase in biomass. of data when very well-­established replicates are used instead of replicates of low establishment success, this treatment of data only pertains to the seeded M. sac × sin hybrid because of its greater establishment problems. The standing crop biomass field measurements show how M × g crops at ZAG suffered in a drought and were poorly established at TWS. The simulated biomass, resulting from a calibration using mean measurements from all less productive sites, will be higher than the measured biomass at poorly established sites because calibration values are in- creased by the better performing sites. To show the poten- tial of a hybrid, well-­established plants should be used for calibration measurements, therefore since the hybrid with the poorest establishment is the seeded M. sac × sin, this has been calibrated for its best established calibration field mea- surements at the PAC field site in green. The second thing to improve the variability of measurements from sites is to de- termine best agronomy practise, to ensure well-­established plants at all sites, then repeat an study such as this. 3.3  |  Method 2b: Logistic fitted light interception curve sac × sin at sites was an issue that warranted an alternative model calibration to deter- mine the crop potential for seeded M. sac × sin; hence, we re-­visited the light interception-­degree days logistic 10 SHEPHERD et al. 10 |  11 SHEPHERD et al. 11 TABLE 3  Statistics of observed and simulated biomass for selected hybrids and sites using logistic light interception curve. Logistic light interception M. sin × sin M × g Seed M. sac × sin Rh. M. sac × sin TWS OLI ZAG PAC r2 correlation 0.98 0.98 0.85 0.86 RMSE 23.86 16.38 35.18 42.40 Mean difference −0.59 0.21 −0.86 4.34 Relative error −9.29 2.08 −7.84 31.37 Maximum error 4.23 3.87 10.18 13.19 No. of values 17 17 17 17 Abbreviations: OLI: Oberer Lindenhof; PAC: Piacenza; Rh.: rhizome; RMSE: root mean square error; TWS: Trawscoed; ZAG: Zagreb. Logistic light interception Abbreviations: OLI: Oberer Lindenhof; PAC: Piacenza; Rh.: rhizome; RMSE: root mean square error; TWS: Trawscoed; ZAG: Zagreb. FIGURE 5  (a, b) Two validations using simulated versus measured harvest biomass across all hybrids: (a) from different field sites 2021 harvest and (b) from the same field sites as calibrations 2022 harvest (four replicates). and shows how the validated model has improved upon the unmodified model (in blue) which was calibrated for M × g only. The validation data provide satisfactory re- sults (r2 0.54, RMSE 28.7). Figure 5b shows validations at the same field sites for 2022, the next harvest after the calibration growing season. This showed a poor r2 of 0.0005, but was due to three outliers shown in red of very low measured harvest yield (each an average of four rep- licates), much lower than other hybrids in the same field under the same environmental conditions and was not connected to the modelling. If we take the three outliers away, the results are satisfactory (Table 4, r2 0.68, RMSE 12.65). selected sites and hybrids derived from a logistic light in- terception curve. (Statistics on every site and hybrid, for third-­order polynomial and logistic derived relationships, can be found in Table S3 of Supplementary information.) Biomass resulting from the logistic method for determin- ing light interception was more accurately simulated than from the third-­order polynomial method; hence, only the logistic method was taken forward for validation and final simulation. The aim of the modelling is to determine the biomass incremental change using daily climatic data and accu- mulate these increments over a whole growing season to predict final biomass yield. To validate the model, we compared simulations to measured harvest yields from different sites or from different years to the calibration data, across any of the hybrids. 3.4  |  Resulting biomass from light interception curves Figure 4 shows the resulting calibrations of measured bio- mass compared against simulations determined from the calculated light interception resulting from third-­order polynomial and logistic relationships with degree days, showing how the logistic simulations shown in red have a better agreement with the field measurements than both the unmodified model and the third order polyno- mial simulation. Early season frosts occurrences were checked against the growth curves (displayed on Figure 4 M. sin × sin plots), but as the timing of frosts were before MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; O Table 3 shows a statistical comparison of the seasonal time series of observed and simulated crop biomass from FIGURE 4  Simulated biomass, from logistic light interception-­degree day relationships plus the original model using leaf area index estimation, compared against measured standing crop biomass for each hybrid and for each site. nelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License rary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are m/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by nditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable C Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Com OA articles are governed by the applicable Creative Commons License FIGURE 4  Simulated biomass, from logistic light interception-­degree day relationships plus the original model using leaf area index estimation, compared against measured standing crop biomass for each hybrid and for each site. FIGURE 4  Simulated biomass, from logistic light interception-­degree day relationships plus the original model using leaf area index estimation, compared against measured standing crop biomass for each hybrid and for each site. 12 Clifton-­Brown, Wattenbach, Mitchell, & Smith, 2009), al- though it is accepted that in harvest:peak ratio, it can vary a little between the hybrids. During 2020–­2030, mean annual harvest yield ranges from 0 to 11 t ha−1 year−1. This is shown in Figure 6a,b for M. sac × sin and M. sin × sin, respectively, with black areas displaying where either the bioenergy land use is constrained by national parks, forestry, mountains, etc. or yield is zero, due to frost or drought crop kill. The crop biomass processes and parameters for the validated site model were input to the spatial model (Equation 5, Table 5) to run simulations across Europe to determine the European-­wide potential of the hybrids. The Europe-­wide simulations for each hybrid display similarly in map form, the differences being in the spa- tially aggregated totals; hence, spatial results are displayed using the seed-­propagated hybrids M. sin × sin and M. sac × sin. The mean peak annual biomass during 2020–­ 2030 ranges from 0 to 18 t ha−1 year−1. The mean annual harvest yield was calculated at 67% of peak yield (Hastings, Growth is closely related to water availability, so north- erly and central European regions with lower water defi- cit and warm growing season temperatures in central Europe have the highest simulated peak yield and harvest yield, on a per hectare basis Switzerland for example con- tains areas with the highest yields in Europe. Ultimately though, spatial area availability matters, so countries with larger areas of grassland and unproductive arable for con- version which are not biomass land use constrained will have the largest aggregated yields. Figure  7 shows the areas of highest harvest biomass projected for the seeded hybrids, this is a small difference of yield in tonnes per hectare but will aggregate spatially. M. sac × sin has the ad- vantage over most areas; however, M. sin × sin appears to be the hybrid to use in warmer drier areas. TABLE 4  Validation statistics (relating to Figure 5) for the different sites (V1 relating to Figure 5a) and next year 2022 harvest data at calibration sites (V2 relating to Figure 5b) (three field data outliers removed). V1 V2 r 2 correlation coef 0.67 0.68 Root mean square error 27.2 12.65 Mean difference −0.2 0.004 Relative error −2.2 0.03 Maximum error 4.1 3.0 No. |  11 The two validations were done at different times, first using 2021 measured harvest data from other field sites' (SCH site near Amsterdam, CHV site near Paris and a Piacenza second site PAC2) and second after the 2022 harvests, data from the same sites as the calibration were used, shown in Figure 5a,b, respectively. Figure  5a displays the validation data (in green) and also calibrations (in black) for various hybrids, For the best (logistic) photosynthetic simulation of bio- mass, we determined that the core photosynthesis proce- dure is to substitute Equation (5) into Equation (1), where RUE is 2.35 g MJ−1. Fraction of light interception is by the applicable Creative Commons License (5) theta1 + ((theta2 −theta1)∕(1 + exp(DDcum −theta3)∕theta4)) (5) )) where the parameters for the different hybrids are listed in Table 5. where the parameters for the different hybrids are listed in Table 5. 12  | SHEPHERD et al. sac × sin for mean annual harvest biomass (t ha−1 year−1) over 2020–­2030 for Europe. M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin, Miscanthus sinensis × sinensis. FIGURE 8  Standard deviation of annual harvest dry matter biomass for Europe 2020–­2030 (simulated using seed-­propagated M. sac × sin potential). M. sac × sin, Miscanthus sacchariflorus × sinensis. 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Lib 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are g SHEPHERD et al. |  13 13 FIGURE 7  Spatial distribution of highest yielding seeded hybrids M. sin × sin hybrid and M. sac × sin for mean annual harvest biomass (t ha−1 year−1) over 2020–­2030 for Europe. M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin, Miscanthus sinensis × sinensis. m/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-co FIGURE 8  Standard deviation of annual harvest dry matter biomass for Europe 2020–­2030 (simulated using seed-­propagated M. sac × sin potential). M. sac × sin, Miscanthus sacchariflorus × sinensis. FIGURE 8  Standard deviation of annual harvest dry matter biomass for Europe 2020–­2030 (simulated using seed-­propagated M. sac × sin potential). M. sac × sin, Miscanthus sacchariflorus × sinensis. the other hybrids only flowered at the Zagreb latitude. The OPTIMISC miscanthus field trial found little evidence of spread of Miscanthus by seed fertile flowering hybrids (Kalinina et al.,  2017), because volunteer seedlings rarely establish and successfully overwinter (Hastings et al., 2017), breeding of sterile triploid seeded hybrids which eliminate invasive risk remains a long-­term goal for Miscanthus breed- ers. Breeding for late or absent flowering reduces invasive risk because plants fail to produce seed before winter frosts (Hastings et al.,  2017). Creeping rhizomes have been ob- served in several M. sacchariflorus genotypes, it is therefore recommended to exclude creeping genotypes from commer- cialization to avoid the problem (Lewandowski et al., 2016). which are, in turn, related to variance in soil type and cli- mate. 4  |  DISCUSSION 4 Athena, Aphrodite and M × g have the same genetic back- ground but the difference is in the origin of the parent ma- terial for these hybrids. Germplasm collected from Asia (303 accessions of M. sinensis, M. sacchariflorus, M. floridu- lus, collected from 158 diverse locations with varied agro- nomic traits) has been used in the Defra-­BBSRC supported of values 10 11 Higher uncertainty in yield (Figure 8) has been shown to be due to higher water deficits (Shepherd et al., 2021) theta1 theta2 theta3 theta4 M. × sinensis 1 0 1000 149.287 M. × giganteus 0.96 0.096 1120.14 190.779 Seeded M. sac × sin ‘Aphrodite’—­all site calibration 0.95 0.095 1114.45 177.901 Seeded M. sac × sin ‘Aphrodite’ potential—­ best site calibration 0.95 0.095 925.33 85.702 Rhizome M. sac × sin ‘Athena’ 0.95 0.095 986.769 103.178 TABLE 5  Light interception parameters for hybrids. FIGURE 6  (a, b) Mean annual harvest dry matter biomass (t ha−1 year−1) over 2020–­2030 for Europe (simulated using growth calibrated for seed-­propagated M. sin × sin (a) and M. sac × sin (b) potential, respectively). M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin, Miscanthus sinensis × sinensis. TABLE 5  Light interception parameters for hybrids. theta1 theta2 theta3 theta4 M. × sinensis 1 0 1000 149.287 M. × giganteus 0.96 0.096 1120.14 190.779 Seeded M. sac × sin ‘Aphrodite’—­all site calibration 0.95 0.095 1114.45 177.901 Seeded M. sac × sin ‘Aphrodite’ potential—­ best site calibration 0.95 0.095 925.33 85.702 Rhizome M. sac × sin ‘Athena’ 0.95 0.095 986.769 103.178 wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License FIGURE 6  (a, b) Mean annual harvest dry matter biomass (t ha−1 year−1) over 2020–­2030 for Europe (simulated using growth calibrated for seed-­propagated M. sin × sin (a) and M. sac × sin (b) potential, respectively). M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin, Miscanthus sinensis × sinensis. FIGURE 6  (a, b) Mean annual harvest dry matter biomass (t ha−1 year−1) over 2020–­2030 for Europe (simulated using growth calibrated for seed-­propagated M. sin × sin (a) and M. sac × sin (b) potential, respectively). M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin, Miscanthus sinensis × sinensis. FIGURE 6  (a, b) Mean annual harvest dry matter biomass (t ha−1 year−1) over 2020–­2030 for Europe (simulated using growth calibrated for seed-­propagated M. sin × sin (a) and M. sac × sin (b) potential, respectively). M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin, Miscanthus sinensis × sinensis. |  13 SHEPHERD et al. FIGURE 7  Spatial distribution of highest yielding seeded hybrids M. sin × sin hybrid and M. Uncertainty in rapidly scaling-­up biomass energy supply, especially in dry climates and in regions where fu- ture climate change could result in drier conditions, has important policy implications in bioenergy effectiveness for lowering atmospheric carbon (Littleton et al.,  2022). Despite different climate and soil datasets, the uncertainty we obtained for European biomass projections is of the same range and spatial distribution as obtained in Hastings, Clifton-­Brown, Wattenbach, Mitchell, and Smith (2009). The European aggregated mean annual totals for bio- mass (Table 6) show a European capacity to produce nearly 90 Mt year−1 of miscanthus harvest yield from the conver- sion of 10% of less productive grassland and 10% of less productive arable land. This would provide 1.34 EJ year−1 energy in electricity generation and a carbon capture po- tential (CCS) of 40 Mt year−1. FIGURE 7  Spatial distribution of highest yielding seeded hybrids M. sin × sin hybrid and M. sac × sin for mean annual harvest biomass (t ha−1 year−1) over 2020–­2030 for Europe. M. sac × sin, Miscanthus sacchariflorus × sinensis; M. sin × sin, Miscanthus sinensis × sinensis. 4  | SHEPHERD et al. 14 TABLE 6  European Projections for Annual Harvest Yield, Energy Produced and Carbon Capture and Storage Potentials over climate period 2020–­2030, over 15.7 Mha area including land constraints based on 10% grassland, 10% arable conversion. Harvest yield Mt year−1 (SD) Electrical energy produced EJ year−1 Carbon capture Mt year−1 M. × sin × sin 87.19 (0.051) 1.30 39.24 M × g 81.28 (0.048) 1.20 36.57 TABLE 6  European Projections for Annual Harvest Yield, Energy Produced and Carbon Capture and Storage Potentials over climate period 2020–­2030, over 15.7 Mha area including land constraints based on 10% grassland, 10% arable conversion. Harvest yield Mt year−1 (SD) Electrical energy produced EJ year−1 Carbon capture Mt year−1 M. × sin × sin 87.19 (0.051) 1.30 39.24 M × g 81.28 (0.048) 1.20 36.57 Seeded M. sac × sin ‘Aphrodite’—­all site calibration 80.72 (0.047) 1.20 36.32 Seeded M. sac × sin ‘Aphrodite’ potential—­best site calibration 89.66 (0.052) 1.34 40.36 Rhizome M. sac × sin ‘Athena’ 89.66 (0.052) 1.34 40.35 Abbreviations: M × g: Miscanthus × giganteus; M. sac × sin: Miscanthus sacchariflorus × sinensis; M. sin × sin: Miscanthus sinensis × sinensis. The calibrations were based on field trials grown on less productive land, where the definition of environmental re- striction on growth is in keeping with the use of lower-­grade arable land and grassland conversion to growing biomass. Climate projections from the RCP2.6 climate scenario have been used, assuming a 2°C or lower global temperature in- crease and associated bioenergy land use change which as- sumes biomass crops for bioenergy with CCS being rolled out at scale in the next 10–­20 years (Littleton et al., 2022). GIANT project, a European miscanthus breeding program (Huang et al., 2019). Various diploid M. sinensis and tetra- ploid M. sacchariflorus were collected that could be used as parents to breed high-­yielding sterile triploid hybrids to ad- dress potential concern about plant invasiveness. Field tri- als in Europe with miscanthus over the past 25 years have demonstrated that interspecies hybrids such as M × g com- bine high yield potentials and low inputs in a wide range of soils and climates (Clifton-­Brown et al., 2017). Despite the main current commercial hybrids, M. sac × sin and M × g, having similar parent material, they have different phe- nological characteristics. For example, different charac- teristics being the late ripening of M. 4  | sac × sin (seeded and rhizome), and M × g having intermediate flowering and se- nescence when compared (Magenau et al., 2022). y All hybrids use the same climate, soil and land use da- tabases, the only differences are from the biomass calibra- tions from field trials. Seeded M. sin × sin and rhizome M. sac × sin European harvest potential show promise to out-­ perform the current commercial crop M × g. Seeded M. sin × sin is planted at double density and therefore being seed-­propagated requires more plugs than the M. sac × sin and rhizome-­propagated plants. It was planted at the recommended rate advised by its developer; however, in- creasing the density of M. sin × sin hybrids has previously not increased the yield (Ouattara et al., 2020). This is the shortest hybrid and height has a much stronger effect on yield than stem count (Awty-­Carroll et al., 2022; Davey, Robson, et al., 2017) but increasing density could result in lower yields in the longer term due to overcrowding (in- terplant competition). Rhizome M. sac × sin will have the same problem as M × g of slower propagation and avail- ability. Meanwhile, seeded M. sac × sin based on a calibra- tion of poorly and well-­established crops performed a little lower than the current commercial crop, but its potential based on well-­established plants, already mature at third year in a warmer climate, outperforms most miscanthus hybrids and shows the same yield potential as rhizome M. sac × sin (the rhizome version was well established, sup- porting what could be expected of the seeded version). The methods chosen demonstrate that simply reduc- ing RUE by a constant rate through the season does not work since RUE is not constant; being influenced greatly by environmental conditions, it is different between sites. Thus, a more seasonally dynamic process is required and one based on the phenological characteristics of a hybrid while reducing the variation from the climate of each field site is required to determine a relationship related to RUE which is common to all sites. 4  | The aim was to parameterize a model in a way that will work for any hybrid; therefore, a modelling process was found which will suit all hybrids at all sites, retain a stan- dardized model coding and processes and change only the crop parameter file rather than change the way that photo- synthesis is represented in the model code for each hybrid. Since for this projects we had measured values of light interception, we extracted a direct relationship with cumu- lative degree days, therefore bypassing a previous calcula- tion for leaf area in the model, and that a single relationships could be used for each hybrid that was applicable at each site. This simplified the model and avoided using environ- mental influences in the algorithm (temperature, water and light), although their direct effects were reflected in estab- lishment levels of the plant, canopy closure and light inter- ception, but not as a variable within the 2-­week measuring frequency as was required for predicting measured RUE. 3.4.1  |  A note on invasiveness The M. sin × sin hybrid was the only hybrid to reach flow- ering at all four locations (Magenau et al., 2022); however, 14  |      SHEPHERD et al. TABLE 6  European Projections for Annual Harvest Yield, Energy Produced and Carbon Capture and Storage Potentials over climate period 2020–­2030, over 15.7 Mha area including land constraints based on 10% grassland, 10% arable conversion. Harvest yield Mt year−1 (SD) Electrical energy produced EJ year−1 Carbon capture Mt year−1 M. × sin × sin 87.19 (0.051) 1.30 39.24 M × g 81.28 (0.048) 1.20 36.57 Seeded M. sac × sin ‘Aphrodite’—­all site calibration 80.72 (0.047) 1.20 36.32 Seeded M. sac × sin ‘Aphrodite’ potential—­best site calibration 89.66 (0.052) 1.34 40.36 Rhizome M. sac × sin ‘Athena’ 89.66 (0.052) 1.34 40.35 Abbreviations: M × g: Miscanthus × giganteus; M. sac × sin: Miscanthus sacchariflorus × sinensis; M. sin × sin: Miscanthus sinensis × sinensis. 14  |      SHEPHERD et al. TABLE 6  European Projections for Annual Harvest Yield, Energy Produced and Carbon Capture and Storage Potentials over climate period 2020–­2030, over 15.7 Mha area including land constraints based on 10% grassland, 10% arable conversion. Harvest yield Mt year−1 (SD) Electrical energy produced EJ year−1 Carbon capture Mt year−1 M. × sin × sin 87.19 (0.051) 1.30 39.24 M × g 81.28 (0.048) 1.20 36.57 Seeded M. sac × sin ‘Aphrodite’—­all site calibration 80.72 (0.047) 1.20 36.32 Seeded M. sac × sin ‘Aphrodite’ potential—­best site calibration 89.66 (0.052) 1.34 40.36 Rhizome M. sac × sin ‘Athena’ 89.66 (0.052) 1.34 40.35 Abbreviations: M × g: Miscanthus × giganteus; M. sac × sin: Miscanthus sacchariflorus × sinensis; M. sin × sin: Miscanthus sinensis × sinensis. If it were also possible to link onto other projects such as the PBC4GGR, carbon fluxes will be combined with similar measurements to this study to understand the dynamics of RUE, which could provide further information on the dynamics of photosynthesis and respiration. Nevertheless, to see the limitations is not to downplay the successes of the field trials and the modelling. The GRACE project field trials developed phenological proto- cols and trained international teams to collect data that can used to assess light interception and conversion and is a particular benefit of European projects. The modelling found generic equations for light interception dynamics with thermal time despite the different site conditions. In summary, the benefit of applying a relationship be- tween light interception measurement and degree days is that it is dynamic through the season, reduces uncer- tainty, is easier to measure in the field, and for calibra- tion standardizes weather variation between field sites, with differences being largely phenotypic based. Using light interception-­degree day curves includes variation between hybrids in phenological timing. Calibrating data against standing crop biomass includes different rates of leaf litter drop between hybrids. A conservative model, calibrated by crops of varying establishment and varying maturity, accompanied by out- put resulting from a calibration showing the potential of a well-­established mature crop, is a more realistic predic- tor of a variable landscape when spatial aggregations are required. It is projected that 10% land use conversion of less productive grassland and arable with seeded hybrids could provide 1.3 exajoule of power annually in Europe, where 1 exajoule is equivalent to 174 million barrels of oil (Koppelaar, 2012). Less productive land in temperate climates and time to maturity are linked, with crops establishing slower and take longer to maturity, for example. at TWS 4–­5 year is required for full establishment of miscanthus (pers. comm. Professor John Clifton-­Brown). Thus, a longer funded period for the project measurements would have been desirable with a five growing season project. A com- mon assumption in modelling is that crops are mature, when in reality aggregating spatial yield in the landscape includes crops at varying age and yield potential and therefore lowers the accumulated total, which is why a conservative projection is a realistic predictor. on meta-­analysis work in the United States, Sharma et al. (2022) show, M × g yield increases at a decreasing rate till the seventh year, beyond which, yield starts de- creasing at an increasing rate. However, work in the UK by Shepherd, Clifton-­Brown, et al. (2020) shows M × g yields to continue increasing at a decreasing rate to 10 years and beyond with expanding rhizome and infilling of crop stems. Regarding the 2-­week sampling frequency of the crop biomass and light interception measurements, frequency is limited by manpower but nuanced details can be lost easily especially at the temporal resolution of 2-­weekly biomass. It is however important to keep in mind the novelty of this project and the scale and coor- dination across several European sites and field teams to achieve simultaneous sampling across the season was an ambitious undertaking. The development of miscanthus varies by climate zone. Third-­year miscanthus will be ma- ture in southern Europe while still developing in temper- ate latitudes. This means that we are inevitably dealing with a varying development of crops that we calibrate over Europe locations and climate zones, and also dealing with a variation of crop establishment level. The standard de- viation map of simulated harvest yield will also show a high variability in areas prone to higher soil water deficit and variable soil types and quality. This is a project to de- termine the potential for miscanthus on less productive lands, calibrations from field measurements will produce projections of yields lower than the those obtained on prime arable land. However, on prime land best agro- nomic practices are applied for the current commercial cultivar of miscanthus, these field measurements and projections are ambitious, newly developed and best agro- nomic practices have yet to be developed. Ongoing work is needed to develop agronomic methods for the best es- tablishment and least risk to the seeded hybrids, since this holds potential for improved yield over the current com- mercial crop plus improved plant upscaling. Agronomy for seeded M. sac × sin is currently being investigated in the UK by the Perennial Biomass Crops 4 Greenhouse Gas Reduction (PBC4GGR) project. The next steps could be to repeat the measurements a later year in a follow on project, using the same plus ad- ditional locations. This is particularly important regard- ing plant maturity. 4.1  |  Model and measurement limits and next steps These calibrations result in conservative model estimates based on third-­year field trial measurements. Based SHEPHERD et al. 15 on meta-­analysis work in the United States, Sharma et al. (2022) show, M × g yield increases at a decreasing rate till the seventh year, beyond which, yield starts de- creasing at an increasing rate. However, work in the UK by Shepherd, Clifton-­Brown, et al. (2020) shows M × g yields to continue increasing at a decreasing rate to 10 years and beyond with expanding rhizome and infilling of crop stems. Regarding the 2-­week sampling frequency of the crop biomass and light interception measurements, frequency is limited by manpower but nuanced details can be lost easily especially at the temporal resolution of 2-­weekly biomass. It is however important to keep in mind the novelty of this project and the scale and coor- dination across several European sites and field teams to achieve simultaneous sampling across the season was an ambitious undertaking. The development of miscanthus varies by climate zone. Third-­year miscanthus will be ma- ture in southern Europe while still developing in temper- ate latitudes. This means that we are inevitably dealing with a varying development of crops that we calibrate over Europe locations and climate zones, and also dealing with a variation of crop establishment level. The standard de- viation map of simulated harvest yield will also show a high variability in areas prone to higher soil water deficit and variable soil types and quality. This is a project to de- termine the potential for miscanthus on less productive lands, calibrations from field measurements will produce projections of yields lower than the those obtained on prime arable land. However, on prime land best agro- nomic practices are applied for the current commercial cultivar of miscanthus, these field measurements and projections are ambitious, newly developed and best agro- nomic practices have yet to be developed. Ongoing work is needed to develop agronomic methods for the best es- tablishment and least risk to the seeded hybrids, since this holds potential for improved yield over the current com- mercial crop plus improved plant upscaling. Agronomy for seeded M. sac × sin is currently being investigated in the UK by the Perennial Biomass Crops 4 Greenhouse Gas Reduction (PBC4GGR) project. Less productive land in temperate climates and time the spatial limit of the databases and the components of the land mask do not allow us to view variation between fields, maps only allow for regional viewing at a 1  km resolution. 1707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and impact of centralized versus distributed BECCS with domestic biomass production in Great Britain. GCB Bioenergy, 11, 1234–­ 1252. https://doi.org/10.1111/gcbb.12630 doi.org/10.1111/gcbb.13026 Buettner, G. (2014). CORINE land cover and land cover change products. In I. Manakos & M. Braun (Eds.), Land use and land cover mapping in Europe: Practices & trends. Remote sensing and digital image processing (pp. 55–­74). Springer. Christian, D. G., Riche, A. B., & Yates, N. E. (2008). Growth, yield and mineral content of Miscanthus × giganteus grown as a bio- fuel for 14 successive harvests. Industrial Crops and Products, Clifton-­Brown, J., Harfouche, A., Casler, M. D., Dylan Jones, H., Macalpine, W. J., Murphy-­Bokern, D., Smart, L. B., Adler, A., Ashman, C., Awty-­Carroll, D., Bastien, C., Bopper, S., Botnari, V., Brancourt-­Hulmel, M., Chen, Z., Clark, L. V., Cosentino, S., Dalton, S., Davey, C., … Lewandowski, I. (2019). Breeding progress and preparedness for mass-­scale deployment of pe- rennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar. GCB Bioenergy, 11, 118–­151. https://doi. org/10.1111/gcbb.12566 Clifton-­Brown, J., Harfouche, A., Casler, M. D., Dylan Jones, H., Macalpine, W. J., Murphy-­Bokern, D., Smart, L. B., Adler, A., ORCID Anita Shepherd  https://orcid.org/0000-0003-1902-5147 Danny Awty-­Carroll  https://orcid. org/0000-0001-5855-0775 Chris Ashman  https://orcid.org/0000-0001-5736-6327 Elena Magenau  https://orcid.org/0000-0003-3859-9402 Mislav Kontek  https://orcid.org/0000-0001-9042-5499 Andrea Ferrarini  https://orcid. org/0000-0001-9390-7004 Mohamad Al Hassan  https://orcid. org/0000-0002-2297-3394 Jon McCalmont  https://orcid.org/0000-0002-5978-9574 Luisa Trindade  https://orcid.org/0000-0003-1541-2094 Rebecca Rowe  https://orcid.org/0000-0002-7554-821X Andreas Kiesel  https://orcid.org/0000-0003-0806-2532 John Clifton-­Brown  https://orcid. org/0000-0001-6477-5452 Anita Shepherd  https://orcid.org/0000-0003-1902-5147 Danny Awty-­Carroll  https://orcid. org/0000-0001-5855-0775 Chris Ashman  https://orcid.org/0000-0001-5736-6327 Elena Magenau  https://orcid.org/0000-0003-3859-9402 Mislav Kontek  https://orcid.org/0000-0001-9042-5499 Andrea Ferrarini  https://orcid. org/0000-0001-9390-7004 Mohamad Al Hassan  https://orcid. org/0000-0002-2297-3394 Jon McCalmont  https://orcid.org/0000-0002-5978-9574 Luisa Trindade  https://orcid.org/0000-0003-1541-2094 Rebecca Rowe  https://orcid.org/0000-0002-7554-821X Andreas Kiesel  https://orcid.org/0000-0003-0806-2532 John Clifton-­Brown  https://orcid. org/0000-0001-6477-5452 A tl H ti htt // id /0000 0001 9863 7613 Clifton-­Brown, J. C., Neilson, B., Lewandowski, I., & Jones, M. B. (2000). The modelled productivity of Miscanthus × giganteus (Greef et Deu.) in Ireland. Industrial Crops and Products, 12, 97–­109. Clifton-­Brown, J. C., Stampfl, P. F., & Jones, M. B. (2004). Miscanthus biomass production for energy in Europe and its potential con- tribution to decreasing fossil fuel carbon emissions. Global Change Biology, 10, 509–­518. Davey, C. L., Jones, L. E., Squance, M., Purdy, S. J., Maddison, A. L., Cunniff, J., Donnison, I., & Clifton-­Brown, J. (2017). Radiation capture and conversion efficiencies of Miscanthus sacchariflo- rus, M. sinensis and their naturally occurring hybrid M. × gi- ganteus. GCB Bioenergy, 9, 385–­399. https://doi.org/10.1111/ gcbb.12331 Astley Hastings  https://orcid.org/0000-0001-9863-7613 Davey, C. L., Robson, P., Hawkins, S., Farrar, K., Clifton-­Brown, J. C., Donnison, I. S., & Slavov, G. T. (2017). Genetic relationships be- tween spring emergence, canopy phenology, and biomass yield increase the accuracy of genomic prediction in Miscanthus. Journal of Experimental Botany, 68(18), 5093–­5102. https://doi. /10 1093/j b/ 339 DATA AVAILABILITY STATEMENT The data that support the findings of this study are avail- able from the corresponding author upon reasonable request. Clifton-­Brown, J., Hastings, A., Mos, M., McCalmont, J. P., Ashman, C., Awty-­Carroll, D., Cerazy, J., Chiang, Y.-­C., Cosentino, S., Cracroft-­Eley, W., Scurlock, J., Donnison, I. S., Glover, C., Gołąb, I., Greef, J. M., Gwyn, J., Harding, G., Hayes, C., Helios, W., … Flavell, R. (2017). Progress in upscaling Miscanthus bio- mass production for the European bio-­economy with seed-­ based hybrids. GCB Bioenergy, 9, 6–­17. https://doi.org/10.1111/ gcbb.12357 CONFLICT OF INTEREST The authors have no conflicts of interest to declare. The authors have no conflicts of interest to declare. ACKNO​WLE​DGE​MENTS We would like to thank the industry partner Terravesta, developers of Miscanthus throughout the UK, the Dutch company Van Dinter Semo, developers of M. sin × sin hybrids, and all collaborators and the members of the GRACE project funded by the Bio-­based Industries Joint Undertaking, grant agreement no. 745012. The authors thank EPSRC, BBSRC and UK Supergen Bioenergy Hub (EP/S000771/1) who funded and supported this research. The work was made possible by a Supergen Bioenergy hub fellowship, funding ref. RG15855—­UKRI (EPSRC) via Aston University and the survey was carried out as part of project SUMMER—­seed-­propagated upscaling of Miscanthus—­modelling and environmental response. This work was also made possible by BBSRC funding (BB/V011553/1) for the Perennial Biomass Crops for Greenhouse Gas Removal (PBC4GGR) Demonstrator pro- ject, and was also undertaken as part of the UK Energy Research Centre research programme. 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Resil​ience.Org (Online Articles). February 16, 2012. https://www.resil​ience.org/stori​es/2012-­02-­16/world​-­energ​y-­ consu​mptio​n-­beyon​d-­500-­exajo​ules/ Lewandowski, I., Clifton-­Brown, J., Trindade, L. M., van der Linden, G. C., Schwarz, K. U., Müller-­Sämann, K., Anisimov, A., Chen, C. L., Dolstra, O., Donnison, I. S., Farrar, K., Fonteyne, S., Harding, G., Hastings, A., Huxley, L. M., Iqbal, Y., Khokhlov, N., Kiesel, A., Lootens, P., … Kalinina, O. (2016). Progress on optimizing miscanthus biomass production for the European bioeconomy: Results of the EU FP7 project OPTIMISC. Frontiers in Plant Science, 7, 1620. https://doi. org/10.3389/fpls.2016.01620 Rosenberger, A., Kaul, H.-­P., Senn, T., & Aufhammer, W. (2002). Costs of bioethanol production from winter cereals: The ef- fect of growing conditions and crop production intensity levels. Industrial Crops and Products, 15, 91–­10. https://doi. org/10.1016/S0926​-­6690(01)00099​-­1 Scarlat, N., Dallemand, J. F., Monforti-­Ferrario, F., & Nita, V. (2015). 17571707, 0, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/0 SHEPHERD et al. 17 |  17 expansion for climate change mitigation explored using land surface, agronomic and integrated assessment models. GCB Bioenergy, 1–­16. https://doi.org/10.1111/gcbb.12982 REFERENCES Albanito, F., Hastings, A., Fitton, N., Richards, M., Martin, M., MacDowell, N., Bell, D., Taylor, S. C., Butnar, I., Li, P.-H., Slade, R., & Smith, P. (2019). Mitigation potential and environmental Albanito, F., Hastings, A., Fitton, N., Richards, M., Martin, M., MacDowell, N., Bell, D., Taylor, S. C., Butnar, I., Li, P.-H., Slade, R., & Smith, P. (2019). Mitigation potential and environmental org/10.1093/jxb/erx339 Farage, P. K., Blowers, D., Long, S. P., & Baker, N. R. (2006). Low growth temperatures modify the efficiency of light use by photosystem II for CO2 assimilation in leaves of two chilling-­ tolerant C4 species, Cyperus longus L. and Miscanthus × gigan- teus. Plant, Cell & Environment, 29, 720–­728. expansion for climate change mitigation explored using land surface, agronomic and integrated assessment models. GCB Bioenergy, 1–­16. https://doi.org/10.1111/gcbb.12982 expansion for climate change mitigation explored using land surface, agronomic and integrated assessment models. GCB Bioenergy, 1–­16. https://doi.org/10.1111/gcbb.12982 18  | 18 SHEPHERD et al. and drawbacks of the bioenergy crop. GCB Bioenergy, 14, 1205–­ 1218. https://doi.org/10.1111/gcbb.12997 Shepherd, A., Clifton-­Brown, J., Kam, J., Buckby, S., & Hastings, A. (2020). Commercial experience with miscanthus crops: Establishment, yields and environmental observations. GCB Bioenergy, 12, 510–­523. https://doi.org/10.1111/gcbb.12690 Wieder, W. R., Boehnert, J., Bonan, G. B., & Langseth, M. (2014). Regridded harmonized world soil database v1.2. Data set. http:// daac.ornl.gov. https://doi.org/10.3334/ORNLD​AAC/1247 Shepherd, A., Littleton, E., Clifton-­Brown, J., Martin, M., & Hastings, A. (2020). Projections of global and UK bioenergy potential from Miscanthus × giganteus –­ Feedstock yield, carbon cycling and electricity generation in the 21st century. GCB Bioenergy, 12, 287–­305. https://doi.org/10.1111/gcbb.12671 Zimmerman, J., Styles, D., Hastings, A., Dauber, J., & Jones, M. B. (2013). Assessing the impact of within crop heterogeneity (“patchiness”) in young Miscanthus × giganteus fields on eco- nomic feasibility and soil carbon sequestration. GCB Bioenergy, 6, 566–­576. https://doi.org/10.1111/gcbb.12084 Shepherd, A., Martin, M., & Hastings, A. (2021). Uncertainty of modelled bioenergy with carbon capture and storage due to variability of input data. GCB Bioenergy, 13, 691–­707. https:// doi.org/10.1111/gcbb.12803 Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/gcbb.13029 by LIVERPOOL JOHN MOORES UNIV, Wiley Online Library on [13/02/2023]. See the Terms and Con The role of biomass and bioenergy in a future bioeconomy: Policies and facts. Environmental Development, 15, 3–­34. https://doi.org/10.1016/j.envdev.2015.03.006 Lewandowski, I., Clifton-­Brown, J. C., Scurlock, J. M. O., & Huisman, W. (2000). Miscanthus: European experience with a novel en- ergy crop. Biomass and Bioenergy, 19(4), 209–­227. https://doi. org/10.1016/S0961​-­9534(00)00032​-­5 Sharma, B. P., Zhang, N., Lee, D., Heaton, E., Delucia, E. H., Sacks, E. J., Kantola, I. B., Boersma, N. N., Long, S. P., Voigt, T. B., & Khanna, M. (2022). Responsiveness of miscanthus and switch- grass yields to stand age and nitrogen fertilization: A meta-­ regression analysis. GCB Bioenergy, 14, 539–­557. https://doi. Littleton, E. W., Shepherd, A., Harper, A. B., Hastings, A. F. S., Vaughan, N. E., Doelman, J., van Vuuren, D. P., & Lenton, T. M. (2022). Uncertain effectiveness of Miscanthus bioenergy 18 SUPPORTING INFORMATION Additional supporting information can be found online in the Supporting Information section at the end of this article. Sieber, A.-­N., Würschum, T., & Longin, C. F. H. (2014). Evaluation of a semi-­controlled test as a selection tool for frost tolerance in durum wheat (Triticum durum). Plant Breeding, 133, 465–­469. https://doi.org/10.1111/pbr.12181 Tóth, G., Hermann, T., Da Silva, M., & Montanarella, L. (2016). Heavy metals in agricultural soils of the European Union with implications for food safety. Environment International, 88, 299–­309. https://doi.org/10.1016/j.envint.2015.12.017 How to cite this article: Shepherd, A., Awty-­ Carroll, D., Kam, J., Ashman, C., Magenau, E., Martani, E., Kontek, M., Ferrarini, A., Amaducci, S., Davey, C., Jurišić, V., Petrie, G.-J., Al Hassan, M., Lamy, I., Lewandowski, I., de Maupeou, E., McCalmont, J., Trindade, L., van der Cruijsen, K. … Hastings, A. (2023). Novel Miscanthus hybrids: Modelling productivity on marginal land in Europe using dynamics of canopy development determined by light interception. GCB Bioenergy, 00, 1–18. https://doi.org/10.1111/gcbb.13029 How to cite this article: Shepherd, A., Awty-­ Carroll, D., Kam, J., Ashman, C., Magenau, E., Martani, E., Kontek, M., Ferrarini, A., Amaducci, S., Davey, C., Jurišić, V., Petrie, G.-J., Al Hassan, M., Lamy, I., Lewandowski, I., de Maupeou, E., McCalmont, J., Trindade, L., van der Cruijsen, K. … Hastings, A. (2023). Novel Miscanthus hybrids: Modelling productivity on marginal land in Europe using dynamics of canopy development determined by light interception. GCB Bioenergy, 00, 1–18. https://doi.org/10.1111/gcbb.13029 United Nations/Framework Convention on Climate Change. (2015). Adoption of the Paris agreement, 21st conference of the parties. United Nations. van der Werf, H. M. G., Meijer, W. J. M., Mathijssen, E. W. J. M., & Darwinkel, A. (1992). Potential dry matter pro- duction of Miscanthus sinensis in The Netherlands. Industrial Crops and Products, 1(2–­4), 203–­210. https://doi. org/10.1016/0926-­6690(92)90020​-­V von Hellfeld, R., Hastings, A., Kam, J., Rowe, R., Clifton-­Brown, J., Donnison, I., & Shepherd, A. (2022). Expanding the Miscanthus market in the UK: Growers in profile and experience, benefits
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The Cish SH2 domain is essential for PLC-γ1 regulation in TCR stimulated CD8+ T cells
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To cite this version: Geoffrey Guittard, Ana Dios-Esponera, Douglas C. Palmer, Itoro Akpan, Valarie A. Barr, et al.. The Cish SH2 domain is essential for PLC-gamma 1 regulation in TCR stimulated CD8(+) T cells. Scientific Reports, 2018, 8 (5336), ￿10.1038/s41598-018-23549-2￿. ￿hal-02143617￿ Distributed under a Creative Commons Attribution 4.0 International License The Cish SH2 domain is essential for PLC-γ1 regulation in TCR stimulated CD8+ T cells Geoffrey Guittard1,3, Ana Dios-Esponera1, Douglas C. Palmer2, Itoro Akpan1, Valarie A. Barr Asit Manna1, Nicholas P. Restifo2 & Lawrence E. Samelson1 Geoffrey Guittard1,3, Ana Dios-Esponera1, Douglas C. Palmer2, Itoro Akpan1, Valarie A. Barr1, Asit Manna1, Nicholas P. Restifo2 & Lawrence E. Samelson1 Received: 23 November 2017 Accepted: 6 March 2018 Published: xx xx xxxx Cish, participates within a multi-molecular E3 ubiquitin ligase complex, which ubiquitinates target proteins. It has an inhibitory effect on T cell activation mediated by PLC-γ1 regulation, and it functions as a potent checkpoint in CD8+ T cell tumor immunotherapy. To study the structural and functional relationships between Cish and PLC-γ1 during CD8+ T cell activation, we tested mutants of the Cish-SH2 (R107K) and D/BC (L222Q, C226Q) domains. We confirmed that Cish-SH2-specific binding was essential for PLC-γ1 ubiquitination and degradation. This domain was essential for the Cish-mediated inhibition of Ca2+ release upon TCR stimulation. No effect on inhibition of cytokine release was observed with SH2 or D/BC mutants, although the absence of Cish led to an increased release of IFN-γ and TNF-α. Using imaging we showed that Cish was expressed mostly in the cytoplasm and we did not see any Cish clustering at the plasma membrane upon stimulation. We conclude that the Cish-SH2 domain is essential for PLC-γ1 regulation in TCR-stimulated CD8+ T cells. Cish (cytokine-inducible SH2 containing protein) belongs to the SOCS (Suppressor of Cytokine signaling) fam- ily of E3-ligases. Emerging evidence indicates that SOCS family members can play critical roles in both innate and adaptive immune responses by mediating negative-feedback inhibition of cytokine signaling1. Lack of Cish expression in cytotoxic CD8+ T cells and NK cells improves their anti-tumor properties2–4. Understanding the precise molecular mechanisms for Cish function is thus of great interest and might suggest possibilities for new targeted cancer therapies. g p We previously observed that Cish is expressed following T cell antigen receptor (TCR) stimulation2. We also showed that Cish is involved in negative regulation of TCR signaling. Cish can bind PLC-γ1 constitutively and negatively regulates its phosphorylation and activation. This interaction leads to PLC-γ1 ubiquitination and sub- sequent degradation. Thus our data identified Cish as a new key negative regulator of TCR signaling and immune function2.h There are eight SOCS family members, SOCS1–7 and Cish. HAL Id: hal-02143617 https://amu.hal.science/hal-02143617v1 Submitted on 28 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 www.nature.com/scientificreports www.nature.com/scientificreports Received: 23 November 2017 Accepted: 6 March 2018 Published: xx xx xxxx Materials and Methods Cells and culture. 293 T Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supple- mented with 10% fetal bovine serum, and 1% penicillin-streptomycin. Cells were incubated at 37 °C in 5% CO2. E6-1 Jurkat cell lines were cultured in RPMI supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin. mented with 10% fetal bovine serum, and 1% penicillin streptomycin. Cells were incubated at 37  C in 5% CO2. E6-1 Jurkat cell lines were cultured in RPMI supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin. Mice. Cish−/− mice were generated and genotyped, as previously described2. Mice were housed according to the guidelines of the Animal Care and Use Committee at the National Institutes of Health (NIH). Transfection 293 T cells. 293 T cells were transfected using a calcium-phosphate transfection method. Briefly, for transfection, 2.5 × 106 cells were plated 24 hrs prior to transfection in a 10-cm dish. On the day of transfection, a 500 μL aqueous mixture of DNA (5 μg max per construct plus pcDNA3 empty vector, to reach 20 μg total DNA per dish) and CaCl2 (62 μl of 2M CaCl2) was added dropwise to 500 μL of 2X HBS (42 mM HEPES, 274 mM Nacl, 10 mM KCL, 1.8 mM Na2PO4) (pH 6.95–7.00). 10 mL of fresh medium was then added to the 293 T cells, and the HBS/DNA mixture was added dropwise to the cells. 24 hrs later the medium was replaced with 10 mL of fresh media. Cloning. The Cish WT expression retroviral vector has already been described2 and encodes N-terminal Flag-tagged (3×) Cish, self-cleaving furin-2A (f2A) peptide, and congenic marker Thy1.1 driven by the intrinsic LTR promoter. We generated the SH2 domain R107K10 and the SOCS-Box D/BC (L222Q, C226Q) mutations11 in the same backbone vector (Genesynthesis Company). Cish and Cish mutant constructs were expressed in pmTur- quoise2-C1 (Addgene #6056012) vectors (Kind gift of Dorus Gadella). In-fusion kit from Clontech was used and cloning was performed according to manufacturer’s instructions. Transfection of Jurkat cells, fixation and immunostaining. Jurkat T cells were transfected using the Amaxa T-kit. Cells were allowed to spread on coverslips as described earlier13. Briefly, poly-lysine cov- ered four-chambered glass coverslips (LabTek II, Nunc/Nalgene) were coated with 10 μg/ml of antibody (anti-CD3-Ucht1) from BD Pharmigen (custom concentration of Catalog # 550367). Materials and Methods The chambers were loaded with 300 μl of normal media without phenol red supplemented with 25 mM HEPES, pH 7.0, and warmed. Cells were resuspended in the same buffer, plated into the bottom of the chamber and incubated at 37 °C. After 3 min, cells were fixed in 2.4% paraformaldehyde for 30 min. The cells were permeabilized with TritonX-100, incubated with blocking buffer for 30 min and then incubated with primary antibodies for 60 min, followed by washes and 60 min incubation with either mouse isotype specific or anti-rabbit Alexa conjugated secondary antibod- ies (ThermoFisher Grand Island NY). Primary antibodies used for immunostaining: pLAT 132 - rabbit poly- clonal IgG from Invitrogen (Catalog # 44–224) - used at 4.38 μg/ml, pY (4G10) - mouse monoclonal IgG2B from Millipore (Catalog # 05–321) - used at 1.1 μg/ml. Secondary antibodies used for immunostaining: Alexa Fluor 647 - goat anti mouse monoclonal IgG2B from Thermo Fisher Scientific (Catalog # A21242) - used at 4 μg/ml, Alexa Fluor 568 - goat anti rabbit IgG from Thermo Fisher Scientific (Catalog #A11036) - used at 2 μg/ml. Imaging. Confocal imaging was performed as previously described14. Microscope images of fixed cells were captured using a Leica SP8 laser-scanning confocal microscope using a 63×, 1.4 numerical aperture (NA) objec- tive (Leica Microsystems Inc, Buffalo Grove IL). 2- to 3-μm z-stacks with a spacing of 0.3 μm were taken of the area contacting the coverslip. Image processing. Leica AF software was used to produce images of fixed cells. Adobe PhotoShop and Illustrator (Adobe Systems Inc, San Jose CA) were used to prepare composite figures. Scale bars were cut from the original images and then were pasted in a more visible position on the final composite image. T cell transduction. Retroviral T cells transduction was performed as previously described2. Briefly, WT and CISH KO CD8+ T-cell blasts were obtained from lymph nodes by negative selection (Mouse CD8+ T cell Isolation Kit, STEM CELL, #19853) and activated with 2 μg/ml CD3, 2 μg/ml CD28 mAbs and 100 U IL2 for 1 day. The virus-containing supernatant form Plat-E packaging cells was added to 24-well non-tissue culture treated plates coated with Retronectin and anti-CD3 mAb and then centrifuged at 2500 rpm at 32 °C for 120 min. Viral particles were removed and then T-cell blasts were added in regular medium containing IL-2. The Cish SH2 domain is essential for PLC-γ1 regulation in TCR stimulated CD8+ T cells Each of these proteins has a conserved struc- ture with a central Src homology 2 (SH2) domain, an amino-terminal domain of variable length and a carboxy-terminal 40-amino-acid module known as the SOCS box. The SOCS box interacts with several ubiq- uitination machinery enzymes: elongin B/C, cullins, ring-box 2 (Rbx2) and an E2 ubiquitin transferase1. This complex forms an E3 ubiquitin ligase complex. Thus SOCS proteins exert their inhibitory role by mediating protein degradation. The central SH2 domain appears critical for binding target molecules, thereby enabling the E2-E3 complex to ubiquitinate them5. Cish was the first identified member of the SOCS family. It was discovered as a gene product induced in response to various cytokines (IL-2, 3, 5 and EPO) that activate STAT56,7. Cish was shown to bind via its SH2 domain to cytokine receptors after ligand-mediated phosphorylation8,9. Cish can act as a negative-feedback regulator of the STAT5 pathway by binding in this manner, thereby masking STAT5 docking sites9,10. 1Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, 20892-4256, USA. 2Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Building 10/CRC, Room 3W-3840, Bethesda, MD, 20892, USA. 3Present address: INSERM, U1068, CNRS UMR7258, Aix-Marseille Université UM105, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, 13009, Marseille, France. Geoffrey Guittard and Ana Dios- Esponera contributed equally to this work. Correspondence and requests for materials should be addressed to G.G. (email: geoffrey.guittard@inserm.fr) or L.E.S. (email: SamelsonL@mail.nih.gov) SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 1 www.nature.com/scientificreports/ In order to define the structural and functional relationships between Cish and PLC-γ1 during CD8+ T cell activation, we used both SH2 domain (Cish SH2*) and D/BC SOCS box (Cish D/BC*) Cish mutants to check for their impact on PLC-γ1 and CD8+ T cell function. Underlying our study is our desire to identify a dominant negative mutant of Cish, which would be of great interest to understand more precisely the regulation of Cish and might give some insight into approaches that would specifically target Cish for inhibition. www.nature.com/scientificreports/ www.nature.com/scientificreports/ material was pre-cleared with 4 μg of normal mouse IgG bound to 20 μl of Protein A/G Plus-Agarose beads (Santa Cruz Biotechnology) for 1 hr at 4 °C. The precleared samples were incubated with 4 μg of the indicated antibody (FLAG M2, Cish, GFP or PLC-γ1) previously conjugated to 30 μl Protein A/G Plus-Agarose beads. After incuba- tion for 2 hr at 4 °C, the immunoprecipitates were washed three times with ice-cold lysis buffer. p p yf Transduced CD8+ T cells, prior to simulation, were rested overnight in regular RPMI medium (supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 50 μM β-mercaptoethanol). For ubiquitination experiments, 293 T cells were treated for 4 hrs with proteasome inhibitor MG-132 at 20 mM (Calbiochem #474790). Samples were resolved by 10% SDS–polyacrylamide gel electrophoresis or 5% gels for ubiquitinyl- ation experiments. Blots were incubated overnight at 4 °C with the corresponding primary antibody directed against ZAP-70 (Cell Signaling Technology #2705), β-actin (Cell Signaling Technology #4970), CISH (Cell Signaling Technology #8731), PLC-γ1 (Cell Signaling Technology #2822). For immunoprecipitations, PLC-γ1 (Santa Cruz Biotechnology #sc-7290), ubiquitin (Santa Cruz Biotechnology #sc-8017), or FLAG M2 (Sigma #F3165 or anti-GFP (Roche# 11814460001) were used. GFP-HRP conjugate (Miltenyi biotec #120-002-105) and HA−Peroxidase (Sigma #H6533-1VL) were used for Western blotting. Blots were incubated with horseradish peroxidase–conjugated secondary antibodies (Millipore) for 1 hr at room temperature. ECL (enhanced chemi- luminescence; SuperSignal West Pico and SuperSignal West Femto, Pierce) was used to visualize protein bands, which were quantified with ImageJ software (NIH). Cytokine stimulation. Cultured T cells were restimulated for 6 hr with different concentrations of anti-CD3ε (#624092, BD Pharmingen) and 2 μg/ml anti-CD28 (#553294, BD Pharmingen) with addition of protein transport inhibitor (2 μl/ml, BD GolgiStop, #51-2092KZ, BD Biosciences). For intracellular staining, cells were surface stained with fixed LIVE/DEAD (Molecular Probes), then fixed and permeabilized (Cytofix/ Cytoperm Plus Fixation/Permeabilization kit, BD Biosciences) to evaluate intracellular cytokine production by flow cytometry with the following antibodies: antitumor necrosis factor-α-PE-Cy7 (1:300, #557644, eBioscience), anti-IFN-γ-Pacific blue (1:500, #487311, eBioscience) and anti-Thy1.1-APC (1:2000, (#202526, Biolegend). Cytometry. Cytometry was performed as previously described15. Cell acquisition was performed on FACSCalibur (Becton Dickinson, Franklin Lakes, NJ, USA) or LSRFortessa (BD Biosciences) flow cytometers. Data analysis was performed using FlowJo software (Tree Star, Inc., Ashland, OR, USA). Calcium flux measurement. www.nature.com/scientificreports/ Cells were incubated in RPMI containing 5 mM Indo-1 dye (#I1223, Invitrogen) and 0.5 mM Probenicid (#P8761, Sigma) for 45 min at 37 °C. Cells were washed with RPMI, re-suspended in RPMI, and incubated at 37 °C for 5 min before Ca2+ measurement. Biotinylated anti-CD3ε (5 μg/ ml) was added, and a baseline reading was taken for 30 sec before cross-linking with streptavidin (20 μg/ml). Samples were analyzed with an LSRFortessa (BD Biosciences) with a UV laser, and data were analyzed with FlowJo software. Calcium increases were monitored as the ratio of Indo-1 (blue) and (violet) emission, and dis- played as a function of time. Responses were quantified from three experiments using the area under curve (AUC) function of PrismGraph. Data availability. The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request. Data availability. The datasets generated during and/or analyzed during the current study are available from he corresponding author on reasonable request. Ethical approval and informed consent. Mice used in this manuscript were maintained under pathogen-free conditions at an American Association for the Accreditation of Laboratory Animal Care-accredited facility. Mice were housed in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health under animal study proposals approved by the NCI-Bethesda Animal Care and Use Committee (ASP#LCMB-013). Materials and Methods After a short centrifugation, 1500 rpm for 5 min, cells were used 3 days after the transduction. Cell, stimulation, lysis, immunoprecipitation and Western blotting analysis. For stimulation of naïve purified CD8+ T cells, cells were re-suspended in RPMI alone at 50 × 106 cells per 100 μL. CD8+ T cells were then incubated for 15 min at 4 °C with biotinylated anti-CD3ε (10 μg/mL 2C11 BD Pharmingen #553060). Cells were washed twice in RPMI, incubated with RPMI for 5 min at 37 °C, and then stimulated for the indicated time by adding streptavidin (20 μg/ml final concentration). After rapid centrifugation, cells were lysed at 4 °C for 10 min in 1% NP-40 lysis buffer (50 mM Tris pH 7.4, 150 mM NaCl, 5 mM EDTA, protease inhibitor cocktail [Roche# 11836170001], 1 mM Na3VO4, 0.1% SDS, adding 200 mM N-ethylmaleimide [NEM] for ubiquitinyla- tion experiments). Lysates were centrifuged at 13000 rpm for 10 min at 4 °C. For immunoprecipitation, soluble SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 2 Results Cish is expressed upon TCR stimulation and regulates PLC-γ1 expression. As previously described, the Cish protein is expressed at a very low amount at steady state and increases upon TCR stimulation2. To more precisely study Cish expression, we stimulated blast CD8+ T cells for the indicated times using increas- ing amounts of plate-bound antibody (Fig. 1A). Interestingly, Cish expression is maximal at 4 hrs of stimulation (Fig. 1A). Indeed, for all concentrations tested, a decrease in Cish expression is detected between 4 and 6 hrs. Using α-CD3 concentrations above 2 μg/ml does not seem to increase Cish expression. g μg p We also have showed that Cish is necessary for the ubiquitination of PLC-γ1 upon TCR activation2. In order to test the impact of Cish expression on PLC-γ1 degradation, we stimulated CD8+ T blast cells from WT or Cish KO mice using increasing amounts of plate-bound α-CD3 for 4hrs (Fig. 1B). As expected, we observed that PLC-γ1 expression decreased in the presence of Cish expression in WT CD8+ T cells (Fig. 1B,C) or in 293 T cells trans- fected with Cish and PLC-γ1 (Suppl. Figure 1). The expression of PLC-γ1 is higher in stimulated Cish KO CD8+ T cell compared to WT T cells, suggesting a direct effect of Cish on PLC-γ1 expression and the degradation that is dependent on TCR stimulation. Cish SH2 and D/BC domains are essential for PLC-γ1 ubiquitination. Each SOCS protein has a con- served structure with a central SH2 domain, an amino-terminal domain of variable length and a carboxy-terminal 40-amino-acid module that is known as the SOCS box. The central SH2 domain appears critical in binding target molecules, enabling the E2-E3 complex to ubiquitinate them, but the structural and functional relationships between Cish and PLC-γ1 during CD8+ T cell activation remain unknown5. To better understand the Cish domains required for its interaction with PLC-γ1 we used mutations known to disable the SH2 domain (R107K) or to disable the SOCS box D/BC domain (L222Q, C226Q)10,11 (Fig. 2A). Because we have previously learned SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 3 www.nature.com/scientificreports/ Figure 1. (A) and (B) Blast T cells from the indicated mice were stimulated with increasing concentration of anti-CD3 coated antibody during the indicated time. Cell lysates were analyzed by immunoblotting for Cish, PLC-γ1 and Zap-70 (Loading control). Numbers below the band indicate PLCγ1 expression quantification. (C) Quantification of PLC-γ1 expression from 3 experiments. Results Non-stimulated conditions represent 100% of PLC-γ1 expression. Bars show mean + SEM out of 3 independent experiments. Statistical significance was determined by two-tailed Student’s t test. *P ≤ 0.05. (NS = Non-stimulated). Figure 1. (A) and (B) Blast T cells from the indicated mice were stimulated with increasing concentration of anti-CD3 coated antibody during the indicated time. Cell lysates were analyzed by immunoblotting for Cish, PLC-γ1 and Zap-70 (Loading control). Numbers below the band indicate PLCγ1 expression quantification. (C) Quantification of PLC-γ1 expression from 3 experiments. Non-stimulated conditions represent 100% of PLC-γ1 expression. Bars show mean + SEM out of 3 independent experiments. Statistical significance was determined by two-tailed Student’s t test. *P ≤ 0.05. (NS = Non-stimulated). that PLC-γ1 was ubiquitinated in the presence of Cish we were able to test the effect of Cish mutant expres- sion on PLC-γ1 ubiquitination2. Cultured 293 T cells were transfected with a vector expressing Cish WT, Cish SH2* or Cish D/BC* and a vector expressing PLC-γ1-YFP and/or Ubiquitin-HA. We then immunoprecipitated PLC-γ1-YFP and blotted for HA (Fig. 2B). We observed that expression of the D/BC mutant decreased PLC-γ1 ubiquitination minimally compared to expression of Cish WT. However, expression of Cish containing the SH2 mutation resulted in a major decrease in the ubiquitination of PLC-γ1 (Fig. 2B). This result is consistent with a model whereby the SH2 domain is critically important for the ubiquitination of the targeted PLC-γ1. The Cish SH2 domain is essential for PLC-γ1 binding. To evaluate more precisely the question of how the domains of Cish affected its physical binding to PLC-γ1, we transfected 293 T cells with vectors expressing Cish WT, Cish SH2* or Cish D/BC* in combination with PLC-γ1-YFP. We then immunoprecipitated Cish from these cells and blotted for GFP (PLC-γ1) (Fig. 2C). These data revealed an interaction of Cish WT and D/BC* with PLC-γ1 but a decreased interaction between Cish SH2* and PLC-γ1 suggesting that the SH2 domain was required for optimal interaction between Cish and PLC-γ1. q p γ To study the Cish/ PLC-γ1 interaction in resting and stimulated T cells we transduced activated Cish KO CD8+ T cells with retroviral N-terminal FLAG-tagged construct expressing Cish WT, SH2* or D/BC*. After resting the transduced T cells we stimulated them with a α-CD3 antibody for five minutes and compared these cells with unstimulated T cells (Fig. 2D). Results To measure the physical interactions of Cish and PLC-γ1, we immuno- precipitated Cish using the Flag M2 antibody, performed electrophoresis and blotted for PLC-γ1. As observed in experiments with 293 T cells, the Cish WT protein and the D/BC* mutant interacted with PLC-γ1, but we clearly saw a decrease in PLC-γ1 binding to Cish with the SH2 mutation. We concluded that mutation of the SH2 domain of Cish, but not a mutation to the D/BC domain diminished the ability of Cish to physically interact with PLC-γ1. The Cish SH2 domain is essential for calcium release inhibition. Once activated, PLC-γ1 hydrolyses PtdIns (4,5)P2 to Inositol tri-phosphate (IP3) and diacylglycerol (DAG), which are responsible for intracellular Ca2+ release and PKC activation, respectively. To evaluate the impact of CISH WT, SH2* and D/BC* expression on calcium release from CD8+ T cells we reconstituted Cish KO CD8+ T cells with retroviruses expressing either an N-terminal FLAG-Cish WT, or Cish with SH2* or D/BC* mutations (Fig. 3A,B). We examined the impact of PLC-γ1–dependent changes in cytosolic Ca2+ flux upon TCR stimulation in these transduced CD8+ T cells SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 4 www.nature.com/scientificreports/ B. C. Cish YFP HA YFP 250 150 150 37 150 WCL IP YFP + + + + + + + + PLC-γ1 YFP HA-ub NT Cish WT Cish D/BC* Cish SH2* A. + + + + PLC-γ1 YFP NT Cish WT Cish D/BC* Cish SH2* Cish YFP YFP IP FLAG M2 WCL Cish KO background NT Cish WT Flag M2 Cish D/BC* Flag M2 Cish SH2* Flag M2 NS 5min NS 5 min NS 5min NS 5min CD3 10µg/ml IP Flag M2 WCL PLC-γ1 Cish PLC-γ1 Flag M2 100 37 100 37 150 150 37 D. 1 0.6 0.15 1 0.9 0.3 Figure 2. (A) Schematic diagram of Cish constructs used in our experiments. (B) 293 T cells were transfected with Tagged plasmids expressing PLC-γ1-YFP, Ubiquitin-HA, and Cish-FLAG constructs (WT, SH2* and D/ BC*) where indicated, in the presence of the proteasome inhibitor, MG-132. PLC-γ1-YFP (GFP antibody) was immunoprecipitated and blotted for HA and YFP. Whole-cell lysates were blotted for Cish and Cish and YFP PLC-γ1. Numbers below the band indicate PLCγ1 ubiquitin quantification. A value of 1 was arbitrarily set for PLCγ1 ubiquitination in the presence of the Cish WT construct. (C) Same as in (B) with no proteasome inhibitor, MG-132. Results (D) Immunoprecipitation of FLAG-tagged Cish and immunoblotting of PLC-γ1 and Cish, in indicated transduced CD8+ T cells with and without CD3 stimulation (5 min). Whole lysates were blotted for PLC-γ1 and Flag M2. Figure 2. (A) Schematic diagram of Cish constructs used in our experiments. (B) 293 T cells were transfected with Tagged plasmids expressing PLC-γ1-YFP, Ubiquitin-HA, and Cish-FLAG constructs (WT, SH2* and D/ BC*) where indicated, in the presence of the proteasome inhibitor, MG-132. PLC-γ1-YFP (GFP antibody) was immunoprecipitated and blotted for HA and YFP. Whole-cell lysates were blotted for Cish and Cish and YFP PLC-γ1. Numbers below the band indicate PLCγ1 ubiquitin quantification. A value of 1 was arbitrarily set for PLCγ1 ubiquitination in the presence of the Cish WT construct. (C) Same as in (B) with no proteasome inhibitor, MG-132. Cish (Flag M2) was immunoprecipitated and blotted for YFP (PLC-γ1) and Cish. Whole-cell lysates were blotted for YFP. Numbers below the band indicate PLCγ1 binding to Cish quantification, a value of 1 was arbitrarily set for PLCγ1 binding in the presence of the Cish WT construct. (D) Immunoprecipitation of FLAG-tagged Cish and immunoblotting of PLC-γ1 and Cish, in indicated transduced CD8+ T cells with and without CD3 stimulation (5 min). Whole lysates were blotted for PLC-γ1 and Flag M2. (Fig. 3A,B). As previously described, Cish KO CD8+ T cells transduced with an empty vector demonstrated an increase in Ca2+ release when compared to cells transduced with WT (Cish WT)2. This result confirmed that Cish WT constitutive expression was sufficient to inhibit Ca2+ release. Importantly, transduction of Cish SH2* in Cish KO CD8+ T cells failed to decrease Ca2+ release. This finding was consistent with the data shown above indicating the functional importance of the SH2 domain in binding PLC-γ1. Importantly, transduction of Cish WT and Cish D/BC* constructs in Cish KO CD8+ T cells had similar effects on PLC-γ1 as indicated by the Ca2+ decrease. These observations indicate that the SH2 domain of Cish is essential for Ca2+ release inhibition, most likely through PLC- γ1 binding. Cish SH2* and D/BC* do not impair cytokine inhibition. We already showed that Cish expression lead to a decreased release of certain cytokines such as IFN-γ and TNF-α in CD8+ T cells2. Results Cish (Flag M2) was immunoprecipitated and blotted for YFP (PLC-γ1) and Cish. Whole-cell lysates were blotted for YFP. Numbers below the band indicate PLCγ1 binding to Cish quantification, a value of 1 was arbitrarily set for PLCγ1 binding in the presence of the Cish WT construct. (D) Immunoprecipitation of FLAG-tagged Cish and immunoblotting of PLC-γ1 and Cish, in indicated transduced CD8+ T cells with and without CD3 stimulation (5 min). Whole lysates were blotted for PLC-γ1 and Flag M2. A. B. Cish YFP HA YFP 250 150 150 37 150 WCL IP YFP + + + + + + + + PLC-γ1 YFP HA-ub NT Cish WT Cish D/BC* Cish SH2* D. 1 0.6 0.15 C. Cish YFP 37 150 WCL + + + + PLC-γ1 YFP NT Cish WT Cish D/BC* Cish SH2* Cish YFP YFP IP FLAG M2 WCL Cish KO background NT Cish WT Flag M2 Cish D/BC* Flag M2 Cish SH2* Flag M2 NS 5min NS 5 min NS 5min NS 5min CD3 10µg/ml IP Flag M2 WCL PLC-γ1 Cish PLC-γ1 Flag M2 100 37 100 37 150 150 37 D. 1 0.9 0.3 D. C. Cish KO background + + + + PLC-γ1 YFP NT Cish WT Cish D/BC* Cish SH2* Cish YFP YFP IP FLAG M2 WCL 150 150 37 1 0.9 0.3 Figure 2. (A) Schematic diagram of Cish constructs used in our experiments. (B) 293 T cells were transfecte Figure 2. (A) Schematic diagram of Cish constructs used in our experiments. (B) 293 T cells were transfected with Tagged plasmids expressing PLC-γ1-YFP, Ubiquitin-HA, and Cish-FLAG constructs (WT, SH2* and D/ BC*) where indicated, in the presence of the proteasome inhibitor, MG-132. PLC-γ1-YFP (GFP antibody) was immunoprecipitated and blotted for HA and YFP. Whole-cell lysates were blotted for Cish and Cish and YFP PLC-γ1. Numbers below the band indicate PLCγ1 ubiquitin quantification. A value of 1 was arbitrarily set for PLCγ1 ubiquitination in the presence of the Cish WT construct. (C) Same as in (B) with no proteasome inhibitor, MG-132. Cish (Flag M2) was immunoprecipitated and blotted for YFP (PLC-γ1) and Cish. Whole-cell lysates were blotted for YFP. Numbers below the band indicate PLCγ1 binding to Cish quantification, a value of 1 was arbitrarily set for PLCγ1 binding in the presence of the Cish WT construct. Results (A) Representative Ca2+ flux as assessed by fluorometric evaluation after αCD3 stimulation of indicated transduced CD8+ T cells. Kinetic of the ratio indo-blue to indo-violet over time shown and assessed by flow cytometry. (B) Calcium responses were integrated and quantified relative to Cish WT+ empty vector. Error bars represent SD from the mean (n = 3). (C) To evaluate cells positive for intracellular expression of TNF-α or IFN-γ, indicated transduced CD8+ T cells were re-stimulated with anti-CD3 coated antibody (at indicated concentration) and soluble CD28 (2 μg/ml) in presence of Golgi stop for 6 hrs. Cells were then labeled for surface Thy1.1 and intracellular TNF-α or IFN-γ. The flow cytometry analysis of Thy1.1+ T cell populations is shown. (D) Absolute cell numbers of Thy1.1+ T cells positive for intracellular TNF-α or IFN-γ. Bars show mean + SEM out of at least 4 independent experiments. Statistical significance was determined by two-tailed Student’s t test. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. (NS = Non-stimulated). 0.24 19.0 20.3 60.5 0 102 103 104 0 -10 2 102 103 TNF-α Cish KO + empty 0.49 9.86 12.3 77.4 0 102 103 104 0 -10 2 102 103 0.45 7.57 10.6 81.3 0 102 103 104 0 -10 2 102 103 Cish KO + Cish D/BC* Cish KO + Cish SH2* 0.44 8.73 12.5 78.4 0 102 103 104 0 -10 2 102 103 0 -10 2 102 103 0.45 7.57 10.6 81.3 0 102 103 104 0 -10 2 102 103 IFN-γ Cish KO + Cish WT Cish KO + Cish D/BC* Cish KO + Cish D/BC* D. D. Figure 3. (A) Representative Ca2+ flux as assessed by fluorometric evaluation after αCD3 stimulation of Figure 3. (A) Representative Ca2+ flux as assessed by fluorometric evaluation after αCD3 stimulation of indicated transduced CD8+ T cells. Kinetic of the ratio indo-blue to indo-violet over time shown and assessed by flow cytometry. (B) Calcium responses were integrated and quantified relative to Cish WT+ empty vector. Error bars represent SD from the mean (n = 3). (C) To evaluate cells positive for intracellular expression of TNF-α or IFN-γ, indicated transduced CD8+ T cells were re-stimulated with anti-CD3 coated antibody (at indicated concentration) and soluble CD28 (2 μg/ml) in presence of Golgi stop for 6 hrs. Cells were then labeled for surface Thy1.1 and intracellular TNF-α or IFN-γ. Results To evaluate the impact of CISH WT, SH2* and D/BC* expression on cytokine expression, we again reconstituted Cish KO CD8+ T cells with a retrovirus expressing N-terminal FLAG-Cish WT, SH2* or D/BC*. We then stimulated cells with plate-bound α-CD3 and soluble α-CD28 for 6 hrs, and checked by FACS for intracellular expression of IFN-γ and TNF-α (Fig. 3C,D). We observed a decrease in IFN-γ and TNF-α expression in Cish KO CD8+ T cells expressing either Cish WT, Cish D/BC* or Cish SH2* constructs compared to Cish KO T cells transduced with an empty vector (Fig. 3C,D). At low-dose of anti-CD3 stimulation (0.1 μg/ml), there was little difference in cytokine inhi- bition between cells expressing Cish WT or Cish D/BC* for production of either cytokine. However, expression SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 5 www.nature.com/scientificreports/ p / C. A. Cish WT + empty Cish KO + empty Cish KO + Cish WT Cish KO + Cish D/BC* Cish KO + Cish SH2* 1 10 19 28 37 46 55 64 73 82 91 100 109 118 127 136 145 154 163 172 181 190 199 208 217 226 235 244 253 262 271 280 289 298 307 ) c e S ( e m i T n o it a l u m it s Indo Violet/Blue 3.5 3 2.5 2 1.5 1 0.5 0 0.24 19.0 20.3 60.5 0 102 103 104 0 -10 2 102 103 0.44 8.73 12.5 78.4 0 102 103 104 0 -10 2 102 103 0.49 9.86 12.3 77.4 0 102 103 104 0 -10 2 102 103 0.45 7.57 10.6 81.3 0 102 103 104 0 -10 2 102 103 TNF-α IFN-γ Cish KO + empty Cish KO + Cish WT Cish KO + Cish D/BC* Cish KO + Cish SH2* D. B. Figure 3. (A) Representative Ca2+ flux as assessed by fluorometric evaluation after αCD3 stimulation of indicated transduced CD8+ T cells. Kinetic of the ratio indo-blue to indo-violet over time shown and assessed by flow cytometry. (B) Calcium responses were integrated and quantified relative to Cish WT+ empty vector. Error bars represent SD from the mean (n = 3). (C) To evaluate cells positive for intracellular expression of TNF-α or IFN-γ, indicated transduced CD8+ T cells were re-stimulated with anti-CD3 coated antibody (at indicated concentration) and soluble CD28 (2 μg/ml) in presence of Golgi stop for 6 hrs. Results Cells were then labeled for surface Thy1.1 and intracellular TNF-α or IFN-γ. The flow cytometry analysis of Thy1.1+ T cell populations is shown. (D) Absolute cell numbers of Thy1.1+ T cells positive for intracellular TNF-α or IFN-γ. Bars show mean + SEM out of at least 4 independent experiments. Statistical significance was determined by two-tailed Student’s t test. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. (NS = Non-stimulated). C. A. Cish WT + empty Cish KO + empty Cish KO + Cish WT Cish KO + Cish D/BC* Cish KO + Cish SH2* 1 10 19 28 37 46 55 64 73 82 91 100 109 118 127 136 145 154 163 172 181 190 199 208 217 226 235 244 253 262 271 280 289 298 307 ) c e S ( e m i T n o it a l u m it s Indo Violet/Blue 3.5 3 2.5 2 1.5 1 0.5 0 B. A. Cish WT + empty Cish KO + empty Cish KO + Cish WT Cish KO + Cish D/BC* Cish KO + Cish SH2* 1 10 19 28 37 46 55 64 73 82 91 100 109 118 127 136 145 154 163 172 181 190 199 208 217 226 235 244 253 262 271 280 289 298 307 ) c e S ( e m i T n o it a l u m it s Indo Violet/Blue 3.5 3 2.5 2 1.5 1 0.5 0 B. A. B. C. 0.24 19.0 20.3 60.5 0 102 103 104 0 -10 2 102 103 0.44 8.73 12.5 78.4 0 102 103 104 0 -10 2 102 103 0.49 9.86 12.3 77.4 0 102 103 104 0 -10 2 102 103 0.45 7.57 10.6 81.3 0 102 103 104 0 -10 2 102 103 TNF-α IFN-γ Cish KO + empty Cish KO + Cish WT Cish KO + Cish D/BC* Cish KO + Cish SH2* C. 0.24 19.0 20.3 60.5 0 102 103 104 0 -10 2 102 103 0.44 8.73 12.5 78.4 0 102 103 104 0 -10 2 102 103 0.49 9.86 12.3 77.4 0 102 103 104 0 -10 2 102 103 0.45 7.57 10.6 81.3 0 102 103 104 0 -10 2 102 103 TNF-α IFN-γ Cish KO + empty Cish KO + Cish WT Cish KO + Cish D/BC* Cish KO + Cish SH2* D. Figure 3. Results The flow cytometry analysis of Thy1.1+ T cell populations is shown. (D) Absolute cell numbers of Thy1.1+ T cells positive for intracellular TNF-α or IFN-γ. Bars show mean + SEM out of at least 4 independent experiments. Statistical significance was determined by two-tailed Student’s t test. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. (NS = Non-stimulated). of the Cish SH2* resulted in TNF-α expression not statistically different than TNF-α expression with the empty vector. The effect of the Cish SH2* protein was more restrained producing lower IFN-γ levels than cells express- ing the empty vector, but higher levels than cells expressing either Cish WT or Cish D/BC*. Higher dose stimulus (1 μg/ml anti-CD3) eliminated any differences of cytokine release from cells expressing the different constructs. Thus, the Cish SH2 domain is essential for binding to PLC-γ1 and this binding is important for PLC-γ1 ubiquiti- nation and for Ca2+ inhibition. However, mutation of the Cish SH2 domain has only a subtle effect on inhibition of cytokine release in the assays we performed. 6 SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 www.nature.com/scientificreports/ /scientificreports/ SH2 mutant Cish Turq PLC YFP pY Merged mTurq alone WT Cish Turq D/BC mutant Cish Turq B. A. Figure 4. (A) and (B) Evaluation of PLC-γ1 and phosphotyrosine in TCR-induced microclusters after αCD3 stimulation in Jurkat T cells transfected with empty mTurq2-C1, Cish WT-mTurq2-C1, Cish-D/BC*- mTurq2-C1 or Cish-SH2*-mTurq2-C1 as indicated. (A) Representative confocal images from transfected Jurkat cells dropped on to stimulatory coverslips, fixed after three minutes, immunostained for PLC-γ1 and phosphotyrosine (pY), and the areas of the clusters were calculated (B). Statistical significance was determin by two-tailed Student’s t test. *P ≤ 0.05, ***P ≤ 0.001. SH2 mutant Cish Turq PLC YFP pY Merged mTurq alone WT Cish Turq D/BC mutant Cish Turq A. A. mTurq alone WT Cish Turq B. B. Figure 4. (A) and (B) Evaluation of PLC-γ1 and phosphotyrosine in TCR-induced microclusters after αCD3 stimulation in Jurkat T cells transfected with empty mTurq2-C1, Cish WT-mTurq2-C1, Cish-D/BC*- mTurq2-C1 or Cish-SH2*-mTurq2-C1 as indicated. (A) Representative confocal images from transfected Jurkat cells dropped on to stimulatory coverslips, fixed after three minutes, immunostained for PLC-γ1 and phosphotyrosine (pY), and the areas of the clusters were calculated (B). Statistical significance was determined by two-tailed Student’s t test. *P ≤ 0.05, ***P ≤ 0.001. Cish WT or mutants construct expression is sufficient to inhibit PLC-γ1 clusters. Discussion l Stimulation of the T cell for the calcium release is measured in seconds and minutes, while activation for the cytokine assay is six hours. The more prolonged assay might allow sufficient function from the Cish proteins to affect cytokine production. pf y p By genetically coupling Cish to the Turquoise fluorescent protein we were able to show that Cish was expressed predominately in the cytoplasm. We did not observe any Cish clustering at the plasma membrane or co-localization with PLC-γ1 or any other tyrosine-phosphorylated proteins upon T cell stimulation. Any effect of the Cish protein might thus occur prior to PLC-γ1 recruitment to microclusters or is so rapid at that site as to be not visible in our assay. We confirmed our previous observation that the area of microclusters containing PLC-γ1 in Cish-deficient T cells decreased in the presence of Cish, whereas the absence or presence of Cish had no effect on the area of microclusters detected using anti- phosphotyrosine antibodies. When we reconstituted the Cish KO cells with either of the SH2 or D/BC mutations, we observed a decrease in the PLC-γ1 microcluster area as we did with WT Cish reconstitution. As with the cytokine assay, the mutated protein likely had sufficient functional capacity to affect clustering of the PLC-γ1 molecule. f Immunotherapy has led to unprecedented responses in patients with advanced-stage tumors with the use of checkpoint inhibitors and adoptive cellular therapy16,17. Additionally, T cells can be engineered to express CAR T cell and adoptively transferred to patients18. All of these strategies target cell surface molecules to improve T cell anti-tumor function. We propose to identify and target intracellular molecules to improve T cell anti-tumor properties2,19. We previously showed that genetic deletion of the Cish molecule, an intracellular protein regulatory molecule, was an efficient strategy to improve CD8+ T cell function and others have shown the importance of Cish in NK anti-tumor properties2,3. In the current study, we performed initial structure-function studies on Cish in an attempt to discover a region of the protein that would be essential to its inhibitory properties and that could be targeted for immunotherapy development. Perhaps due to the complexity of Cish regulation, we were unable to identify an appropriate dominant negative mutant of Cish that consistently inhibited Cish in all assays. Discussion l In an earlier publication we demonstrated that following TCR-mediated T cell activation, the SOCS family mol- ecule, Cish, binds to PLC-γ1 leading to its degradation, thus regulating early T cell signaling and its functional consequences. The aim of our current study was to further define the structural and functional relationships between Cish and PLC-γ1 during CD8+ T cell activation. We show here that Cish is expressed for a very short period of time that peaks after 4 hrs of TCR stimulation. Previous data using a pulse chase assay in other cell models showed that the Cish half-life was very short (1 hr)11. These data indicate that Cish expression is tightly regulated in cells and especially in CD8+ T cells through an as yet unknown mechanism. To study the relationship of Cish protein structure to its function we then used mutants of the Cish SH2 and SOCS-Box domains. We showed that SH2-specific binding was essential for the Cish-mediated PLC-γ1 ubiquit- ination and degradation. The Cish D/BC domain mutant caused a small decrease in ubiquitination. The impact of these mutations on CD8+ T cells functions was also tested and we showed that an intact Cish SH2 domain was essential for full inhibition of Ca2+ release. Expression of a Cish molecule with this mutation resulted in the same level of calcium release as was observed in Cish KO T cells without any Cish-expressing construct. Reconstitution with Cish having a D/BC mutation did not differ from reconstitution with a WT construct in the calcium assay.ii f In cytokine release functional assays, we reproduced our original findings that activation of Cish-deficient T cells resulted in more cytokine release than was observed from similarly activated Cish KO cells re-constituted with WT Cish protein. Levels of IFN-γ and TNF-α produced by the KO cells were significantly different than that produced by the reconstituted cells. We also showed that reconstitution of the KO cells with the Cish SH2 mutant resulted in a slight increase in cytokine expression (TNF-α greater than IFN-γ) compared to the WT while expression of the Cish D/BC mutant brought down the level of cytokine expression to that seen in cells reconstituted with WT Cish. The difference in the results of the calcium and cytokine assays may reflect the length of time of the assay. Discussion l In light of this observation, we believe that a more efficient strategy to target Cish, and perhaps other intracellular proteins for immunotherapy, is to generate genetic deletion of the protein of interest in lymphocytes. Results In our previ- ous study, we also observed that Cish KO CD8+ T cells, upon T cell activation, showed more PLC-γ1 recruit- ment to microclusters as detected by phosphotyrosine content compared to WT CD8+ T cells2. However we were unable to image Cish localization in those experiments due to the poor visualization of Cish protein using antibody-mediated immunofluorescence2. In order to localize Cish during T cell activation we generated a chi- meric Cish molecule by cloning Cish WT, SH2* and D/BC* constructs into a pmTurquoise2-C1 vector12. We expressed these constructs and the empty pmTurquoise2-C1 vector in Jurkat T cells (Supplemental Fig. 2A). The pmTurquoise2-C1 empty vector was expressed diffusely in cytoplasm and nucleus. WT Cish mTurq was seen in the cytoplasm of both activated and unactivated cells. When transfected Jurkat cells expressing WT or mutant Cish were activated on coverslips coated with α-CD3 for 3 min, we were unable to see differences in localization of the Cish WT, SH2* and D/BC* constructs. No Cish constructs were found in any clusters upon activation (Supplemental Fig. 2B). Thus Cish is expressed in the cytoplasm and not in a specific subcellular compartment of SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 7 www.nature.com/scientificreports/ the cell; it is not recruited to the plasma membrane. We also tried immunofluorescence staining of FLAG-tagged retroviral constructs of Cish, transduced into Cish KO activated blast T CD8+ cells with anti-Cish or anti Flag-Tag, but were unable to detect the Cish constructs (data not shown). g g ( ) We then co-expressed Cish WT, SH2* and D/BC* proteins in combination with PLC-γ1-YFP in Jurkat T cells to test the effect of the various Cish constructs on microcluster formation. In this experiment, we observed fewer PLC-γ1-YFP clusters in cells transfected with Cish WT-mTurq2 compared to cells transfected with mTurq2 and stimulated with α-CD3 (Fig. 4A,B). This result confirms our previous results, and demonstrates that cytoplasmic Cish-mTurq2 is functional. Unexpectedly mutation of the SH2 or D/BC domains did not reverse PLC-γ1-YFP inhibition of cluster formation. These mutations were somewhat more efficient than Cish WT in inhibiting PLC-γ1-YFP cluster formation. However, the size of clusters detected by anti-phosphotyrosine staining was not affected by transfection of the various Cish constructs, demonstrating that the effect on PLC-γ1 was specific. References 1. Palmer, D. C. & Restifo, N. P. Suppressors of cytokine signaling (SOCS) in T cell differentiation, maturation, and function. Trends Immunol 30, 592–602, https://doi.org/10.1016/j.it.2009.09.009 S1471-4906(09)00197-5 (2009). 2. Palmer, D. C. et al. Cish actively silences TCR signaling in CD8+ T cells to maintain tumor tolerance. J Exp Med 212, 2095–2113, https://doi.org/10.1084/jem.20150304 (2015). 3. Delconte, R. B. et al. CIS is a potent checkpoint in NK cell-mediated tumor immunity. Nat Immunol 17, 816–824, https://doi. org/10.1038/ni.3470 (2016). 4. Putz, E. M. et al. Targeting cytokine signaling checkpoint CIS activates NK cells to protect from tumor initiation and metastasis. Oncoimmunology 6, e1267892, https://doi.org/10.1080/2162402X.2016.1267892 (2017). 1. Palmer, D. C. & Restifo, N. P. Suppressors of cytokine signaling (SOCS) in T cell differentiation, maturation, and function. Trends Immunol 30, 592–602, https://doi.org/10.1016/j.it.2009.09.009 S1471-4906(09)00197-5 (2009). g 4. Putz, E. M. et al. Targeting cytokine signaling checkpoint CIS activates NK cells to protect from tumor initiation and metastasis. Oncoimmunology 6, e1267892, https://doi.org/10.1080/2162402X.2016.1267892 (2017). Author Contributions G.G., A.D.E., D.C.P., I.A., A.M., V.A.B., N.P.R., and L.E.S. designed experiments. G.G., A.D.E., D.C.P., I.A. and A.M. performed the research. G.G., A.D.E., V.A.B., N.P.R. and L.E.S. supervised the study. G.G., A.D.E. and L.E.S. wrote the paper. www.nature.com/scientificreports/ J Cell Sci 129, 4548–4562, jcs.194886 (2 14. Barr, V. A. et al. Development of nanoscale structure in LAT-based signaling complexes. J Cell Sci 129, 4548–4562, jcs.194886 (2016). 15. Guittard, G. et al. Absence of both Sos-1 and Sos-2 in peripheral CD4(+) T cells leads to PI3K pathway activation and defects in migration. Eur J Immunol 45, 2389–2395, https://doi.org/10.1002/eji.201445226 (2015). 14. Barr, V. A. et al. Development of nanoscale structure in LAT-based signaling complexes. J Cell Sci 129, 4548–4562, jcs.194886 (2016). 15. Guittard, G. et al. Absence of both Sos-1 and Sos-2 in peripheral CD4(+) T cells leads to PI3K pathway activation and defects in migration. Eur J Immunol 45, 2389–2395, https://doi.org/10.1002/eji.201445226 (2015). 15. Guittard, G. et al. Absence of both Sos-1 and Sos-2 in peripheral CD4(+) T cells leads to migration. Eur J Immunol 45, 2389–2395, https://doi.org/10.1002/eji.201445226 (2015). g p g j 6. Rosenberg, S. A. & Restifo, N. P. Adoptive cell transfer as personalized immunotherapy for human cancer. Science 348, 62–68 https://doi.org/10.1126/science.aaa4967348/6230/62 (2015). 17. Couzin-Frankel, J. Breakthrough of the year 2013. Cancer immunotherapy. Science 342, 1432–1433, https://doi.org/10.1126/ science.342.6165.1432342/6165/1432 (2013). 17. Couzin-Frankel, J. Breakthrough of the year 2013. Cancer immunotherapy. Science 342, 1432–1433, https://doi.org/10.1126/ science.342.6165.1432342/6165/1432 (2013). 18. Fesnak, A. D., June, C. H. & Levine, B. L. Engineered T cells: the promise and challenges of cancer immunotherapy. Nat Rev Cancer 16, 566-581, https://doi.org/10.1038/nrc.2016.97(2016).i 18. Fesnak, A. D., June, C. H. & Levine, B. L. Engineered T cells: the promise and challenges of cancer immunotherapy. Nat Rev Cancer 16, 566-581, https://doi.org/10.1038/nrc.2016.97(2016).i , , p g ( ) 19. Patel, S. J. et al. Identification of essential genes for cancer immunotherapy. Nature. https://doi.org/10.1038/nature23477 (2017 19. Patel, S. J. et al. Identification of essential genes for cancer immunotherapy. Nature. https://doi.org/10.1038/nature23477 (2017). Acknowledgementsh References 8 SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 Acknowledgementsh g This work was supported by the Intramural Research Program of the National Cancer Institute Center for Cancer Research. g This work was supported by the Intramural Research Program of the National Cancer Institute Center for Cancer Research. SCIeNtIfIC Reports | (2018) 8:5336 | DOI:10.1038/s41598-018-23549-2 www.nature.com/scientificreports/ www.nature.com/scientificreports/ 5. Landsman, T. & Waxman, D. J. Role of the cytokine-induced SH2 domain-containing protein CIS in growth hormone receptor internalization. J Biol Chem 280, 37471–37480, https://doi.org/10.1074/jbc.M504125200 (2005). g j 6. Matsumoto, A. et al. CIS, a cytokine inducible SH2 protein, is a target of the JAK-STAT5 pathway and modulates STAT5 activation Blood 89, 3148–3154 (1997). 7. Yoshimura, A. et al. A novel cytokine-inducible gene CIS encodes an SH2-containing protein that binds to tyrosine-phosphorylated interleukin 3 and erythropoietin receptors. EMBO J 14, 2816–2826 (1995).h 8. Okabe, S. et al. Thrombopoietin induces an SH2-containing protein, CIS1, which binds to Mpl: involvement of the ubiquitin proteosome pathway. Exp Hematol 27, 1542–1547, doi:S0301-472X(99)00094-6 (1999). p p y p 9. Verdier, F. et al. Proteasomes regulate erythropoietin receptor and signal transducer and activator of transcription 5 (STAT5) ti ti P ibl i l t f th bi iti t d Ci p t i J Bi l Ch 273 28185 28190 (1998) 9. Verdier, F. et al. Proteasomes regulate erythropoietin receptor and signal transducer and activator of transcription 5 (STAT5) activation. Possible involvement of the ubiquitinated Cis protein. J Biol Chem 273, 28185–28190 (1998). 0. Matsumoto, A. et al. Suppression of STAT5 functions in liver, mammary glands, and T cells in cytokine-inducible SH2-containing protein 1 transgenic mice. Mol Cell Biol 19, 6396–6407 (1999). p g 1. Piessevaux, J., De Ceuninck, L., Catteeuw, D., Peelman, F. & Tavernier, J. Elongin B/C recruitment regulates substrate binding by CIS J Biol Chem 283, 21334–21346, https://doi.org/10.1074/jbc.M803742200 (2008).l p g j 12. Goedhart, J. et al. Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%. Nat Commun 3, 751, https://doi.org/10.1038/ncomms1738 (2012). 12. Goedhart, J. et al. Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%. Nat Commun 3, 751, https://doi.org/10.1038/ncomms1738 (2012). p g ( ) 13. Bunnell, S. C., Barr, V. A., Fuller, C. L. & Samelson, L. E. High-resolution multicolor imaging of dynamic signaling complexes in T cells stimulated by planar substrates. Sci STKE 2003, PL8, https://doi.org/10.1126/stke.2003.177.pl8 (2003). g 3. Bunnell, S. C., Barr, V. A., Fuller, C. L. & Samelson, L. E. High-resolution multicolor imaging of dynamic signaling complexes in T cells stimulated by planar substrates. Sci STKE 2003, PL8, https://doi.org/10.1126/stke.2003.177.pl8 (2003). y p , , p g p ( ) 14. Barr, V. A. et al. Development of nanoscale structure in LAT-based signaling complexes. Additional Information Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-018-23549-2.h Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-018-23549-2 Competing Interests: The authors declare no competing interests. Competing Interests: The authors declare no competing interests. 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https://earth-planets-space.springeropen.com/counter/pdf/10.1186/BF03352546
English
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VLBI observation of narrow bandwidth signals from the spacecraft
Earth, planets and space
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cc-by
6,151
1. Introduction the rim of the Moon, we apply very long baseline interfer- ometry (VLBI) technique in VRAD (the differential VLBI radio sources) mission of Japanese lunar exploration project SELENE (SELenological and ENgineering Explorer) in ad- dition to a conventional 2-way Doppler and newly applied 4-way Doppler measurement (e.g., Hanada et al., 2002; Namiki et al., 1999). By measuring the difference of arriv- ing time of the same wave front of a radio signal from the spacecraft (s/c) at two or more separated antennas, VLBI can precisely determine the position and the velocity of the s/c in the direction perpendicular to LOS in contrast to the Doppler measurement. The lunar gravity field has been investigated by Doppler measurement for the last 40 years. Recently its global map- ping has been done by “Clementine” (Zuber et al., 1994) and “Lunar Prospector” (LP) (Konopliv et al., 2001). Al- though these observations contributed to knowing the low degree gravity field and the detail structure of the nearside, the gravity field of the rim of the Moon was not clearly in- vestigated like the nearside. This is because the Doppler measurement is sensitive to the direction of the line of sight (LOS). Over the rim of the Moon, the gravity force from the Moon acts mainly in the direction perpendicular to LOS and we cannot estimate the gravity field precisely only by Doppler measurements. The internal structure, which is conventionally derived from the gravity and the topographic data (Bratt et al., 1985), is interesting especially for the rim of the moon. For example, the observational fact that a crust of the far side is older and thicker than that of the nearside is one of the important phenomena related to the thermal evolution of the moon, and there may be new facts under the rim region of the Moon which give us a key to clear up the cause of the dichotomy. In order to improve the low order and degree components of gravity field especially for The VLBI technique has been applied to tracking of a s/c since 1960s (e.g. Border et al., 1992; Sagdeyev et al., 1992). These VLBI observations of the s/c were success- ful, and recently it has been used for deep space missions of NASA and ESA (Antreasian et al., 2002; Thornton and Border 2003). However, a large amount of VLBI data pre- vented the real time processing. Copy right c⃝The Society of Geomagnetism and Earth, Planetary and Space Sci- ences (SGEPSS); The Seismological Society of Japan; The Volcanological Society of Japan; The Geodetic Society of Japan; The Japanese Society for Planetary Sci- ences; TERRAPUB. (Received May 7, 2004; Revised October 13, 2004; Accepted October 13, 2004) (Received May 7, 2004; Revised October 13, 2004; Accepted October 13, 2004) We carried out a series of VLBI observations of Nozomi by using a dedicated narrow bandwidth VLBI system. The three carrier waves with frequency interval of 515 kHz were recorded in 3 channels of the system and correlated by a software method. As a result of the correlation, the residual fringe phases of the main carrier wave are obtained for every 1.3 seconds. We can also continuously track them for 100 minutes. The variation of the residual fringe phase is +/−150 degrees. Moreover, we can derive succesively the group delay for every 100 seconds by using these three carrier waves. The RMS of the group delays is 13 nsec and its average is well accorded with the delay determined by the range and Doppler measurements within an error of 2 nsec. Consequently, we confirmed the validity of the narrow bandwidth VLBI system, and it could be expected that this system, in addition to range and Doppler measurements, can be applied to three-dimensional tracking of a spacecraft and the precise gravity measurement of the Moon and the planets. Key words: VLBI, spacecraft, narrow bandwidth, group delay, SELENE. Key words: VLBI, spacecraft, narrow bandwidth, group delay, SELENE. Earth Planets Space, 56, 1041–1047, 2004 Earth Planets Space, 56, 1041–1047, 2004 VLBI observation of narrow bandwidth signals from the spacecraft Fuyuhiko Kikuchi1, Yusuke Kono2, Makoto Yoshikawa3, Mamoru Sekido4, Masafumi Ohnishi5, Yasuhiro Murata3, Jinsong Ping6, Qinghui Liu6, Koji Matsumoto6, Kazuyoshi Asari6, Seiitsu Tsuruta6, Hideo Hanada2, and Nobuyuki Kawano6 1Department of Astronomical Science, Graduate University for Advanced Studies, 2-12 Hoshigaoka, Mizusawa, Iwate 023-0861, Japan 2Division of Radio Astronomy, National Astronomical Observatory, 2-21-1 Osawa, Mitaka, Tokyo 181-8588, Japan 3Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Sagamihara, Kanagawa 229-8510, Japan 4Kashima Space Reserch Center, National Institute of Information and Communications Technology, 893-1 Hirai, Kashima, Ibaraki 314-8510, Japan 5Fujitsu Limited, 1-9-3 Nakasen Mihama-ku, Chiba 261-8588, Japan 6Division of Radio Astronomy, National Astronomical Observatory, 2-12 Hoshigaoka, Mizusawa, Iwate 023-0861, Japan 6Division of Radio Astronomy, National Astronomical Observatory, 2-12 Hoshigaoka, Mizusawa, Iwate 023-0861, Japan KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT 1042 Fig. 1. Block diagram of the narrow bandwidth receiving system. the Moon emit three carrier waves in S band and one in X band, and differential VLBI observation between the two sub-satellites is carried out. When we derived the fringe phase with an accuracy of 10 degrees by using differential VLBI, the relative position of two sub-satellites around the moon will be decided with an accuracy of 20 cm for the 2000 km baseline (Kono et al., 2003). This accuracy will be contributed on determination of the low degree coeffi- cients of the spherical harmonics of the lunar gravity field (Matsumoto et al., 2002). In association with this plan, we have developed a narrow bandwidth sampling and recording system for VLBI and a correlation software for processing of the data obtained in the VRAD mission. Fig. 1. Block diagram of the narrow bandwidth receiving system. which are ajusted to the bandwidth of the S-RTP, are mixed to the signals to compensate the phase difference between channels in front of the video converter. Using the systems mentioned above, VLBI observations for tracking of LP were carried out (Kono et al., 2003). In these observations, a phase delay was estimated within an error of a few degrees for a short period, however a group delay could not be estimated because only one frequency signal was used in LP. For applying VLBI to the gravity measurement of the Moon, we must obtain the phase delay for longer period within an error of a few degrees and deter- mine the group delay without cycle ambiguity. In order to confirm the performance and capability of our narrow band- width VLBI system and analysis software, we conducted a fringe phase tracking and group delay determination for a few hours by VLBI observation of Japanese explorer No- zomi, which transmitted a main carrier wave and two sub carriers with frequencies of 515 kHz apart from that of the main carrier. In this article, a detail of the VRAD system, and the result of the fringe phase tracking and the group delay measurement of Nozomi are shown. 2. VRAD System 2.1 Back-end system where Rsc(t) is the predicted position vector of the s/c and Rref (t) represents the position vector of the reference station. t is the time based on the reference station, c is the velocity of light, and τgrav is general relativistic delay. We obtain τref (t) from an iterative procedure as follows, 2.2 Correlation software A correlation software has been also developed for this system. The software is composed of modules of VLBI delay estimation and cross-correlation which includes a bit- shift, a fringe-stopping and a fractional bit correction. 2.2.1 Delay model for a s/c in finite distance In a conventional correlator, a geometric delay is calculated as- suming plane waves coming from the extra galactic radio sources. However, the assumption of the plane wave is not valid in the case of a s/c at a finite distance from the Earth. So we modified the delay model from the plane wave to a spherical wave to estimate the geometric delay for the s/c. In our method, the propagation times from the s/c to each ground station are calculated directly by using the light time equation. The propagation time from the s/c to the reference station is expressed as follows, 2.2.1 Delay model for a s/c in finite distance In a conventional correlator, a geometric delay is calculated as- suming plane waves coming from the extra galactic radio sources. However, the assumption of the plane wave is not valid in the case of a s/c at a finite distance from the Earth. τref (t) = | Rsc(t −τref (t)) −Rref (t)| c + τgrav (1) (1) 1. Introduction Moreover, frequency allo- cation of the downlink signals was not appropriate for pre- cise group delay measurement and limited the accuracy of angular component of the position of the s/c to several tens to nano radians (Thornton and Border 2003). In order to de- tect a small motion of an s/c generated by the regional grav- itational acceleration of the Moon, multi-frequency VLBI (MFV) was proposed (Kono et al., 2003). In MFV method, radio transmitters on board two small sub-satellites around 1041 3. VLBI Observation of Nozomi Nozomi is the Japanese explorer that had two swing- bys by the earth in December 2002 and June 2003 so as to be injected into a Mars orbit in 2004 (Yoshikawa et al., 2001). During the period between these two swing- bys, the onboard high gain antenna could not point to the Earth due to some operational problems. In this period, range and Doppler measurements could not be conducted with sufficient SNR. To overcome this problem, the No- zomi team of JAXA (Japan Aerospace Exploration Agency) and the VLBI group of NICT (National Institute of In- 2.1 Back-end system We also took part in the to 27, 2003, by using our VLBI scopes involved in this observati KASHIMA (KSM), and MIZUS these telescopes are shown in Tab Usually the differential VLBI o and a QSO is carried out to remov phase and propagation delay cau sphere, and the ground systems. observation was not applied in o long-term behavior of fringe phas sitions well known, for example 1 were observed before and after th calibrating the clock offset and th t ti X b d i l f Q Table 2. List of radio telescopes involved in the VLBI observation of Planet-B. Station Antenna diameter (m) System noize temperature (K) Longitude Latitude USUDA 64 70 138◦21′57′′E 36◦07′45′′N KASHIMA 34 85 140◦39′36′′E 35◦57′06′′N MIZUSAWA 10 130 141◦07′56′′E 39◦08′00′′N MIZUSAWA 20 150 141◦07′57′′E 39◦08′01′′N Table 2. List of radio telescopes involved in the VLBI observation of Planet-B. Fig. 2. Block diagram of the correlation process of the software. formation and Communications Technology) collaborated to determine the Nozomi orbit by using the VLBI tech- nique. We also took part in the observation from May 13 to 27, 2003, by using our VLBI systems. The radio tele- scopes involved in this observation were USUDA (USD), KASHIMA (KSM), and MIZUSAWA (MZS). Details of these telescopes are shown in Table 2. p Usually the differential VLBI observation between an s/c and a QSO is carried out to remove the fluctuations in fringe phase and propagation delay caused by ionosphere, tropo- sphere, and the ground systems. However, the switching observation was not applied in our observation to detect a long-term behavior of fringe phase. Several QSOs with po- sitions well known, for example 1842+681 and 1849+670, were observed before and after the tracking of Nozomi for calibrating the clock offset and the clock rate between VLBI stations. X band signals from QSOs were recorded in 4 channels of the K5 system, in which the sampling rate and quantization were 4 MHz and 2 bit, respectively (Kondo et al., 2002). Fig. 2. Block diagram of the correlation process of the software. from an iterative procedure in the same way as τref (t). Finally the geometric delay between the reference and the slave station is obtained as follows, 3.1 Signals of Nozomi τgeometric(t) = τslv(t) −τref (t) (5) Between the two swing-by events, the downlink signal of Nozomi was either in telemetry mode or in ranging mode. There was only one carrier wave in the teleme- try mode. In contrast, the downlink signal consists of a main carrier wave, two range tones, and some ambiguity tones in the ranging mode. We observed Nozomi in rang- ing mode to estimate the group delay. The frequency of the main carrier wave fcarrier was 8411 MHz and those of the two range tones were fcarrier+/−fcarrier/214 ( fcarrier/214 is about 515 kHz). The ambiguity tones with frequencies of fcarrier+/−fcarrier/2n+14 (n = 1, 2. . .) were added ev- ery 100 seconds for 40 seconds to solve the ambiguity of the range tones. However, the carrier to noise ratios (C/N) of the ambiguity tones were so weak that these tones could not be detected. The main carrier wave and the two range tones were separately recorded in three channels of S-RTP station. To compensate the phase difference between these three channels, the phase calibration signals at every 60 kHz were mixed with the IF signals in front of the video con- verter. (5) τgeometric(t) = τslv(t) −τref (t) 2.2.2 Correlation process The correlation process is made by FX mode. The signal recorded at the 1st station is Fourier transformed for every parameter period (PP). On the other hand, the signal recorded at the 2nd station is bit-shifted, fringe-stopped and corrected for the fractional bit by using the predicted geometric delay calculated from Eq. (5). After these corrections, the signal of the 2nd station is Fourier transformed. Finally, each Fourier component is cross-correlated and a residual fringe phase is obtained. Block diagram of the process is shown in Fig. 2. In many cases, the downlink signal from a s/c is a narrow bandwidth carrier wave. So, we use only several tens of Hz around the center frequency of the carrier wave to obtain a high SNR in the course of calculating the residual fringe phase. 2.1 Back-end system In radio astronomical and geodetic VLBI surveys, usu- ally wide bandwidth signals (from several MHz to GHz) from radio stars have been recorded by a fast sampling- rate system. This is because the signal-to-noise ratio (SNR) and the accuracy of the group delay depend on signal band- width. However, the wide bandwidth signals are not ef- fective for real-time tracking of a s/c because they consume higher power in the s/c and they need longer time to obtain a result from the large amount of data. For these reasons, we have developed a narrow bandwidth sampling and record- ing system for VLBI, called S-RTP station, for an s/c VLBI tracking. The performances of this system are listed in Ta- ble 1 and block diagram of this system is shown in Fig. 1. After the frequency down conversion and the video con- version of the signals by using K4 or Mark-4 systems, the S-RTP station samples and digitizes the video signals, and now a hard disk drive is used for recording sampled data instead of the tape recorder in the old system. Moreover, the phase calibration signals at every several tens of kHz, τ i+1 ref (t) = | Rsc(t −τ i ref (t)) −Rref (t)| c + τgrav (2) τ 0 ref (t) = | Rsc(t) −Rref (t)| c + τgrav (3) (2) (3) τ 0 ref (t) is an initial value of τref (t). On the other hand, the propagation time from the s/c to the slave station is expressed as follows, τslv(t) = | Rsc(t −τref (t)) −Rslv(t −τref (t) + τslv(t))| c +τgrav (4) (4) +τgrav where Rslv(t) is the position vector of the slave station and τref (t) is given from the Eq. (1). τslv(t) can be obtained F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT 1043 Table 2. List of radio telescopes involved in the VLBI observation of Planet-B. Station Antenna diameter (m) System noize temperature (K) Longitude USUDA 64 70 138◦21′57′′ KASHIMA 34 85 140◦39′36′′ MIZUSAWA 10 130 141◦07′56′′ MIZUSAWA 20 150 141◦07′57′′ Fig. 2. Block diagram of the correlation process of the software. formation and Communications to determine the Nozomi orbit nique. 3.2 Result of correlation The difference of the ASD for three baselines would be attributed to the difference of the param- eters of the ground systems: system temperature, diameter of the antenna, coherence factor, and aperture efficiency of the antenna. The ratios of the ASD expected from the nomi- nal value of the parameters of the ground systems are 11 for USD-KSM/KSM-MZS, 5 for USD-KSM/MZS-USD, and 3 for MZS-USD/KSM-MZS. These values are roughly con- sistent with Fig. 5. While τ is longer than 10 seconds for USD-KSM and 30 seconds for KSM-MZS and MZS-USD, the fluctuation of the atmosphere became dominant and the ASD hardly decreased. The ASD of the residual fringe phases caused by the atmospheric fluctuation varies from 10−12 to 10−13 according to the atmospheric condition, and 1.5 × 10−13 from Fig. 5 corresponds to the value of clear day. In addition, the ASD for longer than 200 seconds was not calculated. This is because the observation period of about 6,000 seconds is not enough to obtain the ASD for longer than 200 seconds. Fig. 3. The residual fringe phases of the main carrier wave for USD-KSM baseline. These clock parameters were corrected before the correla- tion of the signals from Nozomi. g 3.2.2 Estimation of residual fringe phase The fre- quency of the carrier waves from Nozomi changed slightly by a few Hz in 1 PP of 1.3 seconds. So the Fourier compo- nents of only +/−10 Hz around the center frequency of the carrier wave were used to calculate the residual fringe phase with a high SNR. The frequency resolution was 0.76 Hz for 1 PP. The residual fringe phases for USD-KSM baseline calculated by using the whole recorded bandwidth and only +/−10 Hz around the center frequency of the main carrier wave are shown in Fig. 3. The root mean square (RMS) of the residual fringe phase for the period of 120 seconds de- creased from 39 to 8 degrees by this method. The averaged SNR of the main carrier wave is about 40 for 40 seconds integration. Moreover, we could continuously track the residual fringe phases of the main carrier wave for most obser- vations of all baselines, i.e. USD-KSM, KSM-MZS, and MZS-USD. The residual fringe phases of the main carrier waves in each baseline from 07:00:00 to 08:40:00 on May 27, 2003 in UT and the closure phases are shown in Fig. 4. 3.2 Result of correlation 3.2.1 Clock offset and clock rate The correlation of the signal from QSO was also carried out by the same soft- ware. Correlation process of the QSO was similar to the conventional method and the delay model was the same as the Consensus model (McCarthy, 2003). As a result of the correlation and the group delay analysis, the clock off- set and the clock rate were estimated within an error of 20 pico seconds (psec) and of 0.001 psec/second, respectively. F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT 1044 -150 -100 -50 0 50 100 150 200 250 300 07:00:00 07:30:00 08:00:00 08:30:00 Residual fringe phase [degree] 2003/5/27 [UT] USUDA-KASHIMA KASHIMA-MIZUSAWA MIZUSAWA-USUDA closure phase Fig. 4. The residual fringe phases of the main carrier wave for 3 baselines and the closure phases. USUDA-KASHIMA KASHIMA-MIZUSAWA MIZUSAWA-USUDA closure phase Fig. 4. The residual fringe phases of the main carrier wave for 3 baselines and the closure phases. -250 -200 -150 -100 -50 0 50 100 07:00:00 07:01:00 07:02:00 Residual fringe phase [degree] 2003/5/27 [UT] +/- 10Hz 100kHz Fig. 3. The residual fringe phases of the main carrier wave for USD-KSM baseline. The RMS of the closure phases is 3 degrees for the period of 100 minutes when the integration time of the residual fringe phases are 5.2 seconds. This result suggests that the correlation by the software method has been carried out suc- cessfully, and the intrinsic error of the residual fringe phase, which is caused by the thermal noise of the ground systems or the model of the software, is 3 degrees. Furthermore, the residual fringe phase of each baseline varies with various periods from several tens of seconds through several tens of minutes as shown in Fig. 4. To clarify these fluctuations, the Allan standard deviation (ASD) of the residual fringe phases were calculated for each baseline and are shown in Fig. 5. From Fig. 5, the ASD decreased at the rate of 1/τ (τ is the averaging time) until τ was less than 10 seconds for USD-KSM and 30 seconds for KSM-MZS and MZS- USD. Consequently, the short-term variation of the resid- ual fringe phase would be explained by the thermal noise of the ground systems. 3.2 Result of correlation Two range tones were correlated by the same way as the main carrier wave to carry out the group delay analysis. In contrast to the main carrier wave, we could detect the residual fringe phase of the range tones only for the USD- KSM baseline because their SNR was less than that of the 1045 F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT 10-15 10-14 10-13 10-12 10-11 10-10 1 10 100 Allan standard deviation Averaging time τ [second] USUDA-KASHIMA KASHIMA-MIZUSAWA MIZUSAWA-USUDA Fig. 5. The Allan standard deviations of residual fringe phases of the main carrier wave for 3 baselines. and this result showed that the group delay is obtained with- out cycle ambiguity of about 2 micro seconds, which is the inverse of the frequency intervals of the three carrier waves. On the contrary, the RMS of the differences between the geometric delays is 13 nsec. The tropospheric and the iono- spheric fluctuations were at the order of a few nsec during the observation period, so most of the error of the group delay could be caused by the thermal noise in the ground system. The SNR of the two range tones are almost half of that of the main carrier wave, which is 19 for 40 seconds in- tegration in average. The error of the group delay expected from the SNR of the range tone is 12 nsec and is in con- sistency with the RMS of the differences of the geometric delays. The baseline length is about 200 km for USD-KSM baseline, the precision of the angular distance of Nozomi is 3710 mas. The distance between Nozomi and the ground station is 6 × 106 km in this observation, so the estimated position error of Nozomi is 117 km. Moreover, it could be expected that the accuracy of the angular distance and the position of Nozomi would be improved to 46 mas and 1.4 km respectively, if the SNR of the range tones are as large as the main carrier wave and the frequency intervals are 20 MHz. Fig. 5. The Allan standard deviations of residual fringe phases of the main carrier wave for 3 baselines. main carrier wave. Moreover, the transmission of Nozomi in ranging mode was divided into 2 modes, A and B. 4. Discussion As mentioned in the previous section, we can continu- ously track the residual fringe phase of the main carrier wave for 100 minutes and obtain the group delay of the three carrier waves without cycle ambiguity. These results confirm the validity of the narrow bandwidth hardware and software VLBI systems. In this section, we suppose the fea- sibility of the VRAD mission of SELENE from the result of Nozomi considering the C/N of each observation. 3.2.3 Estimation of group delay Before analyzing the group delay, the phase difference of the separate chan- nels obtained from the phase calibrator signals has to be removed from the residual fringe phase as follows, g The three carrier waves in S-band whose frequency inter- vals are 6 MHz and 75 MHz will be received to obtain the precise group delay on differential VLBI observation of two sub-satellites in VRAD. In order to obtain the group delay without the cycle ambiguity, the phase error of the residual fringe phases of these carrier waves are required to be less than 10 degrees between the switching period of 120 sec- onds. In the case of the main carrier wave of Nozomi for the baseline of USD-KSM, the C/N is 6 and the RMS of the residual fringe phases of every 1 PP of 1.3 seconds during 120 seconds is 8 degrees. In contrast, the specification of the C/N of the carrier waves in VRAD is 3.5, and the phase error is expected to be 14 degrees for 1 PP of 1.3 second in VRAD because the phase error would be proportional to the inverse of the C/N. This phase error would be improved by the square root of the integration period. By integrating the residual fringe phases for 3 PP, the phase error would be reduced to 6 degrees and the requirement of 10 degrees in VRAD would be achieved. This result suggests that the group delay of the three carrier waves would be obtained without cycle ambiguity and the small acceleration of the sub-satellite caused by the gravity field of the Moon will be detected from the geometric delay. δφ′ i = δφi −(φref pcal,i −φslv pcal,i), (i = 1, 2, 3) (6) (6) where δφi is the residual fringe phase of ith channel and φref pcal,i and φslv pcal,i are the phase of the phase calibration signal in ith channel, respectively. 4. Discussion The residual group delay of the signals is given by, δτgroup−delay = δφ′ i+1 −δφ′ i 2π( fi+1 −fi) (7) (7) where fi is the frequency of the carrier wave. The propaga- tion delays of the troposphere and the ionosphere are also corrected. The atmospheric delay is corrected by using the tropospheric model (Davis et al., 1985) and the ionospheric delay is corrected by using a regional ionosphere map (Ping et al., 2002). After these corrections, the geometric delays of the sig- nals from Nozomi are obtained in every 100 seconds by the group delay analysis. These derived geometric delays well accorded with the geometric delay determined by the range and Doppler measurements, and the differences be- tween these geometric delays are shown in Fig. 7. The av- erage of these differences are about 2 nano seconds (nsec) 5. 3.2 Result of correlation In the mode A, the ambiguity tones were added to the downlink signal and decreased the SNR of the range tones. So the residual fringe phases of the range tones were not obtained for this period of 60 seconds as shown in Fig. 6. On the other hand, the ambiguity tones were not added in the mode B and the residual fringe phases of the range tones were obtained in this period of 40 seconds in B of Fig. 6. The averaged SNR of two range tones in the mode B is 19 for 40 seconds integration. Therefore the group delay analysis could only be carried out during the mode B. 5. Conclusion We carried out a VLBI observation of Nozomi. In this observation, we recorded three carrier wave signals by us- F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT 1046 -200 -100 0 100 200 300 07:00:00 07:02:00 07:04:00 07:06:00 07:08:00 07:10:00 Residual fringe phase [degree] 2003/5/27 [UT] B: 40sec. A: 60sec. main carrier range tone 1 range tone 2 Fig. 6. The residual fringe phases of the main carrier wave and two range tones for USD-KSM baseline. -200 -100 0 100 200 300 07:00:00 07:02:00 07:04:00 07:06:00 07:08:00 07:10:00 Residual fringe phase [degree] 2003/5/27 [UT] B: 40sec. A: 60sec. main carrier range tone 1 range tone 2 Fig. 6. The residual fringe phases of the main carrier wave and two range tones for USD-KSM baseline. Fig. 6. The residual fringe phases of the main carrier wave and two range tones for USD-KSM baseline. -40 -20 0 20 40 07:00:00 07:30:00 08:00:00 08:30:00 O-C of geometric delay [nsec] 2003/5/27 [UT] Fig. 7. The difference between the geometric delays in this VLBI obser- vation and those calculated from the orbital motion estimated from the range and Doppler measurements. -40 -20 0 20 40 07:00:00 07:30:00 08:00:00 08:30:00 O-C of geometric delay [nsec] 2003/5/27 [UT] phase error would be less than 10 degrees for 3.9 seconds integration, which is the requirement of VRAD. It could be expected that we can detect the regional gravity field of the Moon precisely by using this system. Furthermore, in addition to the range and Doppler measurements, VLBI observation by this system has a capability of precise three- dimensional positioning of an s/c. Acknowledgments. We would like to thank all the staffs of Kashima space communication research center of NICT, Usuda deep space center of JAXA and Mizusawa observation center of National Astronomical Observatory for their helps in VLBI obser- vations. Acknowledgments. We would like to thank all the staffs of Kashima space communication research center of NICT, Usuda deep space center of JAXA and Mizusawa observation center of National Astronomical Observatory for their helps in VLBI obser- vations. References Antreasian, P. G., D. T. Baird, J. S. Border, P. D. Burkhart, E. J. Graat, M. K. Jah, R. A. Mase, T. P. McElrath, and B. M. Portock, 2001 Mars Odyssey Orbit Determination During Interplanetary Cruise, AIAA/AAS Astrodynamics Specialist Conference and Exhibit, AIAA-2002-4531, Aug. 5–8, 2002. Fig. 7. The difference between the geometric delays in this VLBI obser- vation and those calculated from the orbital motion estimated from the range and Doppler measurements. Border, J. S., W. M. Folkner, R. D. Kahn, and K. S. Zukor, Precise Track- ing of the Magellan and Pioneer Venus Orbiters by Same-Beam Interfer- ometry, Part 1: Data Accuracy Analysis, TDA progress report, 42–110, Aug. 15, 1992. ing dedicated narrow bandwidth VLBI system, and corre- lated these signals by the software method. As a result of correlation, the residual fringe phases of the main carrier wave in each baseline are obtained at every 1.3 seconds. We can also continuously track them for 100 minutes. The variation of the residual fringe phase is +/−150 degrees in peak-to-peak and its Allan standard deviation shows that the variation comes from the fluctuation of the atmosphere. Moreover, we can derive successfully the group delays for every 100 seconds by using three carrier wave signals. The RMS of them is 13 nsec. The average of the obtained ge- ometric delay well accorded with the geometric delay de- termined by the range and Doppler measurement within an error of 2 nsec. From these results, it could be expected that if the SNR of the range tones are as large as the main carrier wave and the frequency intervals are 20 MHz, the accuracy of the angular distance and the position of Nozomi would be improved to be less than 46 mas and 1.4 km respectively. From the result of the correlation and the group delay ing dedicated narrow bandwidth VLBI system, and corre- lated these signals by the software method. As a result of correlation, the residual fringe phases of the main carrier wave in each baseline are obtained at every 1.3 seconds. We can also continuously track them for 100 minutes. The variation of the residual fringe phase is +/−150 degrees in peak-to-peak and its Allan standard deviation shows that the variation comes from the fluctuation of the atmosphere. Moreover, we can derive successfully the group delays for every 100 seconds by using three carrier wave signals. References The RMS of them is 13 nsec. The average of the obtained ge- ometric delay well accorded with the geometric delay de- termined by the range and Doppler measurement within an error of 2 nsec. From these results, it could be expected that if the SNR of the range tones are as large as the main carrier wave and the frequency intervals are 20 MHz, the accuracy of the angular distance and the position of Nozomi would be improved to be less than 46 mas and 1.4 km respectively. From the result of the correlation and the group delay analysis, we confirmed the validity of the new hardware and the software in VLBI system. We also confirmed the feasibility of the VRAD mission of SELENE. That is, the Bratt, S. R., S. C. Solomon, J. W. Head, and C. H. Thurber, The deep struc- ture of lunar basin: Implications for basin formation and modification, J. Geophys. Res., 90, 3049–3064, 1985. Davis, J. L., T. A. Herring, I. I. Shapiro, A. E. E. Rogers, and G. Elgered, Geodesy by radio interferometry: Effects of atmospheric modeling er- rors on estimates of baseline length, Radio Sci., 20, 1593–1607, 1985. Hanada, H., T. Iwata, Y. Kono, and K. Matsumoto, VRAD Mission: Precise Observation of Orbits of Sub-satellites in SELENE, IVS 2002 General Meeting Proceedings, 73–76, 2002. Kondo, T., Y. Koyama, J. Nakajima, M. Sekido, R. Ichikawa, E. Kawai, H. Okubo, H. Osaki, M. Kimura, Y. Ichikawa, and GALAXY team, Real-time Gigabit VLBI System and Internet VLBI System, IVS 2002 General Meeting Proceedings, 142–146, 2002. Kono, Y., H. Hanada, J. S. Ping, Y. Koyama, Y. Fukuzaki, and N. Kawano, Precise positioning of spacecrafts by multi-frequency VLBI, Earth Planets Space, 55, 581–589, 2003. Konopliv, A. S., S. W. Asmer, E. Carranza, W. L. Sjogren, and D. N. Yuan, i d l l f h i i Konopliv, A. S., S. W. Asmer, E. Carranza, W. L. Sjogren, and D. N. Yuan, Recent gravity models as a result of the Lunar Prospector Mission, Icarus, 150, 1–8, 2001. Recent gravity models as a result of the Lunar Prospector Mission, Icarus, 150, 1–8, 2001. Matsumoto, K., K. Heki, and H. Hanada, Global Lunar Gravity Field Recovery from SELENE, IVS 2002 General Meeting Proceedings, 381– 385, 2002. McCarthy, D. D., IERS Conventions 2003, in IERS Technical Note 32, to be published. F. Kikuchi (e-mail: fuyuhiko@miz.nao.ac.jp), Y. Kono, M. Yoshikawa, M. Sekido, M. Ohnishi, Y. Murata, J. Ping, Q. Liu, K. Matsumoto, K. Asari, S. Tsuruta, H. Hanada, and N. Kawano References From the result of the correlation and the group delay analysis, we confirmed the validity of the new hardware and the software in VLBI system. We also confirmed the feasibility of the VRAD mission of SELENE. That is, the Namiki, N., H. Hanada, T. Tsubokawa, N. Kawano, M. Ooe, K. Heki, T. Iwata, M. Ogawa, and T. Takano, Selenodetic experiments of SELENE: Relay satellite, differential VLBI, and laser altimater, Adv. Space Res., F. KIKUCHI et al.: VLBI OBSERVATION OF NARROW BANDWIDTH SIGNALS FROM THE SPACECRAFT 1047 tion Series, edited by J. H. Yuen, 85 pp, Wiley and Sons Inc., US, 2003. 23, 1817–1820, 1999. tion Series, edited by J. H. Yuen, 85 pp, Wiley and Sons Inc., US, 2003. Yoshikawa, M., M. Sekido, N. Kawaguchi, K. Fujisawa, H. Hanada, Y. Kono, H. Hirabayashi, Y. Murata, S. Sawada-satoh, K. Wajima, Y. Asaki, J. Kawaguchi, H. Yamakawa, T. Kato, T. Ichikawa, and T. Ohnishi, Present status and future problems of the orbit determination for Nozomi spacecraft, IVS CRL Technology Development Center News, No. 19, 37–40, 2001. Ping, J. S., Y. Kono, K. Matsumoto, Y. Otsuka, A. Saito, C. Shum, K. Heki, and N. Kawano, Regional ionosphere map over Japanese Islands, Earth Planets Space, 54, e13–e16, 2002. Yoshikawa, M., M. Sekido, N. Kawaguchi, K. Fujisawa, H. Hanada, Y. Kono H Hirabayashi Y Murata S Sawada satoh K Wajima Y Yoshikawa, M., M. Sekido, N. Kawaguchi, K. Fujisawa, H. Hanada, Y. Kono, H. Hirabayashi, Y. Murata, S. Sawada-satoh, K. Wajima, Y. Asaki, J. Kawaguchi, H. Yamakawa, T. Kato, T. Ichikawa, and T. Ohnishi, Present status and future problems of the orbit determination Sagdeyev, R. Z., V. V. Kerzhanovitch, L. R. Kogan, V. I. Kostenko, V. M. Linkin, L. I. Matveyenko, R. R. Nazirov, S. V. Pogrebenko, I. A. Struckov, R. A. Preston, J. Purcel, C. E. Hildebrand, V. A. Grish- manovskiy, A. N. Kozlov, E. P. Molotov, J. E. Blamont, L. Boloh, G. Laurans, P. Kaufmann, J. Galt, F. Biraud, A. Boischot, A. Ortega- Molina, C. Rosolen, G. Petit, P. G. Mezger, R. Schwartz, B. O. Ron- nang, R. E. Spencer, G. Nicolson, A. E. E. Rogers, M. H. Cohen, R. M. Martiroysan, I. G. Moiseyev, and J. S. Jatskiv, Differential VLBI measurements of the Venus atmosphere dynamics by balloons: VEGA project, Astron. and Astrophys., 254, 387–392, 1992. for Nozomi spacecraft, IVS CRL Technology Development Center News, No. 19, 37–40, 2001. Zuber, M. T., D. E. Smith, F. G. Lemoine, and G. A. 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Wind Assisted Ship PropulsionTechnologies – Can they Help in Emissions Reduction?
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Summary According to International Maritime Organization, emissions coming from global shipping are expected to increase 50% to 250% by the year 2050. This concern led to the introduction of various regulations that aims to encourage ship owners and builders to explore innovative renewable technologies. The main focus of this article is on wind-assisted ship propulsion technologies, as a complement to ship propulsion, such as rigid sail, soft sail, wing sail, kite, and Flettner rotor. These technologies are not widely accepted because ship owners have doubts due to the lack of real-life results and their implementation and effi ciency greatly depends on ship design and purpose. This article shows the progress in the fi eld of wind-assisted ship propulsion in the last 15 years which proved the concept as they have the potential to reduce fuel consumption, thus emissions, by double digits. The conclusion is drawn, from fuel savings percentages, that rotor and soft sails technologies have great potential in the future of the shipping industry. Wind Assisted Ship PropulsionTechnologies – Can they Help in Emissions Reduction? Tehnologije propulzije broda s pomoću vjetra – mogu li one pomoći u smanjenju emisija? Marko Zubčić University of Split Faculty of Maritime studies Department for Marine electrical engineering and IT E-mail: mzubcic@pfst.hr Marko Zubčić University of Split Faculty of Maritime studies Department for Marine electrical engineering and IT E-mail: mzubcic@pfst.hr Miro Petković University of Split Faculty of Maritime studies Department for Marine electrical engineering and IT E-mail: mpetkovic@pfst.hr Maja Krčum University of Split Faculty of Maritime studies Department for Marine electrical engineering and IT E-mail: mkrcum@pfst.hr Ivan Pavić University of Split Faculty of Maritime studies Department for Marine electrical engineering and IT E-mail: ipavic@pfst.hr DOI 10.17818/NM/2021/2.6 UDK 629.5.037:626.74 Review / Pregledni rad Paper accepted / Rukopis primljen: 4. 9. 2020. Sažetak KLJUČNE RIJEČI WASP kruto jedro krilno jedro rotorsko jedro kajt Flettner rotor Prema Međunarodnoj pomorskoj organizaciji, očekuje se da će se emisije koje stvara pomorska industrija na globalnoj razini povećati između 50% i 250% do 2050. Ova svijest dovela je do uvođenja različitih propisa koji imaju cilj ohrabriti brodovlasnike i brodograditelje te istraživati inovativne obnovljive tehnologije. Glavni je fokus ovoga članka na tehnologijama propulzije broda s pomoću vjetra kao dopuna propulziji broda kao što su: kruta jedra, mekana jedra, krilna jedra, kajt i Flettner rotor. Ove tehnologije nisu općenito prihvaćene jer brodovlasnici imaju sumnje zbog nedostatka stvarnih pouzdanih rezultata te njihova implementacija i djelotvornost uvelike ovise o dizajnu namjeni broda. Ovaj članak pokazuje napredak u području propulzije broda s pomoću vjetra u posljednjih 15 godina koji potvrđuje tu zamisao jer ima potencijal smanjiti potrošnju goriva, a time i emisije na dvoznamenkasti broj. Izvodi se zaključak na temelju postotaka uštede da rotorske i tehnologije mekanih jedara imaju velik potencijal u budućnosti brodarske industrije. 1. INTRODUCTION / Uvod Energy Effi ciency Design Index (EEDI) which states that all newly built ships, from 2013 and onwards, have to follow EEDI sets of mandatory carbon dioxide emissions reduction targets. Also, to ensure future production of more effi cient ships, reduction targets are tightened every fi ve years up until 2030. Reports [4], [5] submitted to the IMO Marine Environment Protection Committee (MEPC) pointed that the EEDI is only encouraging “mainstream” innovation. Proving that there has been no uptake of innovative measures that yield signifi cant savings, which are necessary to keep shipping’s CO2 emissions in line. To decrease carbon dioxide emissions and improve energy effi ciency in shipping activities, utilization of renewable energy solutions and technologies is considered a necessary direction. According to [6] EEDI is calculated: Energy Effi ciency Design Index (EEDI) which states that all newly built ships, from 2013 and onwards, have to follow EEDI sets of mandatory carbon dioxide emissions reduction targets. Also, to ensure future production of more effi cient ships, reduction targets are tightened every fi ve years up until 2030. Reports [4], [5] submitted to the IMO Marine Environment Protection Committee (MEPC) pointed that the EEDI is only encouraging “mainstream” innovation. Proving that there has been no uptake of innovative measures that yield signifi cant savings, which are necessary to keep shipping’s CO2 emissions in line. To decrease carbon dioxide emissions and improve energy effi ciency in shipping activities, utilization of renewable energy solutions and technologies is considered a necessary direction. According to [6] EEDI is calculated: Global shipping transport demand is increasing around 4% per year, while the world’s trade carried by sea reached over 90% [1]. Shipping is the most energy-effi cient mode of transport which is probably the reason why the sector has got away with ignoring the carbon dioxide emissions problem. In 2014, a greenhouse gas study presented by International Maritime Organization (IMO) [1], carbon dioxide emissions coming from global shipping are expected to increase 50% to 250% by the year 2050. IMO concluded that this rapid increase of emissions proves the need for energy effi ciency regulations, and made them eff ective by January 2013 [2]. The regulation requires all 5000 GT ships and above to record fuel and oil consumption and report them. As of March 2018, MARPOL Annex VI sets of regulations [3], became mandatory. Also, IMO introduced the 102 M. (1) where: – CO2 emission factor based on type of fuel used by given engine – cubic capacity correction factor (for chemical tankers, LNG carriers and RoPax) – correction factor to compensate deadweight losses through cargo-related equipment like cranes – capacity adjustment factor for any technical/regulatory limitation on capacity – coeff icient indicating the decrease in ship speed due to weather and environmental conditions – correction factor for ship-specific design elements correction factor for ship specific design elements – availability factor of individual energy eff iciency technologies. If we influence Peff(i), the main engine power requirement will be reduced, thus the overall EEDI value will be decreased. Wind energy has great potential and advantage since its availability is continuous at the open sea when comparing to the other renewable solutions [7] and can offer significant savings on existing ships [8]. For example, in [9] seasonal forecasting of winds, waves, and currents in the North Pacific were analyzed, with the conclusion that the western North Pacific is the most predictable region and therefore seasonal forecast data could be used for vessel routing and confirms the potential application of some wind-assisted technology. According to [10] wind assisted ship propulsion (WASP) technologies have the potential to decrease fuel consumption, thus emissions, by double digits. This leads to the conclusion that this renewable technology will play important role in the future of the shipping industry. Fuel savings, that can be achieved, depending on the design of the ship (rig and hull), the operating speed, and the wind speeds and directions experienced [10]. Also, it is noted that of the available wind assist technologies, kites and Flettner rotors have received the most attention concerning to helping reduce the fuel consumption and emissions from larger commercial ships. where: – ship speed at reference conditions – deadweight tonnage (DWT) rating for bulk ship and tankers; gross tonnage for passenger ships Rigid sails are a mature technology with low uncertainties on costs and with simple architecture with no huge motor. But, we must keep in mind that the aerodynamic effi ciencies on the vessels are limited by the tip speed ratio. Racing sailboats or foiling catamarans, in specifi c situations, can sail faster than the wind and achieve tip speed ratios above one, allowing their sails to obtain a higher propulsion effi ciency [11]. Also, the author noted when the ship is loaded with all the needs for her serving purpose and cargo, the effi ciency is reduced by the lack of ability to achieve the same tip speed ratios. – individual power of main engines – combined installed power of auxiliary engines – power of individual shaft motors divided by the effi ciency of shaft generators – auxiliary engine power reduction due to individual technologies for electrical energy effi ciency – main engine power reduction due to individual technologies for mechanical energy effi ciency – fuel use per unit of engine power In paper [12] power profi le for a rigid sail is proposed which could assist with modeling potential fuel savings and emission reductions. Strengths, weaknesses, opportunities, and threats (SWOT) analysis was conducted for rigid sail technology by [13]. The analysis recognized that strengths are lower fuel consumption, emission reduction, lower operating costs, improved vessel stability, propulsion in emergencies, and less volume for fuel bunkering. Weaknesses are safety for the crew, additional operational cost, initial cost, interference with cargo operations, increased weight of the ship, additional training, and workload for the crew. Opportunities are the implementation of IMO regulations, higher fuel costs which make this approach economically viable, marketing regarding brand presentation, slow steaming. Threats are shipping industry suspicion, lower fuel cost, alternative or new fuels, route changing, thus placing the ship in the conditions that make rigid sail unfavorable and overall complex structure (hardware and software solutions). 1. INTRODUCTION / Uvod Petković et al: Wind Assisted Ship PropulsionTechnologies... 2.2. Soft sails / Mekana jedral Soft sails are fl exible sails similar to traditional sails characterized by very diff erent innovative features and are automated to a great extent i.e. duplex rigs, freestanding square rigs, rotating masts etc. Some of the innovative technologies are Pinta- Rig, DynaRig, Delta wingsail and Fastrigs. DynaRig became a popular soft sail technology mainly because of its easy to use characteristics and self-sustainability. The main characteristic is the mast, which is lightly guyed and rotatable, making maneuvres of DynaRig safe and secured. When comparing to the wing sail, its lift coeffi cients are lower, but by utilizing the larger surface areas greater lift forces are achieved [14]. It is noted that when sailing upwind effi ciency of this type of sail decreases. In [15] a coastal sailing vessel (3000 DWT) is proposed, aiming to have zero carbon emissions by utilizing the DynaRig soft sail system. By using this technology total required thrust was reduced by 61%. In [16], a sailing Mult- 103 “Naše more” 68(2)/2021., pp. 102-109 Figure 1 Cargo Vessel “Eco liner” Slika 1. Teretni brod „Ecoliner“ Source: (WASP (Ecoliner) - Dykstra Naval Architects, 2019) [16] Figure 1 Cargo Vessel “Eco liner” Slika 1. Teretni brod „Ecoliner“ Figure 1 Cargo Vessel “Eco liner” Slika 1. Teretni brod „Ecoliner“ Source: (WASP (Ecoliner) - Dykstra Naval Architects, 2019) [16] Slika 1. Teretni brod „Ecoliner“ Source: (WASP (Ecoliner) - Dykstra Naval Architects, 2019) [16] Source: (WASP (Ecoliner) - Dykstra Naval Architects, 2019) [16] Figure 1 Illustration of forces acting on wing sail; FT – thrust force, FH – drift force, FL – lift force, FD – drag force, θ – the angle between apparent wind and ship’s longitudinal line. Slika 1. Ilustracija sila koje djeluju na krilno jedro; Fr – porivna sila, Fh – plovna sila, Fl – sila uzgona, Fd – sila povlačenja, θ – kut između prividnog vjetra i longitudinalne linije broda Source: Authors purpose Cargo Vessel “Eco liner” 8000 DWT was proposed. In [17], the characteristics of the “Eco liner” has been compared with similar-sized motorized ship under given estimated time of arrival by using computational fl uid dynamic (CFD) simulations and weather routing programs. At a cruise speed of 12 knots, simulations showed fuel savings up to 35% and approximately 22% fewer costs of operation. 2.2. Soft sails / Mekana jedral When compared to a similar conventional ship, “Eco liner” has a 3% cost benefi t after 10 years of operation if we consider capital costs and depreciation. 2.3. Wing sails / Krilna jedrai The wing sail profi le and the thickness of the airfoil shape can generate a strong lift eff ect and provide a strong propulsive force while decreasing the induced drag that slows down the ship [14].The operating principle of the wing sail is to maximize the aerodynamic lift force by rotating to the optimum wind angle of attack. By using mast which rotates 360˚, the wing sail works in diff erent wind angles and even upwind. Figure 1 illustrates the geometrical relationship between forces acting on the wing sail due to apparent wind. Figure 1 Illustration of forces acting on wing sail; FT – thrust force, FH – drift force, FL – lift force, FD – drag force, θ – the angle between apparent wind and ship’s longitudinal line. Figure 1 Illustration of forces acting on wing sail; FT – thrust force, FH – drift force, FL – lift force, FD – drag force, θ – the angle between apparent wind and ship’s longitudinal line. Slika 1. Ilustracija sila koje djeluju na krilno jedro; Fr – porivna sila, Fh – plovna sila, Fl – sila uzgona, Fd – sila povlačenja, θ – kut između prividnog vjetra i longitudinalne linije broda Source: Authors According to [18] wing sail should be as small as possible and therefore should apply high lift devices, also sails or their skins should be reefable from the wing structure. In [19], [20] a collapsible wing sail is proposed with double fl aps. Also, the best confi guration of parameters was investigated and using a numerical simulation method the aerodynamic performance of the new wing sail was analyzed. These papers show that double-fl ap wing sails provide more thrust force in comparison to arc sail, variable-chamber sail [21], and NACA0021. Another case study [22] states that with wing sail technology, on a route from Ras Tanura (Saudi Arabia) to Yokohama (Japan), 2.6 % fuel savings can be achieved per trip. Four wing sails were considered in this case study. Numerical analysis of aerodynamic performances was conducted by [23] for a two-element wing sail. Also, it is stated that multi- element wing sails are diffi cult to operate so there is a need to thoroughly investigate the fl ow around the wing sail. The paper Slika 1. 2.3. Wing sails / Krilna jedrai Ilustracija sila koje djeluju na krilno jedro; Fr – porivna sila, Fh – plovna sila, Fl – sila uzgona, Fd – sila povlačenja, θ – kut između prividnog vjetra i longitudinalne linije broda Source: Authors Slika 1. Ilustracija sila koje djeluju na krilno jedro; Fr – porivna sila, Fh – plovna sila, Fl – sila uzgona, Fd – sila povlačenja, θ – kut između prividnog vjetra i longitudinalne linije broda Source: Authors investigates the infl uence of the construction parameters on the lift and drag coeffi cients. The WindShip project [24] proposed a new rigid concept of a wing sail, as a case study ship a Product Carrier 50000 DWT was selected. For the given wind direction and speed, a program was developed to predict the ship’s speed, rudder angles, and drift. Within areas with strong winds wing sail technology achieved 10% fuel savings when compared to a similar conventional Product Carrier. But, it is noted that 104 M. Petković et al: Wind Assisted Ship PropulsionTechnologies... Figure 2 Forces acting on the towing kite; FL – Lift force, Ft – Total force, Fd – A drag force Slika 2. Sile koje djeluju na kajt koji tegli; Fl – sila podizanja, Ft – ukupna sila, Fd – sila povlačenja Source: Authors Figure 2 Forces acting on the towing kite; FL – Lift force, Ft – Total force, Fd – A drag force Slika 2. Sile koje djeluju na kajt koji tegli; Fl – sila podizanja, Ft – ukupna sila, Fd – sila povlačenja Figure 2 Forces acting on the towing kite; FL – Lift force, Ft – Total force, Fd – A drag force Slika 2. Sile koje djeluju na kajt koji tegli; Fl – sila podizanja, Ft – ukupna sila, Fd – sila povlačenja Source: Authors Source: Authors Source: Authors carrier “Aghia Marina”). the manufacturer claims that 10 – 15 % fuel saving can be achieved and up to 2 MW of power generation under favorable wind conditions [28]. In paper [29], the power output of a kite on five potential trade routes is estimated. It is calculated that towing kite can provide between 127 and 461 kW of power generation resulting in 1 to 32 % of fuel savings, depending on the ship type. In [30], an analytical model is used to evaluate the performance of a towing kite as an auxiliary power source. 2.5. Rotor sails – Flettner rotor / Rotorska jedra – Flettner rotor The rotor sails or Flettner rotor is a rotating cylinder vertically installed on the deck, the rotation of the cylinder is achieved by using an electrical motor. By utilizing the Magnus effect it generates lift force which is perpendicular to the apparent wind vector as shown in Figure 3 b). The direction of the lift force vector depends on the rotational direction of the cylinder. The first rotors were installed on the ship named Backau in 1925. In 1926 it crossed the Atlantic and anchored in the port of New York. The concept was proven technically sound and plausible but was abandoned because of the economical situation regarding low oil prices [31]. In [8] it is claimed that rotor sails could achieve up to 20% fuel savings for commercial cargo ships, assuming three rotors were installed. The lift and drag coefficient study for the 2D case was conducted by [32] and it showed that rotor spin ratio has significant implications for the flow control strategies. The influence of the Thom disc on the lift and drag coefficient was studied by [33] and is illustrated in Figure 3 a). 2.3. Wing sails / Krilna jedrai On a tanker (50,000 DWT) with 320 m2 towing kite, themodel showed up to 10% of fuel savings on a 10 m/s wind speed and up to 50% savings at 15.6 m/s. The performance of towing kites proves to be volatile [29], but they are a low emissions solution that should be considered. during voyages with high average speeds, in a less windy area, fuel savings could be marginal. Another concept of wing sail was studied during the Wind Challenger project [25] on the Bulk Carrier “UT Wind Challenger” 18000 DWT. The result was the development of the energy prediction program which predicts operational performance, also on the route Yokohama - Seattle simulation showed fuel savings up to 22%. In another project [26], a wing sail concept for the KVLCCM type hull is proposed. Under certain wind and ship speeds computational fluid dynamics (CFD) simulation showed the reduction of thrust, required by the main engine, for approximately 10% with proposed wing sails. The variables investigated in the paper are true wind speed, ship speed, wing sail area, and aspect ratio. Maximum power reduction in this study was achieved for the case were total wing sail area and the height of the sails were kept constant while the variable was the number of the sails. The reduction of 14 % is achieved for 8 wing sails and a true wing angle of 80 °. 2.4. Kites / Kajtovi The operating principle of a kite is to tow the ship when deployed off his bow and Figure 2 illustrates forces acting on the towing kite. They operate at an altitude between 100 – 300 m to tame the power of the higher altitude winds. In paper [27] parameters are used, based on experimental data, to create the point-mass model. A path following strategy was designed so that the kite can follow an eight- shaped trajectory using a simple proportional controller. The result of their simulation showed that a 15 m2 kite was enough to tow a small fishing boat, also a 30 m2 kite was enough to tow a zero greenhouse gas emissions vessel 30.5 meters long by 12.80 meters wide. Skysails is one of the prominent kite technology’s and some ships have used or are using it (general Cargo ship “Michael A.”, container/cargo ship “M/V Theseus”, Bulk 105 “Naše more” 68(2)/2021., pp. 102-109 Figure 3 a) Illustration of Magnus eff ect; FL –Lift force, Fd –Drag force, b) Illustration of Flettner rotor and Thom disc Slika 3. a) Ilustracija Magnus efekta; FL – Sila podizanja, Fd – Sila povlačenja; b) ilustracija Flettner rotora i Thom diska Authors Figure 3 a) Illustration of Magnus eff ect; FL –Lift force, Fd –Drag force, b) Illustration of Flettner rotor and Thom disc Slika 3. a) Ilustracija Magnus efekta; FL – Sila podizanja, Fd – Sila povlačenja; b) ilustracija Flettner rotora i Thom diska Authors Source: Authors Source: Authors In 2015 Ro-Ro Carrier “Estraden” (9700 DWT) was retrofitted with rotors, 18 m in height and 3 m in diameter, made by Norsepower [38]. Sea trials conducted on a route between the Netherlands and the United Kingdom showed a 2.6% fuel saving with only one rotor, after installing second rotor trials showed 6.1% fuel savings. Analytical evaluation of net generated power for different values of rotation coefficient was performed by [34], net generated power decreased as the coefficient of rotation increased. Evaluation of the aerodynamic performance of the Flettner rotor was done in [35] by using CFD simulations which showed the importance of 3D simulations over 2D simulations. While evaluating CFD simulation results, in [29] a performance model for power saving simulation of Flettner rotors is proposed. A cargo ship (5500 DWT) was used as a case study, with three Flettner rotors (27m in height and 4m in diameter) installed. 2.4. Kites / Kajtovi The simulation showed a 50% power reduction used by the main engine. In another study [36], the authors followed the performance and handling tests of the Panamax Bulk Carrier with installed Integrated Greenwave MK1 Rotor. A scaled model of a 182 m Bulk carrier with Flettner rotor installed, was used. The results of the experimental tests were that Flettner rotor provided 50% of nominal thrust during light wind conditions and 100% during moderate winds. Currently, there are six ships with installed rotor technology. All six are stated in the Table 1. 3. ANALYSIS OF WASP TECHNOLOGY RESULTS / Analiza rezultata WASP tehnologija Summary of results from WASP technology’s literature, discussed in this paper, is presented in Table 2. Based on the literature, this paper presents that wing sail technology can achieve fuel saving in the range of 2.6 – 22 %, depending on the route, ship type, sail angle, number of sails. Soft sail, even though having a lower lift coefficient, can achieve fuel saving up to 35 %. For DynaRig soft sail system,it is reported that 61 % reduction of main engine power is possible. Towing kite can provide 1- 32 % fuel savings. Simulations results show that for Flettner rotor technology fuel savings up 50 % can be expected. From the results, it can be seen that Flettner rotor and soft sail technologies have the most potential. In 2010 the Cargo ship “Enercon E-ship” (10500 DWT) came into operation with four rotors, 25m high and 4 m in diameter, installed onboard [37]. On the voyage between Germany and Portugal, fuel consumption was decreased by 23 %. Table 1 Ships in operation with installed Flettner rotor Tablica 1. Brodovi koji djeluju s ugrađenim Flettner rotorom Ship Type Year of Built No. of rotors Rotor dimensions (H x d) [m] Fehn Pollux [39] General Cargo 1996 1 18 x 3 Estraden [38] Ro-Ro Cargo 1999 2 18 x 3 Maersk Pelican [40] Crude Oil Tanker 2008 2 30 x 5 E-Ship 1 [37] General Cargo 2010 4 25 x 4 Viking Grace [41] Ro-Ro/Passenger 2013 1 24 x 4 Afros [42] Bulk Carrier 2018 4 / Source: Authors Source: Authors M. Petković et al: Wind Assisted Ship PropulsionTechnologies... Table 2 Summary of wind-assisted ship propulsion technology Tablica 2. Sažetak tehnologija propulzije broda s pomoću vjetra Table 2 Summary of wind assisted ship propulsion technology Tablica 2. Sažetak tehnologija propulzije broda s pomoću vjetra WASP tech. Ref. Methodology Results Real ship / Simulation Fuel savings Rigid sails [12] Methodology (power profi le) is developed by which key performance values can be calculated and displayed in a standardized format by using a virtual wind tunnel. Power profi le will outline key performance characteristics and allow comparisons to be made between diff erent types of rigid sails. 3. ANALYSIS OF WASP TECHNOLOGY RESULTS / Analiza rezultata WASP tehnologija Simulation [13] SWOT analysis Strengths, weaknesses, and opportunities are emphasized for rigid sail technology Simulation Soft sails [14] Developed software to calculate fuel- saving performance of three wind- assisted ship propulsion technologies – the Flettner rotor, the Soft sails - DynaRig, and a wing sail Comparison of DynaRig soft sail with Wing sail showed lower lift coeffi cients of DynaRig, but greater lift force can be achieved. Simulation [15] Performance of zero carbon emission coastal sailing vessel is simulated Simulation showed 61% reduction of required thrust Simulation [17] Using CFD simulations and weather routing programs “Eco liner” has been compared with similar-sized motorized ship The simulation showed up to 35% fuel savings and approximately 22% fewer costs of operation Simulation 35% Wing sails [19] [20] Using numerical simulations methods aerodynamic performance of collapsible wing sail was studied Double fl ap wing sails provide more thrust force in comparison to other wing sail technologies Simulation [22] ANSYS is used to perform simulation- based study On a route from Ras Tanura to Yokohama, 2.6% fuel savings can be achieved per trip Simulation 2.6% [23] Numerical analysis of aerodynamic performance for two-element wing sail Infl uence of the construction parameters on the lift and drag coeffi cients Simulation [24] A new rigid concept of wing sail with realistic simulations based on measured and simulated performance Rigid wing sail mounted on a case study ship of a Product Carrier achieved 10% fuel savings when compared to similar conventional Product Carrier Real ship 10% [25] Development of energy prediction program for Wind Challenger project on the case study ship The simulation showed fuel savings of up to 22% on the route from Yokohama to Seattle Simulation 22% [26] CFD simulation of a wing sail concept for KVLCCM type hull Under certain wind and ship speeds simulation showed a reduction of required thrust, by the main engine, for approximately 10%. Also, the reduction of 14% is achieved for 8 wing sails and a true wing angle of 80 degrees. 3. ANALYSIS OF WASP TECHNOLOGY RESULTS / Analiza rezultata WASP tehnologija Simulation Kites [27] Based on experimental data parameters are used to create a point mass model The simulation showed that 30 m2 kite was enough to tow zero carbon emission vessel 30.5 m long and 12.8 m wide Real ship [28] Performance test of Skysails kite is conducted on a general Cargo ship 10 - 15 % fuel savings and up to 2 MW of power generation can be achieved under favorable wind conditions Real ship 10 – 15% [29] The numerical model of a kite on fi ve potential trade routes Towing kite can provide between 127 and 461 kW of power generation resulting 1 to 32% of fuel savings Real ship 1 – 32% [30] Analytical model for towing kite performance evaluation Tanker with 320 m2 towing kite, the model showed 10% of fuel savings on a 10 m/s wind speed and up to 50% savings at 15.6 m/s Simulation 10 – 50% Rotor sails [8] Techno-economic and environmental analysis study Authors claim that rotor sails could achieve up to 20% fuel savings Simulation 20% [32] Using the fi nite element method the fl ow past a rotating cylinder in 2D is calculated Rotor spin ratio has signifi cant implication for the fl ow control strategies Simulation [33] CFD simulation of spinning cylindrical rotors for maritime propulsion Infl uence of the Thom disc on the lift and drag coeffi cient Simulation [34] Analytical evaluation of net generated power Net generated power decreases as the rotation coeffi cient increases Simulation [35] Aerodynamic performance of Flettner rotor by using CFD simulations Importance of 3D simulations over 2D simulations Simulation [29] A performance model for power saving simulation of Flettner rotors On a case study, Cargo ship simulation showed 50% power reduction used by the main engine Simulation 50% [36] Authors followed tests on a scaled model of a 182 m Bulk carrier with installed Flettner rotor Experimental tests showed that Flettner rotor provided 50% of nominal thrust during light wind conditions and 100% during moderate winds Simulation 50 – 100% [37] Experimental tests on the Cargo ship “Enercon E-ship” On the voyage between Germany and Portugal, fuel consumption was decreased by 23% Real ship 23% [38] Sea trials on Ro-Ro Carrier “Estraden” retrofi tted with rotor sails Sea trials showed 2.6% fuel savings with only one rotor, after installing second rotor trials showed 6.1% fuel savings Real ship 2.6 – 6.1% “Naše more” 68(2)/2021., pp. 4. CONCLUSION / Zaključak Wind technologies that directly contribute to ship’s propulsion, were presented in this paper. This segment of renewable energy sources is potentially of great meaning to a shipping industry when considering the requirements from IMO for emissions reduction. This conclusion is drawn from the percentages of fuel savings achieved, thus reduction of CO2, NOx, SO , and PM emissions. Due to diff erent construction designs, diff erent WASP technologies contribute more or less to ship propulsion. The utilization of these technologies depends on the ship deck construction, speed, and ship routing (weather situation along the route). WASP technologies are not widely accepted because ship owners have doubts due to the lack of real-life results regarding fuel savings, for example, from 1999 till 2020 there were only six commercial ships in the world fi tted with Flettner rotors. The fact that simulations provide high fuel saving is the motivation for the shipbuilders and owners to consider these technologies as a measure for compliance with IMO emissions regulations. Also, the implementation of fuel cells, solar energy, and other energy-effi cient technologies should be considered for emissions reduction for IMO regulations compliance and these technologies will be scope in our future work. [15] Surplus, D. C. (2011). “B9 Ships: Sail and Virtual Bio-Methane Powered Coastal Vessels”. LCS 2011 - International Conference on Technologies, Operations, Logistics and Modelling for Low Carbon Shipping. [16] WASP (Ecoliner) - Dykstra Naval Architects, Dykstra Naval Architects (2019). Available at: http://www.dykstra-na.nl/designs/wasp-ecoliner/ [accessed 16/6/2020] [17] van Hasselt, R., Feenstra, B. (2015). “Sail into a sustainable future Factsheets hybrid shipping Hybrid shipping market opportunities Niche market”. Available at: http://www.nsrsail.eu/wp-content/uploads/2015/06/Factsheet- Brochure_SAIL_2015.pdf [accessed 18/6/2020] [18] Kralj, D. M., Klarin, B. (2016).”Wing sails for hybrid propulsion of a ship”. J. Sustain. Dev. Energy, Water Environ. Syst., Vol. 4, No. 1, pp. 1-13. https://doi. org/10.13044/j.sdewes.2016.04.0001 [19] Li, D., Li, G., Dai, J., Li, P. (2017). “A new type of collapsible wing sail and its aerodynamic performance”. Proceedings of the International Conference on Off shore Mechanics and Arctic Engineering - OMAE, Vol. 10. https://doi. org/10.1115/OMAE2017-61084 [20] Li, D., Zhang, Y., Li, P., Dai, J., Li, G. (2019). “Aerodynamic Performance of a New Double-Flap Wing Sail”. Polish Marit. Res., Vol. 26, No. 4, pp. 61-68. https://doi. org/10.2478/pomr-2019-0067 [21] Li, Q., Nihei, Y., Nakashima, T., Ikeda, Y. (2015). “A study on the performance of cascade hard sails and sail-equipped vessels”. Ocean Eng., Vol. 98, pp. 23-31. REFERENCES / Literatura Further technical and operational measures for enchancing the energy effi ciency of international shipping, The Existing Shipping Fleet’s CO2 Effi ciency MEPC 68/INF24/REV1. [Online]. Available at: http://www.imo.org/. vA – apparent wind speed [m/s]fi cL – lift coeffi cient fi [6] Ren, H., Ding, Y., Sui, C. (2019). “Infl uence of EEDI (Energy Effi ciency Design Index) on Ship-Engine-Propeller Matching”. J. Mar. Sci. Eng., Vol. 7, No. 12, p. 425. https://doi.org/10.3390/jmse7120425 [6] Ren, H., Ding, Y., Sui, C. (2019). “Infl uence of EEDI (Energy Effi ciency Design Index) on Ship-Engine-Propeller Matching”. J. Mar. Sci. Eng., Vol. 7, No. 12, p. 425. https://doi.org/10.3390/jmse7120425 cD – drag coeffi cientfi cD – drag coeffi cientfi D gfi The effi ciency of these technologies is defi ned by their lift and drag force ratio. Paper [44] reports that for towing kite technology value of lift and drag ratio is from 3 to 8, depending on relative power setting. Paper [43] reports that Skysail towing kite has a lift to drag ratio of 5. For Flettner rotor lift to drag ratio is a function of a spin ratio. In [45] author reported that a lift to drag ratio depends on the ratio of the diameters of Thom disc and spinning rotor. Lift to drag ratio is a non linear function, for spin ratio interval from 0 to 2, its value increases achieving maximum when the spin ratio is around 2. When the value of spin ratio is from 2 to 8, a lift to drag ratio decreases. The maximum values of lift to drag ratio ranges from 2.5 to 6.5. In the study [46] authors reported nine lift to drag ratio curves where each curve diff ers one from another in terms of shape and maximum value. For example, one curve has a maximum value of 2.5, where another curve has a maximum value of 13.5. This shows the discrepancy in research data and proves the need for thorough research in this fi eld. [7] Gudelj, A., Krčum, M. 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Naše more, Vol. 66, No. 1, pp. 1-9. https://doi.org/10.17818/NM/2019/1.1 Where: FL – lift force [N] FD – drag force [N] ρ – air density [kg/m3] A – projected area of the rotor [m2] vA – apparent wind speed [m/s] cL – lift coeffi cient cD – drag coeffi cientfii FL – lift force [N] FD – drag force [N] ρ – air density [kg/m3] A – projected area of the rotor [m2] vA – apparent wind speed [m/s] cL – lift coeffi cient cD – drag coeffi cientfi [4] IMO (2014). EEDI Database - Review of Status of Technological Development - MEPC 67-INF3 - Third IMO GHG Study 2014 - Final Report (Secretariat). [Online]. Available at: http://www.imo.org/. [4] IMO (2014). EEDI Database - Review of Status of Technological Development - MEPC 67-INF3 - Third IMO GHG Study 2014 - Final Report (Secretariat). [Online]. Available at: http://www.imo.org/. [5] IMO (2015). 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IN VENTO 2018: Proceedings of the XV Conference of the Italian Association for Wind Engineering, pp. 110-123. https://doi.org/10.1007/978-3-030-12815-9_9 [43] Costello, S., Costello, C., François, G., Bonvin, D. (2015). “Analysis of the maximum effi ciency of kite-power systems”. J. Renew. Sustain. Energy, Vol. 7, No. 5, p. 053108. https://doi.org/10.1063/1.4931111 [32] Mittal, S., Kumar, B. (2003). “Flow past a rotating cylinder”. Journal of Fluid Mechanics, No. 476, pp. 303-334. https://doi.org/10.1017/S0022112002002938 [44] Hummel, J., Göhlich, D., Schmehl, R. (2019). “Automatic measurement and characterization of the dynamic properties of tethered membrane wings”. Wind Energy Science, Vol. 4, No. 1, pp. 41-55. https://doi.org/10.5194/wes-4-41-2019 [33] Craft, T. J., Iacovides, H., Johnson, N., Launder, B. E. (2012). “Back to the future: Flettner-Thom rotors for maritime propulsion?”. THMT-12. Proceedings of the Seventh International Symposium On Turbulence, Heat and Mass Transfer, Palermo, Italy, 24-27 September, 2012, p. 10. https://doi.org/10.1615/ ICHMT.2012.ProcSevIntSympTurbHeatTransfPal.1150 [45] Seifert, J. (2012). “A review of the Magnus eff ect in aeronautics”. Prog. Aerosp. Sci., Vol. 55, pp. 17-45. https://doi.org/10.1016/j.paerosci.2012.07.001 [46] De Marco, A., Mancini, S., Pensa, C. (2014). “Preliminary Analysis for Marine Application of Flettner Rotors”. 2nd International Symposium on Naval Architecture and Maritime (INT-NAM 2014), Yıldız Technical University, Istanbul, Turkey. DOI: 10.13140/2.1.4921.3765. [34] Lele, A., Rao, K. V. S. (2017). “Net power generated by fl ettner rotor for diff erent values of wind speed and ship speed”. 2017 International Conference on Circuit, Power and Computing Technologies (ICCPCT), Apr. 2017, pp. 1-6. https://doi.org/10.1109/ICCPCT.2017.8074170 “Naše more” 68(2)/2021., pp. 102-109
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The subxiphoid view cannot replace the apical view for transthoracic echocardiographic assessment of hemodynamic status
Critical care
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Abstract Introduction: This prospective study aimed to assess whether use of the subxiphoid acoustic window in transthoracic echocardiography (TTE) can be an accurate alternative in the absence of an apical view to assess hemodynamic parameters. Methods: This prospective study took place in a teaching hospital medical ICU. Over a 4-month period, TTE was performed in patients admitted for more than 24 hours. Two operators rated the quality of parasternal, apical, and subxiphoid acoustic windows as Excellent, Good, Acceptable, Poor, or No image. In the subpopulation presenting adequate (rated as acceptable or higher) apical and subxiphoid views, we compared the left ventricular ejection fraction (LVEF), the ratio between right and left ventricular end-diastolic areas (RVEDA/LVEDA), the ratio between early and late mitral inflow on pulsed Doppler (E/A ratio), the aortic velocity time integral (Ao VTI), and the ratio between early mitral inflow and displacement of the mitral annulus on tissue Doppler imaging (E/Ea ratio). Results: An adequate apical view was obtained in 80%, and an adequate subxiphoid view was obtained in 63% of the 107 patients included. Only 5% of patients presented an adequate subxiphoid view without an adequate apical view. In the subpopulation of patients with adequate apical and subxiphoid windows (n = 65), LVEF, E/A, and RVEDA/LVEDA were comparable on both views, and were strongly correlated (r > 0.80) with acceptable biases and precision. However, the Ao VTI and the E/Ea ratio were lower on the subxiphoid view than on the apical view (18 ± 5 versus 16 ± 5 cm and 9.6 ± 4.6 versus 7.6 ± 4 cm, respectively, P = 0.001 for both). Conclusions: An adequate TTE subxiphoid window was obtained in fewer than two thirds of ICU patients. In addition to the classic indication for the subxiphoid window to study the vena cava and pericardium, this view can be used to study right and left ventricular morphology and function, but does not provide accurate hemodynamic Doppler information. ICU echocardiographers should therefore record both apical and subxiphoid views to assess comprehensively the cardiac function and hemodynamic status. subxiphoid. As recommended in guidelines, the appropri- ate window corresponds to the Doppler mode with the best alignment obtained between the ultrasound beam and the direction of blood flow [5]. RESEARCH Open Access Open Access © 2013 Maizel 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 For that reason, most para- meters recorded for hemodynamic assessment classically require an apical window: left ventricular ejection fraction (LVEF) [6,7], ratio between early and late mitral inflow (E/ A) [8], ratio between early mitral inflow and displacement of the mitral annulus on tissue Doppler imaging (E/Ea) [8], velocity time integral of aortic blood flow (Ao VTI) [9], and the ratio between right (RVEDA) and left (LVEDA) ventricular end-diastolic area [7]. However, many factors in the ICU can interfere with apical image quality. More The subxiphoid view cannot replace the apical view for transthoracic echocardiographic assessment of hemodynamic status Julien Maizel1, Ahmed Salhi1, Christophe Tribouilloy2, Ziad A Massy1, Gabriel Choukroun1 and Michel Slama1* * Correspondence: slama.michel@chu-amiens.fr 1Medical Intensive Care Unit, Department of Nephrology, Amiens University Medical Center, Amiens, France and INSERM U-1088, Jules Verne University of Picardie, Amiens, France Full list of author information is available at the end of the article Maizel et al. Critical Care 2013, 17:R186 http://ccforum.com/content/17/5/R186 Introduction Transthoracic echocardiography (TTE) has become the leading noninvasive examination to assess the hemody- namic status of patients hospitalized in intensive care units (ICUs) [1-3]. It allows the physician to study noninvasively the contractility, relaxation, and fluid responsiveness of the two ventricles [4]. All parameters must be recorded in one of the following three windows: parasternal, apical, or * Correspondence: slama.michel@chu-amiens.fr 1Medical Intensive Care Unit, Department of Nephrology, Amiens University Medical Center, Amiens, France and INSERM U-1088, Jules Verne University of Picardie, Amiens, France Full list of author information is available at the end of the article Maizel et al. Critical Care 2013, 17:R186 http://ccforum.com/content/17/5/R186 Page 2 of 8 Page 2 of 8 sample cursor placed in the lateral mitral annulus, and aor- tic blood flow was measured with the sample volume placed at the aortic annulus. The size of the sample volume was not modified between apical and subxiphoid views. specifically, in this setting, the lung interposition between the probe and the heart, the presence of mechanical venti- lation, the inability to position the patient in left-sided decubitus, tachypnea, and the presence of bandages or tubes on the chest can alter the quality of the images obtained on apical and parasternal views. The two operators then blindly reviewed the quality of the 2D images recorded with these windows offline on a computer (General Electric Healthcare, Fairfield, CT, USA), according to the following scoring system: Excellent (visualization of the four chambers with complete endo- cardial visualization of both ventricles); Good (visualiza- tion of the two ventricles with complete endocardial visualization of both ventricles); Acceptable (visualization of both ventricles, but short segments of endocardium are not correctly visualized); Poor (the endocardium cannot be visualized in most portions of the ventricles); and No image (no visualization of the ventricles). An adequate acoustic window was defined by an acceptable, good, or excellent score. Each physician separately scored the video recording of the three windows (parasternal, apical, and subxiphoid) and compared their results. When both scores were identical, the final score was accepted. When the two scores were different, the physicians jointly visualized the video, discussed their points of view, and reached a con- sensus to establish a final score. To complete the examination in this setting, the echo- cardiographer may perform transesophageal echocardio- graphy. However, transesophageal echocardiography is more invasive and can be difficult to perform, especially in nonintubated ICU patients. Introduction In this setting, use of the transthoracic subxiphoid view can be an attractive alter- native to transesophageal echocardiography for less- experienced operators who may be reluctant to perform an invasive examination. The subcostal view is classically used to study respiratory variations of the inferior vena cava and the presence of pericardial effusion. This view can provide additional hemodynamic parameters, such as LVEF, mitral or aortic flows, and RV/LV areas. Although the subxiphoid view does not provide the same alignment as the apical view, it is not known to what degree this different alignment affects the results of the hemodynamic examination. To address this issue, we tried to determine the accuracy of the subxiphoid window to record various echocardio- graphic parameters usually recorded on the apical view for hemodynamic assessment. In the subpopulation of patients with adequate apical and subxiphoid windows (scored excellent, good, or accepta- ble), LVEF (according to the Monoplane Simpson method) and RVEDA/LVEDA ratio were measured on both the apical and subxiphoid 2D cine-loops. The mitral peak E velocity (E), peak A velocity (A), E/A ratio, Ao VTI, and E/Ea ratio were measured on Doppler images in the apical and subxiphoid windows. All data were the average of three end-expiratory measurements (excluding outliers). In the presence of an outlier, an additional assessment was recorded. In the subxiphoid window, LVEF and RVEDA/ LVEDA were recorded on a longitudinal four-chamber view visualizing both right and left ventricles in their lar- gest dimensions. On a modified four-chamber view, the operator tried to obtain the best alignment between flow and the Doppler axis by obtaining the highest maximum Doppler velocity to record mitral and aortic flows on the subxiphoid view. Materials and methods Patients In accordance with French legislation, the local institu- tional review board (CPP Nord-Ouest II, Amiens Univer- sity Hospital, France) approved the study protocol, and all patients or their relatives gave their informed consent. This single-center prospective study was performed in an eight-bed teaching hospital medical ICU (Amiens, France). Over a 4-month period, all patients admitted to the ICU were included in the study, except when one of the two experienced echocardiographers (JM and AS) was absent and except for patients admitted to the unit for less than 24 hours. Patient characteristics were recorded. Demographic data Patient characteristics are presented in Table 1. Supra- ventricular arrhythmia (atrial fibrillation and atrial flutter) was reported in 23 (21%) patients. The admission diagnoses were shock in 35%, respiratory distress in 23%, acute renal failure in 10%, cardiac arrest in 5%, severe sepsis in 4%, deliberate drug overdose in 5%, scheduled postoperative surveillance in 5%, and other (seizures, pancreatitis, ketoacidosis) in 13%. A higher mean number of the five parameters (LVEF, Ao VTI, E/A, E/Ea, and RVEDA/LVEDA) was obtained on the apical view than on the subxiphoid view (3.7 ± 1.9 and 2.9 ± 2.2, respectively; P = 0.001). When considered sepa- rately, each parameter was recorded significantly more frequently on the apical view than on the subxiphoid view (Table 2). The subpopulation of 65 patients with adequate apical and subxiphoid windows were not significantly different from the overall population, except for the proportion of acceptable apical windows (27% versus 21%; P = 0.04 for the overall population and subpopulation, respectively). The various parameters obtained on each of these two views were compared in this group of 65 patients (Table 3). No significant difference was observed for the parameters based on the two-dimensional mode: LVEF, RVEDA, LVEDA, and the RVEDA/LVEDA ratio. In the Doppler mode, Ao VTI, E, A, Ea, and E/Ea ratio were significantly decreased on the subxiphoid view, suggesting inadequate alignment between the cursor and blood flow. However, E and A velocities on the subcostal view were underesti- mated in the same proportion, so the E/A ratio was equiva- lent to that observed on the apical view. Table 1 Patient characteristics of the overall population Overall population N = 107 Age (years) 63 ± 16 Men, n (%) 59 (55) SAPS II 49 ± 20 BMI, kg/m2 28 ± 8 COPD, n (%) 26 (24) Mechanical ventilation, n (%) VC PSV PEEP, cm H2O 48 (45) 40 (37) 8 (7) 3.4 ± 1.7 MAP, mm Hg 79 ± 17 HR, bpm 97 ± 23 Arrhythmia, n (%) 23 (21) Catecholamines, n (%) 36 (34) Tubes, bandages, n (%) Chest Abdomen 10 (9) 6 (6) 4 (4) Table 1 Patient characteristics of the overall population Similar differences were observed when only patients with a history of COPD or mechanically ventilated patients were considered (data not shown). A strong correlation was observed between apical and subxiphoid values for all parameters (Figure 1). The Bland-Altman graphs are presented in Figure 1. Measurements The mean number of adequate acoustic windows per patient was 2.2 ± 0.9. An adequate parasternal view was obtained in 69% of patients; an adequate apical view was obtained in 86% of patients; and an adequate subxiphoid view was obtained in 66% of patients. The proportion of adequate views was significantly higher for the apical window than for the subxiphoid window for the overall population and the subpopulation of mechanically venti- lated patients and was close to significant in COPD patients (Table 2). Three adequate views were obtained in 45% of patients; two adequate views were obtained in 37%; only one adequate view was obtained in 10%; and no adequate window was obtained in 8% of patients. An adequate subxiphoid view but no adequate apical view was obtained in only 5% of patients. The proportion of adequate subxiphoid windows was not affected by mechanical ventilation (67% versus 66%; P = 0.9 with or without mechanical ventilation, respectively), the mode of ventilation (67% versus 62%; P = 0.9 in VC or PSV mode, respectively), the level of PEEP (67% versus 73%; P = 0.9, PEEP <5 and PEEP ≥5 cm H2O, respectively), or a history of COPD (58% versus 69%; P = 0.4 COPD versus absence of COPD, respectively). The inter- and intraobserver reproducibilities were deter- mined for each parameter (LVEF, E/A, E/Ea, RVEDA/ LVEDA, and Ao VTI) in both the apical and subxiphoid windows. All intraobserver variabilities were <5%, and interobserver variabilities were <9%. Statistical analysis was performed by using MedCalc ver- sion 12.0.4.0 (MedCalc Software, Mariakerke, Belgium). The limit of significance was set at ≤0.05. BMI, body mass index; COPD, chronic obstructive pulmonary disease; HR, heart rate; MAP, mean arterial pressure; PEEP, positive end-expiratory pressure; PSV, pressure-support ventilation; SAPSII, simplified acute physiology score II; VC, volume controlled. Statistics Transthoracic echocardiography was performed during the first 2 days after admission in all patients by one of the two operators (JM or AS) by using a Vivid i (General Electrics Healthcare Fairfield, CT, USA) equipped with a 3-MHz probe. Parasternal (long and short axis), apical four-cham- ber, and subxiphoid four-chamber views were obtained successively in 2D mode, and a cine-loop was stored for offline analysis. In the apical and subxiphoid windows, pulsed Doppler mitral inflow was recorded with the sample cursor placed at the mitral valve tips; early diastolic velocity (Ea) was determined from Doppler tissue imaging with the All variables are expressed as mean ± 1 SD or proportions. The normal distribution was tested with a Kolmogorov- Smirnov test. Quantitative variables were compared by using a Student t test, and proportions were compared with a c2 test. Pearson correlation coefficient and Bland-Altman analy- sis were used to assess the adequacy of the various para- meters obtained in the subxiphoid and apical windows. This analysis was performed in the subpopulation of patients in whom apical and subxiphoid windows were Maizel et al. Critical Care 2013, 17:R186 http://ccforum.com/content/17/5/R186 Page 3 of 8 Page 3 of 8 scored as excellent, good, or acceptable (n = 65). The bias and limit of agreement (LOA) around the bias were given by the Bland-Altman representation. However, no consen- sus has been reached concerning the acceptable LOA to confirm validation of the subcostal view. To define an acceptable LOA, Cecconi et al. [10] proposed assessing the precision of the reference technique (in this case, the apical view) and the tested technique (the subxiphoid view). We prospectively defined the validation criteria for the various parameters studied on the subxiphoid view: to be accepta- ble, the parameter on the subxiphoid view had to be accu- rate (bias <10%) and precise (a lower percentage precision value than on the apical view). Demographic data The per- centage bias, percentage error, and precisions of the apical BMI, body mass index; COPD, chronic obstructive pulmonary disease; HR, heart rate; MAP, mean arterial pressure; PEEP, positive end-expiratory pressure; PSV, pressure-support ventilation; SAPSII, simplified acute physiology score II; VC, volume controlled. Page 4 of 8 Page 4 of 8 Maizel et al. Critical Care 2013, 17:R186 http://ccforum.com/content/17/5/R186 Table 2 Quality of the various windows obtained and proportion of each parameter recorded in apical and subxiphoid windows in the overall population (n = 107) Table 2 Quality of the various windows obtained and proportion of each parameter recorded in apical and subxiphoid windows in the overall population (n = 107) Table 2 Quality of the various windows obtained and proportion of each parameter recorded in apical and subxiphoid windows in the overall population (n = 107) Table 2 Quality of the various windows obtained and proportion of each parameter recorded in apical and subxiphoid windows in the overall population (n = 107) Apical Subxiphoid P Number of patients with adequate apical or subxiphoid acoustic window, n (%) Overall population (n = 107) Mechanically ventilated patients (n = 48) COPD population (n = 26) 92 (86) 38 (78) 21 (81) 71 (66) 32 (67) 15 (58) 0.009 0.002 0.1 Quality of the window A Excellent B Good C Acceptable D Poor E No image 27 (25) 36 (34) 29 (27) 11 (10) 4 (4) 19 (18) 36 (34) 16 (15) 21 (20) 15 (14) 0.7 0.3 0.9 0.06 0.2 LVEF, n (%) 80 (75) 67 (63) 0.001 E/A, n (%) 71 (66) 46 (43) 0.001 E/Ea, n (%) 85 (79) 66 (62) 0.001 Ao VTI, n (%) 83 (78) 66 (62) 0.001 RVEDA/LVEDA, n (%) 79 (74) 67 (63) 0.001 Ao VTI, velocity time integral of aortic blood flow; E/A, ratio between early and late mitral inflow; E/Ea, ratio between early mitral inflow and displacement of the mitral annulus on tissue Doppler imaging; LVEF, left ventricular ejection fraction; RVEDA/LVEDA, ratio between right and left ventricular end-diastolic area. of aortic blood flow; E/A, ratio between early and late mitral inflow; E/Ea, ratio between early mitral inflow and displacement of the pler imaging; LVEF, left ventricular ejection fraction; RVEDA/LVEDA, ratio between right and left ventricular end-diastolic area. and subxiphoid views are presented in Table 4 for each parameter. Demographic data All parameters presented a better precision (lower percentage value) on the subxiphoid view than on the apical view, but two parameters (Ao VTI and E/Ea) presented a bias >10% (12% ± 16 and 22% ± 28, respec- tively) and therefore did not meet the a priori defined criteria. patients did not have an adequate apical view, but had an adequate subxiphoid view. These results emphasize the good feasibility of the apical view in TTE, even in venti- lated or COPD patients. This study also shows that the subxiphoid view is a reliable view to study the right- and left-ventricular morphology and function on two-dimen- sional echocardiography, but not in Doppler mode. The subxiphoid view should be used to explore only the vena cava, pericardium, and the morphology of the left or right ventricles. Semiquantitative evaluation of the diagnostic accuracy of the subxiphoid view was determined for the three para- meters selected (LVEF, E/A, and RVEDA/LVEDA) by identifying several previously published criteria obtained on the apical view (Figure 2). The useful window most frequently obtained in our population was the apical window (86%), followed by the parasternal window (66%), and finally the subxiphoid window (49%), as already reported [11-13]. Only 5% of the patients of our population presented an inadequate apical view and an adequate subxiphoid view. Moreover, a greater number of parameters were recorded on the apical view than on the subxiphoid view. Altogether, these results emphasize the better feasibility of the apical view compared with the subxiphoid view in TTE. Discussion In this study, the apical view was the view most frequently obtained (86%), and only a small proportion (5%) of Table 3 Echocardiographic measurements in apical and subxiphoid windows in the subpopulation of 65 patients (except for A and E/A; n = 51) Apical window Subxiphoid window P value LVEF, % 54 ± 16 55 ± 14 0.9 Ao VTI, cm 18 ± 5 16 ± 5 0.001 E, cm/sec 80 ± 25 59 ± 24 0.001 A, cm/sec 75 ± 32 55 ± 29 0.001 E/A 1.2 ± 0.9 1.1 ± 0.5 0.3 Ea, cm/sec 9.5 ± 3.7 8.8 ± 2.8 0.009 E/Ea 9.6 ± 4.6 7.6 ± 4 0.001 RVEDA, cm2 13 ± 6 13 ± 6 0.9 LVEDA, cm2 26 ± 8 27 ± 8 0.3 RVEDA/LVEDA 0.5 ± 0.19 0.49 ± 0.18 0.2 Ao VTI, velocity time integral of aortic blood flow; E/A, ratio between early and late mitral inflow; E/Ea, ratio between early mitral inflow and displacement of the mitral annulus on tissue Doppler imaging; LVEF, left ventricular ejection fraction; RVEDA/LVEDA, ratio between right and left ventricular end-diastolic area. Table 3 Echocardiographic measurements in apical and subxiphoid windows in the subpopulation of 65 patients (except for A and E/A; n = 51) Table 3 Echocardiographic measurements in apical and subxiphoid windows in the subpopulation of 65 patients (except for A and E/A; n = 51) The proportion of mechanically ventilated patients in our population was 45%, which is lower than the propor- tion usually reported in ICU [14]. However, in our study, TTE was performed within the first 2 days after admission of the patients and mostly at the time of admission. We do not believe that a higher proportion of mechanically ventilated patients would have modified our conclusions, as the proportion of adequate views was significantly higher for the apical view than for the subxiphoid view in the population of mechanically ventilated patients (Table 2). The subxiphoid view is an essential element of echocar- diography in an ICU, particularly to analyze the inferior vena cava (for example, size and collapsibility) and pericar- dium (for example, pericardial effusion). According to our Maizel et al. Critical Care 2013, 17:R186 http://ccforum.com/content/17/5/R186 Page 5 of 8 Figure 1 Regression plot and Bland-Altman analysis between apical and subxiphoid views for the various parameters in the subpopulation of 65 patients. (LVEF, left ventricular ejection fraction; Ao VTI, velocity time integral of aortic blood flow; E/A, ratio between early and late mitral inflow; E/Ea, ratio between early mitral inflow and displacement of the mitral annulus on tissue Doppler imaging; RVEDA/ LVEDA, ratio between right and left ventricular end-diastolic area. Figure 1 Regression plot and Bland-Altman analysis between apical and subxiphoid views for the various parameters in the subpopulation of 65 patients. (LVEF, left ventricular ejection fraction; Ao VTI, velocity time integral of aortic blood flow; E/A, ratio between early and late mitral inflow; E/Ea, ratio between early mitral inflow and displacement of the mitral annulus on tissue Doppler imaging; RVEDA/ LVEDA, ratio between right and left ventricular end-diastolic area. results, only parameters recorded in two-dimensional mode (LVEF and RVEDA/LVEDA) can be recorded on the subxiphoid window without any bias. The bias of E/A was almost nil, but this ratio alone does not constitute a reliable parameter to analyze LV filling pressure in this setting of critically ill patients [15]. The fairly large limits of agreement in the Bland-Altman representations for LVEF, E/A, and RVEDA/LVEDA can also be an argument in favor of the use of a semiquantitative approach for these parameters. approach: preserved or altered LVEF, or normal or dilated right ventricle [16,17]. results, only parameters recorded in two-dimensional mode (LVEF and RVEDA/LVEDA) can be recorded on the subxiphoid window without any bias. CV, coefficient of variation; CE, coefficient of error. Table 3 Echocardiographic measurements in apical and subxiphoid windows in the subpopulation of 65 patients (except for A and E/A; n = 51) The bias of E/A was almost nil, but this ratio alone does not constitute a reliable parameter to analyze LV filling pressure in this setting of critically ill patients [15]. The fairly large limits of agreement in the Bland-Altman representations for LVEF, E/A, and RVEDA/LVEDA can also be an argument in favor of the use of a semiquantitative approach for these parameters. The discrepancy between apical and subxiphoid values for E, A, E/Ea, and Ao VTI can be explained by the angle between the Doppler axis and blood flow or myocardial movement in the various acoustic windows. With the Doppler mode, red blood cell velocity (or myocardial tis- sue movement on tissue Doppler) depends on the cosine of the angle between the axis of the Doppler beam and blood flow (myocardial tissue movement): the smaller the angle, the higher the velocity [18]. On the apical view, the heart is examined in the longitudinal (anteroposterior) axis, ensuring perfect alignment between the Doppler Figure 2 demonstrates the low rate of misclassified patients. Use of the subxiphoid window to analyze ven- tricular morphology therefore allows a point-of-care Table 4 Statistical analysis of the various parameters obtained on the subxiphoid view and on the reference apical view Mean apical CV apical CE apical Precision of apical Mean subxiphoid Bias (± SD) Bias (% of the apical value) Percentage error Precision of subxiphoid LVEF 54% ± 16 29.6 17.1 34% 55% ± 14 -0.1 ± 8.6 -1.5% ± 17 32% 12% Ao VTI 18 cm ± 5 29.1 16.8 34% 16 cm ± 5 2.0 ± 2.8 12% ± 16 31% 13% E/A 1.2 ± 0.9 75.7 43.7 87% 1.1 ± 0.5 0.03 ± 0.2 5% ± 16 33% 81% E/Ea 9.6 ± 4.6 47.5 27.4 55% 7.6 ± 4 1.9 ± 2.4 22% ± 28 50% 23% RVEDA/ LVEDA 0.5 ± 0.19 37.5 21.6 43% 0.49 ± 0.18 0.01 ± 0.1 3% ± 22 40% 16% CV, coefficient of variation; CE, coefficient of error. Table 4 Statistical analysis of the various parameters obtained on the subxiphoid view and on the reference apical view analysis of the various parameters obtained on the subxiphoid view and on the reference apical Table 4 Statistical analysis of the various parameters obtained on the subxiphoid view and on th i Maizel et al. Table 3 Echocardiographic measurements in apical and subxiphoid windows in the subpopulation of 65 patients (except for A and E/A; n = 51) Critical Care 2013, 17:R186 http://ccforum.com/content/17/5/R186 Page 6 of 8 Figure 2 Accuracy of subxiphoid view for classifying various hemodynamic parameters according to the apical view in the subpopulation of 65 patients. (LVEF, left ventricular ejection fraction; E/A, ratio between early and late mitral inflow; RVEDA/LVEDA, ratio between right and left ventricular end-diastolic area). Figure 2 Accuracy of subxiphoid view for classifying various hemodynamic parameters according to the apical view in the subpopulation of 65 patients. (LVEF, left ventricular ejection fraction; E/A, ratio between early and late mitral inflow; RVEDA/LVEDA, ratio between right and left ventricular end-diastolic area). This study presents several limitations. The lower veloci- ties obtained on the subxiphoid view are due to the poor alignment between the Doppler axis and blood flow. Some echocardiography devices apply a correction of this angle by aligning the Doppler beam with blood flow, but this angle correction was not tested in this study. However, accurate determination of the appropriate angle correction for velocity is difficult, essentially because this angle can be measured only in a two-dimensional plane, which therefore disregards the angle in the third dimension of the heart. Moreover, angle correction would not be suffi- cient to correct the velocity of Ea, as the observed decrease is not exclusively due to poor alignment, but also because this view measures a different relaxation property of the myocardium: radial instead of longitudinal. Not all hemo- dynamic parameters were evaluated by TTE in this study. Right ventricular function was not extensively analyzed, apart from RVEDA/LVEDA (an important parameter of biventricular interaction). However, the misalignment observed in Doppler mode would also be expected to affect measurement of the tricuspid proto-systolic S-wave velocity on tissue Doppler, tricuspid annular plane systolic excursion in M mode (TAPSE), or pulmonary artery pres- sure. We also did not study the variation of aortic blood flow during passive leg raising or mechanical ventilation to predict fluid responsiveness, as this would have required a strictly selected population [19]. Although the position of beam and blood flow through the mitral or aortic rings and maximum velocities. On the subxiphoid view, the heart is viewed in a different axis (inferoanterior). Conse- quently, on this view, the alignment between the Doppler beam and aortic flow is not perfect, and the velocity reported by the echocardiographer will be underestimated. Conclusions 2. Vieillard-Baron A, Slama M, Cholley B, Janvier G, Vignon P: Echocardiography in the intensive care unit: from evolution to revolution? Intensive Care Med 2008, 34:243-249. 2. Vieillard-Baron A, Slama M, Cholley B, Janvier G, Vignon P: Echocardiography in the intensive care unit: from evolution to revolution? Intensive Care Med 2008, 34:243-249. 3. Mayo PH, Beaulieu Y, Doelken P, Feller-Kopman D, Harrod C, Kaplan A, Oropello J, Vieillard-Baron A, Axler O, Lichtenstein D, Maury E, Slama M, Vignon P: American College of Chest Physicians/La Société de Réanimation de Langue Française statement on competence in critical care ultrasonography. Chest 2009, 135:1050-1060. 4. Beaulieu Y: Bedside echocardiography in the assessment of the critically ill. Crit Care Med 2007, 35:S235-S249. 5. Sahn DJ: Real-time two-dimensional Doppler echocardiographic flow mapping. Circulation 1985, 71:849-853. 6. Schiller NB, Shah PM, Crawford M, DeMaria A, Devereux R, Feigenbaum H, Gutgesell H, Reichek N, Sahn D, Schnittger I: Recommendations for quantitation of the left ventricle by two- dimensional echocardiography: American Society of Echocardiography Committee on Standards, Subcommittee on Quantitation of Two-Dimensional Echocardiograms. J Am Soc Echocardiogr 1989, 2:358-367. Echocardiography comprises a combination of various acoustic windows. The subxiphoid view is already estab- lished as an essential part of echocardiography in the ICU to explore the inferior vena cava and pericardium. The results of this study also emphasize that the subxiphoid view cannot replace the apical view to perform complete hemodynamic assessment. In the absence of an apical view, the subxiphoid view can provide only partial infor- mation based on analysis of two-dimensional images. To obtain a complete hemodynamic examination, echocardio- graphers should therefore record both apical and subxi- phoid views or use another monitoring device, such as transesophageal echocardiography. 3. Mayo PH, Beaulieu Y, Doelken P, Feller-Kopman D, Harrod C, Kaplan A, Oropello J, Vieillard-Baron A, Axler O, Lichtenstein D, Maury E, Slama M, Vignon P: American College of Chest Physicians/La Société de Réanimation de Langue Française statement on competence in critical care ultrasonography. Chest 2009, 135:1050-1060. 5. Sahn DJ: Real-time two-dimensional Doppler echocardiographic flow mapping. Circulation 1985, 71:849-853. 6. Schiller NB, Shah PM, Crawford M, DeMaria A, Devereux R, Feigenbaum H, Gutgesell H, Reichek N, Sahn D, Schnittger I: Recommendations for quantitation of the left ventricle by two- dimensional echocardiography: American Society of Echocardiography Committee on Standards, Subcommittee on Quantitation of Two-Dimensional Echocardiograms. J Am Soc Echocardiogr 1989, 2:358-367. 7. References 1. Expert Round Table on Ultrasound in ICU: International expert statement on training standards for critical care ultrasonography. Intensive Care Med 2011, 37:1077-1083. 1. Expert Round Table on Ultrasound in ICU: International expert statement on training standards for critical care ultrasonography. Intensive Care Med 2011, 37:1077-1083. 1. Expert Round Table on Ultrasound in ICU: International expert statement on training standards for critical care ultrasonography. Intensive Care Med 2011, 37:1077-1083. Conclusions Lang RM, Bierig M, Devereux RB, Flachskampf FA, Foster E, Pellikka PA, Picard MH, Roman MJ, Seward J, Shanewise J, Solomon S, Spencer KT, St John Sutton M, Stewart W, European Association of Echocardiography, European Society of Cardiology: Recommendations for chamber quantification. Eur J Echocardiogr 2006, 7:79-108. Received: 4 March 2013 Revised: 14 May 2013 Accepted: 3 September 2013 Published: 3 September 2013 Received: 4 March 2013 Revised: 14 May 2013 Accepted: 3 September 2013 Published: 3 September 2013 the heart and consequently our findings should not differ according to the reason for admission, it would be inter- esting to confirm our conclusions in a specific population of acute circulatory failure patients. Competing interests The authors declare that they have no competing interests. p g The authors declare that they have no competing interests. Key messages • The apical view appears to be more accurate and more feasible than the subxiphoid window, even in mechanically ventilated or COPD patients. • The apical view appears to be more accurate and more feasible than the subxiphoid window, even in mechanically ventilated or COPD patients. 8. Nagueh SF, Appleton CP, Gillebert TC, Marino PN, Oh JK, Smiseth OA, Waggoner AD, Flachskampf FA, Pellikka PA, Evangelista A: Recommendations for the evaluation of left ventricular diastolic function by echocardiography. J Am Soc Echocardiogr 2009, 22:107-133. • The E/Ea ratio and Ao VTI appear to be signifi- cantly underestimated on the subxiphoid view and therefore should not be recorded. 9. Quinones MA, Otto CM, Stoddard M, Waggoner A, Zoghbi WA: Recommendations for quantification of Doppler echocardiography: a report from the Doppler Quantification Task Force of the Nomenclature and Standards Committee of the American Society of Echocardiography. J Am Soc Echocardiogr 2002, 15:167-184. 9. Quinones MA, Otto CM, Stoddard M, Waggoner A, Zoghbi WA: Recommendations for quantification of Doppler echocardiography: a report from the Doppler Quantification Task Force of the Nomenclature and Standards Committee of the American Society of Echocardiography. J Am Soc Echocardiogr 2002, 15:167-184. • In addition to its ability to explore the vena cava and pericardium, the subxiphoid view can provide information based on morphologic analysis of the ventricles in two-dimensional mode. g 10. Cecconi M, Rhodes A, Poloniecki J, Della Rocca G, Grounds RM: Bench-to- bedside review: the importance of the precision of the reference technique in method comparison studies: with specific reference to the measurement of cardiac output. Crit Care 2009, 13:201. g 10. Cecconi M, Rhodes A, Poloniecki J, Della Rocca G, Grounds RM: Bench-to- bedside review: the importance of the precision of the reference technique in method comparison studies: with specific reference to the measurement of cardiac output. Crit Care 2009, 13:201. Authors’ contributions 15. Feissel M, Maizel J, Robles G, Badie J, Faller JP, Slama M: Clinical relevance of echocardiography in acute severe dyspnea. J Am Soc Echocardiogr 2009, 22:1159-1164. 15. Feissel M, Maizel J, Robles G, Badie J, Faller JP, Slama M: Clinical relevance of echocardiography in acute severe dyspnea. J Am Soc Echocardiogr 2009, 22:1159-1164. JM and AS contributed to the acquisition and analysis of data and drafting the manuscript JM and AS contributed to the acquisition and analysis of data and drafting the manuscript JM and MS contributed to the conception and design of the study. CT, ZM, GC, and MS were involved in interpretation of data, critically revising the manuscript, and giving final approval. All authors read and approved the final manuscript. 16. Labovitz AJ, Noble VE, Bierig M, Goldstein SA, Jones R, Kort S, Porter TR, Spencer KT, Tayal VS, Wei K: Focused cardiac ultrasound in the emergent setting: a consensus statement of the American Society of Echocardiography and American College of Emergency Physicians. J Am Soc Echocardiogr 2010, 23:1225-1230. 16. Labovitz AJ, Noble VE, Bierig M, Goldstein SA, Jones R, Kort S, Porter TR, Spencer KT, Tayal VS, Wei K: Focused cardiac ultrasound in the emergent setting: a consensus statement of the American Society of Echocardiography and American College of Emergency Physicians. J Am Soc Echocardiogr 2010, 23:1225-1230. Abbreviations l Ao VTI: velocity time integral of aortic blood flow; BMI: body mass index; CE: coefficient of error; COPD: chronic obstructive pulmonary disease; CV: coefficient of variation; E/A: ratio between early and late mitral inflow on pulsed Doppler; E/Ea: ratio between early mitral inflow and displacement of the mitral annulus on tissue Doppler imaging; HR: heart rate; ICU: intensive care unit; LOA: limit of agreement; LVEDA: left ventricular end-diastolic area; LVEF: left ventricular ejection fraction; MAP: mean arterial pressure; PEEP: positive end-expiratory pressure; PSV: pressure support ventilation; RVEDA: right ventricular end-diastolic area; SAPS2: simplified acute physiologic score 2; TTE: transthoracic echocardiography; VC: volume controlled. 11. Vignon P, Chastagner C, François B, Martaillé J-FF, Normand S, Bonnivard M, Gastinne H: Diagnostic ability of hand-held echocardiography in ventilated critically ill patients. Crit Care 2003, 7:R84-R91. 12. Vignon P, Frank MBJ, Lesage J, Mücke F, François B, Normand S, Bonnivard M, Clavel M, Gastinne H: Hand-held echocardiography with Doppler capability for the assessment of critically-ill patients: is it reliable? Intensive Care Med 2004, 30:718-723. 13. Jensen MB, Sloth E, Larsen KM, Schmidt MB: Transthoracic echocardiography for cardiopulmonary monitoring in intensive care. Eur J Anaesthesiol 2004, 21:700-707. 13. Jensen MB, Sloth E, Larsen KM, Schmidt MB: Transthoracic echocardiography for cardiopulmonary monitoring in intensive care. Eur J Anaesthesiol 2004, 21:700-707. 14. Vincent JL, Sakr Y, Sprung CL, Ranieri VM, Reinhart K, Gerlach H, Moreno R, Carlet J, Le Gall JR, Payen D, Sepsis Occurrence in Acutely Ill Patients Investigators: Sepsis in European intensive care units: results of the SOAP study. Crit Care Med 2006, 34:344-353. Table 3 Echocardiographic measurements in apical and subxiphoid windows in the subpopulation of 65 patients (except for A and E/A; n = 51) Interestingly, the E/A ratio is not modified on the subxi- phoid view, as the E and A waves are both decreased to a similar degree. The velocity of the mitral annulus (Ea) is measured in tissue Doppler mode. On the apical view, the Doppler beam is aligned with the longitudinal movement of the mitral annulus, but the subxiphoid view measures the radial movement of the annulus, accounting for the lower Ea velocity obtained in this window. It is noteworthy that the E/Ea and Ao VTI were also underestimated in patients with a history of COPD and in mechanically ven- tilated patients, two situations theoretically associated with a vertical heart axis that could have resulted in better alignment on the subxiphoid view. An adequate apical view could not be obtained in the present study in fewer than 15% of cases, whereas use of the subxiphoid view was incomplete, as Doppler analysis appears to be unreliable. Therefore, in the unusual situa- tion of absence of an apical window, the use of another monitoring device should be considered (particularly in intubated patients, in whom transesophageal echocardio- graphy can usually be performed). Page 7 of 8 Page 7 of 8 Maizel et al. Critical Care 2013, 17:R186 http://ccforum.com/content/17/5/R186 Authors’ details 1 17. Arntfield RT, Millington SJ: Point of care cardiac ultrasound applications in the emergency department and intensive care unit: a review. Curr Cardiol Rev 2012, 8:98-108. 17. Arntfield RT, Millington SJ: Point of care cardiac ultrasound applications in the emergency department and intensive care unit: a review. Curr Cardiol Rev 2012, 8:98-108. 1Medical Intensive Care Unit, Department of Nephrology, Amiens University Medical Center, Amiens, France and INSERM U-1088, Jules Verne University of Picardie, Amiens, France. 2Department of Cardiology, Amiens University Medical Center, Amiens, France and INSERM U-1088, Jules Verne University of Picardie, Amiens, France. 18. Nelson TR, Pretorius DH: The Doppler signal: where does it come from and what does itmean? AJR Am J Roentgenol 1988, 151:439-447. Page 8 of 8 Page 8 of 8 Maizel et al. Critical Care 2013, 17:R186 http://ccforum.com/content/17/5/R186 19. Marik PE, Monnet X, Teboul JL: Hemodynamic parameters to guide fluid therapy. Ann Intensive Care 2011, 1:1. doi:10.1186/cc12869 Cite this article as: Maizel et al.: The subxiphoid view cannot replace the apical view for transthoracic echocardiographic assessment of hemodynamic status. Critical Care 2013 17:R186. 19. Marik PE, Monnet X, Teboul JL: Hemodynamic parameters to guide fluid therapy. Ann Intensive Care 2011, 1:1. 19. Marik PE, Monnet X, Teboul JL: Hemodynamic parameters to guide fluid therapy. Ann Intensive Care 2011, 1:1. doi:10.1186/cc12869 Cite this article as: Maizel et al.: The subxiphoid view cannot replace the apical view for transthoracic echocardiographic assessment of hemodynamic status. Critical Care 2013 17:R186. 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
https://openalex.org/W2135913935
https://journals.iucr.org/e/issues/2005/09/00/lh6485/lh6485.pdf
English
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1,2:3,4-Di-<i>O</i>-isopropylidene-α-<scp>D</scp>-tagatofuranose
Acta crystallographica. Section E
2,005
cc-by
3,371
Received 3 August 2005 Accepted 5 August 2005 Online 12 August 2005 organic papers organic papers Acta Crystallographica Section E Structure Reports Online ISSN 1600-5368 David J. Watkin,a* Andreas F. G. Glawar,a Raquel Soengas,b Ulla P. Skytte,c Mark R. Wormald,d Raymond A. Dwekd and George W. J. Fleetb aDepartment of Chemical Crystallography, Chemical Research Laboratory, Oxford University, Mansfield Road, Oxford OX1 3TA, England, bDepartment of Organic Chemistry, Chemical Research Laboratory, Oxford University, Mansfield Road, Oxford OX1 3TA, England, cArla Foods Ingredients, Viby J, DK-8260 Denmark, and dGlycobiology Institute, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, England 1,2:3,4-Di-O-isopropylidene-a-D-tagatofuranose Acta Crystallographica Section E Structure Reports Online ISSN 1600-5368 The crystal structure of diacetone tagatose, C12H20O6, establishes the stereochemistry of the anomeric spiroacetal as 1,2:3,4-di-O-isopropylidene--d-tagatofuranose. Molecules are linked by O—H  O hydrogen bonds [O  O = 2.862 (2) A˚ ] to form chains running parallel to the b axis. David J. Watkin,a* Andreas F. G. Glawar,a Raquel Soengas,b Ulla P. Skytte,c Mark R. Wormald,d Raymond A. Dwekd and George W. J. Fleetb Acta Cryst. (2005). E61, o2891–o2893 doi:10.1107/S1600536805025092 Comment Carbohydrates provide a rich source of chirons (Lichtenthaler & Peters, 2004). d-Tagatose, (1), is the first example for more than 50 years of a sugar that has changed its status from rare ($5,000 per lb) to common ($2.5 per lb). The driving force for the production of large quantities of hitherto scarce carbo- hydrates is their potential as enhanced dietary targets. d-Tagatose is a healthy sweetener prepared cheaply from galactose (Beadle et al., 1992). Its use as a dietary substitute in soft drinks and ready-to-eat cereals (Skytte, 2002) is rapidly increasing. So far, there has been little exploitation of tagatose as a chiral building block, although recently the easy preparation of branched sugar lactones by the Kiliani cyano- hydrin reaction on d-tagatose has been reported (Soengas, Izumori et al., 2005); the structures of the diacetonide products could only be firmly established by X-ray crystallographic analysis (Harding et al., 2005; Shallard-Brown et al., 2004). For a sugar to be used as a chiral starting material in organic synthesis, it must not only be cheap but also efficiently protected (Bols, 1996). Correspondence e-mail: david.watkin@chem.ox.ac.uk Correspondence e-mail: david.watkin@chem.ox.ac.uk Correspondence e-mail: david.watkin@chem.ox.ac.uk Key indicators Single-crystal X-ray study T = 190 K Mean (C–C) = 0.002 A˚ R factor = 0.036 wR factor = 0.087 Data-to-parameter ratio = 13.7 Key indicators For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e. Acta Cryst. (2005). E61, o2891–o2893 # 2005 International Union of Crystallography Printed in Great Britain – all rights reserved The first reports of the protection of tagatose, (1), with acetone (Reichstein & Bosshard, 1934; Barnett & Reichstein, 1937) gave no indication of the chemistry at the anomeric position of the diacetonide, (3). Otherwise, compound (3) has only been prepared by lengthy synthesis from d-fructose (Cubero et al., 1988); the enantiomer of (3) was derived from a multi-step procedure from l-sorbose (Furneaux et al., 1993). No previous publication has provided any evidence for the anomeric configuration of the diacetonide, (3). In recent studies, treatment of tagatose, (1), which exists in both its crystalline form and in solution in the pyranose form, (2), with acetone produces high yields of crystalline (3) (Soengas, Wormald et al., 2005). The present report of the crystal # 2005 International Union of Crystallography Printed in Great Britain – all rights reserved # 2005 International Union of Crystallography Printed in Great Britain – all rights reserved Watkin et al.  C12H20O6 o2891 doi:10.1107/S1600536805025092 Acta Cryst. (2005). E61, o2891–o2893 organic papers Figure 1 A view of the title compound, with displacement ellipsoids drawn at the 50% probability level. H atoms (except for the hydroxyl atom H15) have been omitted for clarity; atom H15 is shown as a sphere of arbitary radius. structure of (3) unequivocally establishes the anomeric configuration of the diacetonide, (3), as the -form. The crystal structure of (3) consists of O—H  O hydrogen- bonded chains running parallel to the b axis (Table 1 and Fig. 2). There are no other short intermolecular contacts. Atoms C17 and C18 refined to have very anisotropic displa- cement parameters. A difference electron-density map phased on all the structure except for atoms C17 and C18 showed only a single elongated peak at these sites, indicating that the anisotropic displacement parameter model would be appro- priate. The large anisotropic displacement parameters for these atoms are due to disorder of these atoms arising from out-of-plane displacements of atoms in the adjacent ring, and in particular of O15. A single-temperature experiment cannot resolve static from dynamic disorder. Figure 1 Figure 1 A view of the title compound, with displacement ellipsoids drawn at the 50% probability level. H atoms (except for the hydroxyl atom H15) have been omitted for clarity; atom H15 is shown as a sphere of arbitary radius. Figure 1 A view of the title compound, with displacement ellipsoids drawn at the 50% probability level. H atoms (except for the hydroxyl atom H15) have been omitted for clarity; atom H15 is shown as a sphere of arbitary radius. The title material (Soengas, Wormald et al., 2005) was crystallized from petroleum ether (333–353 K). Crystal data C12H20O6 Mr = 260.29 Orthorhombic, P212121 a = 5.8241 (1) A˚ b = 8.4972 (2) A˚ c = 27.1899 (7) A˚ V = 1345.59 (5) A˚ 3 Z = 4 Dx = 1.285 Mg m3 Mo K radiation Cell parameters from 1961 reflections  = 5–30  = 0.10 mm1 T = 190 K Prism, colourless 0.60  0.20  0.20 mm Data collection Nonius KappaCCD area-detector diffractometer ! scans Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) Tmin = 0.84, Tmax = 0.98 7561 measured reflections 2239 independent reflections 1980 reflections with I > 2(I) Rint = 0.027 max = 30.0 h = 8 ! 8 k = 11 ! 11 l = 37 ! 37 Refinement Refinement on F 2 R[F 2 > 2(F 2)] = 0.036 wR(F 2) = 0.087 S = 0.97 2239 reflections 163 parameters H-atom parameters constrained w = 1/[2(F 2) + ( 0.04P)2 + 0.29P] where P = (max(Fo 2,0) + 2Fc 2)/3 (/)max < 0.001 max = 0.31 e A˚ 3 min = 0.18 e A˚ 3 Table 1 Hydrogen-bond geometry (A˚ , ). D—H  A D—H H  A D  A D—H  A O7—H15  O15i 0.81 2.06 2.862 (2) 167 Symmetry code: (i) x; y þ 1; z. In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned from known chiral centres. The relatively large ratio of minimum to maximum corrections applied in the multi-scan process (1:1.16) is due to the prismatic shape of the crystal. Figure 1 The H atoms were all located in a difference map, but those attached to C atoms were repositioned Crystal data C12H20O6 Mr = 260.29 Orthorhombic, P212121 a = 5.8241 (1) A˚ b = 8.4972 (2) A˚ c = 27.1899 (7) A˚ V = 1345.59 (5) A˚ 3 Z = 4 Dx = 1.285 Mg m3 Mo K radiation Cell parameters from 1961 reflections  = 5–30  = 0.10 mm1 T = 190 K Prism, colourless 0.60  0.20  0.20 mm Data collection Nonius KappaCCD area-detector diffractometer ! scans Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) Tmin = 0.84, Tmax = 0.98 7561 measured reflections 2239 independent reflections 1980 reflections with I > 2(I) Rint = 0.027 max = 30.0 h = 8 ! 8 k = 11 ! 11 l = 37 ! 37 Refinement Refinement on F 2 R[F 2 > 2(F 2)] = 0.036 wR(F 2) = 0.087 S = 0.97 2239 reflections 163 parameters H-atom parameters constrained w = 1/[2(F 2) + ( 0.04P)2 + 0.29P] where P = (max(Fo 2,0) + 2Fc 2) (/)max < 0.001 max = 0.31 e A˚ 3 min = 0.18 e A˚ 3 Figure 2 A diagram showing a projection along the a axis of the title compound, with hydrogen bonds indicated as dotted lines. Mo K radiation Cell parameters from 1961 reflections  = 5–30  = 0.10 mm1 T = 190 K Prism, colourless 0.60  0.20  0.20 mm Figure 2 Figure 2 Figure 2 A diagram showing a projection along the a axis of the title compound, with hydrogen bonds indicated as dotted lines. geometrically. The H atoms were initially refined with soft restraints on their bond lengths and angles to regularize their geometry (C—H distances in the range 0.93–0.98 A˚ and O—H distances of 0.82 A˚ ) and displacement parameters [Uiso(H) in the range 1.2–1.5 times Ueq of the parent atom], after which they were refined with riding constraints. Experimental Figure 1 A i f organic papers Lichtenthaler, F. W. & Peters, S. (2004). C. R. Chim. 7, 65–90. Nonius (2001). COLLECT. Nonius BV, Delft, The Netherlands. Table 1 Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduc- tion: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS D—H  A D—H H  A D  A D—H  A O7—H15  O15i 0.81 2.06 2.862 (2) 167 Symmetry code: (i) x; y þ 1; z. In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned from known chiral centres. The relatively large ratio of minimum to maximum corrections applied in the multi-scan process (1:1.16) is due to the prismatic shape of the crystal. The H atoms were all located in a difference map, but those attached to C atoms were repositioned Financial support (RS) provided by the Xunta de Galicia is gratefully acknowledged. Acta Cryst. (2005). E61, o2891–o2893 o2892 Watkin et al.  C12H20O6 Acta Cryst. (2005). E61, o2891–o2893 References Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press. Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435. ( ) pp y Barnett, T. & Reichstein, T. (1937). Helv. Chim. Acta, 20, 1529–1536. Reichstein, T. & Bosshard, W. (1934). Helv. Chim. Acta, 17, 753– 761. ( ) Beadle, J. R., Saunders, J. P. & Wajda, T. J. (1992). US Patent 5078796. Shallard-Brown, H. A., Harding, C. C., Watkin, D. J., Soengas, R., Skytte, U. P. Shallard-Brown, H. A., Harding, C. C., Watkin, D. J., Soengas, R., Skytte, U. P. & Fleet G W J (2004) Acta Cryst E60 o2163 o2164 Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, C. K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487. Shallard Brown, H. A., Harding, C. C., Watkin, D. J., Soengas, R., Skytte, U. P. & Fleet, G. W. J. (2004). Acta Cryst. E60, o2163–o2164. , ( ) y , Soengas, R., Izumori, K., Simone, M. I., Watkin, D. J., Skytte, U. P., Soetaert, W. ( ) pp y Bols, M. (1996). Carbohydrate Building Blocks. New York: John Wiley & Sons. Soengas, R., Izumori, K., Simone, M. I., Watkin, D. J., Skytte, U & Fleet, G. W. J. (2005). Tetrahedron Lett. 46, 5755–5759. Cubero, I., Lopez-Espinosa, M. T. P. & Osorio, P. L. T. (1988). An. Quim. 84, 340–343. Soengas, R., Wormald, M. R., Dwek, R. A., Izumori, K., Watkin, D. J., Skytte U P & Fl G W J (2005) I i Soengas, R., Wormald, M. R., Dwek, R. A., Izumori, K., Watkin, D. J., Skytte, U. P. & Fleet, G. W. J. (2005). In preparation. Furneaux, R. H., Tyler, P. C. & Whitehouse, L. A. (1993). Tetrahedron Lett. 34, 3609–3612. Skytte, U. P. (2002). Cereal Foods World, 47, 224-227. Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, University of Oxford, England. Harding, C. C., Watkin, D. J., Cowley, A. R., Soengas, R., Skytte, U. P. & Fleet, G. W. J. (2005). Acta Cryst. E61, o250–o252. Crystallography Laboratory, University of Oxford, England. Watkin et al.  C12H20O6 o2893 Acta Cryst. (2005). E61, o2891–o2893 supporting information Acta Cryst. (2005). E61, o2891–o2893 sup-1 Acta Cryst. (2005). E61, o2891–o2893 supporting information C4 0.8065 (3) 0.94288 (17) 0.61795 (5) 0.0256 O5 0.95355 (19) 0.80726 (12) 0.62382 (4) 0.0237 C6 0.9294 (4) 1.08802 (18) 0.63558 (6) 0.0348 O7 1.1138 (3) 1.12609 (14) 0.60326 (5) 0.0445 O8 0.6151 (2) 0.94136 (13) 0.69726 (4) 0.0291 C9 0.5377 (3) 0.81064 (19) 0.72565 (5) 0.0249 O10 0.6022 (2) 0.67635 (12) 0.69686 (4) 0.0308 C11 0.2794 (3) 0.8147 (2) 0.73296 (6) 0.0324 C12 0.6658 (3) 0.8066 (2) 0.77381 (6) 0.0339 O13 0.7586 (2) 0.63541 (13) 0.57085 (4) 0.0278 C14 0.9287 (3) 0.52851 (19) 0.55314 (6) 0.0331 O15 1.0252 (3) 0.45663 (14) 0.59641 (4) 0.0413 C16 0.9356 (3) 0.52887 (17) 0.63902 (6) 0.0284 C17 1.1201 (4) 0.6157 (3) 0.52718 (8) 0.0539 C18 0.8104 (6) 0.4066 (3) 0.52222 (10) 0.0721 H21 0.4514 0.6744 0.6302 0.0359* H31 0.4509 0.9496 0.6316 0.0365* H41 0.7674 0.9559 0.5835 0.0352* H61 0.8183 1.1751 0.6360 0.0488* H62 0.9859 1.0683 0.6693 0.0490* H111 0.2308 0.7218 0.7514 0.0568* H112 0.2002 0.8174 0.7024 0.0569* H113 0.2387 0.9082 0.7525 0.0565* H121 0.6235 0.7138 0.7913 0.0598* H122 0.8263 0.8083 0.7675 0.0608* H123 0.6238 0.8987 0.7933 0.0594* H161 0.8265 0.4586 0.6557 0.0409* H162 1.0590 0.5539 0.6614 0.0421* H181 0.9248 0.3339 0.5111 0.1291* H182 0.7341 0.4578 0.4946 0.1288* H183 0.6983 0.3525 0.5434 0.1289* H15 1.1118 1.2217 0.6016 0.0793* H171 1.2372 0.5416 0.5168 0.0958* H172 1.0592 0.6686 0.4986 0.0958* H173 1.1836 0.6950 0.5500 0.0968* sup-2 Acta Cryst. (2005). supporting information Acta Cryst. (2005). E61, o2891–o2893 [https://doi.org/10.1107/S1600536805025092] 1,2:3,4-Di-O-isopropylidene-α-D-tagatofuranose F(000) = 560 Dx = 1.285 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 1961 reflections θ = 5–30° µ = 0.10 mm−1 T = 190 K Prism, colourless 0.60 × 0.20 × 0.20 mm Primary atom site location: structure-invariant direct methods Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ2(F2) + ( 0.04P)2 + 0.29P] where P = (max(Fo2,0) + 2Fc2)/3 (Δ/σ)max < 0.001 Δρmax = 0.31 e Å−3 Δρmin = −0.18 e Å−3 Primary atom site location: structure-invariant sup-1 Acta Cryst. (2005). E61, o2891–o2893 Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) x y z Uiso*/Ueq C1 0.8104 (3) 0.67374 (17) 0.62049 (5) 0.0221 C2 0.5871 (3) 0.71970 (17) 0.64639 (5) 0.0253 C3 0.5892 (3) 0.90127 (17) 0.64648 (5) 0.0264 Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) supporting information Acta Cryst. (2005). E61, o2891–o2893 supporting information E61, o2891–o2893 C4 0.8065 (3) 0.94288 (17) 0.61795 (5) 0.0256 O5 0.95355 (19) 0.80726 (12) 0.62382 (4) 0.0237 C6 0.9294 (4) 1.08802 (18) 0.63558 (6) 0.0348 O7 1.1138 (3) 1.12609 (14) 0.60326 (5) 0.0445 O8 0.6151 (2) 0.94136 (13) 0.69726 (4) 0.0291 C9 0.5377 (3) 0.81064 (19) 0.72565 (5) 0.0249 O10 0.6022 (2) 0.67635 (12) 0.69686 (4) 0.0308 C11 0.2794 (3) 0.8147 (2) 0.73296 (6) 0.0324 C12 0.6658 (3) 0.8066 (2) 0.77381 (6) 0.0339 O13 0.7586 (2) 0.63541 (13) 0.57085 (4) 0.0278 C14 0.9287 (3) 0.52851 (19) 0.55314 (6) 0.0331 O15 1.0252 (3) 0.45663 (14) 0.59641 (4) 0.0413 C16 0.9356 (3) 0.52887 (17) 0.63902 (6) 0.0284 C17 1.1201 (4) 0.6157 (3) 0.52718 (8) 0.0539 C18 0.8104 (6) 0.4066 (3) 0.52222 (10) 0.0721 H21 0.4514 0.6744 0.6302 0.0359* H31 0.4509 0.9496 0.6316 0.0365* H41 0.7674 0.9559 0.5835 0.0352* H61 0.8183 1.1751 0.6360 0.0488* H62 0.9859 1.0683 0.6693 0.0490* H111 0.2308 0.7218 0.7514 0.0568* H112 0.2002 0.8174 0.7024 0.0569* H113 0.2387 0.9082 0.7525 0.0565* H121 0.6235 0.7138 0.7913 0.0598* H122 0.8263 0.8083 0.7675 0.0608* H123 0.6238 0.8987 0.7933 0.0594* H161 0.8265 0.4586 0.6557 0.0409* H162 1.0590 0.5539 0.6614 0.0421* H181 0.9248 0.3339 0.5111 0.1291* H182 0.7341 0.4578 0.4946 0.1288* H183 0.6983 0.3525 0.5434 0.1289* H15 1.1118 1.2217 0.6016 0.0793* H171 1.2372 0.5416 0.5168 0.0958* H172 1.0592 0.6686 0.4986 0.0958* H173 1.1836 0.6950 0.5500 0.0968* Atomic displacement parameters (Å2) U11 U22 U33 U12 U13 U23 C1 0.0280 (7) 0.0193 (6) 0.0190 (6) 0.0001 (6) −0.0002 (6) −0.0015 (5) C2 0.0276 (7) 0.0233 (6) 0.0250 (6) −0.0002 (6) 0.0016 (7) −0.0024 (5) C3 0.0303 (8) 0.0236 (7) 0.0252 (6) 0.0064 (7) −0.0007 (7) −0.0004 (5) C4 0.0340 (8) 0.0193 (6) 0.0236 (6) 0.0055 (7) 0.0010 (7) 0.0023 (5) O5 0.0268 (5) 0.0165 (4) 0.0279 (5) 0.0014 (5) −0.0001 (4) −0.0005 (4) C6 0.0465 (11) 0.0196 (6) 0.0382 (8) −0.0008 (8) 0.0129 (9) 0.0003 (6) O7 0.0510 (8) 0.0227 (5) 0.0599 (8) 0.0018 (6) 0.0241 (7) 0.0059 (6) O8 0.0398 (6) 0.0226 (5) 0.0248 (5) −0.0013 (5) 0.0066 (5) −0.0033 (4) C9 0.0265 (7) 0.0238 (6) 0.0243 (6) 0.0003 (7) 0.0029 (6) −0.0024 (6) Acta Cryst. (2005). supporting information E61, o2891–o2893 sup-2 supporting information O10 0.0449 (7) 0.0229 (5) 0.0245 (5) 0.0028 (6) 0.0091 (5) −0.0001 (4) C11 0.0260 (8) 0.0407 (9) 0.0305 (7) −0.0009 (8) 0.0016 (6) −0.0045 (7) C12 0.0273 (7) 0.0457 (9) 0.0286 (7) −0.0001 (8) −0.0010 (6) 0.0004 (7) O13 0.0340 (6) 0.0280 (5) 0.0214 (5) 0.0051 (5) −0.0024 (5) −0.0055 (4) C14 0.0438 (10) 0.0302 (8) 0.0252 (7) 0.0105 (8) 0.0017 (7) −0.0039 (6) O15 0.0630 (9) 0.0325 (6) 0.0284 (5) 0.0227 (7) 0.0122 (6) 0.0056 (5) C16 0.0400 (9) 0.0198 (6) 0.0252 (6) 0.0057 (7) −0.0009 (7) −0.0003 (5) C17 0.0534 (12) 0.0664 (14) 0.0420 (10) 0.0165 (12) 0.0199 (10) 0.0190 (10) C18 0.0824 (19) 0.0585 (14) 0.0755 (16) 0.0166 (15) −0.0150 (15) −0.0442 (13) Geometric parameters (Å, º) C1—C2 1.530 (2) C9—C12 1.507 (2) C1—O5 1.4108 (18) C11—H111 0.978 C1—O13 1.4209 (16) C11—H112 0.951 C1—C16 1.517 (2) C11—H113 0.985 C2—C3 1.543 (2) C12—H121 0.953 C2—O10 1.4235 (18) C12—H122 0.950 C2—H21 0.983 C12—H123 0.977 C3—C4 1.526 (2) O13—C14 1.428 (2) C3—O8 1.4302 (18) C14—O15 1.4399 (19) C3—H31 0.990 C14—C17 1.513 (3) C4—O5 1.4448 (18) C14—C18 1.501 (3) C4—C6 1.505 (2) O15—C16 1.4110 (19) C4—H41 0.969 C16—H161 0.983 C6—O7 1.425 (2) C16—H162 0.966 C6—H61 0.983 C17—H171 0.970 C6—H62 0.989 C17—H172 0.964 O7—H15 0.814 C17—H173 0.988 O8—C9 1.4256 (19) C18—H181 0.957 C9—O10 1.4339 (18) C18—H182 0.975 C9—C11 1.518 (2) C18—H183 0.984 C2—C1—O5 105.52 (11) C9—O10—C2 107.71 (11) C2—C1—O13 108.37 (13) C9—C11—H111 109.6 O5—C1—O13 111.77 (11) C9—C11—H112 111.5 C2—C1—C16 117.58 (13) H111—C11—H112 109.2 O5—C1—C16 110.31 (13) C9—C11—H113 109.1 O13—C1—C16 103.39 (11) H111—C11—H113 107.7 C1—C2—C3 104.43 (14) H112—C11—H113 109.6 C1—C2—O10 108.97 (13) C9—C12—H121 109.0 C3—C2—O10 104.88 (12) C9—C12—H122 109.2 C1—C2—H21 112.1 H121—C12—H122 111.0 C3—C2—H21 113.5 C9—C12—H123 109.2 O10—C2—H21 112.4 H121—C12—H123 109.1 C2—C3—C4 103.75 (14) H122—C12—H123 109.4 C2—C3—O8 103.92 (12) C1—O13—C14 108.59 (12) C4—C3—O8 110.39 (14) O13—C14—O15 105.38 (11) O10 0.0449 (7) 0.0229 (5) 0.0245 (5) 0.0028 (6) 0.0091 (5) −0.0001 (4) C11 0.0260 (8) 0.0407 (9) 0.0305 (7) −0.0009 (8) 0.0016 (6) −0.0045 (7) C12 0.0273 (7) 0.0457 (9) 0.0286 (7) −0.0001 (8) −0.0010 (6) 0.0004 (7) O13 0.0340 (6) 0.0280 (5) 0.0214 (5) 0.0051 (5) −0.0024 (5) −0.0055 (4) C14 0.0438 (10) 0.0302 (8) 0.0252 (7) 0.0105 (8) 0.0017 (7) −0.0039 (6) O15 0.0630 (9) 0.0325 (6) 0.0284 (5) 0.0227 (7) 0.0122 (6) 0.0056 (5) C16 0.0400 (9) 0.0198 (6) 0.0252 (6) 0.0057 (7) −0.0009 (7) −0.0003 (5) C17 0.0534 (12) 0.0664 (14) 0.0420 (10) 0.0165 (12) 0.0199 (10) 0.0190 (10) C18 0.0824 (19) 0.0585 (14) 0.0755 (16) 0.0166 (15) −0.0150 (15) −0.0442 (13) sup-3 Acta Cryst. Acta Cryst. (2005). E61, o2891–o2893 supporting information (2005). E61, o2891–o2893 supporting information C2—C3—H31 114.1 O13—C14—C17 110.92 (14) C4—C3—H31 111.7 O15—C14—C17 107.53 (16) O8—C3—H31 112.4 O13—C14—C18 108.04 (17) C3—C4—O5 104.52 (11) O15—C14—C18 110.12 (17) C3—C4—C6 115.00 (13) C17—C14—C18 114.48 (19) O5—C4—C6 109.66 (14) C14—O15—C16 110.00 (12) C3—C4—H41 108.8 C1—C16—O15 104.95 (12) O5—C4—H41 109.7 C1—C16—H161 109.6 C6—C4—H41 109.0 O15—C16—H161 110.7 C4—O5—C1 106.49 (11) C1—C16—H162 112.9 C4—C6—O7 110.38 (13) O15—C16—H162 109.8 C4—C6—H61 107.9 H161—C16—H162 108.9 O7—C6—H61 109.4 C14—C17—H171 109.6 C4—C6—H62 108.4 C14—C17—H172 109.4 O7—C6—H62 111.1 H171—C17—H172 109.1 H61—C6—H62 109.6 C14—C17—H173 108.5 C6—O7—H15 104.5 H171—C17—H173 111.2 C3—O8—C9 107.69 (11) H172—C17—H173 109.0 O8—C9—O10 103.99 (10) C14—C18—H181 107.6 O8—C9—C11 111.48 (15) C14—C18—H182 109.4 O10—C9—C11 110.43 (15) H181—C18—H182 111.3 O8—C9—C12 109.38 (13) C14—C18—H183 107.4 O10—C9—C12 109.06 (14) H181—C18—H183 110.2 C11—C9—C12 112.17 (13) H182—C18—H183 110.9 Hydrogen-bond geometry (Å, º) D—H···A D—H H···A D···A D—H···A O7—H15···O15i 0.81 2.06 2.862 (2) 167 Symmetry code: (i) x, y+1, z. sup-4 sup-4 Acta Cryst. (2005). E61, o2891–o2893
https://openalex.org/W2963158600
https://www.swsc-journal.org/10.1051/swsc/2018004/pdf
English
null
The NWRA Classification Infrastructure: description and extension to the Discriminant Analysis Flare Forecasting System (DAFFS)
Journal of space weather and space climate
2,018
cc-by
18,062
The NWRA Classification Infrastructure: description and extension to the Discriminant Analysis Flare Forecasting System (DAFFS) NorthWest Research Associates, Boulder Office, 3380 Mitchell Ln., Boulder, CO 80301, USA Abstract – A classification infrastructure built upon Discriminant Analysis (DA) has been developed at NorthWest Research Associates for examining the statistical differences between samples of two known populations. Originating to examine the physical differences between flare-quiet and flare-imminent solar active regions, we describe herein some details of the infrastructure including: parametrization of large datasets, schemes for handling “null” and “bad” data in multi-parameter analysis, application of non- parametric multi-dimensional DA, an extension through Bayes’ theorem to probabilistic classification, and methods invoked for evaluating classifier success. The classifier infrastructure is applicable to a wide range of scientific questions in solar physics. We demonstrate its application to the question of distinguishing flare- imminent from flare-quiet solar active regions, updating results from the original publications that were based on different data and much smaller sample sizes. Finally, as a demonstration of “Research to Operations” efforts in the space-weather forecasting context, we present the Discriminant Analysis Flare Forecasting System (DAFFS), a near-real-time operationally-running solar flare forecasting tool that was developed from the research-directed infrastructure. Keywords: Sun / statistical analysis / flares / prediction / Discriminant Analysis / Bayes Empirical event-based forecasting is an application of statistical classifiers to historical samples drawn from two known populations: those that did and those that did not produce the event in question. For statistical classification methods, there are essentially four steps: (1) defining the event in question and hence the populations to be sampled, (2) sample acquisition (data acquisition), with attention to bias that may be imposed to the samples of the populations, and parametrization of the data in such a way as to be testable by the classifier, (3) applying the classifier with appropriate safeguards against undue influence from outlier data and statistical flukes, (4) evaluate the classification by way of validation metrics or similar measures. Finally, (5) the results are available for scientific understanding or operational forecasting. *Corresponding author: leka@nwra.com 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 cited. Available online at: www.swsc-journal.org Available online at: www.swsc-journal.org va ab e o e a : www.swsc-journal.org Developing New Space Weather Tools: Transitioning fundamental science to operational prediction systems J. Space Weather Space Clim. 2018, 8, A25 © K.D. Leka et al., Published by EDP Sciences 2018 https://doi.org/10.1051/swsc/2018004 J. Space Weather Space Clim. 2018, 8, A25 © K.D. Leka et al., Published by EDP Sciences 2018 https://doi.org/10.1051/swsc/2018004 J. Space Weather Space Clim. 2018, 8, A25 © K.D. Leka et al., Published by EDP Sciences 2018 https://doi.org/10.1051/swsc/2018004 J. Space Weather Space Clim. 2018, 8, A25 © K.D. Leka et al., Published by EDP Sciences 2018 https://doi.org/10.1051/swsc/2018004 pen Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/license unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1 Introduction The prospect of forecasting rare events such as solar flares is a daunting one, especially in situations where the exact trigger mechanism or threshold for instability is not yet known. Still, due to their impact on the space weather environment, the forecasting of solar flares enjoys some prominence of priority due to the combination of the speed-of-light impact due to X-ray emission, their association with high-energy particle enhance- ments, and their correspondence to coronal mass ejections. , p j Early empirical efforts to forecast solar flares focused on the white-light morphology of their host active regions (Sawyer et al., 1986). Different classes of active region (based on size and sunspot-group characteristics) were observed to produce flares at different rates, and applying Poisson statistics resulted in probabilistic forecasts for flares (McIntosh, 1990; Bornmann & Shaw, 1994). This approach forms the basis for many forecasts published today, including those from the US National Oceanic and Atmospheric Administration (NOAA)/ Space Weather Prediction Center (SWPC) (Sawyer et al., 1986; Gallagher et al., 2002; Murray et al., 2017; Steenburgh & Balch, 2017). We describe herein a classifier infrastructure that has been developed at NorthWest Research Associates (NWRA) based on Non-Parametric Discriminant Analysis (NPDA). Discrimi- nant Analysis (DA) is a tool that has been used for a variety of scientific investigations (Solovyev et al., 1994; Filella et al., 1995; Jombart et al., 2010); it is particularly useful for the analysis of statistically-significant samples of what are believed to be two distinct populations, asking how well are the populations separable in parameter space? While the K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 1. Avery generalized flow chart for the NWRA Classification Infrastructure. Circles generally indicate input, squares are processes, and the diamond is output. ow chart for the NWRA Classification Infrastructure. Circles generally indicate input, squares are processes, and t Fig. 1. Avery generalized flow chart for the NWRA Classification Infrastructure. Circles generally indicate input, squares are processes, and the diamond is output. instruments (the Solar Optical Telescope, Tsuneta et al., 2008, and the EUV Imaging Spectrograph, Culhane et al., 2007). instruments (the Solar Optical Telescope, Tsuneta et al., 2008, and the EUV Imaging Spectrograph, Culhane et al., 2007). 2.1 Posing the question A classifier attempts to separate samples from known populations in the context of the parameter space constructed by variables which describe some physical aspect of the system in question. As such, the questions posed must be constructed in such a way as to be addressable with a statistical classifier. Classifiers can, for example, answer “are these three things uniquely associated with an event?” but cannot answer, “does this thing cause that event to occur?” The crux of posing an appropriate question rests on the event definition. In Section 3, we present a detailed example of NCI in use, specifically NWRA’s ongoing research regarding flare-immi- nent active regions. Following the steps above, this includes a description of the event definitions (Sect. 3.1), data sources and parametrization modules (Sect. 3.2) including parametrization of temporal evolution (Sect. 3.2.8), classifier application examples (Sect. 3.3) and evaluation results (Sect. 3.4). We discuss the results of this updated flare-imminence research in Section 3.5. 1 Introduction NWRA Classification Infrastructure (NCI) has been used for topics including detecting solar emerging flux regions (Leka et al., 2013; Barnes et al., 2014), and filament eruptions (Barnes et al., 2017), it developed from a series of works which examined the question, “what is the difference between a flare- imminent and flare-quiet solar active region?” (Leka & Barnes, 2003b; Barnes & Leka, 2006; Leka & Barnes, 2007; Welsch et al., 2009; Komm et al., 2011). To understand a physical phenomena and guide relevant modeling efforts, it is frequently important to identify what features are unique or predisposed to an event. NCI is a tool for doing that. We describe NCI here in general terms, guided by the steps outlined above (a general flow-chart is provided in Fig. 1). We describe in Section 2 the NCI research-focused infrastructure, with which new questions, new data, param- eters, approaches, etc. are developed and evaluated. We discuss framing the question and event definition consider- ations (Sect. 2.1), data analysis and parametrization (Sect. 2.2), the various flavors of DA employed (Sect. 2.3) and the extension to probabilistic classification by way of Bayes’ theorem (Sect. 2.3.3), evaluation tools (Sect. 2.4), and a discussion of interpreting the results and selecting good parameter combinations (Sect. 2.5). 2.2 Data and parametrization Statistical classifiers attempt to separate samples drawn from different populations within parameter space. The samples are thus representations of the physical state of the systems in question. For image-based or otherwise spatially distributed variables, NCI derives both extensive and intensive parame- ters, meaning those that do and do not depend on the size of the feature in question, respectively (see Leka & Barnes, 2003a, b, 2007; Welsch et al., 2009). The spatially distributed variables (i.e., “x”) are parametrized by the first four moments: mean x, standard deviation s(x), skew &(x), and kurtosis k(x), often weighted by some relevant quantity, plus spatial summations as appropriate. The lower order moments capture the typical properties of the target image, while the higher-order moments capture the presence of small-scale features. The image data themselves can be highly processed derived physical quantities which have a 2-dimensional extent: in the case of imaging spectroscopy, for example, an image of equivalent widths is appropriate. For helioseismology, the image may be phase- shifts or inferred vorticity maps (Komm et al., 2011; Barnes et al., 2014). Linear DA has the advantage of being able to consider large numbers of variables simultaneously even for small sample sizes. If the variables are uncorrelated and in standardized form, the magnitude of each variable’s coefficient in the discriminant function gives its relative predictive power (e.g., Klecka, 1980). If variables are correlated then their predictive power will be shared. In practice diminishing returns are usually found beyond at most 10 parameters, likely due to correlations among variables in the solar contexts tested thus far (Leka & Barnes, 2003b, 2007; Komm et al., 2011). The disadvantage to linear DA is that it assumes a functional form for the probability distribution which may not be valid, and for most parameters considered here is likely invalid. Thus linear DA is best suited to problems for which only small samples are available, and in which large numbers of variables are needed to make accurate classifications. NCI is routinely used to analyze time-series data. The approach taken thus far is to fit time-series data with an appropriate model and then use the retrieved coefficients or model fits as parametrizations. 2.1.1 Event definitions Flare forecasting research tools are becoming somewhat common (Gallagher et al., 2002; Wheatland, 2005; Georgoulis & Rust, 2007; Colak & Qahwaji, 2009; Bloomfield et al., 2012; Bobra & Couvidat, 2015) and their performance an active subject of evaluation (e.g., Barnes & Leka, 2008; Bloomfield et al., 2012; Falconer et al., 2014; Barnes et al., 2016). As a demonstration of Research-to-Operation efforts in the space weather forecasting context, we finally describe here the details of the Discriminant Analysis Flare Forecasting System (DAFFS, Sect. 4), a Near-Real-Time (NRT) operationally- designed forecasting tool which grew from the NCI. DAFFS was recently implemented under a Phase-II Small Business Innovative Research (SBIR) project through the NOAA/ SWPC, as an answer to “Delivering a Solar Flare Forecast Model that Improves Flare Forecast (Timing and Magnitude) Accuracy by 25%.” (topic NOAA 2013-1 9.4.3W). It is presently in use to aid target selection for the Hinode mission (Kosugi et al., 2007), specifically its limited field-of-view The event definition is simply the categorical description of an “event” and the countering “non-event”. In solar physics, event definitions have included whether (or not) a solar active region emerged (Barnes et al., 2014), or whether a filament produced a coronal mass ejection (Barnes et al., 2017). A widespread application has been regarding the occurrence (or not) of a solar flare within the context of photospheric magnetic field measurements (Leka & Barnes, 2003b, 2007), plasma velocity (Welsch et al., 2009) and helioseismology-derived parametrizations (Komm et al., 2011). An event definition can be any such description, the more refined and specific the better. It must uniquely assign data points to one of the two populations (event/non-event) against which the ability to distinguish the populations may be judged. j g By default, the NCI events are defined in a true forecasting sense, with an upcoming interval during which the timing of an Page 2 of 23 Page 2 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 2.2 Data and parametrization In the case of the evolution of photospheric magnetic field over the course of a few hours, for example, a first-order function is fit to the image-derived parameters, then the slope and intercept at a designated future time are considered as two input parameters. 2.3 Discriminant Analysis event is unknown. However, NCI is designed for flexibility for scientific investigations. With the construction of suitable event definitions and event lists, NCI an also be invoked in an super-posed epoch analysis mode (“SPE”; Leka et al., 2013; Barnes et al., 2014) for which the event time is known and analysis is carried out relative to that reference time (Mason & Hoeksema, 2010; Reinard et al., 2010; Bobra & Couvidat, 2015). Discriminant Analysis (DA) (Kendall et al., 1983) is the classifier employed here: DA is a statistical approach to classify new measurements as belonging to one of two populations based on characterizing the Probability Density Functions (PDF) from known examples. In brief, DA divides parameter space into two regions based on where the probability density of one population exceeds the other. Key to success is estimating the PDFs well. There are two general approaches to estimating PDFs: parametric, in which the functional form of the distribution is assumed, and non- parametric, in which it is estimated directly from the data. Both options are available in the NCI. For scientific investigations the emphasis could be on understanding the physical differences between populations. Such a study could use either balanced sample sizes of the populations in question or invoke equal prior probabilities for the two populations, in order to highlight distinguishing characteristics (Leka et al., 2013). This is in contrast to a forecasting system where unequal sample sizes are the norm, and one must incorporate the prior probabilities into the analysis. 2.3.1 Parametric density estimation When each variable is assumed to have a Gaussian distribution, with the same variance for each population, the discriminant boundary is a linear function of the variables. This is quite a strong assumption, and one which is known to be routinely violated for many solar physics relevant para- metrizations; in practice, for some topics, the results have been found to not depend strongly on the assumption (Leka & Barnes, 2007), especially for rarer events. 2.3.2 Non-parametric density estimation In nonparametric DA (NPDA), no assumption is made about the distribution of any parameter. Instead, the distributions are estimated directly from the data. This negates the need for making assumptions, but requires large sample sizes to accurately estimate the distributions, especially when considering the shape of the tails of the distribution, and especially when considering multiple variables simultaneously (see Table 4.2 in Silverman, 1986). As such, NPDA can only reasonably be used for combinations of small numbers of variables. Within NCI, NPDA is generally employed with at most 2-variable combinations. p p The classifier employed here works best with continuous variables, although it can handle discrete values. As discussed below (Sect. 2.3), correlated parameters do not add useful information. Sample size matters. Sufficient data allows for robust estimates of the classifier performance, as demonstrated by the resulting error bars on the validation metrics (see Sect. 2.4.1). Small sample sizes are especially problematic for multi-variable analysis. While each situation is different, samples significantly fewer than 100 data points in any one population are challenging. Sample sizes may be unbalanced. The NCI NPDA code presently estimates the probability density using a kernel method with the Epanechnikov kernel; a single smoothing parameter is set based on its optimum value for a normal distribution (Silverman, 1986). This works well for distributions which are not too far from a normal distribution, but does not accurately represent long tails of Page 3 of 23 Page 3 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 distributions without very large sample sizes. Using a single smoothing parameter has a tendency to undersmooth the tails of a distribution when the peak of the distribution is appropriately smoothed, or to oversmooth the peak if the tails are appropriately smoothed. This is a particularly important effect when multiple variables are considered, as the volume of space occupied by the tails (where key parameter differences can lie) grows rapidly with the number of variables, and thus the difference between the density of observations near the peak and in the tails becomes even more pronounced. To counteract this, the NCI works with the logarithm of positive definite variables with a large skew (or the logarithm of the absolute value of negative definite variables with a large negative skew). 2.4.1 Metrics The success of the classification exercise is judged quantitatively using metrics that are standard in classification and forecast validation (Woodcock, 1976; Jolliffe & Stephen- son, 2003; Bloomfield et al., 2012; Barnes et al., 2016). We focus on the following: the Peirce skill score, also known as the True Skill Statistic, or Hanssen and Kuipers discriminant (H&KSS) and the Appleman skill score (ApSS) for categorical forecasts, and the Brier Skill Score (BSS) for probability forecasts. The Rate Correct (RC) is included for completeness. The full derivations and descriptions can be found in the cited references; of note here are the critical functions of each: the H&KSS measures the discrimination between the Probability of Detection and the False Alarm Rate, the ApSS measures the skill against the climatological forecast, and the BSS evaluates the performance of probabilistic forecasts against observed occurrence. All are normalized such that 1.0 is the highest possible score and 0.0 represents no separation/no skill relative to the appropriate reference. p y pp Since it is impractical to apply NPDA to large numbers of variables simultaneously, it is often helpful to consider the performance of all possible permutations of small numbers of variables to determine which ones are best able to classify the data (see Sect. 2.5). Combining correlated variables does not substantially improve the performance of NPDA over each variable used alone. 2.4.2 Removing bias To make unbiased estimates of the performance of the tested parameters, the NCI system uses cross-validation (Hills, 1966). In cross-validation, one data point is removed from the sample of size n, and the remaining n  1 data points are used to make a probabilistic forecast about or to classify the removed point. This process is then repeated for all n data points and the elements of the standard classification table can be filled in (True Positive, False Positive, False Negative and True Negative). Essentially, this approach minimizes the influence of outliers classifying themselves, and 2.3.4 Missing data The BSS is itself a summary of Reliability plots which graphically display systematic under- and over-forecasting through the comparison of the predicted probabilities to observed frequency (see Barnes et al., 2016, for a discussion). In NCI missing data (e.g., due to outages) is differentiated from “well-measured null values” such as the length of a strongly-sheared magnetic polarity inversion line in a unipolar region (with no such line). Neither of these categories of data are ignored or removed; instead, they are assigned the climatology derived for all other datapoints with the same missing-data assignment. For multiple-parameter analysis, the climatology is determined by those regions which have the same combination of data flags (good, null, bad/missing). In this manner, as much information as is possible (for example if one parameter is good but the other is missing) can be used in the classification. 2.3.2 Non-parametric density estimation NPDA is thus best suited to problems for which large samples are available, and for cases in which only a small numbers of variables are needed to make accurate classifications. With sufficiently large sample sizes, even the tails of a distribution will be well captured by this approach. validation metrics but estimating their uncertainty, identifying and removing bias, and accounting for statistical flukes. Challenges to this and other statistical methods include: small and/or unbalanced sample sizes, bias in the samples, and undue influence from outlier data. However, with the use of appropriate metrics and error estimates, these challenges are not insurmountable to achieving valuable understanding. 2.3.3 Extension to probabilistic forecasts To predict the probability of a data point belonging to a given population, rather than a categorical (yes/no) classifica- tion, Bayes’ theorem is invoked (Barnes et al., 2007). The probability that a measurement x belongs to population j is given by: pp p The categorical skill scores require a probability threshold (Pth) above which an event is classified (or forecast) to occur. By default NCI uses Pth = 0.5, which effectively optimizes the ApSS because the errors of both types are treated equally. As discussed by Bloomfield et al. (2012); Barnes et al. (2016) the optimal H&KSS occurs when Pth ≈R, R being the event rate. The Relative Operating Characteristic (ROC) curve tracks performance of the H&KSS as a function of varying Pth; the Gini coefficient G1 (or ROC Skill Score; Jolliffe & Stephenson, 2003) then quantifies the ROC curve: G1 = 2 * A  1.0 where A is the area under the ROC curve, and again G1 = 1.0 denotes a perfect score. Given the sensitivity of the H&KSS to this Pth, which is to some level a function of customer priority between False Alarms and Misses, we report the Gini coefficient as a concise summary of the behavior of this metric. PjðxÞ ¼ qj f jðxÞ q1 f 1ðxÞ þ q2 f 2ðxÞ ; ð1Þ ð1Þ where qj is the prior probability of belonging to population j, f jðxÞ is the PDF for population j, and (for the flare study) j = 2 refers to the flaring population, while j = 1 refers to the flare-quiet population. This expression is valid for any well behaved probability density function f. 2.5.1 Identifying multiple well-performing parameters A bootstrap method is used to account for random errors (Efron & Gong, 1983), employing 100 draws by default. The draws are performed randomly across all data (meaning the sample sizes in each draw are equal to the sample sizes of the two populations for the data), with points selected randomly with replacement (each sampled point is not removed from the drawn-upon sample, it may be drawn again). The resulting skill scores are computed for each draw, and the uncertainties are estimated by the standard deviation of the draws’ scores. To choose the best-performing single variable, NPDA is performed on all available data including cross-validation and 100-draw bootstrap as outlined above. The single variables with the highest values of the skill score of interest are selected for 1-variable results. Bootstrap draws with no samples in one or all populations (possible for small sample sizes) have a flag assigned for the skill scores, to either include in later computation or to ignore. Small samples will generally result in large uncertainties. For the examples given in Section 3.4, with a sample size of events of 40 (for Xþ1) the typical uncertainty in a skill score is 0.06–0.10, while with a sample of events of 2636 (for Cþ1), the typical uncertainy is 0.01. In both cases, the sample size of non-events is more than a factor of 10 larger than the sample size of events, so the dominant source of the uncertainty is the density estimates for the events. We developed a practical approach to evaluate multi- variable combinations which likely captures the best-perform- ing 2-variable combinations, although it remains a possibility that a well-performing combination is missed. We first compute the skill scores for all possible 2-variable combinations without a bootstrap and using a simplified form of cross-validation in which the contribution from the removed point is subtracted from the density estimate, but the full density estimate is not recomputed with an updated value of the smoothing parameter. Six variables which appear in almost every combination of the top performing combinations are selected. Those are then paired with each of the others available with the full cross- validation and bootstrap draws applied, and the results are sorted on the skill score of choice. There are generally parameters or parameter combinations which perform similarly within the uncertainties (Leka & Barnes, 2003b). This is especially true for classes having larger sample sizes. 2.5 What was learned? Having identified the best-performing parameters (or parameter combinations) and their discriminating power one is then poised to physically interpret the results in the context of the posed question. Conversely, if there are no results which indicate skill, then none of the parameters tested are able to successfully distinguish the populations in parameter space, and are essentially irrelevant to the question posed. Identifying the well-performing parameters also serves as a method for selecting those to be used for successful operational forecasting. After the four steps above, the final one allows for analysis of what are the physically important parameters for the physical question at hand, i.e. “what variables provide the most insight into the physical processes at play in the context of the posed question?” Alternatively, in the operational context, determining the best performing parameters is tantamount to producing a good forecast. For many of the scientific questions addressed and addressable in NCI, hundreds of parameters calculated from the data are considered, which leads to millions of available parameter combinations. In practice only 1- or 2-variable combinations are most appropriate for use, especially with NPDA, where sample-size requirements increase very quickly with the number of variables considered simultaneously. However, with so many parameters under consideration, statistical flukes will occur: variables or variable combinations may seem to perform well (or poorly) when in fact they do not, upon testing further with larger sample size. As noted 2.5.1 Identifying multiple well-performing parameters The point of reporting multiple parameter-combination (classification, forecast) results is not an ensemble result but a guard against statistical flukes (see below). 2.4.4 Accounting for statistical flukes With a large number of parameters being tested, even with cross-validation and bootstrap error estimates, statistical flukes can occur such that a parameter appears to work well when it in fact does not. The best remedy for this is sample size, although the Sun does not always cooperate. As described in Barnes et al. (2014), a Monte Carlo experiment can be used to check that the outcome is not simply a result of random chance: two random samples with sizes equal to the sample sizes of the two samples are drawn from the same normal distribution to represent one variable with no power to distinguish the two populations. This is repeated for a large number of variables, and the same analysis is performed on these random variables as on the actual parameters being studied. In this manner, it can be determined what statistical outliers in the skill scores may be expected given no difference in the two underlying populations (see Sect. 3.4). Different event definitions (Sect. 2.1.1) will lead to different top-performing parameters or parameter combina- tions. Similarly, optimizing the results according to different skill scores will result in different parameters being chosen (Barnes et al., 2016). In practice, however, while there may be a slight re-ordering of the results, we find that the same parameters (or very closely related parameters, such as total magnetic flux vs. total negative magnetic flux) are routinely within the top few percent of the results. 2.4 Evaluation Evaluating the results of a classification exercise is a multi- faceted task that includes not just the calculation of the Page 4 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 is a particularly important process when working with small sample sizes. previously, multi-parameter combinations formed from corre- lated variables do not add discriminating power (Leka & Barnes, 2007). 3 NCI and empirical research into the causes of solar flares As mentioned above, NCI originated from early research into the statistical differences between flare-imminent and flare-quiet time intervals (Leka & Barnes, 2003b; Barnes & Leka, 2006; Leka & Barnes, 2007). The research has continued Page 5 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 will have an extended large-value tail compared to single ARs. Second, most HARP numbers are assigned to regions which do not have a corresponding NOAA number. Such regions are plentiful, are predominantly small (often consisting solely of plage), and hence the parameters (both extensive and intensive) will have distributions which are more densely populated at lower values than AR-based distributions. Table 1. Event definitions. Label Minimum threshold (nomenclature) Minimum threshold (W m2) Latency (h) Validity period (h) Region/full disk C þ 1 C1.0 ≥106 2.2 24 R, FD† M þ 1 M1.0 ≥105 2.2 24 R, FD X þ 1 X1.0 ≥104 2.2 24 R, FD C þ 2† C1.0 ≥106 26.2 24 R, FD M þ 2 M1.0 ≥105 26.2 24 R†, FD X þ 2 X1.0 ≥104 26.2 24 R†, FD C þ 3† C1.0 ≥106 50.2 24 R, FD M þ 3 M1.0 ≥105 50.2 24 R†, FD X þ 3 X1.0 ≥104 50.2 24 R†, FD † Not included in NOAA’s forecasts but included here for completeness. Table 1. Event definitions. p p The full-disk forecasts are created by combining the flaring probabilities of the regions: PFD ¼ 1:0  ∏ AR ð1:0  PARÞ; ð2Þ ð2Þ where PAR are the flaring probabilities of each active region and PFD is the resulting full-disk flaring probability. Of note, combining probabilities in this manner assumes independent events; this assumption may not hold during times of high solar activity when numerous magnetically interconnected regions are present on the solar disk (Schrijver & Higgins, 2015). The NCI can thus provide full-disk forecasts but those are usually less useful for research purposes and more appropriate for the operational tool (see Sect. 4). where PAR are the flaring probabilities of each active region and PFD is the resulting full-disk flaring probability. Of note, combining probabilities in this manner assumes independent events; this assumption may not hold during times of high solar activity when numerous magnetically interconnected regions are present on the solar disk (Schrijver & Higgins, 2015). 3.2 Data sources and parametrization Early NWRA NCI-based research examined the question of differences in flare-imminent vs. flare-quiet active regions (Leka & Barnes, 2003a, b; Barnes & Leka, 2006; Leka & Barnes, 2007) using a substantial database of time-series photospheric vector magnetic field data from the U. Hawai‘i Imaging Vector Magnetograph (Mickey et al., 1996; LaBonte et al., 1999; LaBonte, 2004; Leka et al., 2012). Additional studies (Barnes et al., 2016) used line-of-sight photospheric magnetic field data from the Solar and Heliospheric Observatory/Michelson Doppler Imager (SoHO/MDI Scherrer et al., 1995). Current NWRA research and performance baselines use new data sources, as described here. 3 NCI and empirical research into the causes of solar flares The NCI can thus provide full-disk forecasts but those are usually less useful for research purposes and more appropriate for the operational tool (see Sect. 4). † Not included in NOAA’s forecasts but included here for completeness. with new data sources and parameters; as such, NCI has proven useful as a testbed infrastructure for this research topic. Here we demonstrate NCI with this specific flare-related topic, and thus provide an update of the state of NWRA’s research from earlier publications. 3.1 Event definitions For the NCI research on flare-imminent active regions, we adopted a “forecast” model for event definitions, and essentially match the forecasts issued by NOAA, as summarized in Table 1 based on events as illustrated in Figure 2. The thresholds are defined by the peak Soft X-ray flux as reported by NOAA/SWPC, based on the 1–8 Å Soft X-ray detector on the Geostationary Observing Earth Satellite (GOES) platform at the time of the event. It should be noted that in the application of DA to flaring active regions as defined in this manner, a continuous variable (the Soft X-ray emission) defines the categorical event definition required by DA by means of a fairly arbitrary threshold. Additionally, defining an event by its peak Soft X-ray emission captures only a limited measure of flare-associated energetic output. To characterize the state of the active regions and their likelihood to flare, we perform parametric analysis on the data sets described above. The goal is to reduce the ([x, y, t]) vector magnetic field time series plus the flaring history of each active region into a series of parameters suitable for statistical analysis. The parametrization packages which are now well- established or are under active research are fairly modular; the results from each are often merged after the parameters are calculated, for classifier analysis. g p We included a 2.2 h delay needed for all data processing (including initial Solar Dynamics Observatory/Helioseismic and Magnetic Imager (SDO/HMI) data-reduction at Stanford) between data acquisition time and forecast issuance time, although for research based on the definitive time series, this is effectively moot. In other words, when relying upon the definitive data, the last dataset used is from 21:48 TAI for a forecast (classification) issued at 00:00 UT. The Soft X-Ray (SXR) events considered to match the forecast validity periods, are taken from that issuance time. 3.2.2 Data: SDO/HMI photospheric vector magnetic field data The present NCI research extends earlier work naturally by relying upon time-series of vector magnetic field data from the Helioseismic and Magnetic Imager from the Solar Dynamics Observatory (Pesnell, 2008; Scherrer et al., 2012; Schou et al., 2012; Centeno et al., 2014; Hoeksema et al., 2014). NWRA became an SDO remote SUMS/DRMS (Storage Unit Management System/Data Record Management System) site early in the mission, as NWRA's “ME0” disambiguation code is used for the pipeline data reduction (Leka et al., 2009; Hoeksema et al., 2014) and easy access to the data was needed for pipeline-code implementation. NWRA maintains local copy of the definitive hourly HMI data through the remote- SUMS system and automated updates of the metadata DRMS database. Definitive data are transferred roughly monthly using the JSOC Mirroring Daemon1. The hourly HARP-based sub-areas are extracted, coal- igned, and gathered together as custom in-house Flexible Image Transport System (FITS) files. The filename describes the start time, length of time-series, cadence, and HARP number, and is unique; as such it forms the basis for cross referencing throughout NCI. The hmi.Bharp_720s and hmi. sharp_720s series (both linked to hmi.MEharp_720s) provide disambiguated extracted HARP-area vector field data cut-outs. Following earlier studies (Leka & Barnes, 2003a,b, 2007), the image-plane coordinate system is used by default, with transformations to heliographic components performed using point-by-point observing angle component computation and a propagation of uncertainties based on the uncertainties from the inversion as included in the hmi.ME_720s_fd10 series. The multi-point approach avoids significant errors arising from a planar assumption in the (not infrequent) case that a HARP extends over a significant portion of a visible half-hemisphere. A potential field whose normal component matches the input normal component boundary is computed using a Cartesian Fourier-component method; a guard ring which is a factor of 2 larger than the input boundary size is invoked in order to reduce artifacts which can arise with a boundary occurring on, or too near, strong-field areas. An estimate of the 1s uncertainty in the potential-field components is computed using the computed components themselves: within active pixels, those that are brighter than the mean less the mean absolute deviation of the continuum intensity are used to compute histograms of that component’s field strengths. The field strength where 68% of the area under the histogram curve is achieved is denoted that component’s 1s uncertainty level. 3.2.1 Data: NOAA-generated Soft X-ray event lists NWRA gathers the event lists of solar flares as defined by NOAA/SWPC; the information required includes the start time, peak time, peak flux and associated NOAA-numbered active region source (Fig. 2). These are acquired from the NOAA archives through ftp.swpc.noaa.gov/pub/warehouse and from the NRT updating lists at http://services.swpc.noaa. gov/text/solar-geophysical-event-reports.txt Additionally, NWRA subscribes to the NOAA External Space Weather Data Store (E-SWDS) NRT space weather data access system, where events are recorded with minimal delay. We do not attempt to perform any of the analysis by which to independently determine start time, peak flux, or location. The region-by-region forecasts are based on the HMI active region patches (‘HARPs’ Bobra et al., 2014; Hoeksema et al., 2014, see Sect. 3.2.2) rather than strictly on NOAA Active Regions (ARs). This approach has two consequences if the results are compared to strictly NOAA AR-based methods: first, there are many HARPs which contain more than one NOAA region. As such, the distributions of parameters (in particular extensive parameters such as total magnetic flux) Page 6 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 2. Left: The GOES soft X-Ray plots of the 2011 Sep. 6–9 interval. Right: The event list for flares detected in the GOES soft X-Ray 1–8 Å channel, specifically for NOAA AR 11283, through 20110907 (Active Region and time interval chosen fairly randomly, for additional demonstrations below). Fig. 2. Left: The GOES soft X-Ray plots of the 2011 Sep. 6–9 interval. Right: The event list for flares detected in the GOES soft X-Ray 1–8 Å channel, specifically for NOAA AR 11283, through 20110907 (Active Region and time interval chosen fairly randomly, for additional demonstrations below). Fig. 2. Left: The GOES soft X-Ray plots of the 2011 Sep. 6–9 interval. Right: The event list for flares detected in the GOES soft X-Ray 1–8 Å channel, specifically for NOAA AR 11283, through 20110907 (Active Region and time interval chosen fairly randomly, for additional demonstrations below). In particular, flares for which NOAA does not provide an associated active region, as occurs for a fraction of smaller flares and a few larger flares, are not included in the NCI analysis by default. calibrations that are scheduled at some of the :00 times, we focus on the :48 data. No data are used that have a quality flag different from zero. 3.2.1 Data: NOAA-generated Soft X-ray event lists As described in Section 3.2.8, data covering 6 h inclusive (7 time periods) provide input for short- term temporal-evolution parameters. By default the NCI classification mimics a midnight-issued forecast, thus hourly data from 15:48 to 21:48 are targeted. For definitive data, there is no constraint regarding the HMI data reduction pipeline timing requirements. 1 See http://vso.tuc.noao.edu/VSO/w/index.php/Main_Page. 3.2.3 Data: photospheric line-of-sight magnetic field data 3.2.3 Data: photospheric line-of-sight magnetic field data 3.2.4 Other data sources Photospheric line-of-sight magnetic field data is used in some NCI research on solar flare productivity. The SoHO/MDI mission provided a significant data set, used in one of the first systematic forecasting comparison efforts (Barnes et al., 2016). Presently, the National Solar Observatories (NSO) Global Oscillations Network Group (“GONG”; Hill et al., 2003), in particular the line-of-sight magnetograms, is an ingested dataset for analysis by NCI tools. The GONG data is used in the NRT forecasting system in the event that the vector field data are unavailable (see Sect. 4.1). The GONG data do have the advantage of lengthy coverage, which increases the statistical significance of the training results. For research purposes, the NCI has been used for investigations using helioseismology and coronal emission as related to emerging magnetic flux (Leka et al., 2013; Barnes et al., 2014) as well as flaring. The data sources for these investigations have been or will be described in detail in the relevant publications. 3.2.2 Data: SDO/HMI photospheric vector magnetic field data The analysis of the vector field data extends to viewing angle u ≈80 from disk center. g For the flare-targeted research with NCI the definitive data series are used; we do not generally employ the cylindrical equal-area reprojected data. The hmi.Mharp_720s series, including the bitmap which flags active-pixel “blobs” (see Fig. 3 and Table 8; Hoeksema et al., 2014) is used to identify theHARPsthatareextractedfromthefull-diskMilne-Eddington inversion data series hmi.ME_720s_fd10, including uncertain- ties from the inversion (Centeno et al., 2014). The hmi.B_720s series provides the pipeline disambiguation results and their confidence (Hoeksema et al., 2014). Additionally, we optionally extract the same HARP sub-areas from the continuum images in hmi.Ic_720sandtheline-of-sightmagnetogramsinhmi.M_720s. Anexample HARP and active-pixel map isshown in Figure3 for the region associated with the flares demonstrated in Figure 2. g g To keep the data volume and analysis tenable, an hourly cadence is generally used; to avoid problems from daily Page 7 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 3. An image of NOAA AR 11283 at 2011.09.07 21:48 TAI as an SDO/HARP #833), showing the vertical component of the magnetic field Bz from SDO/HMI (red/positive, blue/negative contours at ±100 Mx cm2); axes are in arcsec, and green/yellow contours indicate the vertical current density Jz at ±50, 100 m Am2. The HARP “active pixel” area is outlined in grey. Fig. 3. An image of NOAA AR 11283 at 2011.09.07 21:48 TAI as an SDO/HARP #833), showing the vertical component of the magnetic field Bz from SDO/HMI (red/positive, blue/negative contours at ±100 Mx cm2); axes are in arcsec, and green/yellow contours indicate the vertical current density Jz at ±50, 100 m Am2. The HARP “active pixel” area is outlined in grey. 3.2.5 Parametrization: prior flare history Future solar energetic events often follow previous activity, with a somewhat predictable distribution in size and frequency (Wheatland, 2005). As such it is not surprising that “flare persistence” can be a good indicator of future activity (Falconer et al., 2012); in fact, it forms one of the primary predictors used for NOAA/SWPC operational forecasts (Sawyer et al., 1986). Data from all available GONG stations are acquired for a target time from the NSO near-real-time GONG website, and assessed. The best is chosen based on metrics (moments of spatial gradients) which quantify the seeing quality with a normalization to account for slightly differing plate scales between the sites. From this module, the parametrization of prior flaring activity provides event probabilities based on peak Soft X-ray output over the prior 6, 12, and 24 h, including the change in flaring output between those intervals. This “Prior Peak Flux” (PFF) parametrization essentially follows Abramenko (2005): GONG-based active-region patches are extracted accord- ing to the NOAA E-SWDS AR data, with a bounding-box generally reflecting the size of the region (latitude, longitude, and area), then adjusted for solar rotation to the target time of the acquired data. FL ¼ X indexC þ 10  indexM þ 100  indexX; ð3Þ FL ¼ X indexC þ 10  indexM þ 100  indexX; ð3Þ FL ¼ X indexC þ 10  indexM þ 100  indexX; ð3Þ ð3Þ q In general when Blos is employed for analysis, an estimate of Bz is derived using a potential field which matches the observed Blos, following Leka et al. (2017). Note that this differs from assuming that Blos ≈Bz. From this potential field, a radial field estimation, Bpot z , is retrieved to be used for the input. The advantage of this treatment of a Blos boundary is twofold, as discussed in Leka et al. (2017): the magnetic field strengths better approximate the radial field strengths and the apparent magnetic polarity inversion lines that are in fact caused only by viewing angle are removed or significantly mitigated. As such, for line-of-sight sources as with vector data sources, the magnetic field analysis functions fully to u ≈80. where indexC ≡2.3, 4.9, etc., as reported by the NOAA GOES 1–8 Å detectors. Example categories include: where indexC ≡2.3, 4.9, etc., as reported by the NOAA GOES 1–8 Å detectors. 3.2.6 Parametrization: photospheric magnetic field The parametrization of the photospheric magnetic field essentially follows Leka & Barnes (2003a and b); Barnes et al. (2007). The goal is to identify signatures of magnetic field complexity, to estimate energy storage, and identify non- potential structures and magnetic twist – in the context that regions showing evidence of minimal available magnetic energy, minimal energy storage, low complexity and nearly- potential (current-free) fields are much less likely to flare, and vice versa. As described in Barnes et al. (2007), the photospheric parameters in many ways quantify the character- istics which are used for the sunspot-group classifications such as the McIntosh (McIntosh, 1990) (modified Zurich) nomenclature. The variables, described in detail in Leka & Barnes (2003a), fall into nine broad categories: ) For each quantity, the parametrization only includes “active pixels” within the full HARP box. For all magnetic field data, we include only those pixels with signal/noise ratio S/N > 4 by default (the S/N threshold is a definable parameter). Masks are created using these criteria, but which are then eroded and dilated using a 2  2 shape operator in order to avoid single-pixel inclusions. For quantities that, for example, require spatial derivatives, the derivatives are taken on the full sub-area, then the appropriate computation (moment analysis, totals, etc.) include only those pixels that meet the selection criteria. Separate but analogous masks are created to identify the magnetic neutral lines, using similar thresholds and boundary-smoothing approaches. ( ) g – the magnetic field vector component magnitudes, Bz and Bh; – the inclination angle of the fields, g ¼ tan1ðBz=BhÞ; – the magnetic field vector component magnitudes, Bz and Bh; h i li i l f h fild 1ðB =B Þ – the inclination angle of the fields, g ¼ tan1ðBz=BhÞ; g g ð = Þ – the horizontal spatial gradients of the magnetic fields, | ∇h B|, | ∇h Bz|, | ∇h Bh|; |, | h z|, | h h|; – the vertical current density, Jz ∼(∂By/∂x  ∂Bx/∂y); – the force-free parameter, a ∼Jz/Bz; – the vertical portion of the current helicity density, hc ∼JzBz; 1 – the shear angle from potential, C ¼ cos1ðBp⋅Bo=BpBoÞ; ð = Þ – the photospheric excess magnetic energy density, re ¼ ðBp  BoÞ2=8p; – the magnetic flux near strong-gradient magnetic neutral lines, ℛnwra. As described above, moment analysis and extensive parameters are used to describe the spatially distributed variables. 3.2.5 Parametrization: prior flare history Example categories include: where indexC ≡2.3, 4.9, etc., as reported by the NOAA GOES 1–8 Å detectors. Example categories include: – the total peak flux of the target active region in the 12 h prior to the forecast; – the total peak flux from the time the region was first identified prior to the forecast; p – the number of flares produced by a target active region in the prior 12 h compared to the prior 24 h. There is no additional statistical sophistication in these parametrizations of flaring history. While the comparisons and summations are performed for the prior 6, 12, and 24 h Page 8 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Barnes et al., 2016). Only strong-flare regions were considered. intervals, there has not yet been any systematic testing of whether these terrestrially-defined periods are optimal (Leka & Barnes, 2017). The approach taken here is to calculate a quantity ℛnwra which more closely represents the physically relevant boundary properties: as such, the vertical component of the field Bz is used rather than Blos; the threshold is based on the noise in the Bz component (and thus varies), and all steps which depend on distances or sizes use an appropriate physical distance in 106 m as computed according to pixel size and observing angle (and thus the number of pixels used will vary with observing angle). Of note, there is no attempt to identify only a single or primary strong-gradient neutral line, and depending on sizes and thresholds chosen, numerous small strong-gradient neutral lines may be identified (Fig. 4). The resulting magnitudes of ℛnwra differ from Schrijver (2007), in part due to the new implementation but also due to the different data source, although the general behavior is very similar (see discussion in Barnes et al., 2016). 3.2.7 Parametrization: magnetic charge topology Most solar energetic events are believed to ultimately originate in the corona, where the magnetic field generally dominates the plasma and the climate is more conducive to the storage and subsequent rapid release of energy via magnetic reconnection. A corona with a very complex magnetic topology is one which should more readily allow magnetic reconnection to initiate, and hence an eruptive event to begin. The Magnetic Charge Topology model describes the coronal topology and its evolution, using as a boundary time-series maps of the photospheric radial field Bz. Concentrations of magnetic flux in an active region are represented by point sources (Fig. 5, top). A gradient-based tessellation scheme, supplemented by the partitioning of a reference time-averaged magnetogram, is used to track each magnetic concentration with time (Barnes et al., 2005). The coronal magnetic field is modeled as the potential field of the point sources, from which a unique magnetic connectivity matrix is derived (Fig. 5, bottom). While arguably inappropriate for very complex active regions, using a potential field is fast (significantly faster than non-linear force-free extrapolations), physics-based (see discussion in Barnes & Leka, 2008), and arguably captures ℛnwra ¼ X f ℬð∇hℬz ± ÞdA; ð4Þ ð4Þ where ℬ(∇h Bz ±) identifies polarity-inversion lines and f is a Gaussian convolution function. Schrijver (2007) identified magnetic neutral lines using polarity-specific bitmaps con- structed using SoHO/MDI (Domingo et al., 1995; Scherrer et al., 1995) Blos magnetograms, including only areas that exceeded a fixed 150 Mx cm2 threshold, and dilating the bitmaps with a 6''  6'' kernel; overlapping regions were thus identified as strong-gradient magnetic neutral lines. A new bitmap with the neutral lines thus identified was convolved with a Gaussian of FWHM Dsep = 15 Mm (fixed at 10 MDI pixels) to obtain a weighting map which, when multiplied by the |Blos| magnetogram and summed (assuming a fixed areal coverage of 2.2  1016 cm2 per pixel), resulted in ℛ. In Schrijver (2007), regions were only considered within 45 of disk center, with the assumption Blos ≈Br, and viewing-angle impacts on pixel-sampled area, etc, were negligible (see also where ℬ(∇h Bz ±) identifies polarity-inversion lines and f is a Gaussian convolution function. 3.2.6 Parametrization: photospheric magnetic field The magnetic character of an active region is thus reduced to approximately 150 variables. In the event that the Blos data are used, only parameters that do not rely on the horizontal component of the field are calculated. where Bp is the computed potential field referred to in Section 3.2.2. All quantities are based on physically- meaningful helioplanar components that include or are weighted by the deprojected pixel area, as approrpiate. The last category follows Schrijver (2007), who developed a parameter to characterize current-carrying emerging flux systems which manifest as magnetic neutral lines displaying strong spatial gradients: 3.3 Discriminant Analysis As discussed in Barnes & Leka (2008), fij is essentially indistinguishable from the “effective connected magnetic field” Beff ¼ cij=jxi  xjj2 (Georgoulis & Rust, 2007) with the primary distinguishing features being the square of the distance and more importantly, a physics-based potential field forming the basis of the connectivity matrix for the MCT parameters. A quantity f2, which uses the potential-field based connectivity in the expression for Beff, is included in the NCI. All forecasting methods include a statistical analysis or machine learning in order to produce a forecast from the observational input. Ranging from the simple (a correlation, e.g. Falconer et al., 2011) to quite complex (a Cascade Correlation Neural Network (e.g., Ahmed et al., 2013)), the basic goal is the same: use a description of past event behavior in the context of past data, to predict future events given new data. DA as a general statistical characteri- zation was first applied to solar flare forecasting in an early attempt to quantify improvements which could be made through multi-parameter analysis (Sawyer et al., 1986). 3.2.7 Parametrization: magnetic charge topology The MCT variables used in the NCI analysis (see Barnes & Leka, 2006) focus on categories describing the distribution of: – the number and separation of magnetic sources S; – the number and separation of magnetic sources S; p g – the flux assigned to each source, |Fi|; – the magnetostatic energy EB ¼ 1 ð2pÞ2 P i<j FiFj jxixjj; – the magnetostatic energy EB ¼ 1 ð2pÞ2 P i<j FiFj jxixjj; – the characteristics of the connectivity matrix cij describing the flux connecting source i to source j; – the characteristics of the connectivity matrix cij describing the flux connecting source i to source j; – the characteristics of the connectivity matrix cij describing the flux connecting source i to source j; The HMI magnetic field data incur a temporal variation as a function of the orbital velocity of the SDO spacecraft, as described in Hoeksema et al. (2014). Although efforts are underway to mitigate the impact (Schuck et al., 2016), for the moment, any analysis based on temporal variation of the magnetic field must accommodate these variations. In the case of DAFFS the “dt” parameters are all calculated using the same part of the orbit, and as such will present a bias in the magnitude of parameters calculated for all samples, but will not preferentially select one population over another. Forecasts or classifications which target a different time and use data from a different time of day (undergoing a different part of the daily orbit) are considered separately. – the flux in each connection weighted by inverse distance between connected sources, ’ij ¼ cij jxixjj; j jj – the angle between the north/south axis and the line segment between connected sources, jij ¼ tan1 xjxi yjyi h i for cij ≠0; j yj yi h i – the distribution of the number of connections from each source Ci. The basic analysis calculates almost 50 parameters based on the above-mentioned characteristics. Of note, due to computational requirements the magnetic null-finding (as was described in Barnes et al., 2005) is not routinely performed for large datasets. 3.2.7 Parametrization: magnetic charge topology Schrijver (2007) identified magnetic neutral lines using polarity-specific bitmaps con- structed using SoHO/MDI (Domingo et al., 1995; Scherrer et al., 1995) Blos magnetograms, including only areas that exceeded a fixed 150 Mx cm2 threshold, and dilating the bitmaps with a 6''  6'' kernel; overlapping regions were thus identified as strong-gradient magnetic neutral lines. A new bitmap with the neutral lines thus identified was convolved with a Gaussian of FWHM Dsep = 15 Mm (fixed at 10 MDI pixels) to obtain a weighting map which, when multiplied by the |Blos| magnetogram and summed (assuming a fixed areal coverage of 2.2  1016 cm2 per pixel), resulted in ℛ. In Schrijver (2007), regions were only considered within 45 of disk center, with the assumption Blos ≈Br, and viewing-angle impacts on pixel-sampled area, etc, were negligible (see also Page 9 of 23 Page 9 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 4. The vertical magnetic field strength (white/black being positive/negative, scaled to 500 G) of HARP 833 i.e. NOAA AR 11283 (cf. Fig. 3), showing regions identified as strong-gradient magnetic neutral lines for which the ℛnwra parameter is calculated (green boxes) with the 0.68-level contour of the Gaussian-convolved bitmap indicated (purple contours). Similar masks are used for the “magnetic neutral line”-related parametrizations. Fig. 4. The vertical magnetic field strength (white/black being positive/negative, scaled to 500 G) of HARP 833 i.e. NOAA AR 11283 (cf. Fig. 3), showing regions identified as strong-gradient magnetic neutral lines for which the ℛnwra parameter is calculated (green boxes) with the 0.68-level contour of the Gaussian-convolved bitmap indicated (purple contours). Similar masks are used for the “magnetic neutral line”-related parametrizations. the key features of coronal complexity associated with event- productive solar active regions (Régnier, 2012). parametrizations discussed in the prior sections. For the photospheric magnetic field parameters and the coronal topology parameters, a linear function is fit to the parameters computed at each of the seven times acquired. The slope and intercept at the forecast issuance time are used (Fig. 6) as two separate parameters. The intercept is used instead of the mean (or similar) of the times considered, in order to account for latency between data acquisition, analysis time, and the forecast issuance time. 3.2.8 Static vs. temporal variation The NCI as implemented for research on flare-imminent active regions is designed to include the recent evolution of the Page 10 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 tration of Magnetic Charge Topology analysis, characterizing the coronal magnetic topology of NOAA AR :48:00 TAI. Top: magnetogram showing the vertical field (greyscale), the partitions (contours), and the locatio ositive and negative). Areas outside of the active-pixel bitmap (cf. Fig. 3) are set to zero. Bottom: same a howing the connectivity matrix (blue lines) with dark/thick lines indicating more flux in the connection than Fig. 5. Demonstration of Magnetic Charge Topology analysis, characterizing the coronal magnetic topology of NOAA AR 11283 (Fig. 3), 2011.09.07 at 21:48:00 TAI. Top: magnetogram showing the vertical field (greyscale), the partitions (contours), and the locations of the sources (þ and  for positive and negative). Areas outside of the active-pixel bitmap (cf. Fig. 3) are set to zero. Bottom: same as top panel, but schematically showing the connectivity matrix (blue lines) with dark/thick lines indicating more flux in the connection than light/thin lines. 3.3.1 NCI flare research error estimation The bootstrap method described above (Sect. 2.4.3) is performed randomly on each HARP for region forecasts; uncertainties for the full disk probabilities are calculated by performing the bootstrap on daily ensembles. The resulting skill scores are computed for each draw, and their uncertainties are calculated by the standard deviation of the draws. 3.3.2 Accounting for statistical flukes The NCI research into flare productivity generally uses NPDA (Sect. 2.3). Examples of 1-variable and 2-variable results are shown in Figure 7, for one event definition (Sect. 3.1). The issues raised regarding small tail sample sizes are readily apparent in the graphic for the 2-variable sample results. As mentioned above, a Monte-Carlo approach can be used to estimate how likely any of the reported scores would be by statistical fluke, given the sample sizes and number of parameters considered. Using the flare-probability parameters described above and the HMI-data sample sizes, we estimate there would be <1% chance of a resulting BSS > 0.001/0.002/ 0.003 by chance alone for single variable NPDA for C1.0þ/ M1.0þ/X1.0þ flares, respectively. 3.4 NCI flare research: evaluation We present first some representative results using the “research-based” modules for flare-imminent classification Page 11 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 of 6 h intervals (7 samples) of time-series parameters from the magnetic field analysis of NOAA AR 11283 for three t the evolution of the total magnetic flux, the evolution of the proxy of the free magnetic energy; evolution of the ear in the vicinity of the magnetic neutral line; Bottom: the evoluton of the log of the ℛparameter. The times relative t own, in these cases the three intervals end just before the X1.8 flare on 2011.09.07, just before the X2.1 flare on 201 eriod of 2011.09.7, respectively. That is, this would be an example invoking a super-posed epoch analysis whereas in e forecast issuance time would likely be a particular time of day. K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 6. Plots of 6 h intervals (7 samples) of time-series parameters from the magnetic field analysis of NOAA AR 11283 for three time intervals. From Top: the evolution of the total magnetic flux, the evolution of the proxy of the free magnetic energy; evolution of the area of strong magnetic shear in the vicinity of the magnetic neutral line; Bottom: the evoluton of the log of the ℛparameter. The times relative to the issuance times are shown, in these cases the three intervals end just before the X1.8 flare on 2011.09.07, just before the X2.1 flare on 2011.09.06, and a flare-quiet period of 2011.09.7, respectively. That is, this would be an example invoking a super-posed epoch analysis whereas in a forecasting approach the forecast issuance time would likely be a particular time of day. at the time of this writing2). This provides almost 30 000 HARP-days (individual HARPs acquired on separate single days). and NCI; this includes the magnetic parameters, the topological parameters, the prior flare parameters, and the temporal behavior of each as appropriate (Table 2). We focus on region forecasts, as that is most appropriate for research purposes. 3.4 NCI flare research: evaluation This report serves at some level as an update to earlier publications (Barnes et al., 2007; Leka & Barnes, 2007), now with updated data and a significantly larger sample size: data covering the full SDO mission for “definitive” vector magnetic field HARPs are used 2010 May 01–2017 June 30 (as available For Table 2, a selection of performance results are shown, specifying the parameter combination used, and some relevant metrics. NCI by default uses Pth = 0.5, and the “well- performing” combinations are generally selected by high BSS as probabilistic forecasts are the most widespread in operational settings and a preferred metric for NOAA/SWPC Page 12 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 7. Examples of non-parametric Discriminant Analysis for one variable (total “excess” photospheric energy, see Leka & Barnes, 2003a) and two variables (same, plus the standard deviation of the horizontal gradients of the horizontal component of the magnetic field, ibid.) for the C1.0þ, 24 h event definition. For both, event/non-event NPDA estimates are shown in red/black respectively, and the 50% probability threshold is shown in blue. Fig. 7. Examples of non-parametric Discriminant Analysis for one variable (total “excess” photospheric energy, see Leka & Barnes, 2003a) and two variables (same, plus the standard deviation of the horizontal gradients of the horizontal component of the magnetic field, ibid.) for the C1.0þ, 24 h event definition. For both, event/non-event NPDA estimates are shown in red/black respectively, and the 50% probability threshold is shown in blue. Table 2. Representative NCI research-mode region-by-region flare classification performance metrics. Region-by-region, 2010.05.01–2017.05.31 Event def. 3.4 NCI flare research: evaluation Event rate Parameter(s) RC BSS ApSS Optimal H&KSS C þ 1 0.0879 ’tot, s (∇h Bz) 0.937 ± 0.005 0.40 ± 0.01 0.28 ± 0.01 0.68 ± 0.01 M þ 1 0.0145 Ee, s(|hc|) 0.987 ± 0.001 0.26 ± 0.02 0.14 ± 0.03 0.76 ± 0.02 X þ 1 0.0013 Ih tot, ℱ(cNL > 45°) 0.9988 ± 0.0003 0.12 ± 0.06 0.12 ± 0.07 0.74 ± 0.07 C þ 2 0.0837 ’tot, s (∇h Bz) 0.936 ± 0.007 0.35 ± 0.01 0.23 ± 0.01 0.64 ± 0.01 M þ 2 0.0134 Ee, s(|hc|) 0.990 ± 0.001 0.22 ± 0.02 0.11 ± 0.03 0.69 ± 0.02 X þ 2 0.0013 FL24, sðCNL;WÞ 0.9988 ± 0.0002 0.13 ± 0.06 0.12 ± 0.06 0.69 ± 0.07 C þ 3 0.0767 ’tot, log(ℛnwra) 0.938 ± 0.007 0.31 ± 0.01 0.19 ± 0.01 0.60 ± 0.01 M þ 3 0.0124 Ih tot, re 0.9884 ± 0.0008 0.15 ± 0.02 0.07 ± 0.02 0.66 ± 0.02 X þ 3 0.0011 log(ℛnwra), ðrij; cÞ 0.9989 ± 0.0002 0.11 ± 0.06 0.08 ± 0.06 0.63 ± 0.10 Variable symbols can be found in Leka & Barnes (2003b); Barnes & Leka (2006) except ℱ(cNL > 45) which indicates the fraction of magnetic neutral line with magnetic shear greater than 45° and FL24 which indicates the prior flare flux (Sect. 3.2.5) for a prior 24 h interval. Table 2. Representative NCI research-mode region-by-region flare classification performance metrics. Variable symbols can be found in Leka & Barnes (2003b); Barnes & Leka (2006) except ℱ(cNL > 45) which in neutral line with magnetic shear greater than 45° and FL24 which indicates the prior flare flux (Sect. 3.2.5) Variable symbols can be found in Leka & Barnes (2003b); Barnes & Leka (2006) except ℱ(cNL > 45) which indicates the fraction of magnetic neutral line with magnetic shear greater than 45° and FL24 which indicates the prior flare flux (Sect. 3.2.5) for a prior 24 h interval. H&KSS which is found by stepping through Pth values, with cross-validation but without bootstrap (leading to some expected discrepancies with Table 2), and the Gini coefficient. Of note is a degradation, but not a substantial one, between increasing latencies. H&KSS which is found by stepping through Pth values, with cross-validation but without bootstrap (leading to some expected discrepancies with Table 2), and the Gini coefficient. 3.4 NCI flare research: evaluation Of note is a degradation, but not a substantial one, between increasing latencies. evaluation. This threshold is used for the quoted RC and ApSS. The “Optimal H&KSS” is the H&KSS for which Pth = Event Rate, which is not necessarily the highest H&KSS but is generally very close, especially once error bars are considered (Bloomfield et al., 2012; Barnes et al., 2016). The full contingency tables are not presented here, since their entries are sensitive to Pth, but all information needed to construct them for any chosen Pth is provided. 2 The NCI demonstration results shown here include parameters from HMI “mode-L” data starting from 2016.04 that were discovered to include alignment errors. As of this manuscript’s acceptence, the affected data are being reprocessed by the HMI team but the task has not yet completed. Substantive quantitative differences are present between parameters generated from the initially released model-L data and examples of reprocessed data. Especially impacted are parameters that rely on the horizontal component of the field. What is presented here are the results given the data available. In Figure 8 the Relative (or Receiver) Operating Characteristic Curves (ROC) are shown for the entries in Table 2. As described in Section 2.4.1, a perfect Gini coefficient or ROC Skill Score results in G1 = 1.0, manifest by an ROC curve consisting of three points: [0,0], [0,1], and [1,1]. The discontinuities are caused at small probability levels due to many regions being assigned the same probability (specifical- ly, the value of climatology). We also indicate the maximum Page 13 of 23 Page 13 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 8. Relative (or Receiver) Operating Characteristic Curve for NCI research on flaring vs. flare-quiet active regions, using a forecasting context as described in the text. Blue/Green/Red curves indicate the three event definitions (C1.0þ, 24 h, M1.0þ, 24 h, X1.0þ, 24 hr) for effectively 0 h, 24 h, and 48 h latencies (left:right), region-by-region “forecasts” using the parameter combinations for each event definition listed in Table 2. Also noted on each plot are the maximum H&KSS (TSS) achieved, the probability threshold Pth used for that maximum TSS score, and the Gini coefficient for the relevant curve. Fig. 8. Relative (or Receiver) Operating Characteristic Curve for NCI research on flaring vs. flare-quiet active regions, using a forecasting context as described in the text. 3.4 NCI flare research: evaluation Blue/Green/Red curves indicate the three event definitions (C1.0þ, 24 h, M1.0þ, 24 h, X1.0þ, 24 hr) for effectively 0 h, 24 h, and 48 h latencies (left:right), region-by-region “forecasts” using the parameter combinations for each event definition listed in Table 2. Also noted on each plot are the maximum H&KSS (TSS) achieved, the probability threshold Pth used for that maximum TSS score, and the Gini coefficient for the relevant curve. 4 The DAFFS Near-Real-Time (NRT) flare forecasting tool – a measure of size (e.g. Ftot, Itot); – a measure of energy storage and non-potential magnetic field (e.g. log(ℛnwra), ℱ(CNL > 45)); – a measure of energy storage and non-potential magnetic field (e.g. log(ℛnwra), ℱ(CNL > 45)); The NCI infrastructure recently bifurcated to include a near-real-time operational flare forecasting tool. The DAFFS is the result of a NOAA SBIR Phase-II contract to NWRA. To achieve a truly operational forecasting tool, many aspects that originated from the NCI were redesigned for automated stand- alone performance (no “human in the loop”), with operational redundancy. In short, the DAFFS cron scripts use the prescribed forecast issuance time as the basis for their schedules, with drivers of all needed modules written in Python. There are a few key differences from the research- based NCI approach above, including some design features not yet implemented due to limited resources, and we describe those below. A generalized flow-chart for DAFFS is provided in Figure 9. ( g g( ) ( )) – a measure of magnetic complexity (e.g. fij, k(Bz)). Often a parameter based on the temporal evolution is included, however within the error bars there are always combinations without temporal evolution which perform similarly. Using two-parameter NPDA, we generally find dozens of parameter combinations that perform similarly within the error bars. When looking at some of the better- performing combinations, we find a gradual decrease in performance for probabilistic forecasts with respect to latency, and a substantial decrease in performance with increasing event magnitude. g These results are consistent with both our earlier results (Leka & Barnes, 2003b; Barnes et al., 2005; Barnes et al., 2007; Leka & Barnes, 2007) and with the present state of the literature (e.g., Falconer et al., 2014; Al-Ghraibah et al., 2015; Bobra & Couvidat, 2015; Murray et al., 2017; Nishizuka et al., 2017), but should not be compared directly due to different event definitions, testing intervals, and validation methodolo- gies (cf. Barnes et al., 2016). 3.5 Flare research: results rarely require that the boundary field to provide distinguish- ing differences of magnetic complexity in addition to a sheared polarity inversion line (although see Kusano et al., 2012). In general, we find that the top-performing parameter pairs routinely include (but are not exclusive to) the following parameters categories (in no particular order): – a measure of recent flare activity (e.g. FL12 or FL24); 4.1 NRT data sources The choice of target time (Table 3) is in part due to GONG data being published “on the fours”, and (similar to HMI NRT data) the time by which the data would be reliably made available. All matching gzipped FITS files are down- loaded for evaluation (see Sect. 3.2.3), and the image with the best seeing is then used. The target times for data sources were chosen according to when the target data products typically become available for transfer (Table 3). The master time was chosen to be 6 min (0.1 h) prior to forecast time, to give the forecast code sufficient time to complete by the forecast issuance time. By referring all of the data acquisition and processing time to a master time (and specifically a master time which is on the same day as the data acquisition), and setting the relative times through keywords, flexibility is afforded for setting different forecast issuance times. Timing tests were performed for each aspect of the pipeline, from data retrieval and staging to producing a forecast and making it live, to come up with a task schedule (implemented via cron) for smooth and automatic operation as well as automated failure handling. In the case of HMI, if the target time is not available, adjacent times are searched as described in Table 3. The HMI NRT data are generally processed and available for transfer within 90 min of the observation time, but delays are not unusual (see Fig. 10). If no HMI sources can be found after a certain amount of time, the forecast is presently issued based on evaluating NOAA- provided flare history parameters (see Sect. 3.2.5). GONG data are intended to serve as a backup for HMI as a fully parallel system. Fig. 10. Histogram of processing delay distributions (elapsed time in between data acquisition and its availability for transfer) for six fairly random weeks between 2014 and 2015 (colored lines) and the distribution for all points (black). While there is a tail to delays greater than 90 min, the majority of data are available within that time. then the target is moved back and forth in time by the HMI vector field cadence (12 min) up to one hour prior and including up to 48 min later – beyond which it is deemed to be missing data (see Table 4). 4.1 NRT data sources The first difference is the source of the vector magnetic field data. For the research system the HMI “definitive” series are used, but for the operational forecasts, the HMI NRT data are used. Specifically the hmi.ME_720s_fd10_nrt full-disk vector field data are retrieved, along with the NRT HARP information from the hmi.Mharp_720s_nrt series and the disambiguation results from the hmi.Bharp_720s_nrt series. The expected latency for the HMI NRT data processing and retrieval was investigated (Fig. 10), and the estimates for expected delays are such that the latest target data practicable are slightly more than 2 h prior to forecast issuance time; this imposes a latency by default, as summarized in Table 3. If the target data are unavailable due to processing or transfer delays, The lack of a few well-identified parameters which definitively distinguish the two defined populations highlights the challenge of using statistical empirical relationships to investigate the fundamental physics of flares. Flares occur in regions which are large and magnetically complex, and preferentially in regions which have flared previously. The latter point is consistent with flare models based on Self Organized Criticality (Lu & Hamilton, 1991; Strugarek et al., 2014). However, one can also view some of the empirical results as guidance for modeling efforts, which (thus far) Page 14 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 9. A very generalized flow chart for the DAFFS system, outlining training to determine best-performing parameter pairs at the top, whose results impact the daily near-real-time operation, in the bottom flow chart. Circles generally indicate input, squares are processes, and diamonds are output. Fig. 9. A very generalized flow chart for the DAFFS system, outlining training to determine best-performing parameter pairs at the top, whose results impact the daily near-real-time operation, in the bottom flow chart. Circles generally indicate input, squares are processes, and diamonds are output. Fig. 10. Histogram of processing delay distributions (elapsed time in between data acquisition and its availability for transfer) for six fairly random weeks between 2014 and 2015 (colored lines) and the distribution for all points (black). While there is a tail to delays greater than 90 min, the majority of data are available within that time. are performed via Python script to find all sources (magneto- gram images from all GONG sites) that exist for a given day and targeted time. K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Training occurs over a set period of time, generally using as much NRT data as are available, e.g., over the full HMI NRT-data availability period of 2012.10.01 through a “recent” month. The top-performing parameter pairs are then used for forecasts, separate pairs for each event definition. The NPDA estimates of the distributions are re-computed on-the- fly, against which new data are compared and thus for which flare probabilities are computed. Additionally, the NRT HARP definitions themselves are generated in near-real-time, and do not have the benefit of size or identity consistency over a disk-passage as is the case for the definitive HARP series (Fig. 11). This difference actually precludes exact region-by-region comparisons between the research NCI results and NRT DAFFS results, although comparisons are possible via full-disk forecasts. Training occurs separately for permutations of param- eters based on those available: e.g., SDO/HMI þ NOAA/ SXR events, NOAA/SXR events by themselves, and eventually GONG þ NOAA/SXR events. For the larger events, single-variable DA and linear DA were considered as well as multi-parameter NPDA, because of the often improved performance by these simpler approaches for small sample sizes, however they are not presently used. The parameters presently used (as of this writing) are listed in Table 5; these are the parameters used for the results reported here. The exact parameter combinations are determined by the training interval used (indicated), and may change upon retraining the system, although as mentioned above there are common parameter “families” that routinely appear in the top-performing results. K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Table 3. DAFFS Near-Real-Time data target timing. Table 3. DAFFS Near-Real-Time data target timing. Table 3. DAFFS Near-Real-Time data target timing. As relevant for a “midnight” forecast: Time Data source Keyword 21:48:00 HMI/MAG target time = Master  2.1 h DAFFS_HMI_LATENCY 22:30:00 NOAA GOES/PFF target time = Master  1.4 h DAFFS_PFF_LATENCY 22:54:00 GONG/LOS_MAG target time = Master  1.0 h DAFFS_GONG_LATENCY 23:54:00 Master time – 00:00:00 Forecast time = Master þ 0.1 h DAFFS_TFORECAST_LATENCY Table 4. DAFFS Data acquisition and processing timeline. As relevant for a “midnight” forecast: Time Task 23:34 Retrieve GONG NRT data, targeting 22:54. 23:36 Retrieve data from HMI magnetogram series (hmi.M_720s_nrt) for full-disk context 23:36 Retrieve NRT HMI full-disk data (hmi.ME_720s_fd10_nrt) via NetDRMS, and extract patches using hmi.MEharp_720s_nrt, hmi.Bharp_720s_nrt series. Attempt 21:48:00 target record; if it does not exist, wait one minute and retry. (21:37) If target record still does not exist, query for data in the following order retrieve closest available record within [-60,þ48] of target: 21:36, 22:00, 21:24, 22:12, 21:12, 22:24, 21:00, 22:36, 20:48 23:37 Query E-SWDS for latest SWPC NRT flare events, AR assignments; simultaneous ftp query and transfer 23:54 0. Plot HARPs on full-disk Blos image, for DAFFS landing page (Fig. 12) 1. Update NWRA database with latest events via NOAA E-SWDS database query 2. Update NRT HARP/NOAA translation table in NWRA database 3. Extract GONG patches via NOAA E-SWDS database query of visible active regions 4. Generate parameters, forecasts 5. Link the main webpage to the new forecast buffer); the disambiguation is performed with a faster cooling schedule. For any specific area, there may be detectable differences on a pixel-by-pixel basis, however there is no systematic under- or over-reporting of magnetic field strengths, azimuthal angle differences, or noise levels (Bobra et al., 2014). Statistically, the distributions of resulting parameters generally agree well between the NRT and definitive HMI data series. HARPs that only ever have a single NOAA number assigned (to account for the frequent delay of NOAA number assignments). DAFFS runs autonomously twice daily by default, producing forecasts issued just before 00:00 UT and 12:00 UT for the event definitions and validity periods listed in Table 1. 4.1 NRT data sources The timeline for producing a NRT DAFFS forecast is summarized in Table 4. The needed NOAA data (up to date flare events and coordinates of visible numbered active regions) are retrieved through queries to “E-SWDS”. The needed data are also retrieved from the public ftp service as backup. Differences between the SDO/HMI definitive and NRT data arise at a few steps in the data reduction, and some are demonstrated in Figure 11. Of note, not all of the full-disk is inverted for the NRT release (only the NRT-HARP areas plus a The GONG data are retrieved from the NSO NRT dissemination page, https://gong2.nso.edu/oQR/zqa/; searches Page 15 of 23 4.2 NRT DAFFS implementation specifics For both the HMI NRTand the GONG data for DAFFS, only a subset of parameters are considered during training (<50% of the full science-investigation list) in order to remove redundancy and highly correlated variables (for example, separately the positive magnetic flux, the negative magnetic flux, and the total magnetic flux). At present, the MCT module is not used for the NRT DAFFS, and data are only examined at a single time; no dX/dt analysis is included. Metadata from hmi.Mharp_720s_nrt is used to match HARPs to AR numbers. For later training efforts, back- propagation of HARP/NOAA matches is performed for those Page 16 of 23 Page 16 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 11. Full-disk line-of-sight magnetograms from SDO/HMI for 2014.03.18 21:48 TAI. Left: NRT data showing the NRT HARPs and their numbering, Right: Definitive data, showing definitive HARP boxes and their numbering. Of note are the differences in coverage and in regions in the NRT which are merged for definitive HARPs. For both NRT and definitive HARPs, boxes may overlap but the “active pixels” (cf. Fig. 3) will not. Fig. 11. Full-disk line-of-sight magnetograms from SDO/HMI for 2014.03.18 21:48 TAI. Left: NRT data showing the NRT HARPs and their numbering, Right: Definitive data, showing definitive HARP boxes and their numbering. Of note are the differences in coverage and in regions in the NRT which are merged for definitive HARPs. For both NRT and definitive HARPs, boxes may overlap but the “active pixels” (cf. Fig. 3) will not. Automated graphical output is generated of the locations of the new data within the parameter space for each event definition (see Fig. 12). This allows the user to understand and confirm the context for the given probability forecast, and enables a user to track movement of a particular active region over time (helping to gauge increasing or decreasing flaring probability). are additionally automatically updated by a separate ftp-based cron job from the NOAA public postings. Of note, NOAA flare forecasts are also retrieved for later evaluation comparisons. GONG data outages With a world-wide 6-station network, data outages from GONG are quite rare. When this does occur, following the protocol for HMI outages, “missing” data values will be assigned and a PFF-based forecast prepared. Performance metrics are generated on demand (see Sect. Hardware redundancy Not yet implemented. SDO/HMI data outages Periodically, there are delays in the SDO/HMI data processing such that no applicable NRT data (see Table 4) are available for a forecast. In this case, then “misssing” data values are assigned and a PFF-based forecast with FLtot and FL24 is prepared. g Retraining The system is retrained on demand, and new variable- combinations can be employed for the forecasts at that point if so desired. This may impact forecasts as results can vary significantly according to the climatology of the training set, especially for larger and rarer events. j Unassigned flares Unassigned Flares are flare events not assigned to a particular active region. Fairly rare for large events (except when they occur behind the limb), they are most frequent for the small events, including C-type flares. For region-by-region forecasts, if they are not assigned, they are not considered as part of the prior flare parameters. For full-disk forecasts, they are included in evaluation but not in the training, leading to a systematic under prediction. 4.3 NRT DAFFS redundancy and operational details An operational system is only as good as its performance when everything fails. While there is still significant room for improvement, the following operational aspects are, or are designed to be, part of the NRT DAFFS implementation: N f 4.2 NRT DAFFS implementation specifics 4.4), as is re-training the full system (which potentially results in different parameter pairs being used from thence forward). Redundant forecasting In order to ensure robustness of the forecasts, DAFFS is designed to consider and report on multiple top performing models; in the case of 2-parameter combinations, forecasts from the three top performing combinations which contain unique parameters would be reported. This would provide essentially an ensemble forecast that considers 6 parameters, albeit without the sample-size requirements of training a true 6-variable NPDA forecast. Although not yet fully imple- mented, this approach also improves the odds of successful bad-data rejection. g p No forecast outages A forecast is always issued. If all redundancies fail, climatology is used. Hardware redundancy p p E-SWDS data outage g The situation of a complete and long-term E-SWDS data outage likely implies larger problems. E-SWDS uses a fail- over server for any outages, and the NWRA database connection will attempt to connect to it if the primary server is not responding. The event lists and active-region locations Page 17 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 ng” page for the NRT DAFFS showing a full-disk line-of-sight magnetogram and defined HARPs f hown: the version of the code running and the training interval being used. Bottom: a context plot fo gion forecasts, contour indicate the event (red)/non-event (black) training-sample distributions, the e green dots indicate the location of the recent data on these distribution plots. The left-hand table sh OAA AR(s) as appropriate, the forecast, and the status flags for the data. The full DAFFS forecast f he demonstration page at www.nwra.com/DAFFS_home/. Fig. 12. Top: “Landing” page for the NRT DAFFS showing a full-disk line-of-sight magnetogram and defined HARPs for context, and the full- disk forecasts. Also shown: the version of the code running and the training interval being used. Bottom: a context plot for the C1.0þ, 24 h, 24 h latency, region-by-region forecasts, contour indicate the event (red)/non-event (black) training-sample distributions, the blue contour is the 50% forecast level, and the green dots indicate the location of the recent data on these distribution plots. The left-hand table shows the HARP number, the corresponding NOAA AR(s) as appropriate, the forecast, and the status flags for the data. The full DAFFS forecast for this date is available for readers through the demonstration page at www.nwra.com/DAFFS_home/. Page 18 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 and evaluation intervals (although full-disk forecasts negate a few of these differences). Table 5. DAFFS forecasting parameter combinations (training interval: 2012.10.01–2016.03.31). Event definition Parameter combination C þ 1 re, Itot M þ 1 s(re), Ih tot X þ 1 FL12, &(Bz) C þ 2 Ftot, log(ℛnwra) M þ 2 Bz, log(ℛnwra) X þ 2 FL24, &(Bz) C þ 3 Bz, Ih tot M þ 3 Bz, Itot X þ 3 FL12, Bz Table 5. DAFFS forecasting parameter combinations (training interval: 2012.10.01–2016.03.31). That being said, DAFFS is running as an autonomous tool designed to address operational needs. p p E-SWDS data outage During the SBIR Phase- I (feasibility) study, an NCI-based demonstration out- performed the NOAA/SWPC forecasts as judged by BSSs that evaluated head-to-head comparisons with matched event definitions and testing intervals, as required by the topic description (Sect. 1). This success enabled Phase-II (prototype development) funding and the NRT operational forecasting tool described here as DAFFS. 5 Future developments The described infrastructure has been designed for flexibility at various junctures, and our hope is to implement improvements at a number of them. Regarding NCI in general, we intend to investigate how to optimize the adaptive-kernel NPDA, where the smoothing parameters are a function of parameter density. This should allow a better estimation of the PDF in high-kurtosis distributions – a useful additional option for all scientific questions for which NCI might be applied. Investigating AKNPDA is a proposed task for future funding. Validation Validation is performed on demand, producing lists of standard skill scores (Fig. 13); Reliability and ROC plots can be generated automatically, as well (e.g. Fig. 14). Customization DAFFS can be customized for event definition, timing of forecasts, and forecast validity periods. Additionally, the categorical forecasts can be optimized against either of the two error types (thus minimizing False Alarms or minimizing Missed Events). p p g Regarding DAFFS specifically3, we intend to finish implementing the GONG-based secondary forecasting – including then a direct comparison of performance as compared to the system when HMI vector field data are available. A bootstrap approach for the training data will be implemented to provide estimates of the performance uncertainties. The event definitions can be modified with respect to forecast interval, latency, and event limits, and these will be acted upon as requested. As mentioned above, parallel forecasts reporting on multiple top-performing combinations can be implemented for the NRT forecasting as a further check against statistical flukes from appearing in the predicted probabilities. Additionally, the DA threshold can be optimized according to the costs of either type of error, or to maximize a particular skill score. While this is not widely used when testing the efficacy of new parameters, it can be of particular importance to customers of the NRT tool. Of note, these proposed enhancements all have some degree of research- based known value to add, but will require resources to implement. Hence, DAFFS is not open source and is not freely available, as there is no automatic funding for NWRA (a small business) to continue its support. However parties interested in using it can be granted limited access for trial periods (see www.nwra.com/DAFFS_home/), and “access only with technical support” levels of contracts are available for very minimal resource levels. Of note, data which are not retrieved for the NRT forecasts, for whatever reason, are queued for retrieval later to ensure a reasonably complete NRT data source database for training purposes. 3 Upon proof state, this is now completed. 4.4 DAFFS results For very few of the event definitions do the ApSS scores show substantial improvement over climatology (Fig. 13), although the ROC plots and G1 coefficients demonstrate some performance significantly away from the “no skill” (x = y) line. (Note that the Peirce (H&KSS) scores quoted in the DAFFS evaluation, Figure 13, use Pth = 0.5 while the ROC plots quote the maximum H&KSS achieved by varying the Pth). Uncertainties are not (yet) quoted when generated from within DAFFS, but the magnitude of the uncertainties in Table 2 can be a guide. g For probabilistic forecasts, the performances are worse for the larger events (due to smaller sample sizes). In fact overall, the larger the event and the longer the latency, generally the worse the performance, which is typical (Barnes et al., 2016; Murray et al., 2017). NCI is a research platform by which many questions can be addressed through the quantitative analysis of appropriate sample sizes. Forecasting solar flares and energetic events is one such question; it is fairly well accepted that the present forecasting methods, DAFFS included, are performing above climatology – but not performing particularly well. The reasons why this is so are starting to become clear: likely culprits include a combination of human-defined events and 4.5 Performance context The results above reflect the general performance of the baseline NRT DAFFS forecast tool. The results will change according to the climatology and training interval, and as such should be interpreted with some care. These results are also not directly comparable to numbers quoted for other methods or even to the NCI results above, as discussed in Barnes et al. (2016), because of differences in samples, event definitions, Page 19 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 Fig. 13. To summarize the metrics for the NRT DAFFS we show a screen-shot from the output of the DAFFS self-evaluation code. Indicated are the evaluation period (20140701–20170630), for which issuance time (23:54:00 UT), and then a variety of skill scores. Note that the H&KSS quoted here is not the “Optimal” quoted above, it is evaluated with Pth = 0.5, which is the system default. “Event” means “event rate”; “FD” indicates full-disk (rather than region-by-region) forecasts. Fig. 14. ROC Curve for DAFFS NRT forecasts (see Fig. 13). Blue/Green/Red curves indicate the three event definitions (C1.0þ, 24 h, M1.0þ, 24 h, X1.0þ, 24 h) for effectively 0 h, 24 h, and 48 h latencies (left:right). Top row: region-by-region, Bottom row: full disk forecasts. Also noted on each plot are the Gini coefficients, the maximum H&KSS (TSS) achieved, and the probability threshold Pth used for that maximum H&KSS score. Fig. 14. ROC Curve for DAFFS NRT forecasts (see Fig. 13). Blue/Green/Red curves indicate the three event definitions (C1.0þ, 24 h, M1.0þ, 24 h, X1.0þ, 24 h) for effectively 0 h, 24 h, and 48 h latencies (left:right). Top row: region-by-region, Bottom row: full disk forecasts. Also noted on each plot are the Gini coefficients, the maximum H&KSS (TSS) achieved, and the probability threshold Pth used for that maximum H&KSS score. Page 20 of 23 Page 20 of 23 K.D. Leka et al.: J. Space Weather Space Clim. 2018, 8, A25 2003b; Barnes & Leka, 2006; Leka & Barnes, 2007) to address an expressed need (Barnes et al., 2007). As a matter of practicality, DAFFS by default mimics the system established at NOAA/SWPC in terms of event definition and output, although it does not have to. Many of the details which make this an operational system (and thus very different from the NCI) are described, and early results are presented. Supplementary Material Supplementary Material Supplementary material supplied by the author. The Supplementary Material is available at https://www.swsc- journal.org/10.1051/swsc/2018004/olm. Acknowledgements. The NCI was developed with funds from numerous sources, including AFOSR contracts F49630-00-C- 004 and F49620-03-C-0019, NASA contracts NNH12CG10C, NNX16AH05G, and NNH09CE72C, and NSF Grant 1630454. The DAFFS tool was developed under NOAA SBIR contracts WC-133R-13-CN-0079 (Phase-I) and WC-133R-14-CN-0103 (Phase-II) with additional support from Lockheed-Martin Space Systems contract #4103056734 for Solar-B FPP Phase E support. The authors also acknowledge NWRA internal development funds and the efforts of the two referees to improve the presentation of this work. The editor thanks Brian Welsch and an anonymous referee for their assistance in evaluating this paper. ( ) Research regarding different event definitions can be constructed within the NCI framework, according to (for example) a CME or lack thereof, the duration of events and total energy released, whatever appropriate database of “events” is available. Presently the NOAA-defined event catalogs form the basis of the GOES event definitions, but this itself could be modified to use other event catalogs based on other instruments. Of note, the NCI is not solely useful for flare research. Topics which have been investigated within the NCI framework include pre-emergence signatures (Barnes et al., 2014), a research topic and approach that is ongoing, and filament eruption (Barnes et al., 2017). The NCI is not, we stress, in and of itself a forecasting tool; it uses DA to evaluate how well samples from two known populations can be distinguished. Indeed, NCI may be used with any appropriately defined populations for diverse investigation topics. We actively invite collaboration to use the NCI framework in broad topics of solar physics. References Abramenko VI. 2005. Relationship between magnetic power spectrum and flare productivity in solar active regions. Astrophys J 629: 1141–1149. DOI:10.1086/431732. Ahmed OW, Qahwaji R, Colak T, Higgins PA, Gallagher PT, Bloomfield DS. 2013. Solar flare prediction using advanced feature extraction, machine learning, and feature selection. Sol Phys 283: 157–175. DOI:10.1007/s11207-011-9896-1. 4.5 Performance context simply a limited amount of information from photospheric magnetic field data that themselves may not directly be related to the flare initiation activity (Leka & Barnes, 2017). As different events, data, and approaches are investigated we invite further collaborative efforts using NCI as means to quantitatively test proposed improvements in establishing distinguishing characteristics of flare-imminent active regions. DAFFS is presently in use by the Chief Observers of the Hinode mission. While the primary data source (SDO/HMI) has an uncertain lifetime, DAFFS was designed to continue without those primary data although the long-term perfor- mance degradation in that situation has yet to be determined. With the oncoming solar minimum and as-of-yet no defined SDO follow-on mission, DAFFS will be supported and maintained to the extent resources allow; it could be of distinct value to new, limited field-of-view facilities and missions slated for operation as solar activity increases again. 5.1 Other research modules Described above are the data, parametrizations, and analysis results for flaring vs. flare-quiet active regions using DA through the NCI. 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Schrijver CJ, Higgins PA. 2015. A Statistical Study of Distant Consequences of Large Solar Energetic Events. Sol Phys 290: 2943–2950. DOI:10.1007/s11207-015-0785-x. Leka KD, Barnes G, Wagner EL. 2017. Evaluating (and improving) estimates of the solar radial magnetic field component from line-of- sight magnetograms. 6 Summary Sol Phys 292: 36. DOI:10.1007/ s11207-017-1057-8. Schuck PW, Antiochos SK, Leka KD, Barnes G. 2016. Achieving consistent Doppler measurements from SDO/HMI vector field inversions. Astrophys J 823: 101. DOI: 10.3847/0004-637X/823/2/ 101. Lu ET, Hamilton RJ. 1991. Avalanches and the distribution of solar flares. Astrophys J Lett 380: L89–L92. DOI:10.1086/186180. Silverman BW, 1986, Density estimation for statistics and data analysis, Chapman and Hall, London. Mason JP, Hoeksema JT. 2010. Testing automated solar flare forecasting with 13 years of Michelson Doppler Imager magneto- grams. Astrophys J 723: 634–640. DOI:10.1088/0004-637X/723/1/ 634. 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Magnetic field structures triggering solar flares and coronal mass ejections. Astrophys J 760: 31. DOI:10.1088/0004-637X/760/1/31. Culhane JL, Harra LK, James AM, Al-Janabi K, Bradley LJ, et al. 2007. The EUV imaging spectrometer for Hinode. Sol Phys 243: 19–61. DOI:10.1007/s01007-007-0293-1. LaBonte B. 2004. The imaging vector magnetograph at Haleakala: III. Effects of instrumental scattered light on stokes spectra. Sol Phys 221: 191–207. DOI:10.1023/B:SOLA.00000 35052.58297.36. Domingo V, Fleck B, Poland AI. 1995. The SOHO mission: an overview. Sol Phys 162: 1–37. DOI:10.1007/BF00733425. Efron B, Gong G. 1983. A leisurely look at the bootstrap, the jackknife, and cross-validation. Am Stat 37: 36–48. LaBonte BJ, Mickey DL, Leka KD. 1999. The imaging vector magnetograph at Haleakala – II. Reconstruction of stokes spectra. Sol Phys 189: 1–24. Falconer D, Barghouty AF, Khazanov I, Moore R. 2011. A tool for empirical forecasting of major flares, coronal mass ejections, and solar particle events from a proxy of Active-Region free magnetic energy. Space Weather 9: S04003. DOI:10.1029/ 2009SW000537. Leka KD, Barnes G. 2003a. Photospheric magnetic field properties of flaring vs. flare-quiet active regions I: data, general analysis approach, and sample results. Astrophys J 595: 1277–1295. Falconer DA, Moore RL, Barghouty AF, Khazanov I. 2012. Prior flaring as a complement to free magnetic energy for forecasting solar eruptions. Astrophys J 757: 32. DOI:10.1088/0004-637X. Leka KD, Barnes G. 2003b. Photospheric magnetic field properties of flaring vs. flare-quiet active regions II: Discriminant Analysis. Astrophys J 595: 1296–1306. Falconer DA, Moore RL, Barghouty AF, Khazanov I. 2014. MAG4 versus alternative techniques for forecasting active region flare productivity. Space Weather 12: 306–317. DOI:10.1002/ 2013SW001024. Leka KD, Barnes G. 2007. Photospheric magnetic field properties of flaring vs. flare-quiet active regions. IV: a statistically significant sample. Astrophys J 656: 1173–1186. DOI:10.1086/510282. Page 22 of 23 K.D. Leka et al.: J. Space Weather Space Clim. Cite this article as: Leka KD, Barnes G, Wagner E. 2018. The NWRA Classification Infrastructure: description and extension to the Discriminant Analysis Flare Forecasting System (DAFFS). J. Space Weather Space Clim. 8: A25 6 Summary Winter LM, Balasubramaniam K. 2015. Using the maximum X-ray flux ratio and X-ray background to predict solar flare class. Space Weather 13: 286–297. DOI:10.1002/2015SW001170. Reinard AA, Henthorn J, Komm R, Hill F. 2010. Evidence that temporal changes in solar subsurface helicity precede active region flaring. Astrophys J Lett 710: L121–L125. DOI:10.1088/ 2041-8205. Woodcock F. 1976. The evaluation of yes/no forecasts for scientific and administrative purposes. Mon Weather Rev 104: 1209–1214. DOI:10.1175/1520-0493(1976)104. Cite this article as: Leka KD, Barnes G, Wagner E. 2018. The NWRA Classification Infrastructure: descrip Discriminant Analysis Flare Forecasting System (DAFFS). J. Space Weather Space Clim. 8: A25 Page 23 of 23 Page 23 of 23
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Review of: "Ecotheology: missiological perspective in awareness"
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Review of: "Ecotheology: missiological perspective in awareness" Dan Smyer Yu1 1 Yunnan University Dan Smyer Yu1 1 Yunnan University Potential competing interests: No potential competing interests to declare. Qeios, CC-BY 4.0 · Review, March 14, 2023 Qeios ID: GWWGDY · https://doi.org/10.32388/GWWGDY Comments and suggestions from the reviewer This submission is potentially a good read if the authors are willing to do a well-rounded revision in these areas: This submission is potentially a good read if the authors are willing to do a well-rounded revision As this submission is Christian specific, the reviewer recommends a revision of the current title to something like this: “Christian Ecotheology: Missiological Perspective in Awareness” or “Ecotheology: Christian Missiological Perspective in Awareness.” From the interfaith perspective, Christianity does not exclusively own the word “theology”; The content of this submission suggests that it does not offer an explanation of what ecological theology means (p.1); instead, it makes an attempt to explain the current environmental crisis and to offer a Christian perspective about how humans should care for the planet earth. This said, the authors are recommended to revise the relevant passages in the opening paragraph; It is not clear from what Christian denominational perspective the authors speak of their “ecotheology” and “missiological perspective”; Other than from “library and web research,” the abstract of the submission claims “collected data from various sources;” however, it does not explicitly inform readers of both the sources and contents of the data. Empirical data will be highly appreciated if they are available; In “Result and Discussion” section, climate change is spoken of in general terms. In currently interdisciplinary studies of climate change as a pressing issue of our time, climate change vary locally although climate scientists offer an averaged assessment of the change. The authors may consider offering readers a picture of the local manifestation of the global climate change in Indonesia; It is not clear what the authors try to convey about the “new paradigm” (p.4); It is not clear what the authors try to convey about the “new paradigm” (p.4); It would make more sense to relocate the section “Missiological Perspective Ecotheology in Indonesian Context” to the earlier part of the submission. Proofreading/copyediting is definitely needed. Proofreading/copyediting is definitely needed. Qeios ID: GWWGDY · https://doi.org/10.32388/GWWGDY 1/1
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Correction: Thin Film Flow in MHD Third Grade Fluid on a Vertical Belt with Temperature Dependent Viscosity
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The PLOS ONE Staff The affiliations for the fourth and fifth authors are incorrect. Ilyas Khan is not affiliated with #4 but with #3 College of Engineering Majmaah University, Majmaah, Saudi Arabia. Sharidan Shafie is not affiliated with #4 but with #4 Department of mathematical Sciences, Faculty of science, University Teknol- ogy Malaysia, UTM Johor Bahru, Johor, Malaysia. Correction: Thin Film Flow in MHD Third Grade Fluid on a Vertical Belt with Temperature Dependent Viscosity The PLOS ONE Staff 1. Gul T, Islam S, Shah RA, Khan I, Shafie S (2014) Thin Film Flow in MHD Third Grade Fluid on a Vertical Belt with Temperature Dependent Viscosity. PLoS ONE 9(6): e97552. doi:10.1371/journal.pone.0097552. Correction Correction: Thin Film Flow in MHD Third Grade Fluid on a Vertical Belt with Temperature Dependent Viscosity Correction Correction: Thin Film Flow in MHD Third Grade Fluid on a Vertical Belt with Temperature Dependent Viscosity Correction Correction: Thin Film Flow in MHD Third Grade Fluid on a Vertical Belt with Temperature Dependent Viscosity PLOS ONE | www.plosone.org Reference Citation: The PLOS ONE Staff (2014) Correction: Thin Film Flow in MHD Third Grade Fluid on a Vertical Belt with Temperature Dependent Viscosity. PLoS ONE 9(10): e110205. doi:10.1371/journal.pone.0110205 Published October 3, 2014 Copyright:  2014 The PLOS ONE Staff. 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 PLOS ONE | www.plosone.org 1 October 2014 | Volume 9 | Issue 10 | e110205 October 2014 | Volume 9 | Issue 10 | e110205
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Determinants of relapse of rehabilitated substance abuse patient in neuropsychiatric hospital, Aro, Abeokuta, Ogun state, Nigeria
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Determinants of relapse of rehabilitated substance abuse patient in neuropsychiatric hospital, Aro, Abeokuta, Ogun state, Nigeria Ogungbesan J. O 1, *, Maitanmi B 1, Aroyewun Oluwayemisi 2 and Maitanmi Julius O 1 1 School of Nursing, Babcock University, Ilishan-Remo, Ogun State, Nigeria. 2 Neuropsychiatric Hospital, Aro, Abeokuta, Ogun State, Nigeria. World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 Publication history: Received on 03 October 2022; revised on 17 November 2022; accepted on 20 November 2022 Article DOI: https://doi.org/10.30574/wjarr.2022.16.2.1197 Determinants of relapse of rehabilitated substance abuse patient in neuropsychiatric hospital, Aro, Abeokuta, Ogun state, Nigeria Ogungbesan J. O 1, *, Maitanmi B 1, Aroyewun Oluwayemisi 2 and Maitanmi Julius O 1 1 School of Nursing, Babcock University, Ilishan-Remo, Ogun State, Nigeria. 2 Neuropsychiatric Hospital, Aro, Abeokuta, Ogun State, Nigeria. World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 Publication history: Received on 03 October 2022; revised on 17 November 2022; accepted on 20 November 2022 Article DOI: https://doi.org/10.30574/wjarr.2022.16.2.1197 Determinants of relapse of rehabilitated substance abuse patient in neuropsychiatric hospital, Aro, Abeokuta, Ogun state, Nigeria 1 School of Nursing, Babcock University, Ilishan-Remo, Ogun State, Nigeria. 2 Neuropsychiatric Hospital, Aro, Abeokuta, Ogun State, Nigeria. World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 Publication history: Received on 03 October 2022; revised on 17 November 2022; accepted on 20 November 2022 Article DOI: https://doi.org/10.30574/wjarr.2022.16.2.1197 Abstract Substance use is a societal and an important public health concern in this 21st century. The number of substance use cases and relapse are increasing geenrally, thus slowing down the progress made in the care and treatment of individuals with substance abuse disorders. The study identified determinant of relapse among the rehabilitated substance use patients in Neuropsychiatric hospital, Aro, Abeokuta. The study adopted cross-sectional, selected 125 relapse substance use patients and their primary informal caregiver on the wards and clinics at neuropsychiatric hospital, Aro, Abeokuta. An interviewer-administered structured questionnaire was used to obtain data on determinants of relapse among the rehabilitated substance use patients and the retrieved data was analysed using SPSS version 21 for descriptive statistics. The findings shows that nearly half (44.4%) of the respondents were below 20 years, majority (64.5%) were male, 40.3% married. Most (69.4%) of the respondents agreed that the patient have friends who use drugs, 71.0% of the patients were currently relapsed, though majority (72.5%) of the patients were on treatment either outside or/and in- ward under control compliance. Conclusively, higher proportion were currently relapsed and had varied factors correlating the relapse; male, under 20years. Hence the client needs be proactively managed to prevent relapse through prompt therapy / care of psychotic patients lengthy to lead a high quality of life. Keywords: Relapse; Rehabilitated; Substance Use; Patient; Substance abuse School of Nursing, Babcock University, Ilishan-Remo, Ogun State, Nigeria. Copyright © 2022 Author(s) retain the copyright of this article. This article is published under the terms of the Creative Commons  Corresponding author: Ogungbesan J. O or(s) retain the copyright of this article. This article is published under the terms of the Creative Commons Attribution Liscense 4.0. Copyright © 2022 Author(s) retain the copyright of this article. This article is published under the terms of the Creative Commons Attribution Liscense 4.0. g g J g, Babcock University, Ilishan-Remo, Ogun State, Nigeria.  Corresponding author: Ogungbesan J. O 1. Introduction Additionally, the national survey on drug use and health in USA revealed that 23.5 million Americans aged 12years and older required treatment for illicit drug and alcohol abuse problem. Of this number, an estimated 2.6million (11.2 %) individual receives treatment at a specialty facility (SAMHSA, 2009). According to Mohammed (2009) revealed that urge, craving, and drug temptation, negative or positive emotional state, negative physical state, testing of personal control, family or others relationship conflicts, social and peer pressures to use substances, and treatment related are correlate with relapse. Predominantly, relapse is one of the most severe problems of mental illness especially among individual with substance use disorder. Despite the current trend in modern treatment, the rate of relapse is alarming. Relapse is estimated as 40 – 75% between three (3) to twenty-four (24) weeks after substance use disorder treatment globally (Hasin et al, 2013; Maehira et al, 2013; Hubbard et al, 2001). Consequently, relapse reduces the chances of substance use disorder individuals from living a productive and responsive life thereby making them not to live up to personal and societal expectation and fulfil life goals. Nevertheless, relapse could occur at any time or stage of treatment; for instance, relapse occur as soon as clients discharge home, on trial discharge, at admission, and/or after successfully avoiding substance use for some period of time as well establishing a routine of substance abstinence. Studies have identified various factors contributing to relapse including; non-adherence to medication regimen and flagrant disregard for relapse prevention strategies (Kabisa, Biracyaza, Habagusenga, et al., 2021). According to Murmane and Howell (2011), reinstatement of drug use after a period of non-use or abstinence is typically initiated by one or a combination of the three main triggers as stress, re-exposure to the drug priming and environmental cues. Although, people of all ages use and abuse substances for a variety of reasons including sensation seeking, peer group pressure, emotional stress, cognitive enhancement, the desire to relieve depression and anxiety and the need to cope with physical illness (Baghurst& Kelley, 2013; Barnett, 2017; Cho et al., 2015). Similarly, there are regional variations in the prevalence rates of substance use in Nigeria. In Nigeria, studies have identified young adults and middle-aged males, less educated individuals, individuals working in technical or commercial jobs, people with marital home, urban areas dwellers and individuals from broken homes are more associated with substance uses (Hamdi et al 2016). 1. Introduction Substance abuse is a foremost societal and important public health concern. Generally, is a mental illness due to the nexus of mental and behavioural disorders. Often time, substance use is used in replace of substance abuse, as substance abuse means using of substances (drugs) for purposes other than it is intended, and characterized with maladaptive pattern of substance uses with a propensity of resulting in to significant impairment in functioning (Sampson et al., 2017). An individual continues using substances despite cognitive, behavioural, and physiological symptoms (Hamdi et al, 2013). Literally, substance abuse is also a drug abuse as it is a harmful, hazardous or excessive use of psychoactive drugs or substances such as alcohol, pain medication, and other drugs in which the user consumes in amount that is different from the prescribed dosage or for purposes other than that which is prescribed but solely for the aim of creating a World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 pleasurable effect (Leikin, 2017; WHO, 2015). Thus with the potential to cause physical, social and emotional harm to the abuser. More so, the World Health Organisation (WHO) conceptualizes substance use as a chronic and relapsing disease confronting the global community in the 21st century due to its relapsing propensities (Mandal, 2021). Subsequently, substance abuse relapse is a gradual or sudden stop or disappearance of abstinence or sobriety status after drug abuse. However, the burden of substance abuse relapse is very high among individuals, family and the society of people abusing substance. As those who are not involve in doing substance are more affected by the behaviour of those doing substances. More so it constantly draining available resources for wellbeing as he might become a danger to self or/and others in the society by causing crisis. In literature, there are evidences that substance abuse related relapse across all age groups but more common among the adolescents and young adult that indulge in substance intake, dependent and a chronic addictive doping/taking of substances. Thus, place severe burden on the informal and formal caregivers managing them especially in the acute phase. The prevalence of chemical dependence relapse among substance abusers had been estimated to be 75 – 90 % within the first year of treatment (Iqbal, 2008). 1. Introduction In general, several social vices are associated with substance use notably, people with criminal tendencies and antisocial behaviours are often under the influence of substances or drugs (Ksir, Oakley and Charles (2011). Objectives of the Study The aimed to determine the factors associated with relapse among rehabilitated substance use patients in Neuropsychiatric hospital, Aro, Abeokuta.  To identify t h e biological determinants of relapse among the rehabilitated substance use patients  To identify the social determinants of relapse among the rehabilitated substance use patients  To identify psychological determinants of relapse among the rehabilitated substance use patients  To identify t h e biological determinants of relapse among the rehabilitated substance use patie T id if h i l d i f l h h bili d b i To identify the social determinants of relapse among the rehabilitated substance use patients To identify psychological determinants of relapse among the rehabilitated substance use patients y p g p  To identify psychological determinants of relapse among the rehabilitated substance use patien  To identify psychological determinants of relapse among the rehabilitated subs 2.1. Research Design The study utilized a hospital-based descriptive cross-sectional survey to identify determinants of relapse among rehabilitated substance abuse patients at the Federal Neuropsychiatric Hospital, Aro, Abeokuta, Ogun State, Nigeria. The study targeted at the rehabilitated substance abuse patient currently in relapse at the Federal Neuropsychiatric Hospital Abeokuta, Ogun State. 748 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 Determinants of Relapse among the Rehabilitated Substance Use Patients Variables Frequency Percentage % Age of patient in years Below 20years 55 44.4 21-30years 36 29.0 31-40 years 20 16.1 41and above 13 10.5 Sex of patient Male 80 64.5 Female 44 35.5 Marital status of patient Single 48 38.7 Marriage 50 40.3 Divorced 16 13.0 Widowed 10 8.0 Has any of the patients’ family members ever abused drugs in the past Yes 90 72.5 No 34 27.5 Specify relationship with patient Parents 45 36.3 Sibling 30 24.2 Brother 27 21.7 Sister 22 17.8 Does the patient suffer from any other chronic infection/illness Mental confusion 50 40.3 Brain damage 36 29.0 Lung disease 22 17.7 Increase stain on the liver 16 13.0 Specific drug(s) is the patient abusing most Skunk 52 42.0 Cannabis 30 24.2 Crystal meth 27 21.8 Colorado 15 12.0 Age did the patient start educing the drugs? Below 1 years 50 40.3 2-4 years 41 33.0 Above 5 years 33 26.7 For how long has the patient been abusing drugs? Below 6 month 58 46.7 6-12 month 40 32.3 13-18 month 26 21.0 Table 1 Biological Determinants of Relapse among the Rehabilitated Substance Use Patients 749 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 A total sample size of 125 relapse patients were conveniently selected. The data was collected with the aid of questionnaire. The caregivers of patient were met at the different wards and clinics, introduced and explained to gain the consent of participants. The collected data was analysed with SPSS version 25 for descriptive statistics. A total sample size of 125 relapse patients were conveniently selected. The data was collected with the aid of questionnaire. The caregivers of patient were met at the different wards and clinics, introduced and explained to gain the consent of participants. The collected data was analysed with SPSS version 25 for descriptive statistics. e 2 Social Determinants of Relapse Among The Rehabilitated Substance Use Patients Variables Frequency Percentage % Does the patient have friends who use drugs? 2.1. Research Design Yes 86 69.4% No 38 30.6% What is the patient's educational level? None 42 33.9% Primary 36 29.0% Secondary 30 24.2% Post-secondary 16 12.9% What is the patient's occupation? Employed 50 40.3% Unemployed 40 32.2% Schooling 34 27.5% How accessible are the drugs that the patient commonly abuses? Readily Accessible 68 54.8% Rarely Accessible 30 24.2 % Never Accessible 26 21.0% How affordable are the drugs that the patient commonly abuses? Readily Affordable 52 42.0% Rarely Affordable 48 38.7% Never Affordable 24 19.3% How often does the patient do drug with friend? Very often 60 48.3% Rarely often 42 33.9% Never 22 17.8% How often does the patient engage in social vices such as fight, rape or scatter the house? Very often 70 56.4% Rarely often 36 29.0% Never 18 14.6% How often does the patient get arrested by the law enforcement agent such as Police or NDLEA? Very often 66 53.3% Rarely often 48 38.7% Never 10 8.0% How often have you tried to stop the patient from doing drug? Very often 80 64.6% Rarely often 36 29.0% Never 8 6.4% able 2 Social Determinants of Relapse Among The Rehabilitated Substance Use Patients 750 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 Table 3 Psychological Determinants of Relapse among the Rehabilitated Substance Use Patients Variables Frequency Percentage % For how long has the patient been ill (current relapse episode)? Below 4 weeks 88 71.0% 1-2 month 22 17.7% 3 month and above 14 11.3% On average how many times in a year does this illness (relapses) usually occur to the patient after successful treatment? Two 80 64.5% Three or more 44 35.5% Does the patient comply to the prescribed medication when his/he recondition is under control (compliance)? Yes 90 72.5% No 34 27.5% Does the patient belong to any support group therapy Yes 100 80.6% No 24 19.4% In the last one year, has the patient felt the need to stop drinking or any other substance? Yes 104 83.8% No 20 16.2% In your own opinion, do you think frequent family conflict contribute to patient frequent relapse? Yes 98 79.0% No 26 21.0% Does the patient ever use any of the following maladaptive coping tactics e.g. smoking, drinking alcohol, chewing Mira, aggression/fights, etc when faced with negative life events and stress? Yes 88 71.0% No 36 29.0% Does the patients have any Personality problem (e.g. 2.1. Research Design introvert, extrovert, impulsive behaviors ,tendency to violence, quarrel some, shyetc Yes 99 79.9% No 25 20.1% Does the patient often have any negative thoughts Yes 100 80.6% No 24 19.4% Are the generative life events that are associated with the present condition of the patient? Yes 94 75.8% No 30 24.2% Does the patient exhibit positive coping mechanisms when faced with stressful events? Yes 88 71.0% No 36 29.0% l Determinants of Relapse among the Rehabilitated Substance Use Patients Table 3 Psychological Determinants of Relapse among the Rehabilitated Substance Use Patients 751 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 Table 1 shows that nearly half 44.4% of the respondents were below 20 years, and 10.5% 41 and above. Majority 64.5% were male, about 38.7% were single, 40.3% were marriage, 13.0% were divorced, while the 8.0% were widowed. The informal caregivers included; parents 36.3%, 24.2% siblings. About 42.0% of the respondent took Skunk, 24.2% Cannabis, 21.8% Crystal meth, while the remaining 12.0% used Colorado. Majority 40.3% started drug 1 years, 33.0% between 2-4 years, and 26.7% above 5 years. Majority 46.7% claimed that they had been on a specific drug below 6 month, 32.3% between 6-12 month, and 21.0% 13-18 months. Table 2 shows that 69.4% of the respondents had friends who used drugs, about 33.9% of the respondents had no formal education, 29.0% had primary, and 24.2% secondary. Two-fifth 40.3% were employed, 32.2% unemployed, and the remaining 27.5% were schooling. Majorly 54.8% of the drug claimed to be readily accessible and about 42.0% were quite affordable. About half 56.4% of the respondents often engaged in social vices such as fight, rape or scatter the house, 53.3% of the respondents had been arrested by the law enforcement agents such as Police or NDLEA, two-third 64.6% of the respondents had tried to stop doing drugs before but finds it hard. Table 3 shows that 71.0% of the respondents had current relapse episode of less than four weeks, few 11.3% had it in 3 month and above. About 64.5% of the respondent said that relapse occurred twice to the patient after successful treatment, majority 72.5% of the respondents claimed that the patient comply to the prescribed medication when his/her condition is under control. About 80.6% of the respondents said that the patient belong to a support group therapy. 2.1. Research Design Most 79.0% of the respondent agreed that the frequent family conflict contributed to patient relapse, and 71.0% of the respondent claimed that the patient ever used maladaptive coping tactics e.g. smoking, drinking alcohol, chewing Mira, aggression/fights, etc when faced with negative life events and stress. Most 79.9% of the respondents agreed that the patients have personality problem (e.g. introvert, extrovert, impulsive behaviors ,tendency to violence, quarrel some, shyetc, while 20.1% did not agreed with the patients have any Personality problem. Majority 80.6% of the respondents agreed that the patient often had negative thoughts, 75.8% of the respondents agreed that the generative life events that are associated with the present condition of the patient. Two-third 71.0% of the respondents agreed that the patient exhibit positive coping mechanisms when faced with stressful events. 3.1. Social determinants of relapse among the rehabilitated substance use patients The present study finds that majority of the respondent agreed that the patient have friends who use drugs, and one- third. One-third of the respondents had no formal education and others had formal education at various levels, 40.3% of the respondent were employed, 32.2% of the respondent were unemployed, while the remaining 27.5% were schooling, Thus, contrary to Swanepoel, Stephen, and Gretel, (2016) that found poverty, unemployment and community adversity been a major contributing factors to relapse in substance abuse people. Half of the respondents readily access drugs that commonly abuses. Most of the respondents have tried to stop the patient from doing drugs and few never tried. This goes with Campbell and Ettore (2011) that social support is a major factor influencing relapse to drugs in males and females. The researchers found that men are more supported from home and in their working environment. Women on the other hand tend to be cut off and secluded from the community and their partners tend to be unfriendly. Also Swanepoel, Stephen, and Gretel, (2016). Poverty, unemployment and community adversity have been major contributing factors to relapse in substance misuse 3. Discussion This present findings is in conversely with Carson et al. 2016, in a study conducted in Canada found that, older patients have a lower relapse rate as compared to young patients. The study associated the difference as due to other age-related factors which impact positively on abstinence post treatment such as higher self-efficacy, greater motivation and social networks among adults. Also, Farkhondeh et al. 2015, agreed that marital status and addiction relapse bear a sufficient relationship. The highest frequency of addiction relapse is observed in single persons, people who have lost spouse through death and those who are divorced Limitation Due to descriptive nature of the study, some importance social demographic data, personal factors, social factor and clinical factors such as, level of income were not recorded. More so, not all factors associated with relapse are considered in the study, factor such as family relationship, genetic factor/hereditary. Generalization of the study should be done with caution as some of the psychotic relapse cases might not be reported Disclosure of conflict of interest No conflict of interest. Implication of the Findings for Nursing Practicing psychiatric nurses should always consider the influence of patient’s demographic-personal characteristics on health decisions as well as treatment adherence when caring for any patient as this will help identify some of the factors that might be contributing to silment and treatment. They need to improve their knowledge on treatment adherence and personal factors that can devoid frequent relapse of patients. The findings of the study would help patients and their relatives to know more about the association between the personal, social and clinical factors that associated with relapse of psychotic illness. 4. Conclusion This study was carried out on relapse among the rehabilitated substance use patient in Neuropsychiatric Hospital, Aro, Abeokuta, Ogun State. Relevant and related literatures were reviewed. Purposive sampling technique used for this study. The study sampled 125 respondents out of 160 that constituted the population. Instrument used for data collection was self-administered questionnaire which was divided into four sections. The analysis done using descriptive statistics such as simple percentage while the presentation will be done using tables and graphs. Recommendations The following are the recommendations from this study. • The therapy / care of psychotic patients must be lengthy if they are to have a high quality of life. In order to prevent the factors linked with relapse, the researcher suggests involving the patient's health care provider/professionals, family/relatives, community, and religious body in the care of the patient. • The therapy / care of psychotic patients must be lengthy if they are to have a high quality of life. In order to prevent the factors linked with relapse, the researcher suggests involving the patient's health care provider/professionals, family/relatives, community, and religious body in the care of the patient. y y g y • Non-governmental organisations and affluent members of society should be encouraged to become more involved in the care of psychotic patients in order to lessen the burden and cost of treatment, which includes the purchase of medication and the transportation of the patient and their family members. • Non-governmental organisations and affluent members of society should be encouraged to become more involved in the care of psychotic patients in order to lessen the burden and cost of treatment, which includes the purchase of medication and the transportation of the patient and their family members. • Government should establish hospitals/clinics that are cheap for both poor and wealthy mentally ill individuals in order to lessen the burden/cost of treatment, which includes the purchase of medication and the emigration of the mentally sick and their relatives. • Government should establish hospitals/clinics that are cheap for both poor and wealthy mentally ill individuals in order to lessen the burden/cost of treatment, which includes the purchase of medication and the emigration of the mentally sick and their relatives. World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 said the patient exhibit positive coping mechanisms when faced with stressful events, this goes in line with (Hames 2013). In a study of untreated heavy drinkers in Britain and their readiness to change, the investigators found that, stress is among the leading causes of relapse among drug addicts. They noted that though all forms of stress can't be avoided, setting priority changes in lifestyle and relationships helps a recovering patient to avoid incidences that spark tension and other negative emotions associated with relapse. Also, Scott, Hemphill, Sampat, Bhaven (2011) shows that, emotional devastation of drug addiction is experienced by the addicts themselves, spouses, children and close friends and the emotional reactions range from pain, stress, discouragement, shame and self-guilty. said the patient exhibit positive coping mechanisms when faced with stressful events, this goes in line with (Hames 2013). In a study of untreated heavy drinkers in Britain and their readiness to change, the investigators found that, stress is among the leading causes of relapse among drug addicts. They noted that though all forms of stress can't be avoided, setting priority changes in lifestyle and relationships helps a recovering patient to avoid incidences that spark tension and other negative emotions associated with relapse. Also, Scott, Hemphill, Sampat, Bhaven (2011) shows that, emotional devastation of drug addiction is experienced by the addicts themselves, spouses, children and close friends and the emotional reactions range from pain, stress, discouragement, shame and self-guilty. [1] American Psychiatric Association (APA) (2013). Diagnostic and statistical manual of Mental disorders(5thedition).Washington DC :American Psychiatric Association. Compliance with ethical standards Disclosure of conflict of interest 3.2. Psychological determinants of relapse among the rehabilitated substance use patients In this study, the findings showed that majority of the patients had current relapse episode, and one-tenth had it in the last three month and above, 64.5% of the respondent agreed that he usually occur to the patient after successful treatment, while the remaining 35.5% were three or more, 72.5% of the respondents agreed that Does the patient comply to the prescribed medication when his/he recondition is under control compliance while 27.5% did not support the patient comply to the prescribed medication. Most of the respondents agreed that the patients have personality problem (e.g. introvert, extrovert, impulsive behaviors ,tendency to violence, quarrel some, shyetc, while 20.1% did not agreed with the patients have any Personality problem (e.g. introvert, extrovert, impulsive behaviors ,tendency to violence, quarrel some, shyetc, likewise most patient often have negative thoughts. About two-third of the respondents 752 No conflict of interest. References [1] American Psychiatric Association (APA) (2013). Diagnostic and statistical manual of Mental disorders(5thedition).Washington DC :American Psychiatric Association. 753 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 World Journal of Advanced Research and Reviews, 2022, 16(02), 747–754 [2] Abuse and Mental Health Services Administration, (2011). The 2010 National Survey on DrugUse and Health: Summary of National Findings, NSDUH Series H-41, Publication No.11-4658,Rockville, Md.: Substance. [3] Annis, H., & Davis, C. S. (2013). Relapse prevention. Adolescent Health and Research World, 15(3). [4] Becker,J.B.,McClellan,M.andReed,B.G.(2016).Socioculturalcontextforsexdifferencesinaddiction.Addiction Biology. [5] Brunette, M. F., Drake, R. E., Xie, H., McHugo, G. J., & Green, A. I. (2006). Clozapine use and relapses of substance use disorder among patients with co-occurring schizophrenia and substance use disorders. Schizophrenia bulletin, 32(4), 637–643. https://doi.org/10.1093/schbul/sbl003 [6] Campbell, N. and Ettore, E. (2011). Gendering Addiction: The Politics of Drug Treatment in a Neuro chemical World. New York: Palgrave Macmillan. [7] Curtin, J. J., McCarthy, D. E., ,Piper, M. E.,Baker, B. (2005). Implicit and explicit drug motivational processes: A model of boundary conditions. [8] Davies, G., Elison, S., Ward, J. et al (2015). The role of lifestyle in perpetuating substance use disorder: the Lifestyle Balance Model. Substance Abuse Treatment and Prevention Policy 10, 2. https://doi.org/10.1186/1747-597X- 10-2 [9] Hames, J. L., Hagan, C. R., Joiner, T. E. (2013). Interpersonal processes in depression. Annual Review of Clinical Psychology. 9:355–377. [PubMed] [Google Scholar] [10] Harstad, E., Levy, S., & Committee on Substance Abuse (2014). 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(2013) Integrated Treatment of Substance Use and Psychiatric Disorders. Soc Work Public H l h 28(0) 388 406 abuse among college students. Addictive Behaviors, 37, 1075 1083. [14] Kelly, T. M., Daley, D. C. (2013) Integrated Treatment of Substance Use and Psychiatric Disorders. References Soc Work Public Health;28(0):388–406. [14] Kelly, T. M., Daley, D. C. (2013) Integrated Treatment of Substance Use and Psychiatric Disord Health;28(0):388–406. [15] Kilgus, S. P., Bonifay, W. E., von der Embse, N. P., Allen, A. N., & Eklund, K. (2018). Evidence for the interpretation of Social, Academic, and Emotional Behavior Risk Screener (SAEBRS) scores: An argument-based approach to screener validation. Journal of school psychology, 68, 129–141. https://doi.org/10.1016/j.jsp.2018.03.002 [16] Koob, G. F., &Schulkin, J. (2019). Addiction and stress: An allostatic view. Neuroscience and bio behavioral reviews, 106, 245–262. [17] Lubman, D. I., King, J. A., & Castle, D. J. (2010). Treating comorbid substance use disorders in schizophrenia. International review of psychiatry (Abingdon, England), 22(2), 191–201. https://doi.org/10.3109/09540261003689958 [18] Mikkonen,J.,Raphael,D.(2010)"SocialDeterminantsofHealth:TheCanadianFacts"(http://www.thecanadianfacts.o rg/The_Canadian_Facts.pdfcited26 Feb2016). [19] Moos, R. H., & Moos, B. S. (2007). Protective resources and long-term recovery from alcohol use disorders. Drug and alcohol dependence, 86(1), 46–54. https://doi.org/10.1016/j.drugalcdep.2006.04.015 [20] Moore, B. A., &Budney, A. J. (2003). Relapse in outpatient treatment for marijuana dependence. Journal of substance abuse treatment, 25(2), 85–89. https://doi.org/10.1016/s0740-5472(03)00083-7 [21] Nayak, P., Domino, K., et al (2005).Risk factors for relapse in Health care professionals withsubstanceusedisorders.Vol.293 DO-10.1001/Jama.293.12.1453. [22] Satre, D. D., Mertens, J. R., Areán, P. A., &Weisner, C. (2004). Five-year alcohol and drug treatment outcomes of older adults versus middle-aged and younger adults in a managed care program. Addiction, 99(10), 1286–1297. [23] Torrens, M., Gilchrist, G., Domingo-Salvany, A., &psyCoBarcelona Group (2011). Psychiatric comorbidity in illicit drug users: substance-induced versus independent disorders. Drug and alcohol dependence, 113(2-3), 147–156. https://doi.org/10.1016/j.drugalcdep.2010.07.013. 754
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https://europepmc.org/articles/pmc3712680?pdf=render
English
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Desmoid Tumors in Pregnant and Postpartum Women
Cancers
2,012
cc-by
4,639
lliam A. Robinson *,1, Colette McMillan 2, Amy Kendall 3 and Nathan Pearlman *,4 Department of Medicine, University of Colorado Denver, Denver, CO 80045, USA Department of Medicine, University of Colorado Denver, Denver, CO 80045, USA 2 Department of Pharmacy, University of Colorado Denver, Denver, CO 80045, USA; E-Mail: colette.mcmillan@uch.edu (C.M.) 3 Department of the Tumor Registry, University of Colorado Denver, Denver, CO 80045, USA; E-Mail: amy.kendall@uch.edu (A.K.) 4 Department of Surgery, University of Colorado Denver, Denver, CO 80045, USA * Authors to whom correspondence should be addressed; E-Mails: william.robinson@ucdenver.edu (W.A.R.); nathan.pearlman@ucdenver.edu (N.P.); Tel.: +1-303-724-3872 (W.A.R.); Fax: +1-303-724-3889 (W.A.R.); Tel.: +1-303-724-2728 (N.P.); Fax: +1-303-724-7377(N.P.). * Authors to whom correspondence should be addressed; E-Mails: william.robinson@ucdenver.edu (W.A.R.); nathan.pearlman@ucdenver.edu (N.P.); Tel.: +1-303-724-3872 (W.A.R.); Fax: +1-303-724-3889 (W.A.R.); Tel.: +1-303-724-2728 (N.P.); Fax: +1-303-724-7377(N.P.). Received: 4 January 2012; in revised form: 11 February 2012 / Accepted: 13 February 2012 / Published: 21 February 2012 Received: 4 January 2012; in revised form: 11 February 2012 / Accepted: 13 February 2012 / Published: 21 February 2012 Abstract: We report here a review of the current medical literature on pregnancy associated desmoids, including 10 cases of our own. The pertinent findings are that a large percentage of desmoids in females arise in and around pregnancy. Most occur in the abdominal muscles, particularly the right rectus abdominus, perhaps related to trauma from abdominal stretching and fetal movement. While these tumors may regress spontaneously after delivery most can be surgically resected with low recurrence rates even with R1 resections and this is clearly the treatment of choice. Subsequent pregnancies do not appear to result in recurrence in either FAP or non FAP patients. It is not clear from currently available data whether pregnancy associated desmoids are molecularly distinct from other desmoids. Keywords: desmoid; pregnancy; post-partum; female Cancers 2012, 4, 184-192; doi:10.3390/cancers4010184 Cancers 2012, 4, 184-192; doi:10.3390/cancers4010184 Cancers 2012, 4 In a previous paper we described four women who all developed post-partum desmoids in the same location, namely the right rectus abdominus muscle. We speculated that this might have resulted from tearing or stretching of the abdominal wall musculature during fetal growth. It is well known that desmoids may be associated with trauma of different sorts. Against such a theory is the fact that in other case reports of pregnancy associated desmoids the tumor has developed in a remote location such as the larynx [3–22]. Others have attempted to link the hormonal and immune system changes that occur with pregnancy with desmoid development. The possible role of these factors is suggested by the description of spontaneous desmoid regression after delivery [23]. Further the possible role of estrogen is suggested by the occasional report of desmoids tumors responding to treatment with the anti-estrogen tamoxifen [24,25]. In contrast however is the finding that it is very uncommon to find estrogen receptors expressed on desmoids, even those that respond to tamoxifen. To date therefore the only thing clear in this unique association is that no clear explanation has been forthcoming. Here we have reviewed our own cases of pregnancy associated desmoids and the current literature in an attempt develops better understanding and future directions for research and management. Cancers 2012, 4 Since then there have multiple single case reports and a few small series including one from our institutions [2]. There have been various definitions of pregnancy associated desmoid. For the purpose of this paper we have elected to define as pregnancy associated desmoids those that arose, or were discovered during pregnancy, grew during pregnancy or developed postpartum within three years after delivery. The reason(s) for the association between pregnancy and development of desmoids remain unclear. A number of possible explanation have been put forward, none very satisfactory. In a previous paper we described four women who all developed post-partum desmoids in the same location, namely the right rectus abdominus muscle. We speculated that this might have resulted from tearing or stretching of the abdominal wall musculature during fetal growth. It is well known that desmoids may be associated with trauma of different sorts. Against such a theory is the fact that in other case reports of pregnancy associated desmoids the tumor has developed in a remote location such as the larynx [3–22]. Others have attempted to link the hormonal and immune system changes that occur with pregnancy with desmoid development. The possible role of these factors is suggested by the description of spontaneous desmoid regression after delivery [23]. Further the possible role of estrogen is suggested by the occasional report of desmoids tumors responding to treatment with the anti-estrogen tamoxifen [24,25]. In contrast however is the finding that it is very uncommon to find estrogen receptors expressed on desmoids, even those that respond to tamoxifen. To date therefore the only thing clear in this unique association is that no clear explanation has been forthcoming. Here we have reviewed our own cases of pregnancy associated desmoids and the current literature in an attempt develops better understanding and future directions for research and management. Since then there have multiple single case reports and a few small series including one from our institutions [2]. There have been various definitions of pregnancy associated desmoid. For the purpose of this paper we have elected to define as pregnancy associated desmoids those that arose, or were discovered during pregnancy, grew during pregnancy or developed postpartum within three years after delivery. The reason(s) for the association between pregnancy and development of desmoids remain unclear. A number of possible explanation have been put forward, none very satisfactory. 1. Introduction Pregnancy associated desmoids tumors have been a subject of interest since the first description by Macfarlene in 1832 [1]. He described a young postpartum woman who had a large fibrous abdominal wall tumor. This was also the first description of surgical resection of a pregnancy associated desmoid. 185 2. Methods All cases with histologically proven desmoid tumors in the Tumor Registry of our institution from 1980 through August 2011 were initially identified. There were 56 total cases of which there were 24 males and 32 females. Among the females 10 fit our criteria for pregnancy associated desmoid: arising in pregnancy, growth of a previously identified desmoid during pregnancy or development in 36 months after parturition. We used this definition since these are slowly growing tumors and it is likely that they were present at the time of pregnancy. Thus in our series 18% of all patients seen here during this time period had a pregnancy associated desmoid. Perhaps more striking is the fact that of all females with desmoids in our registry 31% were pregnancy associated. Details of these patients are shown in Table 1. Four of these were included in a prior paper [2]. In the current series the patients ranged in age from 22 to 39 years with a mean age of 32 and a median age of 33 years. Nine of the 10 cases developed the tumor after completion of pregnancy at an average of 12 months postpartum. One was found in the last month of pregnancy. The most common site was the right rectus abdominus muscle in 6 cases; two were in the left rectus abdominus, one in the mesentery and one on the back in a patient with Gardner’s Syndrome. Surgical resection was the method of primary treatment in 10 patients. The tumors ranged in size from 2 to 16 cm with an average size of 4.5 cm. Two of these had microscopically positive margins, but none of the patients who had surgical resection; even with positive surgical margins have had local or systemic recurrence at a mean follow-up of 3.4 years. No patient received further therapy after surgery. One patient was treated with tamoxifen followed by gleevec prior to surgery with minimal benefit. Two patients subsequently had full term pregnancies without 186 Cancers 2012, 4 Cancers 2012, 4 complications or desmoid recurrence. Two patients have active tumors not thought to be amenable to surgical resection and are currently being treated with tamoxifen and clinoril. Except for the patient with Gardner’s Syndrome no patient had a family history of desmoids tumors. Table 1. Clinical characteristics of 10 patients with pregnancy associated desmoid tumors seen at the University of Colorado. 2. Methods y Patient Age FAP Pre or post Site Treatment Delivery ER Size (cm) Outcome 1 39 No Post 12 mon Rt rectus Surg CS NA 5 NED 5 years 2 39 No Post 1 mon Rt rectus Surg CS NA 2 NED 5 years 3 33 No Post 36 mon Rt rectus Surg CS NA 7.5 NED 2 years 4 32 No Post 12 mon Rt rectus Surg Vag NA 16 NED 5 years 5 36 No Post 13 mon Rt rectus Surg CS NA 2 NED 6 years 6 33 No Post 4 mon Left rectus Surg Vag Neg 8 NED 2 years 7 26 Yes Post 12 mon Back Tam/chemo Vag Neg 37 Alive with 2 years 8 33 No Preg 40 wk Left rectus Tam/chemo CS Neg 8 Alive with 1 years 9 29 No Post 6 mon Mesentery Surg CS NA 5 NED 3 years 10 22 No Post 25 mon Rt rectus Surg CS NA 7 NED 3 years Age range: 22–39 years; Mean: 32 years; mon: month(s), wk: weeks; Rt rectus: right rectus; Size range: 2–37 cm, Mean: 9.75 cm; NED: No evidence of disease. Alive = alive with tumor remaining. 3. Literature Review We reviewed the available literature for reports of pregnancy associated desmoids and this data, minus our own cases, is detailed below in Table 2 [3–22]. We included only those reports in which there was sufficient data on the age of the patient, size of the tumor, location and method of treatment. We also found an abstract describing 15 cases, but this series has not been reported in a full manuscript and is described separately below. For the review we found 20 full length reports in the literature with a total of 24 cases that fit the criteria described and provided sufficient data for analysis. The patients ranged in age from 17 to 42 years with an average age of 27. Seven cases were associated with FAP mutations. The remaining were either non FAP or no mention was made of the genetic status. In 15 cases the desmoid arose during pregnancy, in five during the post-partum period and in four patients a pre- existing desmoid grew during pregnancy. In 14 of the 24 cases (58%) the desmoid involved the muscles of the abdominal wall. The mesentery was the next most common site and the remainder were in a wide variety of locations including the larynx in one case. Most were in the 5 to 10 cm size range, but one in case a tumor in the rectus abdominus grew to 192 cm at 39 weeks gestation. Most of these patients were treated with surgical resection Due to inadequate reporting we are unable to make definitive comments regarding outcome and recurrence in patients other than our own described above. In addition to these cases Rocha et al. [23] have described, in abstract form, limited details of pregnancy associated desmoids seen at The Brigham and Women’s Hospital in Boston. They reviewed 207 total cases of desmoid tumors in their registry and identified 16 of these (8%) as having a pregnancy associated desmoid. Similar to our series, described above, most (75%) were extraabdominal, but the individual sites were not specified. None of these were FAP associated. All 16 patients had surgical resection and of these nine (56%) were R0 and 7(44%) were R1 resections. At a median follow-up 187 Cancers 2012, 4 Cancers 2012, 4 of 39 months only two patients in this series had recurred, both after initial R1 resections. Both underwent successful re-excision. 3. Literature Review These authors concluded that pregnancy associated desmoids represent a less aggressive, subtype of desmoid tumors usually amenable to surgical resection. Table 2. Pregnancy associated desmoid. A review of the literature. Author(s) Ref. Age of Patient FAP Number of Pregnancies Delivery Pre, During, or Post Pregnancy Size Location Treatment Outcome ER Ober et al. [3] 18 N/A 1 (unknown) Pre 1–2 cm Left popliteal fossa Surg NED 1 year N/A Khoo, S.K. [4] 25 No 2 Vag During 8 × 5 × 3 cm obturator Surg NED 6 months 35 N/A 2 CS During 11 week gestation (unknown) Right obturator No treatment N/A Caldwell, E.H. [5] 26 N/A 4 (unknown) Post 15 × 17 cm Lower abdominal wall No treatment NED 5 years N/A Knightly et al. [6] 18 N/A 1 CS Post (unknown) Right upper quadrant Surg; XRT; chemo (unknown) Harvey et al. [7] 23 Yes 1 (unknown) During 3rd trimester N/A Mesentry Surg (unknown) 24 Yes 1 (unknown) Post 12 × 10 × 5 cm Mesentry Surg NED 3 years 34 Yes 1 (unknown) Post (unknown) Terminal ileus Surg (unknown) Camiel & Solish [8] 22 No 2 (unknown) During 7th month 14 × 10 cm Right, upper anterior abdominal wall Surg N/A Ezra et al. [9] 35 No 1 Vag Pre 15 × 13 cm Abdominal wall Surg NED 2 years N/A Sportiello & Hoogerland [10] 40 N/A 1 CS During 3rd trimester 10 × 8 × 6 cm Pelvic mass Surg; XRT; chemo NED at 27 months N/A Allen & Novotny [11] 19 No 1 (unknown) Pre 3 × 3 cm Right labium Surg; XRT NED at 12 months Kunieda et al. [12] 27 N/A 1 (unknown) During 8th month 9 × 7.5 cm Chest wall, xphoid Surg NED Neg Way & Culham [13] 28 N/A 3 Vag Post 3 × 4 × 2.5 cm Left rectus abdominal muscle Surg NED Table 2. Pregnancy associated desmoid. A review of the literature. 188 Cancers 2012, 4 Cancers 2012, 4 Table 2. Cont. Author(s) Ref. Age of Patient FAP Number of Pregnancies Delivery Pre, During, or Post Pregnancy Size Location Treatment Outcome ER Way & Culham [13] 28 N/A 1 (unknown) Post 1.3 × 1.2 cm Left upper rectus muscle just below the costal margin Surg NED Neg Gherman et al. 3. Literature Review [14] 25 N/A 1 Vag During 20 weeks gestation 2.3 × 1.2 × 1.6 cm Larynx Surg (unknown) de Cian et al. [15] 42 N/A 2 CS During 12 weeks gestation 8 × 5 cm Right rectus abdominus c-section scar Surg NED 15 months NE G Firoozmand & Prager [16] 27 Yes 1 (unknown) During 23 weeks gestation 17 × 14 × 10 cm J pouch Surg N/A N/A Mulik et al. [17] 35 Yes 5 Vag; CS During 18 weeks gestation 5 × 4 cm 4 × 4 cm Rectus sheath Surg No follow up Molelekwa, V. [18] 31 N/A 2 CS During 20 weeks gestation 2.7 × 4.5 cm Left lower quadrant abdominal mass Surg N/A Durkin et al. [19] 29 N/A 1 Vag During 1st trimester 3.5 × 7.2 cm Left rectus abdominis muscle Surg; chemo NED 2.5 years Sun et al. [20] 28 N/A 1 CS Post 12.2 × 11.5 × 8.5 cm Mesentery abdomen Surg NED 12 months Viriyaroj et al. [21] 17 N/A 1 (unknown) During 5th month 28 × 21 × 18 cm Lower abdominal wall Surg NED 8 months Le Roc'h et al. [22] 18 N/A 1 Vag Pre 192 cm3 Rectus muscle of the abdomen No treatment N/A N/A Table 2. Cont. Cancers 2012, 4 Cancers 2012, 4 Cancers 2012, 4 without desmoids. The age(s) were not given for the patients in the series reported by Rocha et al. [23]. Most, patients, both in our own series and our review had a prior pregnancy often with a caesarian section. While desmoids have been reported to arise in caesarian section scars this appears to be uncommon. The most common site is in the abdominal musculature particularly the right rectus abdominus muscle. Since these tumors are known to arise in areas of trauma we have speculated that this results from stretching of the abdominal muscles and fascia during gestation. This suggestion of causation does not explain however the development of desmoids in other areas during and after pregnancy indicating that other factors are also involved. The most likely factors are the hormonal and immunologic changes that occur during pregnancy. The fact that some desmoids have been reported to regress without treatment after termination of pregnancy indicates that such factors may be in play. The most important of these are probably hormonal. This suggestion is strengthened by reports of spontaneous regression of pregnancy associated desmoids after delivery and without treatment. Further are many reports that some desmoids, both in pregnant and non-pregnant patients, respond to treatment with the anti-estrogen tamoxifen or the related drug toremifene [24]. This is not a simple estrogen related phenomenon however. Very few desmoids have been reported to express significant estrogen receptors. This may be due to inadequate methods of investigation in the past. These receptors are almost always present if carefully searched for, although their significance is unknown. The effects of tamoxifen are considerably more broad and complex than blocking estrogen uptake [25]. The doses used for desmoids are usually much higher (200 mg/day) [25] than typically used in the treatment of breast cancer (20 mg/day) and usually combined with a non-steroidal anti-inflammatory drug such as sulindac. The response rate to tamoxifen therapy in all desmoids is however in the range of 50% [24] and understanding the mechanisms involved is likely to lead to better understanding of development and new therapies. Finally regression of desmoids has been reported to occur in women as they go through menopause. In contrast prior pregnancy has been reported to ameliorate the course of intra-abdominal desmoids in patients with FAP [26]. 4. Discussion We review here 50 cases of pregnancy associated desmoid tumors including 10 cases from our own institution. These appear to be a unique form of desmoids comprising 8 to 18% of all desmoid tumors in cancer registries. They are usually sporadic but may be associated with the FAP syndrome. If we exclude patients with FAP there does not appear to be any common features that mark women at risk for this problem. The patients in our series were perhaps older (mean age 32 years) than pregnant women 189 Cancers 2012, 4 Cancers 2012, 4 of the three patients did not have mutations of CTNNB1, but did have loss of parts of 5q including the area encoding APC. Together these findings provide a link to the development of spontaneous desmoids and those occurring in FAP patients as the same pathways are involved. Although longer term studies are needed it would appear that those patients without mutations of CTNNB1, such as pregnancy associated desmoids, have a more favorable prognosis for unclear reasons. These same authors [29] have recently reported on outcome and prognostic factors in 426 patients with desmoid tumors. Of these 32 (7.5%) had abdominal wall pregnancy associated desmoids with a 10 year progression survival of 62%, the highest of any subgroup in this large series. One of the questions frequently asked by patients with pregnancy associated desmoids is what the risk of recurrence with subsequent pregnancies is. We could not find any non FAP cases in which this occurred. In our own series two patients had subsequent pregnancies, Rocha’s series had one [23] and Way et al. [13] reported two further patients with no recurrence with a subsequent pregnancy. Of interest in this regard is a patient reported by Caldwell [5] who described a 26 year old woman who a large, unresectable desmoid during pregnancy which regressed without therapy even during a subsequent pregnancy. 5. Conclusions Desmoid tumors in females are often associated with pregnancy or occur post-partum. The reasons behind this association are unclear. The most common sites are in the abdominal muscles, but they have been reported in multiple other areas of the body. Surgical resection is the treatment of choice and is usually curative even when surgical margins are involved. Subsequent pregnancies do not appear to be contraindicated. Acknowledgements We thank Brenda Batlle for her help in preparation of the manuscript. Cancers 2012, 4 These authors compared the growth and progression of FAP related desmoids in 22 never pregnant patients with 25 similar patients who had been pregnant at least once. The patients who had been pregnant had smaller tumors, less surgery and a more benign course overall. These authors go as to far as to suggest that consideration should be given to possible therapy with hormone combinations of progesterone, prolactin and estrogen. It should be noted that these findings were reported only for FAP related desmoids and whether they are applicable to sporadic pregnancy associated desmoids is not clear. In order to better understand the mechanisms involved in the development of desmoids and develop new therapies a number of studies have examined molecular pathways, though not specifically in pregnancy associated desmoids. Heinrich et al. [27] examined tumor specimens from 19 patients looking for possible imatinib targets. No mutations were found in KIT, PDGFRA or PDGFRB, but 16 of the 19 had mutations involving the WNT pathway (APC or CTNNB1). These findings provide a link to the development of spontaneous desmoids and those occurring in FAP patients as the same pathways are involved. These findings were confirmed by Salas et al. in a larger study of 194 patients [28] using comparative genomic and DNA sequencing. This study included 13 women of child bearing age, during or shortly following pregnancy. Of these detailed molecular data is reported for only three. Two 190 Cancers 2012, 4 Cancers 2012, 4 Cancers 2012, 4 8. Camiel, M.R.; Solish, G.I. Desmoid tumor during pregnancy. Am. J. Obstet. Gynecol. 1982, 144, 988–989. 9. Ezra, Y.;Krausz, M.M.; Rivkind, A.; Antebey, S.O. Successful pregnancy and normal delivery with Marlex mesh replacement of the abdominal wall. Am. J. Obstet. Gynecol. 1990, 162, 97–98. 10. Sportiello, D.J.; Hoogerland, D.L. A recurrent pelvic desmoid tumor successfully treated with tamoxifen. Cancer 1991, 67, 1443–1446. 11. Allen, M.V.; Novotny, D.B. Desmoid tumor of the vulva associated with pregnancy. Arch. Pathol. Lab. Med. 1997, 121, 512–514. 12. Kunieda, K.; Saji, S.; Tanaka, Y.; Katoh, M.; Fucada, D.; Shimokawa, K. An abdominal desmoid tumor involving the xyphoid and costal chondrium associated with pregnancy: Report of a case. Surg. Today 1999, 29, 927–930. 13. Way, J.C.; Culham, B.A. Desmoid tumour. The risk of recurrent or new disease with subsequent pregnancy: A case report. Can. J. Surg. 1999, 42, 51–54. 14. Gherman, R.B.; Bowen, E.; Eggleston, M.K.; Karakia, D. Desmoid tumor of the larynx complicating pregnancy: A case report. Am. J. Obstet. Gynecol. 1999, 180, 1036–1037. 15. de Cian, F.; Delay, E.; Rudigoz, R.C.; Ranchere, D.; Rivoire, M. Desmoid tumor arising in a cesarean section scar during pregnancy: Monitoring and management. Gynecol. Oncol. 1999, 75, 145–148. 16. Firoozmand, E.; Prager, E. Pelvic desmoid tumor: threat to mother and fetus. Am. Surg. 2001, 67, 1213–1215. 17. Mulik, V.; Griffiths, A.N.; Beattie, R.B. Desmoid tumours with familial adenomatous polyposis in pregnancy. J. Obstet. Gynaecol. 2003, 23, 307–308. 18. Molelekwa, V. Conservative management of a desmoid tumour in pregnancy. J. Obstet. Gynaecol. 2004, 24, 700. 19. Durkin, A.J.; Korkolis, D.P.; Al-Saif, O.; Zervos, E.E. Full-term gestation and transvaginal delivery after wide resection of an abdominal desmoid tumor during pregnancy. J. Surg. Oncol. 2005, 89, 86–90. 20. Sun, L.; Wu, H.; Zhuang, Y.Z.; Guan, Y.S. A rare case of pregnancy complicated by mesenteric mass: What does chylous ascites tell us? World J. Gastroenterol. 2007, 13, 1632–1635. 21. Viriyaroj, V.;Yingsakmongkol, N.; Pasukdee, P.; Rermluk, N. A large abdominal desmoid tumor associated with pregnancy. J. Med. Assoc. Thai. 2009, 92, S72–S75. 22. Le Roc'h, A.; Montaigne, K.; Leblond, P.; Subtil, D.; Boukerrou, M. Desmoid tumour of the rectus abdominis muscle during pregnancy. J. Obstet. Gynaecol. 2009, 29, 668–669. 23. Rocha, F.; George, S.; Fletcher, C.; Bertagnolli, M.; Butrynski, J.; Demetri, G.; Morgan, J.; Wagner, A.; Raut, C. Pregnancy-associated desmoid tumors: A distinct clinical entity. Ann. Surg. Oncol. References 1. Macfarlane, J. Clinical Reports of the Surgical Practice of the Glasgow Royal Infirmary; David Robertson: Glasgow, UK, 1832; pp. xvi, 314. 1. Macfarlane, J. Clinical Reports of the Surgical Practice of the Glasgow Royal Infirmary; David Robertson: Glasgow, UK, 1832; pp. xvi, 314. 2. Carneiro, C.; Hurtubis, C.; Sing, M.; Robinson, W. Desmoid tumors of the right rectus abdominus muscle in postpartum women. Arch. Gynecol. Obstet. 2009, 279, 869–873. 2. Carneiro, C.; Hurtubis, C.; Sing, M.; Robinson, W. Desmoid tumors of the right rectus abdominus muscle in postpartum women. Arch. Gynecol. Obstet. 2009, 279, 869–873. 3. Ober, W.B.; Velardo, J.T.; Greene, R.T.; Taylor, R.J. Desmoid tumor of the popliteal space occurring during pregnancy: Report of a case with bioassays. J. Natl. Cancer Inst. 1955, 16, 569–577. 4. Khoo, S.K. The desmoid tumor, a diagnostic problem in the gynaecological patient: A report of 3. Ober, W.B.; Velardo, J.T.; Greene, R.T.; Taylor, R.J. Desmoid tumor of the popliteal space occurring during pregnancy: Report of a case with bioassays. J. Natl. Cancer Inst. 1955, 16, 569–577. g g p g y p y , , 4. Khoo, S.K. The desmoid tumor, a diagnostic problem in the gynaecological patient: A report of four patients. Aust. N. Z. J. Surg. 1972, 42, 170–174. 4. Khoo, S.K. The desmoid tumor, a diagnostic problem in the gynaecological patient: A report of four patients. Aust. N. Z. J. Surg. 1972, 42, 170–174. 5. Caldwell, E.H. Desmoid tumor: Musculoaponeurotic fibrosis of the abdominal wall. Surgery 1976, 79, 104–106. 5. Caldwell, E.H. Desmoid tumor: Musculoaponeurotic fibrosis of the abdominal wall. Surgery 1976, 79, 104–106. 6. Knightly, J.J.; Machiedo, G.W.; Merke, E.A.; Blackwood, G.M. Giant recurrent desmoid tumor: A case report. Am. Surg. 1977, 43, 613–616. 6. Knightly, J.J.; Machiedo, G.W.; Merke, E.A.; Blackwood, G.M. Giant recurrent desmoid tumor: A case report. Am. Surg. 1977, 43, 613–616. 7. Harvey, J.C.; Quan, S.H.; Fortner, J.G. Gardner’s syndrome complicated by mesenteric desmoid tumors. Surgery 1979, 85, 475–477. 7. Harvey, J.C.; Quan, S.H.; Fortner, J.G. Gardner’s syndrome complicated by mesenteric desmoid tumors. Surgery 1979, 85, 475–477. 191 © 2012 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 license (http://creativecommons.org/licenses/by/3.0/). Cancers 2012, 4 2008, 15, 66. 24. Bocale, D.; Rotelli, M.T.; Cavallini, A.; Altomare, D.F. Anti-oestrogen therapy in the treatment of desmoid tumours. A systematic review. Colorectal Dis. 2011, 13, e388–e395. 25. Hansmann, A. High-dose tamoxifen and sulindac as first-line treatment for desmoid tumors. Cancer 2004, 100, 612–620. 26. Church, J.M.; McGannon, E. Prior pregnancy ameliorates the course of intra-abdominal desmoid tumors in patients with familial adenomatous polyposis. Dis. Colon Rectum 2000, 43, 445–450. 192 Cancers 2012, 4 27. Heinrich, M.C.; McArthur, G.; Demetri, G.; Joensuu, H.; Bono, P.; Herrmann, R.; Hirte, H.; Cresta, S.; Koslin, B.; Corless, C.; et al. Clinical and molecular studies of the effect of imatinib on advanced aggressive fibromatosis (desmoid tumor). J. Clin. Oncol. 2006, 24, 1195–1203. 27. Heinrich, M.C.; McArthur, G.; Demetri, G.; Joensuu, H.; Bono, P.; Herrmann, R.; Hirte, H.; Cresta, S.; Koslin, B.; Corless, C.; et al. Clinical and molecular studies of the effect of imatinib on advanced aggressive fibromatosis (desmoid tumor). J. Clin. Oncol. 2006, 24, 1195–1203. 28. Salas, S.; Chibon, F.; Noguchi, T.; Terrier, P.; Rancher-Vince, D.; Lagarde, P.; Benard, J.; Forger, S.; Blanchard, C.; Domont, J.; et al. Molecular characterization by array comparative genomic hybridization and DNA sequencing of 194 desmoid tumors. Genes Chromosomes Cancer 2010, 49, 560–568. 29. Salas, S.; Dufresne, A.; Bui, B.; Blay, J.Y.; Terrier, P.; Ranchere-Vince, D.; Bonvalot, S.; Stoeckle, E.; Guillou, L.; Le Cesne, A.; et al. Prognostic factors influencing progression-free survival determined from a series of sporadic desmoid tumors: A wait-and-see policy according to tumor presentation. J. Clin. Oncol. 2011, 29, 3553–3558. © 2012 by the authors; licensee MDPI, Basel, Switzerland. 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Professor Sir Desmond Pond (1978–1981)
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Professor Sir Desmond Pond (1978-1981) Sir Martin Roth and Professor Linford Rees have well documented the achievements of the past ten years, to which I can add but little except to say how proud I am to have been able to join in with these activities and try to continue their far-sighted policies. Nevertheless, there is much that remains to be done, not so much because of what we have failed to do as because of the constantly changing situation in which we work. views more at the undergraduate than the postgraduate level. We are probably further on than most specialties in pro viding better arrangements for part-time trainees and part- time consultant appointments, though there is still a long way to go. More difficult is the question of the ratio of trainees to consultants, though there is now movement here, at least at the levels of DHSS and Joint Consultants Com mittee policy planning. More consultants has always been our policy, but it carries with it the inevitable consequence that some hospitals will be without trainees. What sort of non-trainee, non-consultant doctors may share the work load with the consultant staff is so far an unsolved issue, but 1 think we are nearer than most specialties to having and accepting a role for career-grade part-time (and probably whole-time) specialists. However. I do not think we have adequately considered the advantages of using general practitioners more, nor the possibilities of the non-medical professionals, like community psychiatric nurses, counsellors, clinical psychologists, etc. As an example, I should like first to mention recruitment and manpower. Though I raised this as a major issue when I became President, little progress has been made. However, the general lines of future policy are now clearer, and the will to implement change will undoubtedly be increased by the recommendations of the House of Commons Select Com mittee under RenéeShort, whose report has just been pub lished. The main difficulty is that, though manpower problems are different in different specialties, we have, never theless, to keep roughly in step with the career structure of the medical profession as a whole. Psychiatry. Other active Groups are those for Dependence and Addiction and Biological Psychiatry. All these appear to be thriving in a very healthy manner. During these years the College has taken an active inter est in the matter of human rights, particularly with regard to the abuse of psychiatry for political purposes (see Sidney Levine's article in the Bulletin, May 1981. p 94). The College passed a number of resolutions condemning this abuse, par ticularly in the USSR. During my Presidency, I was able to enlist the agreement of the General Council of the Bar to take part in an investigatory commission jointly with the College to visit the USSR and investigate allegations of psychiatric abuse, but permission was not received from the USSR for the visit to take place. The College proposed a resolution for the General Assembly of the World Psychiatric Association meeting in Hawaii, which after amendment by the Australian and New Zealand College of Psychiatrists, was passed by the Assembly. The World Psychiatric Association set up two committees, one to deal with ethical matters in psychiatry, and the College set up its own special committee to consider matters relating to the political abuse of psychiatry, under the Chairmanship of Dr Peter Sainsbury. This committee has considered allegations of the abuse of psychiatry in other countries, including Argentina. Chile and South Africa. The Research Committee is not only always ready to help individual research workers in the plan methodology of their research, but has also la College's first research project, an inquiry into EC Other standing committees have also gone fr to strength. The Programmes and Meetings arranges excellent meetings throughout the year, tion Committee, in its manifold activities, plays a the College's affairs, the Collegiate Trainees C actively engaged and is particularly conce manpower and the Membership Examination training throughout the United Kingdom and Ireland. A key person during the period preceding the the College and throughout the past decade has Natalie Cobbing who. as Secretary of the Colleg a co-ordinating role without which the College function effectively. We are indebted to her a leagues, and to Mr and Mrs Brooks, for all the have so faithfully given the College. This has really been a very brief summary of important activities of the College, and inevita been unable to mention all its achievements an who have contributed to its success during the p The College continues to evolve and has alread status and recognition throughout the world, fo can all bejustly proud. This has really been a very brief summary of some of the important activities of the College, and inevitably 1 have been unable to mention all its achievements and all those who have contributed to its success during the past decade. The College continues to evolve and has already gained in status and recognition throughout the world, for which we can all bejustly proud. The Research Committee is not only always ready to help Psychiatry. Other active Groups are those for Dependence and Addiction and Biological Psychiatry. All these appear to be thriving in a very healthy manner. During these years the College has taken an active inter est in the matter of human rights, particularly with regard to the abuse of psychiatry for political purposes (see Sidney Levine's article in the Bulletin, May 1981. p 94). The College passed a number of resolutions condemning this abuse, par ticularly in the USSR. During my Presidency, I was able to enlist the agreement of the General Council of the Bar to take part in an investigatory commission jointly with the College to visit the USSR and investigate allegations of psychiatric abuse, but permission was not received from the USSR for the visit to take place. The College proposed a resolution for the General Assembly of the World Psychiatric Association meeting in Hawaii, which after amendment by the Australian and New Zealand College of Psychiatrists, was passed by the Assembly. The World Psychiatric Association set up two committees, one to deal with ethical matters in psychiatry, and the College set up its own special committee to consider matters relating to the political abuse of psychiatry, under the Chairmanship of Dr Peter Sainsbury. This committee has considered allegations of the abuse of psychiatry in other countries, including Argentina. Chile and South Africa. The Research Committee is not only always ready to help individual research workers in the plan methodology of their research, but has also la College's first research project, an inquiry into EC Other standing committees have also gone fr to strength. The Programmes and Meetings arranges excellent meetings throughout the year, tion Committee, in its manifold activities, plays a the College's affairs, the Collegiate Trainees C actively engaged and is particularly conce manpower and the Membership Examination training throughout the United Kingdom and Ireland. A key person during the period preceding the the College and throughout the past decade has Natalie Cobbing who. as Secretary of the Colleg a co-ordinating role without which the College function effectively. We are indebted to her a leagues, and to Mr and Mrs Brooks, for all the have so faithfully given the College. This has really been a very brief summary of important activities of the College, and inevita been unable to mention all its achievements an who have contributed to its success during the p The College continues to evolve and has alread status and recognition throughout the world, fo can all bejustly proud. All these appear to be thriving in a very healthy manner. Psychiatry. Other active Groups are those for Dependence and Addiction and Biological Psychiatry. All these appear to be thriving in a very healthy manner. g y y During these years the College has taken an active inter est in the matter of human rights, particularly with regard to the abuse of psychiatry for political purposes (see Sidney Levine's article in the Bulletin, May 1981. p 94). The College passed a number of resolutions condemning this abuse, par ticularly in the USSR. During my Presidency, I was able to enlist the agreement of the General Council of the Bar to take part in an investigatory commission jointly with the College to visit the USSR and investigate allegations of psychiatric abuse, but permission was not received from the USSR for the visit to take place. The College proposed a resolution for the General Assembly of the World Psychiatric Association meeting in Hawaii, which after amendment by the Australian and New Zealand College of Psychiatrists, was passed by the Assembly. The World Psychiatric Association set up two committees, one to deal with ethical matters in psychiatry, and the College set up its own special committee to consider matters relating to the political abuse of psychiatry, under the Chairmanship of Dr Peter Sainsbury. This committee has considered allegations of the abuse of psychiatry in other countries, including Argentina. Chile and South Africa. Other standing committees have also gone from strength to strength. The Programmes and Meetings Committee arranges excellent meetings throughout the year, the Educa tion Committee, in its manifold activities, plays a vital part in the College's affairs, the Collegiate Trainees Committee is actively engaged and is particularly concerned with manpower and the Membership Examination and with training throughout the United Kingdom and Republic of Ireland. A key person during the period preceding the inception of the College and throughout the past decade has been Miss Natalie Cobbing who. as Secretary of the College, exercises a co-ordinating role without which the College could not function effectively. We are indebted to her and her col leagues, and to Mr and Mrs Brooks, for all the work they have so faithfully given the College. Psychiatry. Other active Groups are those for Dependence and Addiction and Biological Psychiatry. All these appear to be thriving in a very healthy manner. During these years the College has taken an active inter est in the matter of human rights, particularly with regard to the abuse of psychiatry for political purposes (see Sidney Levine's article in the Bulletin, May 1981. p 94). The College passed a number of resolutions condemning this abuse, par ticularly in the USSR. During my Presidency, I was able to enlist the agreement of the General Council of the Bar to take part in an investigatory commission jointly with the College to visit the USSR and investigate allegations of psychiatric abuse, but permission was not received from the USSR for the visit to take place. The College proposed a resolution for the General Assembly of the World Psychiatric Association meeting in Hawaii, which after amendment by the Australian and New Zealand College of Psychiatrists, was passed by the Assembly. The World Psychiatric Association set up two committees, one to deal with ethical matters in psychiatry, and the College set up its own special committee to consider matters relating to the political abuse of psychiatry, under the Chairmanship of Dr Peter Sainsbury. This committee has considered allegations of the abuse of psychiatry in other countries, including Argentina. Chile and South Africa. The Research Committee is not only always ready to help individual research workers in the plan methodology of their research, but has also la College's first research project, an inquiry into EC Other standing committees have also gone fr to strength. The Programmes and Meetings arranges excellent meetings throughout the year, tion Committee, in its manifold activities, plays a the College's affairs, the Collegiate Trainees C actively engaged and is particularly conce manpower and the Membership Examination training throughout the United Kingdom and Ireland. A key person during the period preceding the the College and throughout the past decade has Natalie Cobbing who. as Secretary of the Colleg a co-ordinating role without which the College function effectively. We are indebted to her a leagues, and to Mr and Mrs Brooks, for all the have so faithfully given the College. This has really been a very brief summary of important activities of the College, and inevita been unable to mention all its achievements an who have contributed to its success during the p The College continues to evolve and has alread status and recognition throughout the world, fo can all bejustly proud. This has really been a very brief summary of important activities of the College, and inevita been unable to mention all its achievements an who have contributed to its success during the p The College continues to evolve and has alread status and recognition throughout the world, fo can all bejustly proud. are those for Dependence chiatry. All these appear to er. has taken an active inter particularly with regard to tical purposes (see Sidney y 1981. p 94). The College ondemning this abuse, par y Presidency, I was able to ral Council of the Bar to mmission jointly with the investigate allegations of was not received from the . The College proposed a Assembly of the World in Hawaii, which after d New Zealand College of e Assembly. The World o committees, one to deal and the College set up its er matters relating to the er the Chairmanship of Dr has considered allegations other countries, including . only always ready to help individual research workers in the plannin methodology of their research, but has also launc College's first research project, an inquiry into ECT. Other standing committees have also gone from to strength. The Programmes and Meetings Com arranges excellent meetings throughout the year, the tion Committee, in its manifold activities, plays a vita the College's affairs, the Collegiate Trainees Comm actively engaged and is particularly concerne manpower and the Membership Examination an training throughout the United Kingdom and Rep Ireland. A key person during the period preceding the ince the College and throughout the past decade has be Natalie Cobbing who. as Secretary of the College, e a co-ordinating role without which the College co function effectively. We are indebted to her and h leagues, and to Mr and Mrs Brooks, for all the wo have so faithfully given the College. This has really been a very brief summary of som important activities of the College, and inevitably been unable to mention all its achievements and a who have contributed to its success during the past The College continues to evolve and has already ga status and recognition throughout the world, for w can all bejustly proud. individual research workers in the planning and methodology of their research, but has also launched the College's first research project, an inquiry into ECT. Psychiatry. Other active Groups are those for Dependence and Addiction and Biological Psychiatry. Psychiatry. Other active Groups are those for Dependence and Addiction and Biological Psychiatry. All these appear to be thriving in a very healthy manner. During these years the College has taken an active inter est in the matter of human rights, particularly with regard to the abuse of psychiatry for political purposes (see Sidney Levine's article in the Bulletin, May 1981. p 94). The College passed a number of resolutions condemning this abuse, par ticularly in the USSR. During my Presidency, I was able to enlist the agreement of the General Council of the Bar to take part in an investigatory commission jointly with the College to visit the USSR and investigate allegations of psychiatric abuse, but permission was not received from the USSR for the visit to take place. The College proposed a resolution for the General Assembly of the World Psychiatric Association meeting in Hawaii, which after amendment by the Australian and New Zealand College of Psychiatrists, was passed by the Assembly. The World Psychiatric Association set up two committees, one to deal with ethical matters in psychiatry, and the College set up its own special committee to consider matters relating to the political abuse of psychiatry, under the Chairmanship of Dr Peter Sainsbury. This committee has considered allegations of the abuse of psychiatry in other countries, including Argentina. Chile and South Africa. The Research Committee is not only always ready to help individual research workers in the plan methodology of their research, but has also la College's first research project, an inquiry into EC Other standing committees have also gone fr to strength. The Programmes and Meetings arranges excellent meetings throughout the year, tion Committee, in its manifold activities, plays a the College's affairs, the Collegiate Trainees C actively engaged and is particularly conce manpower and the Membership Examination training throughout the United Kingdom and Ireland. A key person during the period preceding the the College and throughout the past decade has Natalie Cobbing who. as Secretary of the Colleg a co-ordinating role without which the College function effectively. We are indebted to her a leagues, and to Mr and Mrs Brooks, for all the have so faithfully given the College. This has really been a very brief summary of important activities of the College, and inevita been unable to mention all its achievements an who have contributed to its success during the p The College continues to evolve and has alread status and recognition throughout the world, fo can all bejustly proud. Psychiatry. Other active Groups are those for Dependence and Addiction and Biological Psychiatry. All these appear to be thriving in a very healthy manner. During these years the College has taken an active inter est in the matter of human rights, particularly with regard to the abuse of psychiatry for political purposes (see Sidney Levine's article in the Bulletin, May 1981. p 94). The College passed a number of resolutions condemning this abuse, par ticularly in the USSR. During my Presidency, I was able to enlist the agreement of the General Council of the Bar to take part in an investigatory commission jointly with the College to visit the USSR and investigate allegations of psychiatric abuse, but permission was not received from the USSR for the visit to take place. The College proposed a resolution for the General Assembly of the World Psychiatric Association meeting in Hawaii, which after amendment by the Australian and New Zealand College of Psychiatrists, was passed by the Assembly. The World Psychiatric Association set up two committees, one to deal with ethical matters in psychiatry, and the College set up its own special committee to consider matters relating to the political abuse of psychiatry, under the Chairmanship of Dr Peter Sainsbury. This committee has considered allegations of the abuse of psychiatry in other countries, including Argentina. Chile and South Africa. The Research Committee is not only always ready to help individual research workers in the plan methodology of their research, but has also la College's first research project, an inquiry into EC Other standing committees have also gone fr to strength. The Programmes and Meetings arranges excellent meetings throughout the year, tion Committee, in its manifold activities, plays a the College's affairs, the Collegiate Trainees C actively engaged and is particularly conce manpower and the Membership Examination training throughout the United Kingdom and Ireland. A key person during the period preceding the the College and throughout the past decade has Natalie Cobbing who. as Secretary of the Colleg a co-ordinating role without which the College function effectively. We are indebted to her a leagues, and to Mr and Mrs Brooks, for all the have so faithfully given the College. Professor Sir Desmond Pond (1978-1981) We are particularly fortunate in having very good relations with the doctors in the DHSS concerned with mental health in all its aspects. Not all the other Royal Colleges have such close contacts. It has enabled us to have informal discussions about many sensitive medico-political issues before they reach the level of formal negotiation. Perhaps Sir Henry Yellowlees' distinguished psychiatric forebears have had a benign ghostly influence! As I write we are awaiting the news of a possible new Mental Health Act. and this will undoubtedly be a major issue for our new Presi dent—wecould not be in safer and stronger hands to steer us through this and the many other problems that will doubtless emerge in the next few years. class Journal with an international reputation. But it has little influence in the corridors of power. I have often wondered why it is less influential than many of the bodies to which most of its members belong. Probably it is because ACPP does not control entry into any profession, nor training schemes, nor certificates of competence. These functions which the existing organization that do these things, such as the medical Royal Colleges, guard very jealously, and I suspect that they would be very reluctant to give them up or even accept the need for rationalization across disciplines. at least three areas in which we have many common inter ests with numerous other professional groups: the first, the whole matter of training in psychotherapy and counselling. Trainees differ greatly in the intensity of their training, the breadth of their experience and their background of academic knowledge, and the various levels do not corre spond easily to usual professional boundaries. I believe that there is enough in common between all of the methods of treatment for a greater effort to be made to integrate train ing schemes. Secondly, there ought to be certain common standards of professional behaviour. A start has been made in this direction in the long on-going Committee on Con fidentiality. In spite of tremendous efforts by Professor Linford Rees and Dr Brian Ward, the Chairman and Secretary, respectively, of this inter-disciplinary group, agreement is proving difficult to reach, though much valuable discussion has taken place and it is hoped that a report will soon be published. Professor Sir Desmond Pond (1978-1981) The Zangwill Committee Report on a Code of Behaviour for Behaviour Therapy is another example of trying to apply standards of profes sional behaviour across disciplines. The Registration of Psychotherapists is a third topic where standards and training matters overlap. Finally, many of these organiza tions, including ourselves, have common interests in the pre vention of mental disorder and in treatment in the com munity. The community-based work inevitably implies going beyond the treatment of the individual patient which is the traditional role of the doctor. It implies going beyond even the treatment of the family which is now well-established in psychiatry. I am not sure how many of us are ready to be involved even indirectly in changing the attitudes and behaviour of social groups, including some sort of social action. The problems here will probably be the most intract able, as social and political actions are hard to separate and political action is something that many professional people fight shy of. class Journal with an international reputation. But it has little influence in the corridors of power. I have often wondered why it is less influential than many of the bodies to which most of its members belong. Probably it is because ACPP does not control entry into any profession, nor training schemes, nor certificates of competence. These functions which the existing organization that do these things, such as the medical Royal Colleges, guard very jealously, and I suspect that they would be very reluctant to give them up or even accept the need for rationalization across disciplines. Although many people express satisfaction at the flourish ing state of the numerous Sections and Groups that the College has and of the numerous meetings held (even includ ing committees!), I must express some concern at this proliferation—we might do better if we met less often for longer. The central core of general psychiatry needs to be jealously maintained as it is of primary importance for us all. Medicine and surgery, of course, have similar fissiparous tendencies, but I am sure the Royal College of Physicians and the Royal College of Surgeons are right to insist on the MRCP and the FRCS, repectively, as general examinations without which specialization and further training cannot be undertaken. on 1 January, 1982. There are still some subscriptions out standing, and in their own interest members are requested to make prompt payment of their dues. on 1 January, 1982. There are still some subscriptions out standing, and in their own interest members are requested to make prompt payment of their dues. The response from members who signed mandates to enable subscriptions to be paid by direct debit has exceeded our early expectations. However, it is hoped that members who have not already agreed to this method of payment will soon do so. Thus continuity of payment is assured even though the subscription varies and no further action is required by the member. Notification of the amount due will be seni annually. C. M. B. PAREHonorary Treasurer Professor Sir Desmond Pond (1978-1981) What I say in this connection could be seen to be in conflict with what I have said in the previous para graph about the need for multidisciplinary training and standards, but I think the contradiction is probably healthy, and I hope it will continue to stimulate discussion and debate. We are particularly fortunate in having very good relations with the doctors in the DHSS concerned with mental health in all its aspects. Not all the other Royal Colleges have such close contacts. It has enabled us to have informal discussions about many sensitive medico-political issues before they reach the level of formal negotiation. Perhaps Sir Henry Yellowlees' distinguished psychiatric forebears have had a benign ghostly influence! As I write we are awaiting the news of a possible new Mental Health Act. and this will undoubtedly be a major issue for our new Presi dent—wecould not be in safer and stronger hands to steer us through this and the many other problems that will doubtless emerge in the next few years. As many of you know, before I became President of this College I was Chairman of the Association of Child Psychology and Psychiatry. This is a flourishing multi disciplinary body whose membership is rightly increasing all the time. I hope that all child psychiatrists feel that they should belong to it. Amongst other things, it publishes a first Annual Subscription on 1 January, 1982. There are still some subscriptions out standing, and in their own interest members are requested to make prompt payment of their dues. The response from members who signed mandates to enable subscriptions to be paid by direct debit has exceeded our early expectations. However, it is hoped that members who have not already agreed to this method of payment will soon do so. Thus continuity of payment is assured even though the subscription varies and no further action is required by the member. Notification of the amount due will be seni annually. C. M. B. PAREHonorary Treasurer Professor Sir Desmond Pond (1978-1981) Our recruitment from British graduates may improve as a result of the 'popular' specialties of general medicine and surgery making greater efforts to bring home to graduates the advantages of going into the 'shortage' specialties, though it is difficult to know quite what determines popularity and unpopularity among us and whether efforts should be made to change students' This last consideration brings me to the second matter on which further action is increasingly necessary. This is to remedy the lack of a proper body to represent the interests of the numerous workers in the psychosocial caring field.There are many ad hoc committees and standing committees, but no on-going body which can speak with authority. There are 223 https://doi.org/10.1192/S0140078900012621 Published online by Cambridge University Press at least three areas in which we have many common inter ests with numerous other professional groups: the first, the whole matter of training in psychotherapy and counselling. Trainees differ greatly in the intensity of their training, the breadth of their experience and their background of academic knowledge, and the various levels do not corre spond easily to usual professional boundaries. I believe that there is enough in common between all of the methods of treatment for a greater effort to be made to integrate train ing schemes. Secondly, there ought to be certain common standards of professional behaviour. A start has been made in this direction in the long on-going Committee on Con fidentiality. In spite of tremendous efforts by Professor Linford Rees and Dr Brian Ward, the Chairman and Secretary, respectively, of this inter-disciplinary group, agreement is proving difficult to reach, though much valuable discussion has taken place and it is hoped that a report will soon be published. The Zangwill Committee Report on a Code of Behaviour for Behaviour Therapy is another example of trying to apply standards of profes sional behaviour across disciplines. The Registration of Psychotherapists is a third topic where standards and training matters overlap. Finally, many of these organiza tions, including ourselves, have common interests in the pre vention of mental disorder and in treatment in the com munity. The community-based work inevitably implies going beyond the treatment of the individual patient which is the traditional role of the doctor. It implies going beyond even the treatment of the family which is now well-established in psychiatry. Professor Sir Desmond Pond (1978-1981) I am not sure how many of us are ready to be involved even indirectly in changing the attitudes and behaviour of social groups, including some sort of social action. The problems here will probably be the most intract able, as social and political actions are hard to separate and political action is something that many professional people fight shy of. As many of you know, before I became President of this College I was Chairman of the Association of Child Psychology and Psychiatry. This is a flourishing multi disciplinary body whose membership is rightly increasing all the time. I hope that all child psychiatrists feel that they should belong to it. Amongst other things, it publishes a first class Journal with an international reputation. But it has little influence in the corridors of power. I have often wondered why it is less influential than many of the bodies to which most of its members belong. Probably it is because ACPP does not control entry into any profession, nor training schemes, nor certificates of competence. These functions which the existing organization that do these things, such as the medical Royal Colleges, guard very jealously, and I suspect that they would be very reluctant to give them up or even accept the need for rationalization across disciplines. Although many people express satisfaction at the flourish ing state of the numerous Sections and Groups that the College has and of the numerous meetings held (even includ ing committees!), I must express some concern at this proliferation—we might do better if we met less often for longer. The central core of general psychiatry needs to be jealously maintained as it is of primary importance for us all. Medicine and surgery, of course, have similar fissiparous tendencies, but I am sure the Royal College of Physicians and the Royal College of Surgeons are right to insist on the MRCP and the FRCS, repectively, as general examinations without which specialization and further training cannot be undertaken. What I say in this connection could be seen to be in conflict with what I have said in the previous para graph about the need for multidisciplinary training and standards, but I think the contradiction is probably healthy, and I hope it will continue to stimulate discussion and debate. Annual Subscription It was with great reluctance that subscription rates for United Kingdom members were increased at the Annual General Meeting in July 1981. Details appear in the Minutes of the Annual Meeting on page 232. You are reminded that your subscription falls due on 1 January, 1982. and that if you do not pay by direct debit or banker's order payment should now be sent to me at the College. on 1 January, 1982. There are still some subscriptions out standing, and in their own interest members are requested to make prompt payment of their dues. on 1 January, 1982. There are still some subscriptions out standing, and in their own interest members are requested to make prompt payment of their dues. The response from members who signed mandates to enable subscriptions to be paid by direct debit has exceeded our early expectations. However, it is hoped that members who have not already agreed to this method of payment will soon do so. Thus continuity of payment is assured even though the subscription varies and no further action is required by the member. Notification of the amount due will be seni annually. C. M. B. PAREHonorary Treasurer The response from members who signed mandates to enable subscriptions to be paid by direct debit has exceeded our early expectations. However, it is hoped that members who have not already agreed to this method of payment will soon do so. Thus continuity of payment is assured even though the subscription varies and no further action is required by the member. Notification of the amount due will be seni annually. C. M. B. PAREHonorary Treasurer Members whose subscriptions are outstanding for the current year were informed at the beginning of September that unless payment was received by the end of October, they would cease to receive the British Journal of Psychiatry 224 https://doi.org/10.1192/S0140078900012621 Published online by Cambridge University Press
https://openalex.org/W3217604012
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Determining propensity for sub-optimal low-density lipoprotein cholesterol response to statins and future risk of cardiovascular disease
PloS one
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PLOS ONE PLOS ONE RESEARCH ARTICLE Editor: Carmine Pizzi, University of Bologna, ITALY Received: April 7, 2021 Accepted: November 17, 2021 Published: December 2, 2021 OPEN ACCESS Citation: Weng SF, Akyea RK, Man KKC, Lau WCY, Iyen B, Blais JE, et al. (2021) Determining propensity for sub-optimal low-density lipoprotein cholesterol response to statins and future risk of cardiovascular disease. PLoS ONE 16(12): e0260839. https://doi.org/10.1371/journal. pone.0260839 Citation: Weng SF, Akyea RK, Man KKC, Lau WCY, Iyen B, Blais JE, et al. (2021) Determining propensity for sub-optimal low-density lipoprotein cholesterol response to statins and future risk of cardiovascular disease. PLoS ONE 16(12): e0260839. https://doi.org/10.1371/journal. pone.0260839 RESEARCH ARTICLE Determining propensity for sub-optimal low- density lipoprotein cholesterol response to statins and future risk of cardiovascular disease Stephen Franklin Weng1☯, Ralph Kwame AkyeaID1☯*, Kenneth KC ManID2,3, Wallis C. Y. Lau2,3, Barbara IyenID1, Joseph Edgar BlaisID3, Esther W. Chan3, Chung Wah Siu4, Nadeem Qureshi1‡, Ian C. K. Wong2,3‡, Joe Kai1‡ a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Primary Care Stratified Medicine (PRISM), Division of Primary Care, University of Nottingham, Nottingham, United Kingdom, 2 Centre for Medicine Optimisation Research and Education (CMORE), Research Department of Practice and Policy, UCL School of Pharmacy, London, United Kingdom, 3 Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China, 4 Cardiology Division, Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China ☯These authors contributed equally to this work. ‡ These authors also contributed equally to this work. * Ralph.Akyea1@nottingham.ac.uk Background Variability in low-density lipoprotein cholesterol (LDL-C) response to statins is underappreci- ated. We characterised patients by their statin response (SR), baseline risk of cardiovascu- lar disease (CVD) and 10-year CVD outcomes. Editor: Carmine Pizzi, University of Bologna, ITALY Introduction Funding: Funded by scientific donation by AMGEN Ltd. The funders of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. Cardiovascular disease (CVD) is a significant cause of mortality and morbidity, accounting for almost a third of all deaths globally [1]. Statins, the most widely prescribed class of drug world- wide, are an effective and low-cost solution in lowering cholesterol levels and reducing future risk of CVD [2]. Statin use is set to rise further in many countries as guidelines recommend their use in greater proportions of the population [3, 4]. In the United States alone, the proportion of adults whom statins are indicated has increased from 17.9% (21.8 million) to 27.8% (39.2 million) from 2002 to 2013 [5], with similar magnitude increases in most European [6] and Asian countries [7]. Following meta-analyses of cholesterol treatment trials [8, 9], the safety and intended per- centage reductions in LDL-C achieved by specific statins (and their doses) have been well- established. Guidelines in the United States (US), United Kingdom (UK), Europe (EU) and Hong Kong (HK) recommend intended LDL-C reduction targets for statin therapy to reduce CVD. The 2013 American College of Cardiology/American Heart Association (ACC/AHA) guideline suggests a fixed dose (or intensity) of statin depending on absolute CVD risk, with intended LDL-C reduction of 30–50% [4]. The UK National Institute of Clinical Excellence (NICE) Guideline aims for a greater than 40% reduction in non-high-density lipoprotein cho- lesterol (non-HDL-C) [3]. An LDL-C reduction of 50% is recommended by European Society of Cardiology guidelines [10]. Hong Kong primary prevention guidelines follow similar ACC/ AHA, NICE, and ESC guideline targets for LDL-C reduction [11]. Cardiovascular disease (CVD) is a significant cause of mortality and morbidity, accounting for almost a third of all deaths globally [1]. Statins, the most widely prescribed class of drug world- wide, are an effective and low-cost solution in lowering cholesterol levels and reducing future risk of CVD [2]. Statin use is set to rise further in many countries as guidelines recommend their use in greater proportions of the population [3, 4]. In the United States alone, the proportion of adults whom statins are indicated has increased from 17.9% (21.8 million) to 27.8% (39.2 million) from 2002 to 2013 [5], with similar magnitude increases in most European [6] and Asian countries [7]. Introduction Competing interests: NQ is a member of the most recent NICE Familial Hypercholesterolaemia & Lipid Modification Guideline Development Groups (CG71 & CG181). SW, IW are members of the Clinical Practice Research Datalink (CPRD) Independent Scientific Advisory Committee (ISAC). RKA currently holds an NIHR-SPCR funded studentship (2018-2021). SW reports honorarium from AMGEN and is also an employee of Janssen. KM holds the CW Malpethorpe Fellowship Award and reports personal fees from IQVIA Ltd have been received outside the submitted work. JB is supported by the Hong Kong Research Grants Council as a recipient of the Hong Kong PhD Fellowship Scheme. EC and IW report grants from Amgen. The remaining authors have no competing interests. This does not alter our adherence to PLOS ONE policies on sharing data and materials. Following meta-analyses of cholesterol treatment trials [8, 9], the safety and intended per- centage reductions in LDL-C achieved by specific statins (and their doses) have been well- established. Guidelines in the United States (US), United Kingdom (UK), Europe (EU) and Hong Kong (HK) recommend intended LDL-C reduction targets for statin therapy to reduce CVD. The 2013 American College of Cardiology/American Heart Association (ACC/AHA) guideline suggests a fixed dose (or intensity) of statin depending on absolute CVD risk, with intended LDL-C reduction of 30–50% [4]. The UK National Institute of Clinical Excellence (NICE) Guideline aims for a greater than 40% reduction in non-high-density lipoprotein cho- lesterol (non-HDL-C) [3]. An LDL-C reduction of 50% is recommended by European Society of Cardiology guidelines [10]. Hong Kong primary prevention guidelines follow similar ACC/ AHA, NICE, and ESC guideline targets for LDL-C reduction [11]. These guidelines are designed to curb CVD deaths; however, recent evidence has shown that over 50% of a cohort of 165,411 patients prescribed statins for primary prevention in the UK fail to reach treatment targets, which significantly increases risk of heart disease and stroke [12]. The reasons are varied, but there is evidence to suggest individual variability in LDL-C response [13] and significant non-adherence [14]. It is unclear which patient characteristics may be associated with variation in LDL-C reduction after commencing statin therapy for pri- mary prevention of CVD and if these clinical characteristics can be used to predict an individ- ual’s likelihood of achieving recommended LDL-C targets. Methods and results 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.pone.0260839 A multivariable model was developed using 183,213 United Kingdom (UK) patients without CVD to predict probability of sub-optimal SR, defined by guidelines as <40% reduction in LDL-C. We externally validated the model in a Hong Kong (HK) cohort (n = 170,904). Patients were stratified into four groups by predicted SR and 10-year CVD risk score: [SR1] optimal SR & low risk; [SR2] sub-optimal SR & low risk; [SR3] optimal SR & high risk; [SR4] sub-optimal SR & high risk; and 10-year hazard ratios (HR) determined for first major adverse cardiovascular event (MACE). Our SR model included 12 characteristics, with an area under the curve of 0.70 (95% confidence interval [CI] 0.70–0.71; UK) and 0.68 (95% CI 0.67–0.68; HK). HRs for MACE in predicted sub-optimal SR with low CVD risk groups (SR2 to SR1) were 1.39 (95% CI 1.35–1.43, p<0.001; UK) and 1.14 (95% CI 1.11–1.17, p<0.001; HK). In both cohorts, patients with predicted sub-optimal SR with high CVD risk (SR4 to SR3) had elevated risk of MACE (UK HR 1.36, 95% CI 1.32–1.40, p<0.001: HK HR 1.25, 95% CI 1.21–1.28, p<0.001). Copyright: © 2021 Weng 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 third-party data for this study were obtained from the Clinical Practice Research Datalink (CPRD) and the University of Hong Kong/Hospital Authority Hong 1 / 17 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 PLOS ONE Propensity of LDL-C response to statins and CVD Kong West Cluster. CPRD is a research service that provides primary care and linked data for public health research. CPRD and University of Hong Kong/Hospital Authority data governance and our own license to use data do not allow us to distribute or make available patient data directly to other parties. However, data is available upon application to CPRD (www.cprd.com) and the University of Hong Kong/Hospital Authority (www. ha.org.hk). Conclusions Patients with sub-optimal response to statins experienced significantly more MACE, regard- less of baseline CVD risk. To enhance cholesterol management for primary prevention, statin response should be considered alongside risk assessment. Introduction There are currently no management strategies in clinical practice to determine if patients will experience sub-optimal reduction in LDL-C when prescribed statins, nor the impact this may have on future CVD out- comes. First, we conducted an international study using two large geographically distinct cohorts to characterise LDL-C response to statin therapy in relation to baseline cardiovascular risk. We then determined the association between LDL-C response, baseline CVD risk and future CVD outcomes. Outcomes The primary outcome for this analysis was the incidence of first major adverse cardiovascular event (MACE) over 10-year follow-up after initiation of statins. We defined MACE as a com- posite of coronary heart disease (CHD), stroke, transient ischemic attack (TIA), peripheral vascular disease (PVD), and cardiovascular (CV) death [19]. CHD included acute myocardial infarction, coronary revascularisations, stable and unstable angina. CVD events were identi- fied from linked primary, secondary, and death registries. These are coded diagnoses based on National Health Service (NHS) Read codes and ICD-10 in the UK and mapped to ICD-9-CM in HK. Secondary outcomes include all-cause mortality, and CVD outcomes by sub-type. Data source This study used the anonymized electronic health records from the UK Clinical Practice Research Datalink (CPRD) and the Hong Kong (HK) Clinical Data Analysis and Reporting System (CDARS). 2 / 17 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 PLOS ONE Propensity of LDL-C response to statins and CVD CPRD contains anonymized patient data for more than 15 million patients and is represen- tative of the general UK population [15]. CPRD is one of the largest quality-assured databases of longitudinal medical records from primary care in the world, with over 800 UK primary medical care practices. Regulatory approval for this study (protocol number: 17_200RA) was obtained from the CPRD Independent Scientific Advisory Committee. The CDARS contains data from the Hong Kong Hospital Authority, which serves a popula- tion of over 7.4 million through 43 hospitals and institutions, 48 specialist outpatient clinics, 73 general outpatient clinics, covering approximately 80% of all hospital admissions in Hong Kong [16]. The use of CDARS data for this study was approved by the Institutional Review Board of the University of Hong Kong/Hospital Authority Hong Kong West Cluster (protocol number: UW 17–135). Study population The study cohorts comprised 183,213 patients initiating statin therapy with repeat prescrip- tions between 3rd September 1990 and 7th June 2016 in UK CPRD and 170,904 patients between 1st of January 2003 and 31st of December 2011 in HK CDARS. Patients were eligible for inclusion if they were registered with their health care provider for at least 12 months. Patients were required to have at least two recorded LDL-C measurements (directly mea- sured). The baseline LDL measure was within 12 months before or at the initiation of statins and the follow-up measure was within 24 months after initiation of statins. Patients on statin treatment for primary prevention of CVD who failed to achieve greater than 40% reduction in their untreated baseline LDL-C, recorded within the first 24 months, were defined as sub-opti- mal LDL-C responders. This was based on the lower bound expected reduction of LDL-C rec- ommended in CVD prevention guidelines [3, 10, 11, 17] and also recognised in meta-analyses [8]. Percentage LDL-C reduction, which considers individual baseline levels, has been shown to have better prognostic value than attained LDL-C for future CVD events [18]. For on-treat- ment response, the most recent LDL-C record at or closest to 24 months was used. This was because many routine annual medication reviews or cholesterol assessments in clinical prac- tice are unlikely to be documented in the EHRs until beyond 12 months. All individuals with a diagnosis of CVD (defined as coronary heart disease, cerebrovascular disease and peripheral arterial disease) before initiating statin therapy were excluded. Candi- date predictors (documented in S1 Table) were assessed for inclusion by clinical review and prior evidence. Study design and statistical analyses The study involved two phases, detailed in the study flowchart (Fig 1). Phase I involved the development and validation of the statin response (SR) propensity model and Phase II strati- fied groups according to statin response and evaluated future CVD and mortality outcomes. PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 3 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD Fig 1 https://doi.org/10.1371/journal.pone.0260839.g001 Full methods on model development, validation, statistical methods and evaluation of future CVD outcomes are detailed in S1 Text. Stata SE version 15 and RStudio were used for all analysis. Full methods on model development, validation, statistical methods and evaluation of future CVD outcomes are detailed in S1 Text. Stata SE version 15 and RStudio were used for all analysis. PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 Characteristics of the cohorts Within 24 months following initiation of statin therapy, 51.3% of UK patients had sub-optimal cholesterol response in the derivation cohort. However, a higher proportion of HK patients had a sub-optimal LDL-C response (60.8%) compared to the UK. Both derivation and valida- tion cohorts had similar mean age, mean baseline LDL-C, and proportion of females. Baseline mean LDL-C was higher in UK patients than in HK patients (156.5 mg/dL and 156.6 mg/dL for UK cohorts compared to 149.8 mg/dL for the HK cohort). Higher potency statins tended to be prescribed more frequently in in the UK than in HK (with 23.6% prescribed low potency in the UK compared to 68.5% prescribed low potency in HK). Full baseline characteristics are presented in Table 1, with S2 Table detailing the grouping of statins based on potency. Disease outcomes over 10-year follow-up for both cohorts are shown in Fig 2. Overall, there were 40,928 cases of MACE (22.3%) in the UK population and 37,777 cases of MACE PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 4 / 17 PLOS ONE PLOS ONE Propensity of LDL-C response to statins and CVD Table 1. Clinical characteristics of patients initiating statin treatment and free from cardiovascular disease at baseline (n = 183,213). PLOS ONE Characteristic Units UK CPRD derivation cohort UK CPRD internal validation cohort HK CDARS external validation cohort Total sample size N 128,248 54,965 170,904 Follow-up time (years) Median (IQR) 5.29 (2.28–8.78) 5.26 (2.29–8.70) 6.92 (3.78–8.61) Sex (Females) N (%) 60,891 (47.5) 26,161 (47.6) 89,315 (52.3) Sub-optimal LDL-C response to statin N (%) 65,777 (51.3) 28,141 (51.2) 103,899 (60.8) Age (years) Mean (SD) 62.9 (11.9) 62.9 (11.8) 63.0 (12.0) Median (IQR) 63.0 (55.0–71.0) 63.0 (55.0–71.0) 62.8 (54.7–72.0) Baseline LDL-C (mg/dL) Mean (SD) 156.5 (44.2) 156.6 (44.2) 150.0 (41.2) Median (IQR) 154.7 (127.6–184.1) 154.7 (127.6–184.5) 147.6 (125.0–171.9) Body mass index (kg/m2) Mean (SD) 28.72 (4.63) 28.70 (4.61) N/A Median (IQR) 28.3 (25.9–30.8) 28.25 (25.9–30.8) Systolic blood pressure (mmHg) Mean (SD) 142 (19) 142 (19) N/A Median (IQR) 140 (130–150) 140 (130–150) Diastolic blood pressure (mmHg) Mean (SD) 82 (10) 82 (10) N/A Median (IQR) 81 (76–88) 81 (76–88) Ethnicity White N (%) 11,026 (8.6) 4,738 (8.6)  Asian 563 (0.4) 262 (0.5) Black/African/Caribbean 448 (0.3) 180 (0.3) Mixed/multiple 684 (0.5) 282 (0.5) Other 380 (0.3) 163 (0.3) Unknown 115,147 (89.8) 49,340 (89.8) Comorbidities (prior to 1st statin) Atrial fibrillation N (%) 4,200 (3.3) 1,821 (3.3) 3,828 (2.2) Chronic kidney disease N (%) 3,574 (2.8) 1,592 (2.9) 3,150 (1.8) Diabetes N (%) 20,843 (16.3) 8,928 (16.2) 32,457 (19.0) Dyslipidaemias N (%) 10,262 (8.0) 4,375 (8.0) 10,059 (5.9) Family history of cardiovascular disease N (%) 13,491 (10.5) 5,837 (10.6) N/A Family history of hyperlipidaemia N (%) 281 (0.2) 120 (0.2) N/A Treated hypertension N (%) 33,631 (26.2) 14,319 (26.1) 22,670 (13.3) Hypothyroidism N (%) 5,340 (4.2) 2,243 (4.1) 2,636 (1.5) Liver disease N (%) 1,221 (1.0) 517 (0.9) 497 (0.3) Migraine N (%) 2,766 (2.2) 1,182 (2.2) 359 (0.2) Nephrotic syndrome N (%) 83 (0.1) 40 (0.1) 1,062 (0.6) Rheumatoid arthritis N (%) 1,185 (0.9) 480 (0.9) 1,377 (0.8) Systemic lupus erythematosus N (%) 157 (0.1) 54 (0.1) 622 (0.4) Medications (prescribed within 12 months prior to 1st statin) Medication count Median (IQR) 4 (1–6) 4 (1–6) 8 (5–12) Antipsychotics N (%) 5,421 (4.2) 2,295 (4.2) 3,279 (1.9) Other lipid lowering medication N (%) 535 (0.4) 223 (0.4) 10,885 (6.4) Oral corticosteroids N (%) 5,390 (4.2) 2,396 (4.4) 8,906 (5.2) (Continued) atients initiating statin treatment and free from cardiovascular disease at baseline (n = 183,213). PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 5 / 17  According to the most recent Hong Kong population census, about 92% of its residents are Han Chinese. PLOS ONE PLOS ONE Propensity of LDL-C response to statins and CVD Table 1. (Continued) Characteristic Units UK CPRD derivation cohort UK CPRD internal validation cohort HK CDARS external validation cohort Potency of initial statin prescribed† Low N (%) 30,310 (23.6) 12,994 (23.6) 11,7107 (68.5) Medium 90,514 (70.6) 38,747 (70.5) 47,825 (28.0) High 7,424 (5.8) 3,224 (5.9) 5,972 (3.5) Missing data Missing body mass index N (%) 57,782 (45.1) 24,641 (44.8) N/A Missing systolic blood pressure N (%) 15,076 (11.8) 6,354 (11.6) N/A Missing diastolic blood pressure N (%) 15,029 (11.7) 6,337 (11.5) N/A Table 1. (Continued) Characteristic Units UK CPRD derivation cohort UK CPRD internal validation cohort HK CDARS external validation cohort Potency of initial statin prescribed† Low N (%) 30,310 (23.6) 12,994 (23.6) 11,7107 (68.5) Medium 90,514 (70.6) 38,747 (70.5) 47,825 (28.0) High 7,424 (5.8) 3,224 (5.9) 5,972 (3.5) Missing data Missing body mass index N (%) 57,782 (45.1) 24,641 (44.8) N/A Missing systolic blood pressure N (%) 15,076 (11.8) 6,354 (11.6) N/A Missing diastolic blood pressure N (%) 15,029 (11.7) 6,337 (11.5) N/A  According to the most recent Hong Kong population census, about 92% of its residents are Han Chinese. † Statin potency–see S2 Table for detailed definitions. CDARS: Clinical Data Analysis and Reporting System; CPRD: Clinical Practice Research Datalink; HK: Hong Kong; IQR: interquartile range; LDL-C: low-density lipoprotein cholesterol; SD: standard deviation; UK: United Kingdom.  According to the most recent Hong Kong population census, about 92% of its residents are Han Chinese.  According to the most recent Hong Kong population census, about 92% of its residents are Han Chinese. Fig 2. https://doi.org/10.1371/journal.pone.0260839.g002 https://doi.org/10.1371/journal.pone.0260839.g002 6 / 17 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 PLOS ONE Propensity of LDL-C response to statins and CVD (22.1%) in the HK population. There were some notable differences between the proportion of stroke/TIA and CHD between cohorts, the most common MACE outcomes. There was a higher proportion of CHD (14.9%) and PVD (2.6%) outcomes in UK patients compared to HK patients (10.2% CHD, 0.9% PVD). There was a lower proportion of stroke/TIA (3.8%) in UK patients compared to HK patients (8.4%). The proportion of non-CVD death in the HK patients (13.9%) was twice that of UK patients (6.2%). Development of sub-optimal LDL-C statin response model The multivariable logistic model using the derivation cohort retained age, sex, atrial fibrillation (AF), diabetes, dyslipidaemia, potency or intensity of initial statin prescribed, treated hyper- tension, prescription of corticosteroid and other lipid lowering medications, LDL-C level at time of statin prescription and medication count. S3 Table provides the adjusted odds ratios, with regression coefficients and constants presented in S4 Table. The results of the model showed those with higher baseline levels of LDL-C, atrial fibrilla- tion (in men only), diabetes, treated hypertension, increasing number of concurrent medica- tions (in men only), high potency statins, and other lipid lowering drugs (in men only) were less likely to have sub-optimal LDL-C reduction. Dyslipidaemias and corticosteroids were associated with a higher likelihood of sub-optimal LDL-C reduction. The interaction terms showed that when considered in relation to higher LDL-C levels, those on higher potency stat- ins and had a diagnosis of dyslipidaemias were less likely to have sub-optimal response. Validation of sub-optimal LDL-C statin response model The discriminatory accuracy of the model in predicting sub-optimal LDL-C response per- formed similarly in both UK cohorts (derivation AUROC 0.704, 95% CI 0.701–0.707, internal validation AUROC 0.703 (95% CI 0.698–0.707) with a slightly lower performance in the HK cohort (external validation AUC 0.677 (95% CI 0.675–0.680) (Table 2). Calibrations plots (S1 Fig) show that the model was perfectly calibrated (slope = 1.0) for UK populations by comparing the predicted and observed probability of sub-optimal statin response across each tenth of predicted probabilities. For HK populations, the model under- predicted risk with predicted probabilities consistently lower than observed probabilities (slope = 0.86). An adjustment to the intercept term of the risk model in the HK population would improve its calibration. The sensitivity and specificity plots for the model are presented in S2 Fig. The optimum trade-off occurred at 50% probability as determined by the maximum product index [20] between sensitivity and specificity (shown at the intersection), and hence we classified individ- uals with SR propensity >50% as “predicted sub-optimal response” and individuals 50% as “predicted optimal response”. This binary classification resulted in a sensitivity of 64% (95% CI 63.4% - 64.5%) and specificity of 64.9% (95% CI 64.3% - 65.5%). Table 2. Model discrimination for sub-optimal LDL-C response to statins. Statin Optimisation Model Sample Size AUROC (95% CI) Standard Error Derivation cohort: UK CPRD 128,248 0.704 (0.701–0.707) 0.002 Internal validation cohort: UK CPRD 54,965 0.703 (0.698–0.707) 0.002 External validation cohort: HK CDARS 170,904 0.677 (0.675–0.680) 0.001 Jack-knife procedure to estimate standard errors. AUROC (c-statistic): area under the receiver operating curve; CDARS: Clinical Data Analysis and Reporting System; CI: confidence interval; CPRD: Clinical Practice Research Datalink; HK: Hong Kong; UK: United Kingdom. https://doi.org/10.1371/journal.pone.0260839.t002 Table 2. Model discrimination for sub-optimal LDL-C response to statins. Statin Optimisation Model Sample Size AUROC (95% CI) Standard Error Derivation cohort: UK CPRD 128,248 0.704 (0.701–0.707) 0.002 Internal validation cohort: UK CPRD 54,965 0.703 (0.698–0.707) 0.002 External validation cohort: HK CDARS 170,904 0.677 (0.675–0.680) 0.001 Jack-knife procedure to estimate standard errors. AUROC (c-statistic): area under the receiver operating curve; CDARS: Clinical Data Analysis and Reporting System; CI: confidence interval; CPRD: Clinical Practice Research Datalink; HK: Hong Kong; UK: United Kingdom. https://doi.org/10.1371/journal.pone.0260839.t002 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 7 / 17 Table 2. Model discrimination for sub-optimal LDL-C response to statins. Validation of sub-optimal LDL-C statin response model Statin Optimisation Model Sample Size AUROC (95% CI) Standard Error Derivation cohort: UK CPRD 128,248 0.704 (0.701–0.707) 0.002 Internal validation cohort: UK CPRD 54,965 0.703 (0.698–0.707) 0.002 External validation cohort: HK CDARS 170,904 0.677 (0.675–0.680) 0.001 Jack-knife procedure to estimate standard errors. Table 2. Model discrimination for sub-optimal LDL-C response to statins. Jack-knife procedure to estimate standard errors. AUROC (c-statistic): area under the receiver operating curve; CDARS: Clinical Data Analysis and Reporting System; CI: confidence interval; CPRD: Clinical Practice Research Datalink; HK: Hong Kong; UK: United Kingdom. PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 7 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD Table 3. Model performance stratified by statin adherence rates over 2-year follow-up in the United Kingdom CPRD validation cohort (n = 54,965). Statin Adherence Rate (%) Mean reduction in LDL-C (SD), mg/dL Percentage mean reduction in LDL-C (%) Percentage achieving targeted 40% reduction in LDL-C AUROC c-statistic (95% CI) <20% -17.1 (36.7) -19.1% 9.9% 0.637 (0.606–0.670) 20-< 40% -30.6 (41.6) -35.8% 22.2% 0.633 (0.613–0.653) 40-< 60% -44.2 (61.3) -53.7% 35.0% 0.642 (0.627–0.658) 60-< 80% -54.6 (40.5) -69.9% 48.2% 0.672 (0.661–0.684) 80% -65.7 (76.7) -81.6% 58.2% 0.737 (0.731–0.742)  Proxy marker for adherence by medication possession count over two-year follow-up from each patient’s prescribing record. Estimation of start/stop dates representing discontinuation periods are based on statin pack size and prescribed daily dosage. AUROC: area under the receiver operating curve; CI: confidence interval; CPRD: Clinical Practice Research Datalink; LDL-C: low-density lipoprotein cholesterol; SD: atified by statin adherence rates over 2-year follow-up in the United Kingdom CPRD validation cohort (n = 54,965). r 2-year follow-up in the United Kingdom CPRD validation cohort (n = 54,965). Table 3. Model performance stratified by statin adherence rates over 2-year follow-up in the United Kingdom CPRD  Proxy marker for adherence by medication possession count over two-year follow-up from each patient’s prescribing record. Estimation of start/stop dates representing discontinuation periods are based on statin pack size and prescribed daily dosage. AUROC: area under the receiver operating curve; CI: confidence interval; CPRD: Clinical Practice Research Datalink; LDL-C: low-density lipoprotein cholesterol; SD: standard deviation. https://doi.org/10.1371/journal.pone.0260839.t003 Impact of adherence on model Approximately 60% of the UK validation cohort (n = 33,491) had a discontinuation period over two-years from starting statins. The statin adherence rate had explained 11% of the varia- tion in the mean reduction in LDL-C (Pearson’s r = -0.33; R^2 = 0.108) and followed an expected inverse association with both absolute and percentage mean reduction in LDL-C and positive association with percentage patients achieving the targeted 40% reduction in LDL-C from baseline (Table 3). The model performance ranged from AUROC of 0.637 (95% CI 0.606–0.670) for patients who had <20% adherence to an AUROC of 0.737 (95% CI 0.731– 0.742) in patients who had 80% adherence.  Proxy marker for adherence by medication possession count over two-year follow-up from each patient’s prescribing record. Estimation of start/stop dates representing discontinuation periods are based on statin pack size and prescribed daily dosage. AUROC: area under the receiver operating curve; CI: confidence interval; CPRD: Clinical Practice Research Datalink; LDL-C: low-density lipoprotein cholesterol; SD: standard deviation. PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 Stratifying groups by LDL-C statin response and CVD risk Ten-year CVD risk recommended by ESC guidelines and two-year sub-optimal LDL-C reduc- tion propensity was calculated for all patients in both cohorts from baseline risk factors (histo- grams and distributions shown in S3 Fig). By jointly stratifying patients into “high” (> 5%) or “low” ( 5%) CVD risk and “sub-optimal” (> 50%) or “optimal” ( 50%) LDL-C reduction, four groups for statin response (SR) were created (shown in S4 Fig). For the UK cohort, 45,684 patients (24.9%) were predicted to have optimal statin response and low CVD risk (SR1), 64,997 patients (35.5%) were predicted to have sub-optimal statin response and low CVD risk (SR2), 48,460 patients (26.5%) were predicted to have optimal statin response and high CVD risk (SR3), and 24,072 patients (13.1%) were predicted to have sub-optimal statin response and high CVD risk. For the HK cohort, 47,842 patients (27.9%) were predicted to have optimal statin response and low CVD risk (SR1), 61,725 patients (36.1%) were predicted to have sub-optimal statin response and low CVD risk (SR2), 43,514 patients (25.4%) were predicted to have optimal statin response and high CVD risk (SR3), and 17,823 patients (10.4%) were predicted to have sub-optimal statin response and high CVD risk. Characteristics of the groups for the UK patients are provided in S5 Table and HK patients in S6 Table. For UK patients, classified as being at low CVD risk, patients predicted to have sub-optimal compared to optimal response were more likely to be male (55.6% compared to 41.5%), less likely to be treated for hypertension (17.5% compared to 26.7%), with lower mean LDL-C (133.4 mg/dL compared to 187.6 mg/dL), and more frequently initiated on a low potency statin (34.2% compared to 5.4%). Following similar trends, UK patients classified as being at high CVD risk, patients predicted to have sub-optimal response were more likely to be male (64.6% compared to 52.6%), with lower mean LDL-C (123.2 mg/dL compared to PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 8 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD 174.9 mg/dL), less likely to be treated for hypertension (27.4% compared to 35.4%), and were much more likely to initiated on a low potency statin (52.8% compared to 12.2%). In HK patients, SR groups were also significantly different across groups but with some dif- ferences compared to UK patients. Stratifying groups by LDL-C statin response and CVD risk In HK patients classified as being at low CVD risk, patients predicted to have sub-optimal compared to optimal response were more likely to be male (53.3% compared to 32.1%), lower mean LDL-C (207.4 mg/dL compared to 259.8 mg/dL), less likely to be diabetic (14.2% compared to 23.4%), and less likely to be treated for hypertension (7.1% compared to 14.5%). Similarly, HK patients predicted to have sub-optimal compared to optimal response in high CVD risk groups also were more likely to be male (70.9% compared to 47.6%), have lower mean LDL-C (113.6 mg/dL compared to 166.7 mg/dL), less likely to be diabetic (11.0% compare to 24.2%) or treated for hypertension (10.1% compared to 22.0%). Potency of statin prescribing remained stable in HK patients across all groups, favouring lower dosage statins compared to UK patients. Similar to UK patients, HK patients in high CVD risk groups were generally older, with higher numbers of men, medication count, and smokers. Long-term follow-up MACE outcomes Long-term follow-up MACE outcomes Incidence rates (per 1000 person-years) over 10-years for MACE increased significantly across groups (S7 Table). Increasing incidence across SR groups followed similar trends for all-cause mortality, CHD, stroke/TIA, PVD and CVD death for both cohorts. CHD was the most com- mon MACE event to occur during follow-up. Cumulative incidence graphs for 10-year MACE are displayed in Fig 4. In high CVD risk groups, the absolute difference in MACE cumulative event rate at the end of 10-year follow-up was 8% greater in UK patients and 11% greater in HK patients between predicted sub-optimal statin responders (SR4) and predicted optimal statin responders (SR3). Even in low-risk CVD groups, the absolute difference in MACE cumulative event rate at the end of 10-year follow-up was 5% greater in UK patients and 7% greater in HK patients between predicted sub-optimal statin responders (SR2) and predicted optimal statin responders (SR1). Ten-year models (Table 4) showed that predicted sub-optimal SR in patients with low CVD risk (comparing SR2 to SR1), resulted in hazard ratios for MACE of 1.39 (95% CI 1.35– 1.43, p < 0.001) for UK patients and 1.14 (95% CI 1.11–1.17, p < 0.001) for HK patients. Pre- dicted sub-optimal SR in patients with high CVD risk (comparing SR4 to SR3) resulted in haz- ard ratios for MACE of 1.36 (95% CI 1.32–1.40, p < 0.001) for UK patients and 1.25 (95% CI 1.21–1.28, p < 0.001) for HK patients. In UK patients, the risk of constituent MACE outcomes increased significantly in patients predicted to be sub-optimal responders for CHD, stroke/ TIA, and PVD in both high and low CVD risk groups. There was an increased risk of all-cause mortality in UK patients in high CVD risk groups but not in low CVD risk groups. There was no significant difference in CVD death in UK patients. In HK patients, risk of CHD was increased in both low and high CVD risk groups in predicted sub-optimal SR groups. Stroke/ TIA and PVD was, however, only increased for sub-optimal SR in high CVD risk groups. Sub- optimal SR groups had significantly lower risks of CVD death and all-cause mortality in patients with low CVD risk (HR<1.0), which can be explained by this group being younger and healthier. Two-year follow-up of LDL-C reduction Baseline and 2-year follow-up LDL-C levels after statin initiation for UK and HK patients are shown in Fig 3. Higher baseline LDL-C levels resulted in more prominent reductions in LDL-C over two years. In UK patients, low and high CVD risk groups, respectively, achieved 40.5% and 41.9% reduction in mean LDL-C in predicted optimal response groups whereas the mean reduction in LDL-C in predicted sub-optimal responders was only 26.8% and 28.6%. In HK patients, low and high CVD risk groups, respectively, achieved 35.0% and 36.7% reduction in mean LDL-C in predicted optimal response groups whereas the mean reduction in LDL-C in predicted sub-optimal responders was only 20.5% and 22.4%. Overall, variability of the LDL-C response in patients in both UK and HK cohorts remained quite high ranging from 60% reduction in LDL-C to increase of 50% in LDL-C after two years of treatment (S5 Fig). Fig 3. https://doi.org/10.1371/journal.pone.0260839.g003 https://doi.org/10.1371/journal.pone.0260839.g003 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 9 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 Discussion This international study in two countries has identified clinical characteristics of patients that predict variation in LDL-C in response to statin therapy commenced for primary prevention of CVD. We have found that irrespective of their baseline CVD risk, patients with poorer LDL-C response experience much greater rates and risk of adverse cardiovascular outcomes than those likely to achieve target reductions in LDL-C. Groups who have low predicted likeli- hood to achieve LDL-C treatment targets will experience overall 5–10 more CVD events per 1000 person-years with low baseline CVD risk. The effect is even greater in populations with high baseline CVD risk, with 19–20 more CVD events per 1000-years, compared to population groups with predicted optimal response. An individual’s response to statins should be considered alongside cardiovascular risk assessment to enhance cholesterol treatment strategies and to inform shared decision-making with patients as part of primary prevention of CVD. To our knowledge, this is the first study to demonstrate sub-optimal LDL-C response to statins can be reliably predicted. Our statin response model uses patient characteristics that are routinely available in electronic health rec- ords and was robust in both validation cohorts. Considering the effects of adherence, we showed the model predicts LDL-C response when patients are more compliant to their medi- cines, suggesting there is biological variation in treatment response. In less compliant individ- uals, expectedly, there is less certainty in predicting LDL-C response. PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 10 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD Statin response was associated with age, dyslipidaemias, potency of prescribed statin, base line LDL-C level and the use of other medications (other lipid therapies and corticosteroids). These factors have been previously found to be associated with variability in LDL-C response [21, 22]. Corticosteroids are usually prescribed to patients with conditions associated with higher levels of inflammation and thus interact with the effectiveness of statins. Patients in Fig 4. https://doi.org/10.1371/journal.pone.0260839.g004 al.pone.0260839 December 2, 2021 11 / Fig 4. https://doi.org/10.1371/journal.pone.0260839.g004 https://doi.org/10.1371/journal.pone.0260839.g004 https://doi.org/10.1371/journal.pone.0260839.g004 Statin response was associated with age, dyslipidaemias, potency of prescribed statin, base- line LDL-C level and the use of other medications (other lipid therapies and corticosteroids). These factors have been previously found to be associated with variability in LDL-C response [21, 22]. Corticosteroids are usually prescribed to patients with conditions associated with higher levels of inflammation and thus interact with the effectiveness of statins. PLOS ONE PLOS ONE PLOS ONE Table 4. Hazard ratios (95% confidence intervals) for 10-year major adverse cardiovascular events and all-cause mortality for predicted statin response and cardio- vascular risk groups. Group MACE All-Cause Mortality Specific CVD Outcomes CHD Stroke/TIA PVD CVD Death United Kingdom CPRD cohort 10-year outcomes Number of events, N (%) 40,928 (22.3) 13,199 (7.2) 27,257 (14.9) 7,017 (3.8) 4,835 (2.6) 1,819 (1.0) SR2: Predicted sub-optimal statin response & low CVD risk† 1.39 (1.35–1.43)  0.94 (0.88–1.01) 1.45 (1.40–1.50)  1.30 (1.21–1.41)  1.27 (1.16–1.38)  0.86 (0.72–1.03) SR4: Predicted sub-optimal statin response & high CVD risk‡ 1.36 (1.32–1.40)  1.10 (1.06–1.15)  1.47 (1.42–1.52)  1.24 (1.16–1.32)  1.18 (1.09–1.28)  1.10 (0.98–1.23) Hong Kong CDARS cohort 10-year outcomes Number of events, N (%) 37,777 (22.1) 28,321 (16.5) 17,371 (10.2) 14,321 (8.4) 1,554 (0.9) 4,531 (2.7) SR2: Predicted sub-optimal statin response & low CVD risk† 1.14 (1.11–1.17)  0.78 (0.75–0.82)  1.51 (1.45–1.57)  1.00 (0.95–1.04) 0.95 (0.83–1.09) 0.73 (0.66–0.81)  SR4: Predicted sub-optimal statin response & high CVD risk‡ 1.25 (1.21–1.28)  1.06 (1.03–1.09)  1.69 (1.60–1.78)  1.10 (1.04–1.16)  1.17 (1.00–1.37)  0.97 (0.90–1.05) p <0.05. †reference group: SR1-predicted optimal statin response & low CVD risk. ‡reference group: SR3-predicted optimal statin response & high CVD risk. CDARS: Clinical Data Analysis and Reporting System; CHD: coronary heart disease; CPRD: Clinical Practice Research Datalink; CVD: cardiovascular disease; MACE: major adverse cardiovascular event; PVD: peripheral vascular disease; TIA: transient ischemic attack. -year major adverse cardiovascular events and all-cause mortality for predicted statin response and cardio- †reference group: SR1-predicted optimal statin response & low CVD risk. ‡reference group: SR3-predicted optimal statin response & high CVD risk. CDARS: Clinical Data Analysis and Reporting System; CHD: coronary heart disease; CPRD: Clinical Practice Research Datalink; CVD: cardiovascular disease; MACE: major adverse cardiovascular event; PVD: peripheral vascular disease; TIA: transient ischemic attack. ‡reference group: SR3-predicted optimal statin response & high CVD risk. CDARS: Clinical Data Analysis and Reporting System; CHD: coronary heart disease; CPRD: Clinical Practice Research Datalink; CVD: cardiovascular disease; MACE: major adverse cardiovascular event; PVD: peripheral vascular disease; TIA: transient ischemic attack. ‡reference group: SR3-predicted optimal statin response & high CVD risk. CDARS: Clinical Data Analysis and Reporting System; CHD: coronary heart disease; CPRD: Clinical Practice Research Datalink; CVD: cardiovascular disease; MACE: major adverse cardiovascular event; PVD: peripheral vascular disease; TIA: transient ischemic attack. Discussion Patients in Statin response was associated with age, dyslipidaemias, potency of prescribed statin, base- line LDL-C level and the use of other medications (other lipid therapies and corticosteroids). These factors have been previously found to be associated with variability in LDL-C response [21, 22]. Corticosteroids are usually prescribed to patients with conditions associated with higher levels of inflammation and thus interact with the effectiveness of statins. Patients in PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 11 / 17 Propensity of LDL-C response to statins and CVD PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 PLOS ONE The strengths of this study include its large sample size, long-term follow-up, from general patient populations in two countries, derived from high quality electronic patient health PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 12 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD records. Data linkages to hospital records and death registries enhanced the quality of outcome ascertainment for the cohorts of patients derived from these databases. Although the model was developed using a UK cohort, the applicability of the model in the ethnically different HK cohort, enhances external validity and generalisability of more aggressive lipid management across both Western and Asian populations. By adopting an open cohort design and account- ing for statin type and intensity, the predicted statin response and event rates across time peri- ods reflect real-world changes in practice over time. Both populations have experienced prescribing trends towards stronger statin intensity over time [7, 28]. Some limitations of this study are recognized. Although the proxy for statin adherence explained a third of the variation in LDL-C response, prescribing records cannot confirm whether a patient actually takes their medication, which is a shared limitation of all observa- tional studies and trials. Moreover, patients who are on cardioprotective therapies are likely to be on other medications other than statins and are more likely to discontinue multiple thera- pies, which has also been shown to influence the mortality outcomes [29]. In common with other large population studies using routinely collected data, this limitation together with oth- ers including ascertainment and information bias, potential bias due to missing data and unmeasured confounding is acknowledged. Newer medications such as PCSK9 are not yet indicated for primary prevention, hence no data was available to assess its effect on cholesterol response. We used the ESC guidelines to stratify CVD risk due to its simplicity, accessibility to the published risk equations, and being recommended by ESC and HK guideline committees as acceptable for use in both the UK and HK. We acknowledge that different national guide- lines may recommend use of other CVD risk equations. Finally, we did not consider the effects of medication switching during follow-up. Future analysis could consider modelling the effects of time-varying exposure periods to account for any changes of dosing. Conclusions Predicted sub-optimal LDL-C lowering response to statins consistently resulted in higher rates of MACE. To enhance cholesterol management for primary prevention of CVD, clinicians should consider a patient’s likely response to statins as a component of CVD risk assessment. PLOS ONE both cohorts who were less likely to achieve targeted LDL-C reduction were also more likely to have lower baseline LDL-C levels and be initiated on low potency statins. However, there was greater use of more potent statins in the UK cohort compared to the HK cohort, while greater use of other non-statin lipid lowering drugs in the HK cohort compared to the UK cohort. Recent updates to cholesterol guidelines have broadened the population of individuals eligi- ble for statins for primary prevention [3, 10, 11, 17]. For example, the UK NICE guideline [3] now suggest statin therapy be considered for individuals who have a cardiovascular risk score > 10%, which has been reduced from a previous threshold of > 20%. In the current study, over half of patients who initiated statins had a sub-optimal LDL-C response in both HK and UK. This would equate to about 6.1 million of the estimated 12 million adults aged 30–84 in the UK who could be eligible for statins, for primary prevention [23]. Other factors, such as physical activity, diet and statin or treatment side-effects (which are less reliably recorded) should clearly also be considerations alongside statin alternatives to achieve shared clinical decision making with patients for appropriate cholesterol management. However, identifying patients likely to have sub-optimal LDL-C response to statins could enable clinicians to be more aggressive in cholesterol management by identifying those who need closer monitoring, or initiated on higher statin doses, given in combination with ezeti- mibe [24]. Recent evidence suggests that reduction in cardiovascular events is significant even to ultra-low levels of LDL-C less than 0.2 mmol/L (7.7 mg/dL) [25]. Our study shows that many patients are initiated on low dose statins in the predicted sub-optimal groups suggesting many clinicians may not be aware of the clinical benefits of a stronger treatment regime even in those with lower baseline levels of LDL-C with high risk of CVD. Medications that aim to reduce LDL-C such as PCSK9 inhibitors and Ezetimibe [26, 27] are presently indicated for both primary and secondary prevention of CVD. When taken in combina- tion with statin and diet therapies, additional reduction in LDL-C levels have been shown in trials. Supporting information S1 Fig. Validation plots for logistic model applied in (a) UK CPRD internal validation cohort, n = 54,985 and (b) HK CDARS external validation cohort, n = 170,904. E:O–log of the expected/observed number of events; CITL–calibration-in-the-large; AUC–area under the curve; slope–calibration slope. The circles represent deciles of patients grouped by similar pre- dicted risk. The distribution of patients (stratified by outcome) is indicated with spikes at the bottom of the graph. Patients with sub-optimal response are represented by spikes above the x-axis (red line), and patients with optimal response, below the x-axis). (DOCX) S2 Fig. Plot of sensitivity and specificity to determine optimum cut-off for the classifica- tion of sub-optimal LDL response risk to statins using the standard approach model in the UK CPRD validation cohort (n = 54,985). (DOCX) S2 Fig. Plot of sensitivity and specificity to determine optimum cut-off for the classifica- tion of sub-optimal LDL response risk to statins using the standard approach model in the UK CPRD validation cohort (n = 54,985). (DOCX) S3 Fig. Histograms of predicted 10-year CVD risk score by ESC guidelines and 2-year pro- pensity of sub-optimal LDL-C reduction for UK and HK cohorts. (DOCX) S3 Fig. Histograms of predicted 10-year CVD risk score by ESC guidelines and 2-year pro- pensity of sub-optimal LDL-C reduction for UK and HK cohorts. (DOCX) 13 / 17 PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 PLOS ONE Propensity of LDL-C response to statins and CVD S4 Fig. Joint stratification of 10-year CVD risk by ESC guidelines and 2-year propensity of sub-optimal LDL-C reduction in both UK and HK patient cohorts. ESC: European Society of Cardiology CVD SCORE >5% is defined as high CVD risk; Low-density lipoprotein choles- terol statin response propensity of > 50% is defined as sub-optimal response. (DOCX) S4 Fig. Joint stratification of 10-year CVD risk by ESC guidelines and 2-year propensity of sub-optimal LDL-C reduction in both UK and HK patient cohorts. ESC: European Society of Cardiology CVD SCORE >5% is defined as high CVD risk; Low-density lipoprotein choles- terol statin response propensity of > 50% is defined as sub-optimal response. (DOCX) S5 Fig. Waterfall plots of 2-year percentage LDL-C reduction from baseline based on initi- ated statin potency. Potency classification by expected LDL-C reduction (see S2 Table for specific statin types); 20%–30%: low potency; 31%–40%: medium potency; Above 40%: high potency. (DOCX) S1 Table. Potential predictors of sub-optimal statin response propensity model. The choice of medications of medications is informed by review of clinical guidelines and previous litera- ture on CVD risk (UK NICE Guidelines, QRISK3). (DOCX) S2 Table. Grouping of statins by potency. 1 20%–30%: low intensity; 2 31%–40%: medium intensity; 3 Above 40%: high intensity. Note: combination therapies with a statin and ezetimibe 10 mg would push potency up one group (i.e., low to medium, medium to high). (DOCX) S3 Table. Multivariable logistic regression for mutually adjusted diagnostic variables of sub-optimal LDL-C response to statins using UK CPRD derivation cohort (n = 128,298). p < 0.05; No–reference category for dichotomous variables. (DOCX) S4 Table. Logistic regression coefficients and constants derived from the UK Clinical Prac- tice Research Datalink (CPRD) for determining sub-optimal LDL-C response to statistics. Unit: per mmol/L. (DOCX) S4 Table. Logistic regression coefficients and constants derived from the UK Clinical Prac- tice Research Datalink (CPRD) for determining sub-optimal LDL-C response to statistics. Unit: per mmol/L. (DOCX) S5 Table. Characteristics of 183,213 patients from the UK CPRD dataset by statin response group based on ESC score. + Significance determined by Kruskal-Wallis non-parametric H test between two or more groups; ESC: European Society of Cardiology; CPRD: Clinical Prac- tice Research Datalink; HDL: high-density lipoprotein; LDL: low-density lipoprotein; CVD: cardiovascular disease; SR1 –Patients with predicted optimal statin response and low CVD risk; SR2 –Patients with predicted sub-optimal statin response and low CVD risk; SR3 – Patients with predicted optimal statin response and high CVD risk; SR4 –Patients with pre- dicted sub-optimal statin response and high CVD risk. (DOCX) S5 Table. Characteristics of 183,213 patients from the UK CPRD dataset by statin response group based on ESC score. + Significance determined by Kruskal-Wallis non-parametric H test between two or more groups; ESC: European Society of Cardiology; CPRD: Clinical Prac- tice Research Datalink; HDL: high-density lipoprotein; LDL: low-density lipoprotein; CVD: cardiovascular disease; SR1 –Patients with predicted optimal statin response and low CVD risk; SR2 –Patients with predicted sub-optimal statin response and low CVD risk; SR3 – Patients with predicted optimal statin response and high CVD risk; SR4 –Patients with pre- dicted sub-optimal statin response and high CVD risk. (DOCX) S6 Table. Characteristics of 170,904 patients from the HK CDARS dataset by statin response group based on ESC score. + Significance determined by Kruskal-Wallis non- parametric H test between two or more groups; ESC: European Society of Cardiology; CPRD: Clinical Practice Research Datalink; HDL: high-density lipoprotein; LDL: low-density lipopro- tein; CVD: cardiovascular disease; SR1 –Patients with predicted optimal statin response and low CVD risk; SR2 –Patients with predicted sub-optimal statin response and low CVD risk; SR3 –Patients with predicted optimal statin response and high CVD risk; SR4 –Patients with predicted sub-optimal statin response and high CVD risk. (DOCX) PLOS ONE | https://doi.org/10.1371/journal.pone.0260839 December 2, 2021 14 / 17 PLOS ONE Propensity of LDL-C response to statins and CVD S7 Table. 10-year incidence rates (per 1000 person-years) for major adverse cardiovascular events (MACE) and all-cause mortality for predicted statin response and ESC cardiovascu- lar risk groups. 95% Confidence Intervals are provided in () for all incidence rates. SR1 – Patients with predicted optimal statin response and low CVD risk; SR2 –Patients with pre- dicted sub-optimal statin response and low CVD risk; SR3 –Patients with predicted optimal statin response and high CVD risk; SR4 –Patients with predicted sub-optimal statin response and high CVD risk. Acknowledgments We are grateful to all the patients contributing data to both CPRD and CDARS. We are grateful to all the patients contributing data to both CPRD and CDARS. Author Contributions Conceptualization: Stephen Franklin Weng, Nadeem Qureshi, Joe Kai. Data curation: Stephen Franklin Weng, Ralph Kwame Akyea, Kenneth KC Man, Wallis C. Y. Lau, Joseph Edgar Blais. Formal analysis: Stephen Franklin Weng, Ralph Kwame Akyea, Kenneth KC Man, Wallis C. Y. Lau. Funding acquisition: Stephen Franklin Weng. Investigation: Stephen Franklin Weng, Kenneth KC Man, Wallis C. Y. Lau, Barbara Iyen. Methodology: Stephen Franklin Weng, Ralph Kwame Akyea, Kenneth KC Man, Wallis C. Y. Lau, Nadeem Qureshi, Ian C. K. Wong, Joe Kai. Project administration: Stephen Franklin Weng. Resources: Stephen Franklin Weng. Resources: Stephen Franklin Weng. Supervision: Stephen Franklin Weng, Ian C. K. Wong. Supervision: Stephen Franklin Weng, Ian C. K. Wong. Validation: Stephen Franklin Weng. Visualization: Stephen Franklin Weng, Ralph Kwame Akyea. Visualization: Stephen Franklin Weng, Ralph Kwame Akyea. Writing – original draft: Stephen Franklin Weng, Ralph Kwame Akyea. Writing – review & editing: Stephen Franklin Weng, Ralph Kwame Akyea, Kenneth KC Man, Wallis C. Y. Lau, Barbara Iyen, Joseph Edgar Blais, Esther W. Chan, Chung Wah Siu, Nadeem Qureshi, Ian C. K. Wong, Joe Kai. S1 Text. Supplemental methods. (DOCX) S1 Text. Supplemental methods. (DOCX) S4 Table. Logistic regression coefficients and constants derived from the UK Clinical Prac- tice Research Datalink (CPRD) for determining sub-optimal LDL-C response to statistics. Unit: per mmol/L. (DOCX) ESC: European Society of Cardiology; CPRD: Clinical Practice Research Datalink; CDARS: Clinical Data Analysis and Reporting System; CVD: cardiovascular disease; TIA: Transient Ischemic Attack; CHD: Coronary Heart Disease; PVD: Peripheral Vascular Disease; UK: United Kingdom; HK: Hong Kong. (DOCX) References 1. Timmis A, Townsend N, Gale CP, Torbica A, Lettino M, Petersen SE, et al. European society of cardiol- ogy: Cardiovascular Disease Statistics 2019. 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Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe. Budapest and New York: Central European University Press. 386 pp.
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Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finlan Christianity and Modernity in Eastern Europe is a collection of thirteen essays about the results of a collaborative project that lasted from 2005 to 2010 and involved over twenty historians from Europe and North America who sought to “address methodological approaches and interpretative problems in the larger fields of church history and religious studies” (XV). The volume proposes two major goals, one of which is to show the significance of Christianity in Eastern Europe to unfamiliar readers who are searching for the meaning of Christianity and/or religion in the twentieth and twenty-first centuries. The way these goals are formulated suggests that from the perspective of history studies, these essays focus on the interrelatedness of what is defined as Eastern Europe (geography), Christianity (religion) and modernity (historical period), and emphasize the relevance of this interrelatedness within a broad context of inquiries. The contributors also aim to show how in reality the relationship of time, place and religion was and is far more complex than what is suggested by currently pervasive stereotypes. p gg y y p yp In the abovementioned framework, the contributions of editors Bruce R. Berglund and Brian Porter-Szűcs act as an instrumental infrastructure that provides the reader with necessary insights into the project as well as some of the results presented in the essays of the other historian contributors. In his introductory chapter, Porter-Szűcs refers to Hans Georg Gadamer’s (1900-2002) term of hermeneutic circles to describe the contributors of the volume as mediators and translators who “are moving from explanation to a search for meaning and understanding […] to narrow the gap between alien worldviews and to appreciate as fully as possible the motives and the goals of historical agents (without […] surrendering one’s own critical perspectives)” (9-10). In order to achieve this goal, the contributors not only have to pay careful attention to individual subjectivity and agency, but also critically reconsider those theories and terminologies that previously failed to reflect the everyday experiences and actions of believers. These considerations entail a critical approach to existing historiographies and their foci of interest by keeping in mind that Christianity is more than publicly confessed doctrines, officially accepted theologies and institutional embodiments. New articles in this journal are licensed under a Creative Commons Attribution 4.0 International 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 ISSN 1936-8879 (online) Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe. Budapest and New York: Central European University Press. 386 pp. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland However, the purpose of such a broad definition is to empathize how Christianity and any of its conceptual counterparts can be meaningfully addressed, discussed and reflected upon from the perspective of human agents and their approach to and understanding of the world through their respective beliefs. After reading the essays, one may conclude that these abstractions of Christianity are simply tools for addressing questions about identity. For instance, Natalia Shlikhta’s essay on the Ukrainian Greek Catholic Church or Galia Valtchinova’s inquiries into what it means to be Orthodox Christian in Bulgarian society are but two poles that address the fluidity of human identities as studied through the abstraction of Christianity, while both Paul Hanebrink’s research on interwar Christian Hungary and James Felak’s case study of individuals in Slovakia aim to show that identities should be conceived as reflexive processes instead of as static worldviews (see also Michal Pagis, “Religious Self-Constitution: A Relational Perspective,” in Courtney Bender et al. eds., Religion on the Edge; Oxford: Oxford University Press, 96-97). , g g ; y , ) The concept of modernity in this volume emerges within the fluid dynamic of human agency described above and is conceived as a rubric denoting “tumultuous transformations” within, mainly, the twentieth century such as “capitalist industrialization and the Great Depression, the rise of the radical right and racial politics, World War II, Stalinism, the actually existing socialism from the 1960s to the 1980s, and the apparent triumph of neoliberalism since the 1990s” (17). Within this broad framework that emphasizes the fluidity and diversity of human agents and the worldviews they produce, the volume suggests that those who study modernity and its relationship with Christianity should be able to interpret the acts of the will made under various socio-political settings of the various nation-states. The following essays of the volume translate these concerns into a fascinating array of topics based on will and person, two crucial concepts “when questions of action and agency” are concerned according to Thomas Pfau’s Minding the Modern: Human Agency, Intellectual Traditions, and Responsible Knowledge (Notre Dame: University of Notre Dame Press, 2013, 14). For instance, human rights (Katharina Kunter), education (Hanebrink), peace (David Doellinger), belief and socio-political order (Patrick Hyder Patterson), religious diversity (James Bjork and Andreas Kossert), as well as the person and his/her situatedness (Anca Şincan) within culture (Martin C. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland One of the ways in which the contributing historians of the volume bring human agency into a focal point is by making a clear distinction between Christianity defined as “a set of broad frameworks for perceiving and understanding the world” and Christians viewed as “the people who lived within those frameworks” (3), with both definitions kept intentionally vague in order to capture the fluidity of human agents and their relationship to the world. Both categories are defined so loosely that they could essentially be replaced by any other identifier such as Judaism, Islam, “worldview,” “culture” or even “modernity.” The book does acknowledge the nondescript nature of these definitions and soon clarifies that Christianity is discussed in this volume as a New articles in this journal are licensed under a Creative Commons Attribution 4.0 International 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 ISSN 1936-8879 (online) ISSN 1936-8879 (online) Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 broader category encompassing many subcategories such as Catholics, Protestants and Orthodox Christians, and where Protestants are broken down further into Lutherans and Calvinists, the Catholics into Ukrainian Greek Catholics, and the Orthodox believers are categorized according to their respective nation states. These additional categories are just as vague as the original categories of Christianity or Christians, which may be the reason why in his attempt to provide a working definition for Christianity, Porter-Szűcs came to the conclusion that “Christianity is delineated yet fluid, constraining yet enabling and always under construction” (13). Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland Putna) are but a few topics through which the diverse history of “modernity” is presented to the reader. The way the conceptual framework of the project translates into essays also reveals the methodological struggle of combining the abstractions of Christianity and “modernity,” especially when we consider that the noun “modernity” and its derivative adjective “modern” can be used to denote a worldview, an understanding of the world as well as one’s identity and place in the social order. The fact that most of the essays do not or hardly use the terms “modernity” or “modern” further underlines the necessity of addressing the theoretical questions entailed in examining the relationship of Christians, Christianity and modernity. In this regard, the discussion initiated by some of the contributors to the volume could certainly benefit from dwelling more substantially into on theological understandings of modernity and touching on The way the conceptual framework of the project translates into essays also reveals the methodological struggle of combining the abstractions of Christianity and “modernity,” 406 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 other aspects of everyday life such as family, sexuality, gender, leadership and entrepreneurship. “Modernity,” then, is largely presented in the volume as an un-problematized and invariably masculine construct, with a few exceptions such as Valtchinova’s article on the “remaking” of religion in Socialist Bulgaria, in which the author offers a deconstruction of the traditionally accepted religious field in Bulgaria through the case of Vanga (Evangelia) Pandeva Gushterova (1911-1996). Vanga was a blind and poor Orthodox woman who attracted a massive following on account of her visions, premonitions and spiritual experiences and soon caught the attention of political leaders as well, who viewed her as challenging politics to address the issue of religion in Bulgaria. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland Valtchinova illustrates how in their eagerness to settle the issue of faith and modernity in Bulgaria, different political ideologies as well as the Orthodox Church continuously assessed Vanga in ways that strengthened their own arguments. The third key term of the volume is Eastern Europe, which at first glance seems to suggest area studies but which comes to be used across the essays in ways that do not clarify to the reader whether the volume’s choice of terminology hides an epistemological assumption of the legitimacy of an east-west paradigm or not. The transparency of the term is greatly reduced by the way several contributors seemingly use the terms “Central and Eastern Europe” and “East Central Europe” to refer to the same area, and how the concept of “Eastern Europe” is also broken down into certain nation states for the purposes of individual contributors, but the fact that the case of the German Democratic Republic strongly features in the selection (Kunter and Doellinger) seems to confirm the presence of an east-west axis. Nevertheless, whenever the construct of “Eastern Europe” becomes a focal point in research, this happens through the identification and geographical demarcation of regions where “the social, economic, and political processes that have characterized the continent’s modernity were experienced belatedly, if at all” and where “communist regimes held power from the 1940s to the 1989s” (16). Berglund builds on Walter Brueggemann’s theological conceptualization of place to argue that “Eastern Europe” is also a “conceptual place, with no visible boundaries or objective features, yet it remains fixed in most people’s geographic imaginations” and in this sense, “it can influence religious belief and practice” (330). Berglund’s argument also implies that the juxtaposition of the elements mentioned in the title of the volume could be perceived as a triangulation of the concepts of Christianity, modernity and Eastern Europe. y y p Hanebrink partly explores the dynamics of the above mentioned triangulation in an article titled “Christianity, Nation, State: The Case of Christian Hungary,” in which he contemplates the complexities of Christianity and the Hungarian socio-political order by examining the interwar period rhetoric of Hungary being or once again becoming a purely Christian nation. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland Hanebrink eases his readers into the subject through a detailed description of the interwar period in Hungary, during which both politicians and church leaders engaged in politics called for a moral revival and the revitalization of Christianity and Christian values in Hungarian society as the only path towards a brighter future for the Hungarian nation. Hanebrink then proceeds to deconstruct the apparently unified program for realizing a Christian Hungary by highlighting the conflicts, negotiations and compromises among Christians from every tier of society and regardless of their economic, political or religious affiliation as they faced the pressing question of what was the right relationship between religion and state in the age of modernity. As a result, the reader is presented with a wide spectrum of options between nationalism and missionization, where the consensus between Hungarian Christians invariably seems to have emerged with regard to the subject of the “Jewish question.” Hanebrink argues that the line of Anti-Semitic rhetoric calling for a united Christian nation stems from the 1880’s, a time when the concept of a 407 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Nagy, Dorottya. “Berglund, Bruce R. and Brian Porter-Szűcs, eds. 2013. Christianity and Modernity in Eastern Europe.” Hungarian Cultural Studies. e-Journal of the American Hungarian Educators Association, Volume 7 (2014): http://ahea.pitt.edu DOI: 10.5195/ahea.2014.155 Christian Hungary was envisioned “against the predations of “Jewish power” (64) and can be traced up to “the moment of crisis” in 1944 (81). This article also supports Berglund’s argument about Eastern Europe as a place (versus “space”) with historical meanings where certain things are remembered in certain ways and through remembrance, and where different identities remain and manage to relate in spite of all their contradictions. g p One of the volume’s strong points, as demonstrated above, is that it offers fresh takes on old questions, but looking at the relationship of the editors’ programmatic framework and its implementation by the contributions might cause a sense of dissatisfaction in readers as the frame seems to be larger than the actual picture portrayed. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland While I do not dispute the legitimacy of focusing on Catholics, Protestants and Orthodox Christians and investigating their participation in the history of the twentieth and twenty-first centuries in Eastern Europe, it would have been useful to include other Christians in a discussion of modernity as it was exactly within this historical period that the issue of diversity in the Eastern European region was further complicated by the emergence of Christian Others (see Catherine Wanner, Communities of the Converted: Ukrainians and Global Evangelism; New York: Cornell University Press, 2007). In this regard, concepts such as Berglund’s “spiritual geography” become even more problematic since Berglund’s own construct of religiosity is largely based on Catholic or Orthodox terminology (e.g. sacred sites, holy lands, sacramental places), and as such may prove inapplicable to other tenets of Christianity that would be worth investigating. The reader is also left wondering why the historians contributing to the volume neglected the primary sources of other religions such as Judaism or Islam in addressing the question of how non-Christians assessed the role of Christians and Christianity in shaping the history of Eastern Europe. Some of these questions could have been addressed either through a more detailed description of the process of essay selection for the volume, or by a narrower framework that stretches no further than the actual picture emerging within it. g p One of the volume’s strong points, as demonstrated above, is that it offers fresh takes on old questions, but looking at the relationship of the editors’ programmatic framework and its implementation by the contributions might cause a sense of dissatisfaction in readers as the frame seems to be larger than the actual picture portrayed. While I do not dispute the legitimacy of focusing on Catholics, Protestants and Orthodox Christians and investigating their Although the reflective reader might be able to see the triangulation of Christianity, modernity and Eastern Europe throughout the essays, the purpose of the volume might have been better served by establishing a connection between the presented case studies and the rest of the world at large. Offering levels of comparison and extending the east-west dichotomy (Kossert) would have certainly been beneficial to readers who are not familiar with the Eastern European region but have an extended knowledge about other parts of the world. Reviewed by Dorottya Nagy, University of South Africa, Helsinki, Finland Placing the issue of Christianity and modernity in Eastern Europe within an extended global framework would have also allowed readers to engage more easily in dialogue with the volume, especially when it invites us to perceive Eastern Europe as “a relational story, a drama of differences perceived and real, of associations and rejections” (353). Nevertheless, even if these shortcomings might leave some readers frustrated, one should keep in mind Berglund’s words of hope that the “volume will open up new lines of research” into what he calls “East European Christianity” (332). As a volume of selected essays addressing the interrelatedness of geography, religion and a historical period, Christianity and Modernity in Eastern Europe will appeal to a large spectrum of readers. It calls for historians to explore new ways of writing/composing historiographies on Christianity and modernity, challenges theologians to enter into a dialogue with non-theological research on Christianity and modernity, and invites students of Hungarian Cultural Studies to investigate the ways in which the contributing historians tackle these basic concepts. All these directions and possibilities would make the volume an exciting addition to academic courses centered on the juxtaposition of Christianity and modernity. 408
https://openalex.org/W2156627402
https://www.hal.inserm.fr/inserm-00663642/file/cc10270.pdf
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High-sensitivity versus conventional troponin in the emergency department for the diagnosis of acute myocardial infarction
Critical care
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cc-by
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To cite this version: Yonathan Freund, Camille Chenevier-Gobeaux, Pascale Bonnet, Yann-Erick Claessens, Jean- Christophe Allo, et al.. High-sensitivity versus conventional troponin in the emergency department for the diagnosis of acute myocardial infarction.. Critical Care, 2011, 15 (3), pp.R147. ￿10.1186/cc10270￿. ￿inserm-00663642￿ High-sensitivity versus conventional troponin in the emergency department for the diagnosis of acute myocardial infarction. Yonathan Freund, Camille Chenevier-Gobeaux, Pascale Bonnet, Yann-Erick Claessens, Jean-Christophe Allo, Benoit Doumenc, François Leumani, Claudine Cosson, Bruno Riou, Patrick Ray HAL Id: inserm-00663642 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. Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 RESEARCH RESEARCH Open Access * Correspondence: yonatman@gmail.com 1Department of Emergency Medicine and Surgery, Hôpital Pitié-Salpétrière, Assistance Publique-Hôpitaux de Paris (APHP), Université Pierre et Marie Curie-Paris 6 (UPMC), 47-83 boulevard de l’hôpital, F-75651 Paris cedex 13, France Full list of author information is available at the end of the article © 2011 Freund 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 Introduction: Recently, newer assays for cardiac troponin (cTn) have been developed which are able to detect changes in concentration of the biomarker at or below the 99th percentile for a normal population. The objective of this study was to compare the diagnostic performance of a new high-sensitivity troponin T (HsTnT) assay to that of conventional cTnI for the diagnosis of acute myocardial infarction (AMI) according to pretest probability (PTP). Methods: In consecutive patients who presented to our emergency departments with chest pain suggestive of AMI, levels of HsTnT were measured at presentation, blinded to the emergency physicians, who were asked to estimate the empirical PTP of AMI. The discharge diagnosis was adjudicated by two independent experts on the basis of all available data. Results: A total of 317 patients were included, comprising 149 (47%) who were considered to have low PTP, 109 (34%) who were considered to have moderate PTP and 59 (19%) who were considered to have high PTP. AMI was confirmed in 45 patients (14%), 22 (9%) of whom were considered to have low to moderate PTP and 23 (39%) of whom were considered to have high PTP (P < 0.001). In the low to moderate PTP group, HsTnT levels ≥0.014 μg/ L identified AMI with a higher sensitivity than cTnI (91%, 95% confidence interval (95% CI) 79 to 100, vs. 77% (95% CI 60 to 95); P = 0.001), but the negative predictive value was not different (99% (95% CI 98 to 100) vs. 98% (95% CI 96 to 100)). There was no difference in area under the receiver operating characteristic (ROC) curve between HsTnT and cTnI (0.93 (95% CI 0.90 to 0.98) vs. 0.94 (95% CI 0.88 to 0.97), respectively). Conclusions: In patients with low to moderate PTP of AMI, HsTnT is slightly more useful than cTnI. Our results confirm that the use of HsTnT has a higher sensitivity than conventional cTnI. High-sensitivity versus conventional troponin in the emergency department for the diagnosis of acute myocardial infarction Yonathan Freund1*, Camille Chenevier-Gobeaux2, Pascale Bonnet1, Yann-Erick Claessens3, Jean-Christophe Allo3, Benoit Doumenc4, François Leumani1, Claudine Cosson5, Bruno Riou1,6 and Patrick Ray1,6 Introduction with suspected acute coronary syndrome (ACS), including risk stratification of ACS, and the use of cTn measure- ments is recommended by current guidelines [6]. A cutoff point at the 99th percentile has been endorsed, as values above this level have repeatedly proven to be associated with adverse cardiovascular outcomes, including death [7-13]. However, the delay (4 to 6 hours, and 12 hours for peak level) in its elevation remains of concern, since it can delay AMI diagnosis and its treatment and increases the burden on EDs. Thus, cTn measurement does not reliably exclude AMI without repeated negative measurements over the course of 4 to 6 hours. These last years, newer assays have been developed, and High Sensitivity Troponin (HsTn) has been associated with higher sensitivity and Early detection of acute myocardial infarction (AMI) remains a major concern, with approximately 15 million patients per year presenting to US emergency departments (EDs) with symptoms suggestive of the diagnosis [1,2]. Among such patients, a strong association between ele- vated cardiac troponin (cTn) levels and myocardial necro- sis has been clearly demonstrated [3-5]. Conventional cTn has revolutionised the management of patients presenting Page 2 of 9 Page 2 of 9 Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 NPV than conventional cTn. Recent studies have shown excellent diagnostic performance, even with early presen- tation to the ED [14], and a better diagnostic accuracy than cTn [15]. However, the latter studies did not evaluate the diagnostic accuracy of high-sensitivity troponin T (HsTnT) according to the pretest probability (PTP) of AMI. For example, ST elevation on an electrocardiogram of a patient with chest pain would be diagnosed as AMI, and then the patient would undergo cardiac catheteriza- tion without any measurement of a cardiac biomarker. Furthermore, one of the potential strengths of HsTnT might be the exclusion of AMI earlier than it would be with conventional cTn measurement as suggested by pre- vious studies [15]. Therefore, the objectives of the current study were to confirm whether HsTnT is more sensitive than conventional cTnI to detect AMI according to the patient’s PTP. evaluation and treatment or directly to the catheteriza- tion laboratory for primary percutaneous coronary inter- vention. However, the timing and treatment of patients were left to the discretion of the attending physicians according to the suspected diagnosis. Introduction ED physicians in charge were blinded to the results of HsTnT, and biolo- gists were blinded to the emergency diagnosis suspected by physicians. To determine the etiologic diagnosis of chest pain at presentation for each patient, two independent experts (ED physicians) who were blinded to the results of HsTnT reviewed all available medical records (including patient history, physical findings, results of laboratory and radiolo- gic testing, ECG, echocardiography, cardiac exercise test, coronary angiography and summary chart at discharge) pertaining to the patient from the time of ED presentation to 30-day follow-up. In the event of diagnostic disagree- ment, cases were reviewed and adjudicated in conjunction with a third expert (also an ED physician). Routine assessment As part of the routine assessment in our institutions, all patients underwent an initial clinical evaluation that included clinical history, a physical examination, 12-lead electrocardiography (ECG), pulse oximetry, routine blood tests and chest X-rays. After these routine tests were done, and before cardiac biomarker results were available, ED physicians were asked to offer an ‘empiri- cal’ clinical probability of AMI (low, medium or high PTP) based on cardiovascular risk factors, type of chest pain, physical findings and electrocardiogram abnormal- ities [17,18]. Conventional cardiac troponin I (cTnI) was measured at presentation and, if needed, was repeated after 3 to 9 hours as long as it was clinically indicated. Thus, according to the diagnosis of non-ST elevation MI (NSTEMI) or ST elevation MI (STEMI), the patients were admitted either to the cardiology unit for further To assess the influence of renal function on cTn mea- surement accuracy, the creatinine level was measured in each patient and then renal function was estimated using the Modification of Diet in Renal Disease study equation [19]. Materials and methods Clinical setting AMI was diagnosed according to the joint European Society of Cardiology/American College of Cardiology/ American Heart Association/World Heart Federation Task Force redefinition of MI guidelines [6]. Diagnosis of AMI required a cTnI increase above the 10% coefficient of variation (CV) value associated with at least one of the fol- lowing: symptoms of ischaemia, new ST-T changes or a new Q wave on an electrocardiogram, imaging of new loss of viable myocardium or normal cTnI on admission. Unstable angina was diagnosed in patients with constant normal cTnI levels and a history or clinical symptoms consistent with ACS. Predefined further diagnostic cate- gories included AMI (STEMI with the presence of ST- segment elevation in at least two continuous leads on ECG, new onset of left bundle branch block or NSTEMI), unstable angina, and a third group including cardiac but not coronary symptoms (for example, stable angina, myo- carditis, arrhythmias and heart failure), noncardiac symp- toms (for example, pulmonary embolism) and chest pain of unknown origin. During the period from August 2005 to January 2007 in three urban teaching hospitals, we prospectively enrolled consecutive hospital outpatients (> 18 years of age) who presented to the ED with chest pain suggestive of ACS with the onset or peak occurring within the previous 6 hours. Patients with acute or chronic kidney failure requir- ing dialysis were excluded. The study was performed according to the principles of the Declaration of Helsinki and approved by the local ethics committee (Comité de Protection des Personnes Ile-de-France VI, CHU Pitié- Salpétrière Hospital, Paris, France). Because routine medi- cal care was unchanged, waiver of informed consent was authorised. We followed most of the recommendations concerning the reporting of diagnostic studies set forth by the Standards for Reporting of Diagnostic Accuracy initia- tive [16]. Statistical analysis Continuous variables are presented as means ± SD or medians (25th to 75th percentile), and categorical variables are expressed as numbers and percentages. Continuous variables were compared by using the Mann-Whitney U test, and categorical variables were assessed using Pear- son’s c2 test. Correlations among continuous variables were assessed using the Spearman’s rank correlation coef- ficient. Receiver operating characteristic (ROC) curves were constructed to assess the sensitivity and specificity, positive predictive value (PPV) and negative predictive value (NPV), positive likelihood ratio (LR+) and negative likelihood ratio (LR-) (all data presented with their 95% confidence intervals (95% CIs)) throughout the concentra- tions of cTnI and HScTnT to compare the accuracy of these markers in the diagnosis of AMI. Comparison of areas under the ROC curve was performed [20]. As this comparison is recognised as potentially insensitive, the net reclassification index (NRI) method was used as recently described [21]. For tests with binary outcomes (such as cTn for the diagnosis of AMI), NRI is defined as the gain in certainty of the first test (cTnI) minus the gain in cer- tainty of the second test (HScTnT) or, alternatively stated, the difference of the sum of the sensitivity and specificity expressed as follows: Table 1 Contingency data according to pretest probabilitya All patients Patient characteristics AMI No AMI Total Positive cTnI 32 9 41 Negative cTnI 13 263 276 Total 45 272 317 Positive HsTnT 42 48 90 Negative HsTnT 3 224 227 Total 45 272 317 Low to moderate PTP AMI No AMI Total Positive cTnI 17 7 24 Negative cTnI 5 229 234 Total 22 236 258 Positive HsTnT 20 36 56 Negative HsTnT 2 200 202 Total 22 236 258 aNet reclassification improvement (NRI) from the use of highly sensitive troponin T (HsTnT) was 7.9% (95% CI = 0.9 to 14.9; P = 0.034). Comparison of the model including HsTnT with cTnI was significant for low PTP patients (NRI = 10.3%, 95% CI = 1.9 to 18.7; P = 0.027), but NRI was not significantly different in moderate PTP patients (NRI = 11.6%, 95% CI = -0.5 to 23.7; P = 0.084) or in high PTP patients (NRI = -14.4%, 95% CI = -32.6 to -3.6; P = 0.181). Table 1 Contingency data according to pretest probabilitya NRIHScTnT vs. cTnI = (sensitivity + specificity)HScTnT −(sensitivity + specificity)cTnI. Results After 18 months, 317 consecutive patients were enrolled in the study. The baseline characteristics of the patients are shown in Table 2. The mean age of the patients was 57 ± 17 years (range, 40 to 90 years), and 205 (65%) were men. There were significant proportions of older adult patients (31% patients were age 65 years or older, n = 98) and patients with a history of cardiovascular events (26%, n = 83). Chest pain was considered typical of ACS in 43% (n = 136) of the patients. In our study HScTnT measurement d l Heparinised samples collected upon admission and, if available, samples collected 3 to 9 hours later were ana- lysed. Plasmatic highly sensitive cardiac TnT (HScTnT) concentrations were measured using the HScTnT one- step electrochemiluminescence immunoassay on an Elecsys 2010 analyzer (Roche Diagnostics, Meylan, France). The measuring range extended from 0.003 to 10 μg/L. The threshold for this method is 0.014 μg/L and corresponds to the 99th percentile. The CV was found to be < 10% at 0.014 μg/L. In our laboratory, CVs obtained in Roche Diagnostics quality controls containing 0.027 and 2.360 μg/L of HScTnT were < 4%. These analytical performance levels were in accordance with data pro- vided by the manufacturer. All hypothesis testing was two-tailed, and P < 0.05 was considered statistically significant. Statistical analysis was performed using StatView for Windows version 5.0 soft- ware (SAS Institute, Cary, NC, USA) and MedCalc soft- ware for ROC analysis (MedCalc Software, Mariarkerke, Belgium). Graphs were built with GraphPad Prism 5 software (GraphPad Software Inc., La Jolla, CA, USA). Biochemical analysis In two EDs (Cochin Hospital and La Pitié Salpêtrière Hos- pital, Paris, France), plasmatic cTnI concentrations were routinely measured on an Xpand HM analyzer using the Cardiac Troponin I one-step enzyme immunoassay system (Siemens Healthcare Diagnostics Inc., Newark, NJ, USA). The measurement range extended from 0.04 to 40.00 μg/L. The threshold for this method (0.14 μg/L) corresponds to the lowest substrate concentration that can be reproducibly Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 Page 3 of 9 Page 3 of 9 measured with a CV ≤10%. In the remaining ED (Bicêtre Hospital, Le Kremlin-Bicêtre, France), plasmatic cTnI con- centrations were routinely measured on an Access analyser (Beckman Coulter, Inc., Brea, CA, USA). The measurement range of this one-step chemiluminescence immunoassay extends from 0.01 to 100.00 μg/L. The threshold (10% CV) given by the manufacturer is 0.06 μg/L. down in a category and the proportion of individuals with nonevents who move up or down in a category. Table 1 is a contingency table comparing diagnostic classifications according to cTnI and HsTnT, with shifts between the two classifications, to represent the possible benefit of HScTnT in terms of the number of patients correctly reclassified. As stated in the Routine assess- ment subsection above, we separated the study popula- tion into two groups: one included the patients assessed as having low or moderate PTP of AMI and the other assessed as having high PTP of AMI. NRIHScTnT vs. cTnI = (sensitivity + specificity)HScTnT −(sensitivity + specificity)cTnI. Statistical analysis NRI is the combination of four components: the pro- portion of individuals with events who move up or Freund et al. Statistical analysis Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 Page 4 of 9 Page 4 of 9 Table 2 Baseline characteristics of the population according to the pretest probabilitya Population characteristics All patients Low or moderate PTP High PTP P value* Number of patients 317 258 59 Age, years 57 ± 17 56 ± 17 60 ± 17 0.168 Men 205 (65) 166 (64) 39 (66) 0.88 Systolic BP, mmHg 141 ± 28 141 ± 27 144 ± 30 0.396 Diastolic BP, mmHg 80 ± 16 80 ± 16 82 ± 16 0.428 Heart rate, beats/minute 85 ± 45 84 ± 23 80 ± 19 0.177 Pulse oxymetry, % 97 ± 3 97 ± 3 97 ± 2 0.651 TIMI risk score 1 (0 to 3) 1 (0 to 2) 2 (1 to 4) < 0.001 Family history of CAD 100 (32) 77 (30) 23 (59) 0.161 Personal history of CAD 83 (26) 56 (22) 27 (46) 0.0003 Dyslipidemia 113 (36) 86 (33) 27 (46) 0.069 Smoking 128 (40) 99 (38) 29 (49) 0.145 Diabetes 44 (14) 31 (12) 13 (22) 0.059 Hypertension 116 (37) 89 (34) 27 (46) 0.134 History of heart failure 21 (7) 14 (5) 7 (12) 0.083 Typical thoracic pain 136 (43) 105 (41) 31 (53) 0.11 Positive cTnI at admission 41 (13) 24 (9) 17 (29) < 0.001** eGFR, mL/minute/1.73 m2 77 (62 to 94) 77 (64 to 94) 76 (56 to 91) 0.187 Treatment within first 24 hours after admission Aspirin 119 (38) 79 (31) 40 (68) <0.001 Clopidogrel 54 (17) 29 (11) 25 (42) < 0.001 LMWH 68 (21) 41 (16) 27 (46) < 0.001 Anti GPIIb/IIIa 3 (1) 1 (0) 2 (3) 0.09 Coronarography 83 (26) 51 (20) 32 (54) < 0.001 Outcomes Hospital admission 192 (61) 140 (54) 52 (88) < 0.001 Admission to CCU 134 (42) 88 (34) 46 (78) < 0.001 Final diagnosis AMI 45 (14) 22 (9) 23 (39) < 0.001 STEMI 13 (4) 0 (0) 13 (22) < 0.001 NSTEMI 32 (10) 22 (9) 10 (17) < 0.001 Unstable angina 11 (3) 4 (2) 7 (12) < 0.001 Other diagnosis 261 (82) 232 (90) 29 (49) < 0.001*** aAMI, acute myocardial infarction; BP, blood pressure; CAD, coronary artery disease; cTnI, conventional troponin I; eGFR, estimated glomerular filtration rate; LMWH, low-molecular-weight heparin; anti-GPIIb/IIIa, Anti-glycoprotein IIb-IIIa; CCU, cardiologic care unit; NSTEMI, non-ST elevation myocardial infarction; PTP, pretest probability; STEMI, ST elevated myocardial infarction. Statistical analysis TIMI, Thrombolysis in Myocardial Infarction. Results are expressed as means ± standard deviations, medians (25th to 75th percentile) or n (%); *statistical comparisons are between low to moderate PTP and high PTP groups unless otherwise indicated; **P > 0. μg/L in Pitie-Salpetriere and Cochin, P > 0.06 μg/L in Bicêtre; ***Statistical comparison including stable angina (n = 63), pulmonary embolism (n = 16), myopericarditis (n = 43), heart failure (n = 5) and others. Table 2 Baseline characteristics of the population according to the pretest probabilitya aAMI, acute myocardial infarction; BP, blood pressure; CAD, coronary artery disease; cTnI, conventional troponin I; eGFR, estimated glomerular filtration rate; LMWH, low-molecular-weight heparin; anti-GPIIb/IIIa, Anti-glycoprotein IIb-IIIa; CCU, cardiologic care unit; NSTEMI, non-ST elevation myocardial infarction; PTP, pretest probability; STEMI, ST elevated myocardial infarction. TIMI, Thrombolysis in Myocardial Infarction. Results are expressed as means ± standard deviations, medians (25th to 75th percentile) or n (%); *statistical comparisons are between low to moderate PTP and high PTP groups unless otherwise indicated; **P > 0.14 μg/L in Pitie-Salpetriere and Cochin, P > 0.06 μg/L in Bicêtre; ***Statistical comparison including stable angina (n = 63), pulmonary embolism (n = 16), myopericarditis (n = 43), heart failure (n = 5) and others. higher final diagnosis of AMI (39% vs. 9%) in the high PTP group (P < 0.001). At 30 days after admission, there were three deaths (two in the AMI group and one in the other cause group) and four relapses of ACS (all in the AMI group). population, 149 patients (47%) were assessed as having a low PTP of AMI, 109 patients (34%) were assessed as moderate and 59 patients (19%) were assessed as high. AMI was confirmed in 45 patients (14%), 13 of whom had sustained STEMI, and all of these 13 patients were in the high PTP group; 32 of the patients had sustained NSTEMI. Table 2 shows that patients in the two groups (high PTP and low or moderate PTP) had significantly different characteristics. There was a higher rate of a personal history of AMI in the high PTP group and a HsTnT diagnostic performances The area under the ROC curve (AUC) for the diagnosis of AMI was 0.940 (95% Confidence Intervall 0.901 to 0.980) (P < 0.001) for initial cTnI compared to 0.926 Page 5 of 9 Page 5 of 9 Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 Table 3 Diagnostic accuracy of HScTnT compared to that of cTnI for the diagnosis of AMI according to pretest probabilitya Patient characteristics Sensitivity Specificity PPV NPV Acc LR+ LR- Table 3 Diagnostic accuracy of HScTnT compared to that of cTnI for the diagnosis of AMI according to pretest probabilitya Patient characteristics Sensitivity Specificity PPV NPV Acc LR+ LR- All patients (N = 317) Positive cTnI 71 (55-84) 97 (94 to 98) 78 (62 to 89) 95 (92 to 97) 93 (90 to 96) 21.5 (20.1 to 22.9) 0.32 (0.23 to 0.36) Positive HScTnT 93 (89 to 100)* 82 (77 to 87)* 47 (36 to 58)* 99 (96 to 100) 84 (79 to 88)* 5.3 (4.8 to 5.8) 0.08 (0.04 to 0.12) Low to moderate PTP group (n = 258) Positive cTnI 77 (54 to 92) 97 (94 to 99) 71 (49 to 87) 98 (95 to 99) 95 (92 to 97) 26.1 (24.0 to 28.1) 0.23 (0.17 to 0.30) Positive HScTnT 91 (69 to 98) 85 (79 to 89)* 36 (24 to 49)** 99 (96 to 100) 85 (80 to 89)* 6.0 (5.3 to 6.6) 0.11 (0.06 to 0.15) High PTP group (n = 59) Positive cTnI 65 (43 to 83) 94 (79 to 99) 88 (62 to 98) 81 (65 to 91)* 83 (71 to 91)** 11.7 (10.1 to 13.4) 0.37 (0.18 to 0.55) Positive HScTnT 96 (76 to 100)*** 67 (49 to 81)*** 65 (47 to 81) 96 (78 to 100) 78 (65 to 87) 2.9 (2.3 to 3.4) 0.07 (0 to 0.17) aHScTnT, highly sensitive cardiac troponin T; PPV: positive predictive value; NPV: negative predictive value; Acc: diagnostic accuracy; LR: likelihood ratio. Values are expressed as percentages (except for LR) and their 95% confidence intervall. Positive cTnI > 0.14 μg/L in Pitie-Salpetriere and Ccochin, > 0.06 μg/L in Bicetre; positive HScTnT >0.014 μg/mL. *P < 0.05 versus positive cTnI in all patients; **P < 0.05 versus cTnI in low to moderate PTP group; ***P < 0.05 versus cTnI in high PTP group. (0.881 to 0.971) (P < 0.001) for HsTnT. However, there was no significant difference between AUCs (Figure 1). Net reclassification improvement Table 3 shows patient classification on the basis of using cTnI or HsTnT to diagnose AMI and highlights the shifts between the two classifications. HsTnT diagnostic performances ROC analysis indicated an optimal threshold of HsTnT for the diagnosis of AMI at 0.014 μg/L, with a high sen- sitivity of 89% (78 to 98) and a high specificity of 82% (78 to 87). The overall diagnostic accuracy of HsTnT was not significantly different compared to that of cTnI, regardless of PTP. Similar results (data not shown) were observed when we considered only NSTEMI patients (that is, after exclusion of the 13 STEMI patients). For the diagnosis of AMI, the sensitivities of HsTnT were higher and the specificities were lower than those of cTnI, regardless of PTP (Table 3). When we assessed the low and moderate PTP populations, the sensitivity of HsTnT was higher (91% (79 to 100) vs. 77% (60 to 95)) but NPV was not (99% (96 to 100) vs. 98% (95 to 99) for cTnI). Discussion h During the past two decades, cTn has been adopted as the preferred biomarker for the diagnosis of acute MI, a position reaffirmed in recent consensus guidelines [14,22]. However, until recently, cTn methods were unable to deliver the requisite analytic performance at the 99th percentile, an extremely low cutoff point within the range of analytic ‘noise’ in most conventional assays. The present prospective multicenter study of unselected patients who presented to the ED with chest pain of < 6 0,001 0,01 0,1 1 10 100 eGFR tertiles cTnI µg/L 1 2 3 AMI 0 1 *** *** *** 0.04 0.04 0.04 1.10 0.12 1.30 0,001 0,01 0,1 1 10 eGFR tertiles cTnT µg/L 1 2 3 AMI 0 1 *** *** *** 0.007 0.004 0.003 0.241 0.034 0.225 a) b) Figure 2 Boxplots for cTnI (A) and HSTnT (B) values as a function of AMI and according to eGFR tertiles. ***P < 0.001 versus AMI patients in the same eGFR tertile. Tertile 1 (eGFR < 67.2 mL-1 minute-1 1.73 m-2), tertile 2 (eGFR from 67.2 to 86.8 mL-1 minute-1 1.73 m-2) and tertile 3 (eGFR ≥86.9 mL-1 minute-1 1.73 m-2). Medians are indicated for each box. 0,01 0,1 1 10 100 cTnI µg/L AMI 0 1 *** *** *** 0.04 0.04 0.04 1.10 0.12 1.30 a) Second, we confirmed the value of 0.014 μg/L as an optimal threshold [14,22]. We confirmed the high diag- nostic accuracy of HsTnT; the AUC of HsTnT was 0.93, similar to that found by investigators in previous studies. Thus, Keller et al. [22] and Reichlin et al. [14] found AUCs that ranged from 0.94 to 0.96. However, and con- versely to other reports, our findings do not show a better AUC for HsTnT than for conventional cTnI measure- ments. Several reasons could explain this discrepancy. First, we used cTnI (from Siemens and Beckman Coulter) instead of cTnT as the comparator, thus with a different assay than was previously used, and our com- parator cTnI could have slightly better analytical quali- ties than the one called the ‘standard assay’ that was used in the Reichlin et al. study [14]. Second, in our study, the AUC for cTnI, or ‘conventional troponin’, that is, the comparator, was 0.94 (95% CI, 0.90 to 0.98), which in fact is included in the 95% CIs of the AUCs of other comparators previously used. For example, Christ et al. Influence of renal function on cTn performances Patients were classified into tertiles: tertile 1 (estimated glomerular filtration rate (eGFR) < 67.2 ml-1 minute-1 1.73 m-2), tertile 2 (eGFR from 67.2 to 86.8 ml-1 min- ute-1 1.73 m-2) and tertile 3 (eGFR ≥86.9 ml-1 minute-1 1.73 m-2). Cardiac TnI levels were not significantly dif- ferent across tertiles. However, HsTnT increased signifi- cantly across tertiles (P < 0.001): the lower the eGFR, the higher the HsTnT value. However, in each eGFR tertile, cTnI and HsTnT levels remained significantly the higher the HsTnT value. However, in each eGFR tertile, cTnI and HsTnT levels remained significantly Figure 1 ROC curves for the diagnosis of AMI. Values were log- transformed before analysis. AUC: area under the curve; cTnI: conventional troponin I; HSTnT: highly sensitive troponin T. Table 3 Diagnostic accuracy of HScTnT compared to that of cTnI fo Patient characteristics Sensitivity Specificity All patients (N = 317) Positive cTnI 71 (55-84) 97 (94 to 98 Positive HScTnT 93 (89 to 100)* 82 (77 to 87) Low to moderate PTP group (n = 258) Positive cTnI 77 (54 to 92) 97 (94 to 99 Positive HScTnT 91 (69 to 98) 85 (79 to 89) High PTP group (n = 59) Positive cTnI 65 (43 to 83) 94 (79 to 99 Positive HScTnT 96 (76 to 100)*** 67 (49 to 81)* aHScTnT, highly sensitive cardiac troponin T; PPV: positive predictive value; NPV: negative p 95% confidence intervall. Positive cTnI > 0.14 μg/L in Pitie-Salpetriere and Ccochin, > 0.06 moderate PTP group; ***P < 0.05 versus cTnI in high PTP group. Figure 1 ROC curves for the diagnosis of AMI. Values were log- transformed before analysis. AUC: area under the curve; cTnI: conventional troponin I; HSTnT: highly sensitive troponin T. Figure 1 ROC curves for the diagnosis of AMI. Values were log- transformed before analysis. AUC: area under the curve; cTnI: conventional troponin I; HSTnT: highly sensitive troponin T. Figure 1 ROC curves for the diagnosis of AMI. Values were log- transformed before analysis. AUC: area under the curve; cTnI: conventional troponin I; HSTnT: highly sensitive troponin T. Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 Page 6 of 9 Page 6 of 9 hours’ duration produced major different findings about the new HsTnT assay. different between AMI and no AMI (P < 0.001 for both) (Figure 2). Influence of renal function on cTn performances We found no significant differences in the AUCs of cTnI and HsTnT regarding eGFR tertiles, and the optimal threshold value of cTnI did not change across tertiles. Conversely, the optimal threshold value of HsTnT increased only in tertile 1 (0.036 μg/L com- pared to 0.014 μg/L). First, the sensitivity of the HsTnT assay remains high at all PTP levels. The excellent sensitivity of 93% was comparable to that found in a previous study (84% to 90% [22]) and significantly higher than conventional cTn (69% in our study and 72% previously described [14]). However, despite its good sensitivity of 91% in the low and moderate PTP groups, the use of HsTnT assays would not allow physicians to rule out AMI in these patients with a unique measurement of HsTnT, as the NPV is not quite perfect, that is, a unique value < 0.014 μg/L cannot avoid a second blood test several hours later to control HsTnT level. It should be noted that in the high PTP group, HsTnT showed excellent diagnostic accuracy, with 93% sensitivity (compared to 80% for cTnI) and 96% NPV (compared to 93% for cTnI). Recently, Januzzi et al. [15] showed that HsTnT was able to detect ACS more sensitively than a correspond- ing conventional cTnT method in a population of low to moderate PTP patients with chest pain. Limitations The main limitation of our study is the small sample of patients, especially patients with AMI. We cannot exclude the possibility that better results might have been found with a larger sample. Our sample is compar- able to those used in previous studies, however, and most of all, we believe that the imperfect NPV that we describe herein is the major result of our study, which could not have been corrected by including more patients. Our study has some other limitations. First, we per- formed only a single measurement of HsTnT. We did not evaluate its kinetics, which would have been interesting, especially in the ‘grey zone’ (between 0.014 μg/L and 0.050 μg/L). A second value could have provided more data, as previously described in the Giannitsis et al. study [27], which reported that a doubling in the HsTnT concentra- tion within 3 hours of chest pain (with first negative HsTnT and no electrocardiogram abnormality) was asso- ciated with a 100% PPV of a diagnosis of NSTEMI. Conventional cTn is widely used and is recommended for the management of patients presenting with sus- pected ACS [6]. However, the delay in detecting its ele- vation prevents early, safe discharge from the ED without repeated negative measurements during the course of 4 to 6 hours. Recent studies have shown excel- lent diagnostic performance of HsTnT measurement, even with early presentation to the ED [14], and better diagnostic accuracy than cTn [15]. Despite its higher sensitivity, we did not find that HsTnT had better NPV, diagnostic accuracy or AUC, conversely to the findings of previous studies [15]. Furthermore, as expected, spe- cificity and PPV were lower. The clinical setting, time of inclusion, rate of AMI in our patient population and our focus on low or moderate PTP of AMI could explain this discrepancy. Second, we used empirical PTP and not a standardised, validated one [17,18]. However, outcomes in the low and moderate PTP population (only nine with confirmed NSTEMI), and differences in clinical characteristics at admission suggested that even though empirical, this eva- luation by the clinician was accurate. Furthermore, one of the strengths of our study was that it evaluated differ- ences in diagnostic performance for the HsTnT regarding PTP as demonstrated for D-dimers and empirical suspi- cion of pulmonary embolism [28]. Discussion h [23] found an AUC of the standard fourth-genera- tion cTnT assay, that is, its comparator, of 0.89 (95% CI, 0.81 to 0.98). Unfortunately, Keller et al. [22] did not detail the 95% CIs of their AUCs for cTn, and Reichlin et al. [14] used an old standard assay which in fact underestimated the diagnostic performance of the cTn assay. Other reasons could explain this discrepancy in the AUC of ROC curves for cTnI. Our inclusion criteria differ from those of Reichlin et al. [14], Keller et al. [22] and others who included patients with chest pain of less than 12 hours’ duration with high rates of AMI and unstable angina. Our population markedly differs from those in previous studies. Thus, other conventional cTnT assays (also called third-generation cTnTs, from 0,001 eGFR tertiles 1 2 3 0,001 0,01 0,1 1 10 eGFR tertiles cTnT µg/L 1 2 3 AMI 0 1 *** *** *** 0.007 0.004 0.003 0.241 0.034 0.225 b) Figure 2 Boxplots for cTnI (A) and HSTnT (B) values as a function of AMI and according to eGFR tertiles. ***P < 0.001 versus AMI patients in the same eGFR tertile. Tertile 1 (eGFR < 67.2 mL-1 minute-1 1.73 m-2), tertile 2 (eGFR from 67.2 to 86.8 mL-1 minute-1 1.73 m-2) and tertile 3 (eGFR ≥86.9 mL-1 minute-1 1.73 m-2). Medians are indicated for each box. Page 7 of 9 Page 7 of 9 Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 Roche Diagnostics) that could be used in studies as comparators for HSTnT have been reported to have excellent AUCs. Collinson et al. [24] found that at 6 hours postpain, the AUC of cTnT was 0.989 (95% CI, 0.966 to 1.0). However, although the comparison of AUCs remains the most popular metric by which to capture discrimination, it appears that for models con- taining clinical risk and possessing reasonably good dis- crimination, very important associations between the biomarker and the end point are required to provide significantly different AUCs. In other words, compari- sons of AUCs might be considered powerless in identi- fying biomarkers of interest in such situations [20]. To address this problem, new ways of evaluating the useful- ness of biomarkers have been described, but they are used very rarely in studies evaluating diagnostic tests or biomarkers [14,22]. Discussion h In the present study, reclassification, for example, NRI, demonstrated that the use of HsTnT with a clinical assessment (including ECG findings) only slightly improved the discriminative power and perfor- mance in predicting AMI [14,22,25]. As described in previous studies, we have demonstrated a worsening of specificity and lower PPV of HsTnT measurement com- pared to those of conventional cTn; that is, we observed an increase in false-positive findings. Last, the present study is the first to investigate the impact of kidney function on HsTnT levels. We found no significant dif- ference in the AUCs of HsTnT regarding eGFR tertiles. Only in tertile 1 was the optimal threshold value of HsTnT increased (0.036 μg/ml compared to 0.014 μg/L). cannot translate into a real clinical improvement. A NPV of 99% can be interpreted as excellent, but this slight gain from that of cTnI is not sufficient to change the conven- tional method of chest pain investigation in our ED, even in low to moderate PTP patients. This subgroup is the one of most interest in our study, as high PTP patients (and even more so for STEMI patients) are not to be promptly discharged and will more easily undergo further investiga- tions and care. To rapidly and reliably rule out AMI, the answer may be assessment of a combination of different biomarkers, as suggested by Reichlin et al. [26] in their study, where they found that with a copeptin level < 14 pmol/L and a TnT level < 0.01 μg/L, AMI was excluded with 99.7% NPV in an unselected population of chest pain patients. References 1 T k F 1. Task Force for Diagnosis and Treatment of Non-ST-Segment Elevation Acute Coronary Syndromes of European Society of Cardiology, Bassand JP, Hamm CW, Ardissino D, Boersma E, Budaj A, Fernández-Avilés F, Fox KA, Hasdai D, Ohman EM, Wallentin L, Wijns W: Guidelines for the diagnosis and treatment of non-ST-segment elevation acute coronary syndromes. Eur Heart J 2007, 28:1598-1660. 1. Task Force for Diagnosis and Treatment of Non-ST-Segment Elevation Acute Coronary Syndromes of European Society of Cardiology, Bassand JP, Hamm CW, Ardissino D, Boersma E, Budaj A, Fernández-Avilés F, Fox KA, Hasdai D, Ohman EM, Wallentin L, Wijns W: Guidelines for the diagnosis and treatment of non-ST-segment elevation acute coronary syndromes. Eur Heart J 2007, 28:1598-1660. 2. Nawar EW, Niska RW, Xu J: National Hospital Ambulatory Medical Care Survey: 2005 emergency department summary. Adv Data 2007, 386:1-32. 3. Hamm CW, Ravkilde J, Gerhardt W, Jørgensen P, Peheim E, Ljungdahl L, Goldmann B, Katus HA: The prognostic value of serum troponin T in unstable angina. N Engl J Med 1992, 327:146-150. 2. Nawar EW, Niska RW, Xu J: National Hospital Ambulatory Medical Care Survey: 2005 emergency department summary. Adv Data 2007, 386:1-32. 2. Nawar EW, Niska RW, Xu J: National Hospital Ambulatory Medical Care Survey: 2005 emergency department summary. Adv Data 2007, 386:1-32. 3. Hamm CW, Ravkilde J, Gerhardt W, Jørgensen P, Peheim E, Ljungdahl L, Goldmann B, Katus HA: The prognostic value of serum troponin T in unstable angina. N Engl J Med 1992, 327:146-150. 3. Hamm CW, Ravkilde J, Gerhardt W, Jørgensen P, Peheim E, Ljungdahl L, Goldmann B, Katus HA: The prognostic value of serum troponin T in unstable angina. N Engl J Med 1992, 327:146-150. Competing interests CCG PR d BR i CCG, PR and BR received honoraria from Thermo Fisher Scientific B.R.A.H.M.S. (Hennigsdorf, Germany). PR received an honorarium from bioMérieux, Roche Diagnostics France (Lyon, France). Limitations Another limitation of our study is that different conventional Tn assays have been used at the two study sites with different threshold values and CVs. These assays were used because they were both local and well-understood methods at the time of the study. The emergency medicine field would greatly benefit from a new biomarker that eases and hastens the triage of non- cardiac chest pain patients. The main incremental value that could have provided a new highly sensitive assay for Tn would have allowed emergency physicians to rule out AMI and discharge patients with a normal Tn value. This study suggests that even when considering only low to moderate PTP patients, the better sensitivity of HsTnT Third, we used two different assays for the comparator (that is, conventional TnI): a Siemens cTnI assay in two centres (CCH and PSL) and a Beckman Coulter assay in Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 Page 8 of 9 Page 8 of 9 Huchard, F-75018, Paris, France. 5Department of Biochemistry, Hôpital Bicêtre, APHP, 78 rue du Général Leclerc 94270, Le Kremlin-Bicêtre, France. 6INSERM UMRS 956, UPMC, 91 Boulevard de l’Hôpital, F-75013 Paris, France. Huchard, F-75018, Paris, France. 5Department of Biochemistry, Hôpital Bicêtre, APHP, 78 rue du Général Leclerc 94270, Le Kremlin-Bicêtre, France. 6INSERM UMRS 956, UPMC, 91 Boulevard de l’Hôpital, F-75013 Paris, France. the third centre (BCT). The ROC curve for the cTnI is, then, a combined ROC curve of two different assays, making it imprecise. However, the two different ROC curves (for each assay) have similar AUCs. Conclusions We have confirmed that HsTnT is accurate for diagno- sis of AMI, with a sensitivity slightly higher than that of conventional cTnI, regardless of PTP of AMI in patients with chest pain presenting to an ED. However, we did not show a better NPV. Intervention studies are clearly warranted to support the use of HsTnT to help ED phy- sicians achieve clinical improvement in treating patients with chest pain and providing them with an early, safe discharge from the hospital. Received: 1 February 2011 Revised: 19 April 2011 Accepted: 10 June 2011 Published: 10 June 2011 Received: 1 February 2011 Revised: 19 April 2011 Accepted: 10 June 2011 Published: 10 June 2011 Received: 1 February 2011 Revised: 19 April 2011 Accepted: 10 June 2011 Published: 10 June 2011 Abbreviations y 7. Eggers KM, Jaffe AS, Lind L, Venge P, Lindahl B: Value of cardiac troponin I cutoff concentrations below the 99th percentile for clinical decision- making. Clin Chem 2009, 55:85-92. 7. Eggers KM, Jaffe AS, Lind L, Venge P, Lindahl B: Value of cardiac troponin I cutoff concentrations below the 99th percentile for clinical decision- making. Clin Chem 2009, 55:85-92. ACS: acute coronary syndrome; AMI: acute myocardial infarction; AUC: area under the curve; cTn: conventional troponin; CV: coefficient of variation; ED: emergency department; HsTn: high-sensitivity troponin; LR: likelihood ratio; NPV: negative predictive value; NRI: net reclassification improvement; NSTEMI: non-ST elevation myocardial infarction; PPV: positive predictive value; PTP: pretest probability; ROC: receiver operating characteristic; SD: standard deviation; STEMI: ST elevation myocardial infarction. ACS: acute coronary syndrome; AMI: acute myocardial infarction; AUC: area under the curve; cTn: conventional troponin; CV: coefficient of variation; ED: emergency department; HsTn: high-sensitivity troponin; LR: likelihood ratio; NPV: negative predictive value; NRI: net reclassification improvement; 8. Apple FS, Pearce LA, Smith SW, Kaczmarek JM, Murakami MM: Role of monitoring changes in sensitive cardiac troponin I assay results for early diagnosis of myocardial infarction and prediction of risk of adverse events. Clin Chem 2009, 55:930-937. 9. Apple FS, Smith SW, Pearce LA, Ler R, Murakami MM: Use of the Centaur TnI-Ultra assay for detection of myocardial infarction and adverse events in patients presenting with symptoms suggestive of acute coronary syndrome. Clin Chem 2008, 54:723-728. Authors’ contributions CCG, BR and PR designed the study. PB, YEC, JCA, BD, FL and CC helped in collecting the data. CC and YF carried out the statistical analyses and the biochemical assays. YF, CCG, BR and PR wrote the paper. All authors read and approved the final manuscript. CCG, BR and PR designed the study. PB, YEC, JCA, BD, FL and CC helped in collecting the data. CC and YF carried out the statistical analyses and the biochemical assays. YF, CCG, BR and PR wrote the paper. All authors read and approved the final manuscript. Last, this study was underpowered to find any signifi- cant change in the detection of AMI in the low to mod- erate PTP patients. However, as the NPV is not perfect in our patient population, we expect that this would remain the case with a larger sample. Acknowledgements We thank Roche Diagnostics France (Meylan, France) for providing free reagents and kits for HsTnT assays. The tests and kits for the HsTnT assays were provided free of charge by Roche Diagnostics France. Other sources of support were provided solely from departmental sources. We also thank Dr DJ Baker (Department of Anaesthesiology, CHU Necker- Enfants Malades, Assistance Publique des Hôpitaux de Paris (AP-HP), Paris, France) for reviewing the manuscript. This study was partially presented at the research forum of the 2010 scientific assembly of the American College of Emergency Physicians, Las Vegas, NV, USA, 29 September 2010. 10. Eggers KM, Lagerqvist B, Venge P, Wallentin L, Lindahl B: Persistent cardiac troponin I elevation in stabilized patients after an episode of acute coronary syndrome predicts long-term mortality. Circulation 2007, 116:1907-1914. 11. James SK, Lindahl B, Armstrong P, Califf R, Simoons ML, Venge P, Wallentin L: A rapid troponin I assay is not optimal for determination of troponin status and prediction of subsequent cardiac events at suspicion of unstable coronary syndromes. Int J Cardiol 2004, 93:113-120. 12. Venge P, Lagerqvist B, Diderholm E, Lindahl B, Wallentin L: Clinical performance of three cardiac troponin assays in patients with unstable coronary artery disease (a FRISC II substudy). Am J Cardiol 2002, 89:1035-1041. Key messages • Fast and reliable detection of ACS remains a great concern in the ED. g g 4. Lindahl B, Toss H, Siegbahn A, Venge P, Wallentin L, for the FRISC Study Group: Markers of myocardial damage and inflammation in relation to long-term mortality in unstable coronary artery disease. N Engl J Med 2000, 343:1139-1147. • Novel assays for troponin have been developed and tested recently. 5. Antman EM, Tanasijevic MJ, Thompson B, Schactman M, McCabe CH, Cannon CP, Fischer GA, Fung AY, Thompson C, Wybenga D, Braunwald E: Cardiac-specific troponin I levels to predict the risk of mortality in patients with acute coronary syndromes. N Engl J Med 1996, 335:1342-1349. 5. Antman EM, Tanasijevic MJ, Thompson B, Schactman M, McCabe CH, Cannon CP, Fischer GA, Fung AY, Thompson C, Wybenga D, Braunwald E: Cardiac-specific troponin I levels to predict the risk of mortality in patients with acute coronary syndromes. N Engl J Med 1996, 335:1342-1349. • HsTnT is more sensitive than cTn. • In this study, the weak gains realised by measuring HsTnT rather than cTn in terms of NPV is not suffi- cient to change daily clinical practice. • In this study, the weak gains realised by measuring HsTnT rather than cTn in terms of NPV is not suffi- cient to change daily clinical practice. 6. Thygesen K, Alpert JS, White HD, Joint ESC/ACCF/AHA/WHF Task Force for the Redefinition of Myocardial Infarction: Universal definition of myocardial infarction. J Am Coll Cardiol 2007, 50:2173-2195. 6. Thygesen K, Alpert JS, White HD, Joint ESC/ACCF/AHA/WHF Task Force for the Redefinition of Myocardial Infarction: Universal definition of myocardial infarction. J Am Coll Cardiol 2007, 50:2173-2195. Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 14. Reichlin T, Hochholzer W, Bassetti S, Steuer S, Stelzig C, Hartwiger S, Biedert S, Schaub N, Buerge C, Potocki M, Noveanu M, Breidthardt T, Twerenbold R, Winkler K, Bingisser R, Mueller C: Early diagnosis of myocardial infarction with sensitive cardiac troponin assays. N Engl J Med 2009, 361:858-867. 15. Januzzi JL Jr, Bamberg F, Lee H, Truong QA, Nichols JH, Karakas M, Mohammed AA, Schlett CL, Nagurney JT, Hoffmann U, Koenig W: High- sensitivity troponin T concentrations in acute chest pain patients evaluated with cardiac computed tomography. Circulation 2010, 121:1227-1234. 16. Bossuyt PM, Reitsma JB, Bruns DE, Gatsonis CA, Glasziou PP, Irwig LM, Moher D, Rennie D, de Vet HC, Lijmer JG, Standards for Reporting of Diagnostic Accuracy: The STARD statement for reporting studies of diagnostic accuracy: explanation and elaboration. Ann Intern Med 2003, 138:W1-W12. 17. Chandra A, Lindsell CJ, Limkakeng A, Diercks DB, Hoekstra JW, Hollander JE, Kirk JD, Peacock WF, Gibler WB, Pollack CV, EMCREG i*trACS Investigators: Emergency physician high pretest probability for acute coronary syndrome correlates with adverse cardiovascular outcomes. Acad Emerg Med 2009, 16:740-748. 18. Pollack CV Jr, Braunwald E: 2007 update to the ACC/AHA guidelines for the management of patients with unstable angina and non-ST-segment elevation myocardial infarction: implications for emergency department practice. Ann Emerg Med 2008, 51:591-606. 19. Levey AS, Bosch JP, Lewis JB, Greene T, Rogers N, Roth D: A more accurate method to estimate glomerular filtration rate from serum creatinine: a new prediction equation. Modification of Diet in Renal Disease Study Group. Ann Intern Med 1999, 130:461-470. p 20. Ray P, Le Manach Y, Riou B, Houle TT: Statistical evaluation of a biomarker. Anesthesiology 2010, 112:1023-1040. p 20. Ray P, Le Manach Y, Riou B, Houle TT: Statistical biomarker. Anesthesiology 2010, 112:1023-1040. 20. Ray P, Le Manach Y, Riou B, Houle TT: Statistical evaluation of a biomarker. Anesthesiology 2010, 112:1023-1040. 21. Pencina MJ, D’Agostino RB Sr, D’Agostino RB Jr, Vasan RS: Evaluating the added predictive ability of a new marker: from area under the ROC curve to reclassification and beyond. Stat Med 2008, 27:157-172, discussion 207-112. 21. Pencina MJ, D’Agostino RB Sr, D’Agostino RB Jr, Vasan RS: Evaluating the added predictive ability of a new marker: from area under the ROC curve to reclassification and beyond. Stat Med 2008, 27:157-172, discussion 207-112. 22. Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 Keller T, Zeller T, Peetz D, Tzikas S, Roth A, Czyz E, Bickel C, Baldus S, Warnholtz A, Fröhlich M, Sinning CR, Eleftheriadis MS, Wild PS, Schnabel RB, Lubos E, Jachmann N, Genth-Zotz S, Post F, Nicaud V, Tiret L, Lackner KJ, Münzel TF, Blankenberg S: Sensitive troponin I assay in early diagnosis of acute myocardial infarction. N Engl J Med 2009, 361:868-877. 23. Christ M, Popp S, Pohlmann H, Poravas M, Umarov D, Bach R, Bertsch T: Implementation of high sensitivity cardiac troponin T measurement in the emergency department. Am J Med 2010, 123:1134-1142. 24. Collinson PO, Gaze DC, Morris F, Morris B, Price A, Goodacre S: Comparison of biomarker strategies for rapid rule out of myocardial infarction in the emergency department using ACC/ESC diagnostic criteria. Ann Clin Biochem 2006, 43:273-280. 24. Collinson PO, Gaze DC, Morris F, Morris B, Price A, Goodacre S: Comparison of biomarker strategies for rapid rule out of myocardial infarction in the emergency department using ACC/ESC diagnostic criteria. Ann Clin Biochem 2006, 43:273-280. 25. Levinson SS: Clinical validation of biomarkers for predicting risk. Adv Clin Chem 2009, 48:1-25. 25. Levinson SS: Clinical validation of biomarkers for predicting risk. Adv Clin Chem 2009, 48:1-25. 26. Reichlin T, Hochholzer W, Stelzig C, Laule K, Freidank H, Morgenthaler NG, Bergmann A, Potocki M, Noveanu M, Breidthardt T, Christ A, Boldanova T, Merki R, Schaub N, Bingisser R, Christ M, Mueller C: Incremental value of copeptin for rapid rule out of acute myocardial infarction. J Am Coll Cardiol 2009, 54:60-68. 26. Reichlin T, Hochholzer W, Stelzig C, Laule K, Freidank H, Morgenthaler NG, Bergmann A, Potocki M, Noveanu M, Breidthardt T, Christ A, Boldanova T, Merki R, Schaub N, Bingisser R, Christ M, Mueller C: Incremental value of copeptin for rapid rule out of acute myocardial infarction. J Am Coll Cardiol 2009, 54:60-68. 27. Giannitsis E, Becker M, Kurz K, Hess G, Zdunek D, Katus HA: High-sensitivity cardiac troponin T for early prediction of evolving non-ST-segment elevation myocardial infarction in patients with suspected acute coronary syndrome and negative troponin results on admission. Clin Chem 2010, 56:642-650. doi:10.1186/cc10270 Cite this article as: Freund et al.: High-sensitivity versus conventional troponin in the emergency department for the diagnosis of acute myocardial infarction. Critical Care 2011 15:R147. Author details 1 f 1Department of Emergency Medicine and Surgery, Hôpital Pitié-Salpétrière, Assistance Publique-Hôpitaux de Paris (APHP), Université Pierre et Marie Curie-Paris 6 (UPMC), 47-83 boulevard de l’hôpital, F-75651 Paris cedex 13, France. 2Department of Biochemistry, Hôpital Cochin-Hôtel Dieu, APHP, 27 rue du Faubourg Saint-Jacques, F-75679 Paris cedex 14, France. 3Department of Emergency Medicine, Hôpital Cochin-Hôtel Dieu, APHP, Université Paris Descartes-Paris 5, 27 rue du Faubourg Saint-Jacques, F-75679 Paris cedex 14, France. 4Department of Emergency, Hôpital Bichat, APHP, 46 rue Henri 13. Morrow DA, Cannon CP, Rifai N, Frey MJ, Vicari R, Lakkis N, Robertson DH, Hille DA, DeLucca PT, DiBattiste PM, Demopoulos LA, Weintraub WS, Braunwald E: Ability of minor elevations of troponins I and T to predict benefit from an early invasive strategy in patients with unstable angina and non-ST elevation myocardial infarction: results from a randomized trial. JAMA 2001, 286:2405-2412. Page 9 of 9 Page 9 of 9 Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 Freund et al. Critical Care 2011, 15:R147 http://ccforum.com/content/15/3/R147 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: Submit your next manuscript to BioMed Central and take full advantage of: Submit your next manuscript to BioMed Central and take full advantage of: 28. Carrier M, Righini M, Djurabi RK, Huisman MV, Perrier A, Wells PS, Rodger M, Wuillemin WA, Le Gal G: VIDAS D-dimer in combination with clinical pre- test probability to rule out pulmonary embolism: a systematic review of management outcome studies. Thromb Haemost 2009, 101:886-892. • Convenient online submission doi:10.1186/cc10270 Cite this article as: Freund et al.: High-sensitivity versus conventional troponin in the emergency department for the diagnosis of acute myocardial infarction. Critical Care 2011 15:R147.
https://openalex.org/W3016480775
http://irep.ntu.ac.uk/id/eprint/46736/1/1568112_Sher.pdf
English
null
Kinetic and thermodynamic evaluation of effective combined promoters for CO2 hydrate formation
Journal of natural gas science and engineering
2,020
cc-by
18,167
*Corresponding author: E-mail address: Farooq.Sher@coventry.ac.uk (F.Sher); Tel.: +44 (0) 24 7765 7754 1 Kinetic and thermodynamic evaluation of effective combined 1 promoters for CO2 hydrate formation 2 3 4 Mohd Hafiz Abu Hassana,b, Farooq Sherc,*, Gul Zarrend, Norhidayah Suleimane, Asif Ali Tahirf, 5 Colin E. Snapea 6 7 a. Department of Chemical and Environmental Engineering, University of Nottingham, University 8 Park, Nottingham NG7 2RD, UK 9 b. Faculty of Science and Technology, Islamic Science University of Malaysia, Bandar Baru Nilai, 10 71800 Nilai, Negeri Sembilan, Malaysia 11 c. School of Mechanical, Aerospace and Automotive Engineering, Faculty of Engineering, 12 Environmental and Computing, Coventry University, Coventry CV1 2JH, UK 13 d. Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan 14 e. Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra 15 Malaysia, 43400 UPM Serdang, Selangor, Malaysia 16 f. Environment and Sustainability Institute, University of Exeter, Penryn Campus, Cornwall TR10 17 9FE, UK 18 19 20 Abstract 21 The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature. 22 CO2 emissions are closely related to human induced activities such as burning of fossil fuels and 23 deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is 24 required to reduce CO2 emissions. In this study, CO2 hydrate (CO2:6H2O) formation has been 25 explored as an approach to capture CO2 in the integrated gasification combined cycle (IGCC) 26 conditions. The formation of hydrate was experimentally investigated in an isochoric system with 27 high-pressure volumetric analyzer (HPVA). The solubility of CO2 in water using experimental 28 *Corresponding author: E-mail address: Farooq.Sher@coventry.ac.uk (F.Sher); Tel.: +44 (0) 24 7765 7754 1 Kinetic and thermodynamic evaluation of effective combined 1 promoters for CO2 hydrate formation 2 3 4 Mohd Hafiz Abu Hassana,b, Farooq Sherc,*, Gul Zarrend, Norhidayah Suleimane, Asif Ali Tahirf, 5 Colin E. Snapea 6 7 a. Department of Chemical and Environmental Engineering, University of Nottingham, University 8 Park, Nottingham NG7 2RD, UK 9 b. Faculty of Science and Technology, Islamic Science University of Malaysia, Bandar Baru Nilai, 10 71800 Nilai, Negeri Sembilan, Malaysia 11 c. School of Mechanical, Aerospace and Automotive Engineering, Faculty of Engineering, 12 Environmental and Computing, Coventry University, Coventry CV1 2JH, UK 13 d. Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan 14 e. Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra 15 Malaysia, 43400 UPM Serdang, Selangor, Malaysia 16 f. Environment and Sustainability Institute, University of Exeter, Penryn Campus, Cornwall TR10 17 9FE, UK 18 19 20 Abstract 21 The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature. 22 CO2 emissions are closely related to human induced activities such as burning of fossil fuels and 23 deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is 24 required to reduce CO2 emissions. In this study, CO2 hydrate (CO2:6H2O) formation has been 25 explored as an approach to capture CO2 in the integrated gasification combined cycle (IGCC) 26 conditions. The formation of hydrate was experimentally investigated in an isochoric system with 27 high-pressure volumetric analyzer (HPVA). The solubility of CO2 in water using experimental 28 *Corresponding author: E-mail address: Farooq.Sher@coventry.ac.uk (F.Sher); Tel.: +44 (0) 24 7765 7754 Kinetic and thermodynamic evaluation of effective combined 1 promoters for CO2 hydrate formation 2 3 4 Mohd Hafiz Abu Hassana,b, Farooq Sherc,*, Gul Zarrend, Norhidayah Suleimane, Asif Ali Tahirf, 5 Colin E. Snapea 6 7 a. Department of Chemical and Environmental Engineering, University of Nottingham, University 8 Park, Nottingham NG7 2RD, UK 9 b. Faculty of Science and Technology, Islamic Science University of Malaysia, Bandar Baru Nilai, 10 71800 Nilai, Negeri Sembilan, Malaysia 11 c. School of Mechanical, Aerospace and Automotive Engineering, Faculty of Engineering, 12 Environmental and Computing, Coventry University, Coventry CV1 2JH, UK 13 d. Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan 14 e. Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra 15 Malaysia, 43400 UPM Serdang, Selangor, Malaysia 16 f. 1 Kinetic and thermodynamic evaluation of effective combined 1 promoters for CO2 hydrate formation 2 3 4 Mohd Hafiz Abu Hassana,b, Farooq Sherc,*, Gul Zarrend, Norhidayah Suleimane, Asif Ali Tahirf, 5 Colin E. Snapea 6 7 a. Department of Chemical and Environmental Engineering, University of Nottingham, University 8 Park, Nottingham NG7 2RD, UK 9 b. Faculty of Science and Technology, Islamic Science University of Malaysia, Bandar Baru Nilai, 10 71800 Nilai, Negeri Sembilan, Malaysia 11 c. School of Mechanical, Aerospace and Automotive Engineering, Faculty of Engineering, 12 Environmental and Computing, Coventry University, Coventry CV1 2JH, UK 13 d. Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan 14 e. Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra 15 Malaysia, 43400 UPM Serdang, Selangor, Malaysia 16 f. Environment and Sustainability Institute, University of Exeter, Penryn Campus, Cornwall TR10 17 9FE, UK 18 19 20 Abstract 21 The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature. 22 CO2 emissions are closely related to human induced activities such as burning of fossil fuels and 23 deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is 24 required to reduce CO2 emissions. In this study, CO2 hydrate (CO2:6H2O) formation has been 25 explored as an approach to capture CO2 in the integrated gasification combined cycle (IGCC) 26 conditions. The formation of hydrate was experimentally investigated in an isochoric system with 27 high-pressure volumetric analyzer (HPVA). The solubility of CO2 in water using experimental 28 *Corresponding author: E-mail address: Farooq.Sher@coventry.ac.uk (F.Sher); Tel.: +44 (0) 24 7765 7754 Environment and Sustainability Institute, University of Exeter, Penryn Campus, Cornwall TR10 17 9FE, UK 18 19 20 Abstract 21 The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature. 22 CO2 emissions are closely related to human induced activities such as burning of fossil fuels and 23 deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is 24 *Corresponding author: Abstract 21 The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature. 22 CO2 emissions are closely related to human induced activities such as burning of fossil fuels and 23 deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is 24 required to reduce CO2 emissions. In this study, CO2 hydrate (CO2:6H2O) formation has been 25 explored as an approach to capture CO2 in the integrated gasification combined cycle (IGCC) 26 conditions. The formation of hydrate was experimentally investigated in an isochoric system with 27 high-pressure volumetric analyzer (HPVA). The solubility of CO2 in water using experimental 28 The increase in carbon dioxide (CO2) concentration in the atmosphere raises earth’s temperature. 22 CO2 emissions are closely related to human induced activities such as burning of fossil fuels and 23 deforestation. So to make the environment sustainable, carbon capture and storage (CCS) is 24 required to reduce CO2 emissions. In this study, CO2 hydrate (CO2:6H2O) formation has been 25 explored as an approach to capture CO2 in the integrated gasification combined cycle (IGCC) 26 conditions. The formation of hydrate was experimentally investigated in an isochoric system with 27 high-pressure volumetric analyzer (HPVA). The solubility of CO2 in water using experimental 28 1 pressure–time (P-t) curves were analyzed to determine the formation of hydrate. Additionally, the 29 effect of newly synthesized combined promoters and various driving forces were evaluated. The 30 experimental results demonstrated that the CO2 uptake expanded as ∆P expanded and designated 31 combined promoters type T1-5 and type T3-2 were the two best, acquiring a uptake of 5.95 and 32 5.57 mmol of CO2 per g of H2O separately. Ethylene glycol mono-ethyl ether (EGME) was 33 demonstrated to be a good option to THF when linked with SDS, with a CO2 uptake of 5.45 mmol 34 for the designated combined promoters T1A-2. Additionally, the total sum of CO2 devoured 35 through hydrate development maximize as the measure of water inside mesoporous silica 36 increased. All results of the studied parameters confirmed the reliability of experiments and 37 successful implementation. 38 pressure–time (P-t) curves were analyzed to determine the formation of hydrate. Additionally, the 29 effect of newly synthesized combined promoters and various driving forces were evaluated. Abstract 21 The 30 experimental results demonstrated that the CO2 uptake expanded as ∆P expanded and designated 31 combined promoters type T1-5 and type T3-2 were the two best, acquiring a uptake of 5.95 and 32 5.57 mmol of CO2 per g of H2O separately. Ethylene glycol mono-ethyl ether (EGME) was 33 demonstrated to be a good option to THF when linked with SDS, with a CO2 uptake of 5.45 mmol 34 for the designated combined promoters T1A-2. Additionally, the total sum of CO2 devoured 35 through hydrate development maximize as the measure of water inside mesoporous silica 36 increased. All results of the studied parameters confirmed the reliability of experiments and 37 successful implementation. 38 g p , 2 p for the designated combined promoters T1A-2. Additionally, the total sum of CO2 devoure 35 through hydrate development maximize as the measure of water inside mesoporous silic 36 increased. All results of the studied parameters confirmed the reliability of experiments an 37 successful implementation. 38 39 Keywords: Global warming; Gas hydrate; CO2 capture and storage (CCS); HPVA; combine 40 promoters, thermodynamics and kinetics. 41 42 1 Introduction 43 The energy demands of the globe have increased very rapidly. Energy consumption rises day b 44 day globally by increasing industries, electric automobiles and developing economic demand 45 According to recent scenario, the energy consumption demand will increase by one third over nex 46 25 years and will become more than double in 2060 [1]. The increased demands of energy als 47 caused a high level of greenhouse gas (GHG) emissions in the environment, therefore as a resu 48 increased global warming [2]. Due to increased global warming, the European Union (EU) set th 49 reduction target of CO2 emission at least by 80% until 2050 [3]. According to the Internationa 50 Plant Protection Convention (IPPC) fifth assessment report, the leading issue of global warmin 51 39 Keywords: Global warming; Gas hydrate; CO2 capture and storage (CCS); HPVA; combined 40 promoters, thermodynamics and kinetics. 41 promoters, thermodynamics and kinetics. 41 1 Introduction 43 The energy demands of the globe have increased very rapidly. Energy consumption rises day by 44 day globally by increasing industries, electric automobiles and developing economic demands. 45 According to recent scenario, the energy consumption demand will increase by one third over next 46 25 years and will become more than double in 2060 [1]. The increased demands of energy also 47 caused a high level of greenhouse gas (GHG) emissions in the environment, therefore as a result 48 increased global warming [2]. Due to increased global warming, the European Union (EU) set the 49 reduction target of CO2 emission at least by 80% until 2050 [3]. According to the International 50 Plant Protection Convention (IPPC) fifth assessment report, the leading issue of global warming 51 2 2 has caused a rise in temperatures approximately by 1.50 °C due to human induced activities [4, 5]. 52 Mainly, the sources of carbon dioxide (CO2) emissions are industrial activities and thermal power 53 plants [6]. Therefore, the issue to capture CO2 emissions emitting from the industrial processes 54 have gained increasing concern. 55 56 Different schemes were used in the past to reduce global warming specifically carbon emissions 57 in which renewable energy technologies are very important [5, 7]. The process called carbon 58 capture and storage (CCS) emerged as the most important technology to capture and store CO2 59 emitting directly from power and chemical plants [8, 9]. This technology mainly involves 60 separation, conditioning, transportation and storage of CO2. This four-step technology first 61 captures the contents with rich CO2 from any industrial sources, then condense and liquefies CO2 62 before transporting it to the storage site usually through a pipeline and geologically stored it in the 63 formation site of deep saline [10]. Among the whole process, the separation step of CO2 is the one 64 with high energy taking pathway that accounts for about 75–80% of the total cost of CCS [11]. 65 Still, CCS is being recognized as a vital technology with the least cost against climate change 66 mitigation that will be able to limit global warming below 2 °C [12]. 67 68 There are several new strategies developed in the past that can physically and chemically capture 69 has caused a rise in temperatures approximately by 1.50 °C due to human induced activities [4, 5]. 1 Introduction 43 52 Mainly, the sources of carbon dioxide (CO2) emissions are industrial activities and thermal power 53 plants [6]. Therefore, the issue to capture CO2 emissions emitting from the industrial processes 54 have gained increasing concern. 55 has caused a rise in temperatures approximately by 1.50 °C due to human induced activities [4, 5]. 52 Mainly, the sources of carbon dioxide (CO2) emissions are industrial activities and thermal power 53 plants [6]. Therefore, the issue to capture CO2 emissions emitting from the industrial processes 54 have gained increasing concern. 55 56 Different schemes were used in the past to reduce global warming specifically carbon emissions 57 in which renewable energy technologies are very important [5, 7]. The process called carbon 58 capture and storage (CCS) emerged as the most important technology to capture and store CO2 59 emitting directly from power and chemical plants [8, 9]. This technology mainly involves 60 separation, conditioning, transportation and storage of CO2. This four-step technology first 61 captures the contents with rich CO2 from any industrial sources, then condense and liquefies CO2 62 before transporting it to the storage site usually through a pipeline and geologically stored it in the 63 formation site of deep saline [10]. Among the whole process, the separation step of CO2 is the one 64 with high energy taking pathway that accounts for about 75–80% of the total cost of CCS [11]. 65 Still, CCS is being recognized as a vital technology with the least cost against climate change 66 mitigation that will be able to limit global warming below 2 °C [12]. 67 There are several new strategies developed in the past that can physically and chemically capture 69 CO2 using blended solution [13, 14], nanostructured membranes of polymers, zeolites and various 70 carbon or inorganic nanocomposites [15], adsorption media, cryogenic systems [16], integrated 71 gasification combined cycle (IGCC) [17], hydrate based gas separation (HBGS) [18] and chemical 72 looping combustion [19]. In IGCC technology, synthetic gas is reformed from fossil fuels (coal, 73 oil and nature gas). In spite of IGCC promising utilization, it faces a major challenge of high 74 3 3 separation cost of CO2 from CO2/H2 product gas [20]. Hence, energy saving and inexpensive 75 technologies are required to capture CO2 efficiently. 1 Introduction 43 Among all of the above mentioned strategies 76 hydrate based gas separation (HBGS) is one of the novels approaches to capture and store CO2 77 with relatively low consumption of energy [21]. HBGS can be used for both pre and post- 78 combustion from the fuel and flue gas respectively. Though, the process of HBGS is likely more 79 appropriate for pre-combustion of CO2 capture. This is because of the partial pressure of fuel gas 80 (consisting of 40% of CO2 and 60% H2) is thousand times greater than that of flue gas (consisting 81 of 17% of CO2 and 83% N2) in case of post-combustion capture [22]. 82 83 Therefore, in this study HBGS has been chosen because of the continuous operation property of 84 CO2 hydrate formation which enables the treatment of large volumes of gaseous stream, less 85 operating cost and recuperative ability of CO2 capture about 99 mol% from the flue gas [23]. 86 Recently Zheng et al. [24] stated that even at ambient temperature carbon dioxide molecules could 87 be arrested and stored by using HBGS improved properties, it provides the leeway for industrialists 88 to use this pathway for further industrial applications. The process of HBGS relies on the ability 89 of gas hydrate formation that is formed by water molecules and CO2, N2, O2, H2 or natural gas 90 component (methane or ethane) at low temperature (near about 237 K) and at elevated pressure of 91 about 10–70 bar [25, 26]. CO2 hydrate is formed in case of pure CO2 gaseous system at a pressure 92 range of 12.70–45 bar and temperature range of 273.20–283 K [27]. 93 94 separation cost of CO2 from CO2/H2 product gas [20]. Hence, energy saving and inexpensive 75 technologies are required to capture CO2 efficiently. Among all of the above mentioned strategies 76 hydrate based gas separation (HBGS) is one of the novels approaches to capture and store CO2 77 with relatively low consumption of energy [21]. HBGS can be used for both pre and post- 78 combustion from the fuel and flue gas respectively. Though, the process of HBGS is likely more 79 appropriate for pre-combustion of CO2 capture. 1 Introduction 43 This is because of the partial pressure of fuel gas 80 (consisting of 40% of CO2 and 60% H2) is thousand times greater than that of flue gas (consisting 81 of 17% of CO2 and 83% N2) in case of post-combustion capture [22]. 82 separation cost of CO2 from CO2/H2 product gas [20]. Hence, energy saving and inexpensive 75 technologies are required to capture CO2 efficiently. Among all of the above mentioned strategies 76 hydrate based gas separation (HBGS) is one of the novels approaches to capture and store CO2 77 with relatively low consumption of energy [21]. HBGS can be used for both pre and post- 78 combustion from the fuel and flue gas respectively. Though, the process of HBGS is likely more 79 appropriate for pre-combustion of CO2 capture. This is because of the partial pressure of fuel gas 80 (consisting of 40% of CO2 and 60% H2) is thousand times greater than that of flue gas (consisting 81 of 17% of CO2 and 83% N2) in case of post-combustion capture [22]. 82 Therefore, in this study HBGS has been chosen because of the continuous operation property of 84 CO2 hydrate formation which enables the treatment of large volumes of gaseous stream, less 85 operating cost and recuperative ability of CO2 capture about 99 mol% from the flue gas [23]. 86 Recently Zheng et al. [24] stated that even at ambient temperature carbon dioxide molecules could 87 be arrested and stored by using HBGS improved properties, it provides the leeway for industrialists 88 to use this pathway for further industrial applications. The process of HBGS relies on the ability 89 of gas hydrate formation that is formed by water molecules and CO2, N2, O2, H2 or natural gas 90 component (methane or ethane) at low temperature (near about 237 K) and at elevated pressure of 91 about 10–70 bar [25, 26]. CO2 hydrate is formed in case of pure CO2 gaseous system at a pressure 92 range of 12.70–45 bar and temperature range of 273.20–283 K [27]. 93 In the past, numerous parameters have been scrutinized to improve the efficiency of CO2 uptake, 95 less operational cost and ease of hydrate formation. The parameters used for the increased 96 efficiency of CO2 capture are mainly promoters, types of silica, experimental dynamic force, 97 4 4 height of the bed and amount of moisture content. 1 Introduction 43 These parameters were investigated by 98 employing a solid adsorbent approach in HBGS, which is most preferred method in the industry 99 for CCS [18, 28, 29]. Nambiar et al. [30] worked with the biodegradable porous materials that 100 enabled almost double rate of hydrates formation with only 50% water saturation level. While Park 101 et al. [31] used only porous silica gel which increased the gas uptake due to high availability of 102 surface area to increase water and gas contact. Li et al., [32] employed nano-sized Al2O3 and found 103 that gas separation efficiency was improved by approximately 43.62% due to micro-sized 104 particles. 105 106 In spite of the remarkable advancements in HBGS technology, however, this technology still 107 requires a large amount of energy for compression and extraction of CO2 and decrease in optimum 108 conditions of temperature and pressure. Thus, different thermodynamic promoters were used in 109 the past to optimize the conditions of hydrate formation. These promoters include Cyclopentane 110 (CP) [33], Tetra-n-butyl ammonium Chloride (TBAC) [34], Tetra-n-butyl ammonium bromide 111 (TBAB) [35], Tetra-n-butyl ammonium fluoride (TBAF) [29] and Tetrahydrofuran (THF) [36]. 112 However, despite the usage of these promoters, still the time taking for process of hydrate 113 formation and limited gaseous solubility in water restrict the successful application of CO2 capture 114 schemes. That is why more investigation regarding the definite solution of this problem is required. 115 Therefore, the present study investigates two parameters i.e. best type of silica and novel combined 116 type promoters to evaluate their effect for hydrate formation. The main focus was to evaluate the 117 optimum hydrate based separation in the operating conditions of an integrated gasification 118 combined cycle. Herein, the fact is highlight that hydrate formation is possible in integrated 119 gasification combined cycle conditions. Furthermore, the hydrate formation driving force and non- 120 height of the bed and amount of moisture content. These parameters were investigated by 98 employing a solid adsorbent approach in HBGS, which is most preferred method in the industry 99 for CCS [18, 28, 29]. Nambiar et al. [30] worked with the biodegradable porous materials that 100 enabled almost double rate of hydrates formation with only 50% water saturation level. While Park 101 et al. 2.1 Materials 124 Tetrahydrofuran (THF), Ethylene glycol mono-ethyl ether (EGME), sodium dodecyl sulfate (SDS) 125 and tetrabutylammonium bromide (TBAB) promoters with the purity of 99.70, 99.60, 99.90 and 126 97.50% respectively were purchased from Fisher Scientific. Silica gel with standard particle size 127 of 200–500 μm, pore volume of 0.630 cm3/g, surface area of 499 m2/g and mean pore size of 5.14 128 nm were purchased from Fisher Scientific. Antifreeze was provided by ASDA. A member of Linde 129 group i.e. BOC supplied Helium and Nitrogen gas for cleaning and controlling the valve of high 130 pressure volumetric analyzer (HPVA). 131 1 Introduction 43 [31] used only porous silica gel which increased the gas uptake due to high availability of 102 surface area to increase water and gas contact. Li et al., [32] employed nano-sized Al2O3 and found 103 that gas separation efficiency was improved by approximately 43.62% due to micro-sized 104 particles. 105 In spite of the remarkable advancements in HBGS technology, however, this technology still 107 requires a large amount of energy for compression and extraction of CO2 and decrease in optimum 108 conditions of temperature and pressure. Thus, different thermodynamic promoters were used in 109 the past to optimize the conditions of hydrate formation. These promoters include Cyclopentane 110 (CP) [33], Tetra-n-butyl ammonium Chloride (TBAC) [34], Tetra-n-butyl ammonium bromide 111 (TBAB) [35], Tetra-n-butyl ammonium fluoride (TBAF) [29] and Tetrahydrofuran (THF) [36]. 112 However, despite the usage of these promoters, still the time taking for process of hydrate 113 formation and limited gaseous solubility in water restrict the successful application of CO2 capture 114 schemes. That is why more investigation regarding the definite solution of this problem is required. 115 Therefore, the present study investigates two parameters i.e. best type of silica and novel combined 116 type promoters to evaluate their effect for hydrate formation. The main focus was to evaluate the 117 optimum hydrate based separation in the operating conditions of an integrated gasification 118 combined cycle. Herein, the fact is highlight that hydrate formation is possible in integrated 119 gasification combined cycle conditions. Furthermore, the hydrate formation driving force and non- 120 5 5 hydrate forming conditions especially in IGCC conditions were investigated with the employment 121 of pure CO2 gas. 122 2.2 Sample preparation 132 Then promoter-water solution equal to 47.50 g was 156 added to make the total mass of dry silica gel-promoter-water mixture equal to 50 g. These samples 157 were prepared by implementing the highest rates of stirring. The degassing unit was used to 158 calculate an exact amount of moisture content residing inside the pores of silica gel. The amount 159 of water content was necessary to calculate the final conversion of water to CO2 hydrate. 160 2.2 Sample preparation 132 149 water mixture were vigorously stirred at a speed of 37,000 rpm [38] by using a high-speed blender 144 for 90 seconds. Then, the mixture was left at atmospheric conditions until the final mass reached 145 equilibrium. To obtain the final moisture content, the final equilibrium mass was subtracted from 146 dry silica gel mass. Four promoter samples were named as; THF, EGME, TBAB and SDS. Each 147 promoter was diluted in water to obtain, SDS with 0.01 mol% concentration [39] and 3 mol% 148 concentration of THF [39]. 149 150 The combined-promoter designated type named T1-5 (5.60 mol% THF + 0.01 mol% SDS), T3-2 151 (0.01 mol% SDS +0.10 mol% TBAB) and T1A-2 (0.10 mol% EGME +0.01 mol% SDS) were 152 used in analysis. The discovery of two new combined-promoters (designated types T3-2 and T1A- 153 2) in this work could provide more options for HBGS research field in future. 154 150 The combined-promoter designated type named T1-5 (5.60 mol% THF + 0.01 mol% SDS), T3-2 151 (0.01 mol% SDS +0.10 mol% TBAB) and T1A-2 (0.10 mol% EGME +0.01 mol% SDS) were 152 used in analysis. The discovery of two new combined-promoters (designated types T3-2 and T1A- 153 2) in this work could provide more options for HBGS research field in future. 154 Table 1 summarizes the concentration required for each combined-promoter employed. 2.50 g of 155 silica gel was used to prepare each sample. Then promoter-water solution equal to 47.50 g was 156 added to make the total mass of dry silica gel-promoter-water mixture equal to 50 g. These samples 157 were prepared by implementing the highest rates of stirring. The degassing unit was used to 158 calculate an exact amount of moisture content residing inside the pores of silica gel. The amount 159 of water content was necessary to calculate the final conversion of water to CO2 hydrate. 160 The combined-promoter designated type named T1-5 (5.60 mol% THF + 0.01 mol% SDS), T3-2 151 (0.01 mol% SDS +0.10 mol% TBAB) and T1A-2 (0.10 mol% EGME +0.01 mol% SDS) were 152 used in analysis. The discovery of two new combined-promoters (designated types T3-2 and T1A- 153 2) in this work could provide more options for HBGS research field in future. 154 Table 1 summarizes the concentration required for each combined-promoter employed. 2.50 g of 155 silica gel was used to prepare each sample. 2.2 Sample preparation 132 The adsorbent employed was standard because silica gel due its high porosity and reproducibility 133 can supply a large amount of contact area between water and gas molecules in a short time. Thus, 134 it increases the kinetics of hydrate formation and enhances the CO2 uptake as compared to other 135 adsorbents. Furthermore, it was noted that silica gel with chosen specific properties, as a solid 136 adsorbent can effectively overcome the gas/water contact limitation where in the gas phase will 137 have better contact with water dispersed in pores of silica gel [37]. Four methods were used for 138 the preparation of wet silica gel, the method with the best result was reported in this study. For 139 preparation, silica gel was initially dried inside the oven for one night at 200 oC, before the 140 commencement of the experiment. Oven with the model of AX30 manufactured by Carbolite was 141 used. Dry silica gel (0.50 g) was placed inside blender and water was added in excess (19 times 142 6 6 the mass of dry silica gel) so that the total mass of the mixture became 50 g. The silica gel and 143 water mixture were vigorously stirred at a speed of 37,000 rpm [38] by using a high-speed blender 144 for 90 seconds. Then, the mixture was left at atmospheric conditions until the final mass reached 145 equilibrium. To obtain the final moisture content, the final equilibrium mass was subtracted from 146 dry silica gel mass. Four promoter samples were named as; THF, EGME, TBAB and SDS. Each 147 promoter was diluted in water to obtain, SDS with 0.01 mol% concentration [39] and 3 mol% 148 concentration of THF [39]. 149 the mass of dry silica gel) so that the total mass of the mixture became 50 g. The silica gel and 143 water mixture were vigorously stirred at a speed of 37,000 rpm [38] by using a high-speed blender 144 for 90 seconds. Then, the mixture was left at atmospheric conditions until the final mass reached 145 equilibrium. To obtain the final moisture content, the final equilibrium mass was subtracted from 146 dry silica gel mass. Four promoter samples were named as; THF, EGME, TBAB and SDS. Each 147 promoter was diluted in water to obtain, SDS with 0.01 mol% concentration [39] and 3 mol% 148 concentration of THF [39]. 2.3 Experimental procedure 161 The pneumatic valves of HPVA were also controlled by the gas chambers. Prior to the 169 initiation of analysis, to clean the line from any sort of polluting influences, physical cleaning of 170 the system was done by gas. 171 172 The working conditions, such as; analyze time, examination gas port, working weight, and 173 temperature were pre-characterized. From that point forward, the cells valve was firstly closed and 174 sample cell was accused with silica gel having a sufficient amount of water that was placed inside 175 the water bath. During the experimental work, the desired working temperature was built up 176 through a steady temperature bath and simultaneously the required pressure was built up through 177 a supply vessel. The cells valve was directed to completely open, after the maintenance of 178 operating conditions. Then the analysis was done for 1200 minutes. At that point, the weight was 179 diminished to barometrical pressure at the equivalent working temperature for hydrate 180 disintegration. After that, the sample cell was removed from HPVA and the cells valve was 181 allowed to completely shut. At long last, the development of hydrate in the HPVA was inspected 182 by examining the P-t bends and furthermore the examination on CO2 dissolution in water. 183 The working conditions, such as; analyze time, examination gas port, working weight, and 173 temperature were pre-characterized. From that point forward, the cells valve was firstly closed and 174 sample cell was accused with silica gel having a sufficient amount of water that was placed inside 175 the water bath. During the experimental work, the desired working temperature was built up 176 through a steady temperature bath and simultaneously the required pressure was built up through 177 a supply vessel. The cells valve was directed to completely open, after the maintenance of 178 operating conditions. Then the analysis was done for 1200 minutes. At that point, the weight was 179 diminished to barometrical pressure at the equivalent working temperature for hydrate 180 disintegration. After that, the sample cell was removed from HPVA and the cells valve was 181 allowed to completely shut. At long last, the development of hydrate in the HPVA was inspected 182 by examining the P-t bends and furthermore the examination on CO2 dissolution in water. 183 2.3 Experimental procedure 161 Fig. 1 shows the work station for hydrate formation experiments consisting of a high-pressure 162 volumetric analyzer (model HPVA-100, manufactured by Micromeritics). It contains a computer 163 unit, a constant temperature bath, gas cylinders and a vacuum pump. The mixture of 70 vol% water 164 + 30 vol% antifreeze was used to avoid the formation of ice inside the temperature control vessel 165 7 7 and to make sure that the water mixture was consistently circulated throughout the process. Gas 166 chambers were important to give an investigation of gas with 99.99% purity having 103 bar 167 pressure and Helium gas with the same purity having 34.40 bar pressure for expelling and cleaning 168 purposes. The pneumatic valves of HPVA were also controlled by the gas chambers. Prior to the 169 initiation of analysis, to clean the line from any sort of polluting influences, physical cleaning of 170 the system was done by gas. 171 172 The working conditions, such as; analyze time, examination gas port, working weight, and 173 temperature were pre-characterized. From that point forward, the cells valve was firstly closed and 174 sample cell was accused with silica gel having a sufficient amount of water that was placed inside 175 the water bath. During the experimental work, the desired working temperature was built up 176 through a steady temperature bath and simultaneously the required pressure was built up through 177 a supply vessel. The cells valve was directed to completely open, after the maintenance of 178 operating conditions. Then the analysis was done for 1200 minutes. At that point, the weight was 179 diminished to barometrical pressure at the equivalent working temperature for hydrate 180 disintegration. After that, the sample cell was removed from HPVA and the cells valve was 181 allowed to completely shut. At long last, the development of hydrate in the HPVA was inspected 182 by examining the P-t bends and furthermore the examination on CO2 dissolution in water. 183 2.3.1 Uncertainty analysis 184 All prepared samples were used to investigate hydrate formation in the HPVA by using pure CO2 185 and to make sure that the water mixture was consistently circulated throughout the process. Gas 166 chambers were important to give an investigation of gas with 99.99% purity having 103 bar 167 pressure and Helium gas with the same purity having 34.40 bar pressure for expelling and cleaning 168 purposes. 2.3.1 Uncertainty analysis 184 However, the average 196 differences, standard deviation and estimation of the uncertainty of mean maximum water 197 conversion to hydrate and mean maximum CO2 uptake data through the estimation of 90% 198 confidence intervals (CI) calculated with the help online statistics calculator to verify the reported 199 results. 200 2.3.1 Uncertainty analysis 184 All prepared samples were used to investigate hydrate formation in the HPVA by using pure CO2 185 gas (99.99% purity). The P-t curve for all experiments that exhibited hydrate formation either in 186 pure CO2 or fuel gas mixture showed a similar trend. In this study, the P-t (Pressure-time) curves 187 obtained were determined through the formation of hydrate together with the study of CO2 188 8 dissolution in water according to Henry’s Law and then followed by the analysis of water 189 conversion to hydrate, CO2 uptake and rate of hydrate formation. All experiments were conducted 190 for 1200 minutes to obtain maximum water conversion to hydrate and maximum CO2 uptake. For 191 accurate measurement, the rate of hydrate formation was reported every 30 minutes because the 192 data was very large. The sampling time for data acquisition of pressure and temperature were taken 193 every 5 s by HPVA. Thus, the rate for every 30 minutes helps for proper visualization of the rate 194 change during 1200 minutes. Furthermore, to ensure the accuracy and statistical validity of the 195 reported results two runs for each sample promoters were performed. However, the average 196 differences, standard deviation and estimation of the uncertainty of mean maximum water 197 conversion to hydrate and mean maximum CO2 uptake data through the estimation of 90% 198 confidence intervals (CI) calculated with the help online statistics calculator to verify the reported 199 results. 200 dissolution in water according to Henry’s Law and then followed by the analysis of water 189 conversion to hydrate, CO2 uptake and rate of hydrate formation. All experiments were conducted 190 for 1200 minutes to obtain maximum water conversion to hydrate and maximum CO2 uptake. For 191 accurate measurement, the rate of hydrate formation was reported every 30 minutes because the 192 data was very large. The sampling time for data acquisition of pressure and temperature were taken 193 every 5 s by HPVA. Thus, the rate for every 30 minutes helps for proper visualization of the rate 194 change during 1200 minutes. Furthermore, to ensure the accuracy and statistical validity of the 195 reported results two runs for each sample promoters were performed. 3 Results and discussion 201 [41] 226 described the time from point a-c as an induction time for hydrate formation. Moreover, the fast 227 induction time observed in this work was almost less than 10 minutes by employing FBR this 228 agrees with the one reported in the literature [18, 43, 44]. Then, the second stage of pressure drop 229 was observed immediately after point c and this significant pressure drop is known as the hydrate 230 growth stage. From point c-d sudden decrease in pressure was observed which is expected due to 231 the availability of enough driving force required for the growth of hydrate. Thus, the significant 232 two-stage pressure drop observed in the initial stage (the first 20 minutes) before being followed 233 by the second small pressure drop (until 100 minutes) until almost no more drop in pressure was 234 According to Tang et al. [41], there must be at least a two-stage pressure drop upon completion of 213 the experiment to ensure the formation of hydrate. The first stage of pressure drop indicates the 214 dissolution of CO2 in water and the subsequent stages indicate hydrate growth. This trend was 215 observed for baseline experiment during the hydrate formation experiment at the constant 216 temperature of 275 K (Fig. 2), where the total pressure drop achieved after 1200 minutes was 217 around 2 bar. The complete dissolution of CO2 in water inside silica gel pores was observed after 218 the pressure dropped approximately to 33.8 bar. As seen in Fig. 2, the first 120 minutes showed 219 two stages of pressure drop. Point a-c is considered the first stage of pressure drop. Initially, a 220 pressure drop from point a-b indicates that the dissolution of CO2 in water happened around 5 221 minutes in which Sloan and Koh [42] stated that upon dissolution of gas in water, labile clusters 222 form immediately. Concurrently, labile clusters started to agglomerate by sharing faces, thus 223 increasing disorder which explained the little rise in pressure from point b-c. This process 224 continued until the size of the cluster agglomerate reached a critical value at point c, wherein Sloan 225 and Koh [42] said this was the point where primary nucleation happens. Also, Tang et al. [41] 226 described the time from point a-c as an induction time for hydrate formation. 3 Results and discussion 201 The prepared samples T1-5, T3-2, T1A-2 and standard silica gel with water (baseline experiment) 202 was used to investigate hydrate formation in HPVA at 275–293 K and 22–36 bar by using pure 203 CO2 gas (99.99% purity). All experiments were conducted for 1200 minutes to obtain maximum 204 CO2 uptake. The P-t curve obtained was firstly used to justify the successful formation of hydrate 205 together with the study of CO2 dissolution in water and then followed by the analysis of CO2 uptake 206 and rate of hydrate formation. Due to the limitation of crystallizer in which the formation of 207 hydrate could not be seen directly by the eyes, there was a necessity to justify the formation of 208 hydrate. Subsequently, two methodologies were utilized to analyze the formation of hydrate; 209 examination of P-t bends and investigation of CO2 disintegration in the water suggested by Servio 210 and Englezos, [40]. 211 9 9 212 According to Tang et al. [41], there must be at least a two-stage pressure drop upon completion of 213 the experiment to ensure the formation of hydrate. The first stage of pressure drop indicates the 214 dissolution of CO2 in water and the subsequent stages indicate hydrate growth. This trend was 215 observed for baseline experiment during the hydrate formation experiment at the constant 216 temperature of 275 K (Fig. 2), where the total pressure drop achieved after 1200 minutes was 217 around 2 bar. The complete dissolution of CO2 in water inside silica gel pores was observed after 218 the pressure dropped approximately to 33.8 bar. As seen in Fig. 2, the first 120 minutes showed 219 two stages of pressure drop. Point a-c is considered the first stage of pressure drop. Initially, a 220 pressure drop from point a-b indicates that the dissolution of CO2 in water happened around 5 221 minutes in which Sloan and Koh [42] stated that upon dissolution of gas in water, labile clusters 222 form immediately. Concurrently, labile clusters started to agglomerate by sharing faces, thus 223 increasing disorder which explained the little rise in pressure from point b-c. This process 224 continued until the size of the cluster agglomerate reached a critical value at point c, wherein Sloan 225 and Koh [42] said this was the point where primary nucleation happens. Also, Tang et al. 3 Results and discussion 201 Moreover, the fast 227 induction time observed in this work was almost less than 10 minutes by employing FBR this 228 agrees with the one reported in the literature [18, 43, 44]. Then, the second stage of pressure drop 229 was observed immediately after point c and this significant pressure drop is known as the hydrate 230 growth stage. From point c-d sudden decrease in pressure was observed which is expected due to 231 the availability of enough driving force required for the growth of hydrate. Thus, the significant 232 two-stage pressure drop observed in the initial stage (the first 20 minutes) before being followed 233 by the second small pressure drop (until 100 minutes) until almost no more drop in pressure was 234 10 observed in batch FBR as indicated by point e, could be a basic guideline to determine the 235 formation of CO2 hydrate and CO2 dissolution in water. After point e, several stages of pressure 236 drop were observed for the sample before it became a plateau. For the sample prepared by the 237 highest rates of stirring, the pressure became constant approximately after 700 minutes. Moreover, 238 the growth of hydrate and the fast induction time around 5–10 minutes for hydrate formation 239 validates by different studies conducted in the literature [18, 40, 41]. Since the formation of hydrate 240 was justified, next to the study on final water to hydrate conversion, CO2 uptake and rate of hydrate 241 formation are presented in the next section. 242 observed in batch FBR as indicated by point e, could be a basic guideline to determine the 235 formation of CO2 hydrate and CO2 dissolution in water. After point e, several stages of pressure 236 drop were observed for the sample before it became a plateau. For the sample prepared by the 237 highest rates of stirring, the pressure became constant approximately after 700 minutes. Moreover, 238 the growth of hydrate and the fast induction time around 5–10 minutes for hydrate formation 239 validates by different studies conducted in the literature [18, 40, 41]. Since the formation of hydrate 240 was justified, next to the study on final water to hydrate conversion, CO2 uptake and rate of hydrate 241 formation are presented in the next section. 242 3.2 Integrated gasification combined cycle (IGCC) process 264 Generally, most of the literature has investigated CO2 hydrate formation from fuel gas mixture in 265 non-IGCC operating conditions whereas experiments performed in this work used the IGCC 266 conditions. Mostly, the operating conditions of the IGCC are in the range of 283–290 K and 20– 267 70 bar (fuel gas mixture) and are outside the hydrate forming conditions. The minimum pressure 268 required for CO2 hydrate to form at 283 K is 30 bar (pure CO2) as discovered by Servio and 269 Englezos, [40]. Nevertheless, the initial investigation on the implementation of promoters directed 270 our attention to the hydrate formation in non-hydrate forming conditions. Therefore, the focus of 271 the study was to obtain optimum hydrate formation in the IGCC operating conditions. Hence, 272 additional experimental parameters were investigated and reported which indicated that hydrate 273 formation is possible in IGCC conditions. The experimental parameters that were studied include 274 hydrate formation driving force (∆P) and various non-hydrate forming conditions (temperature 275 and pressure), especially in the IGCC conditions. 276 3.1 Hydrate formation analysis 243 In contrast, the solubility of CO2 260 in water reduced as the temperature increased in non-hydrate forming region. This trend was 261 comparable to the equilibrium mole fraction of CO2 in water as shown in the literature [46] which 262 explains the non-existence of hydrate at elevated temperature. 263 3.1 Hydrate formation analysis 243 Hydrate formation experiments were investigated in the HPVA by using a prepared sample with 244 approximately 0.50 g of wet silica. The hydration number of 5.75 [45] was used to calculate the 245 water conversion to hydrate as 6 water molecules are needed to form CO2 hydrate (CO2.6H2O). 246 The sample prepared by the highest rates of stirring had the maximum water conversion to hydrate 247 with a value of 40.50 ± 2.28 mol%. The amount of gas uptake was directly related to the amount 248 of water conversion to hydrate. Hence, the gas uptake obtained for the prepared sample was the 249 highest amount of CO2 molecules with a value of 0.29 mmol. Additionally, it was observed that 250 the sample with the greater equilibrium moisture contents yielded the maximum water conversion 251 to hydrate. 252 Hydrate formation experiments were investigated in the HPVA by using a prepared sample with 244 approximately 0.50 g of wet silica. The hydration number of 5.75 [45] was used to calculate the 245 water conversion to hydrate as 6 water molecules are needed to form CO2 hydrate (CO2.6H2O). 246 The sample prepared by the highest rates of stirring had the maximum water conversion to hydrate 247 with a value of 40.50 ± 2.28 mol%. The amount of gas uptake was directly related to the amount 248 of water conversion to hydrate. Hence, the gas uptake obtained for the prepared sample was the 249 highest amount of CO2 molecules with a value of 0.29 mmol. Additionally, it was observed that 250 the sample with the greater equilibrium moisture contents yielded the maximum water conversion 251 to hydrate. 252 253 Moreover, the sample prepared by the highest rates of stirring demonstrated the fastest kinetics in 254 which the initial rate of hydrate formation was more than 0.05 mmol of CO2/g of H2O/min. Overall, 255 the silica contacted with water from vigorous stirring showed the best results and reproducibility. 256 Thus, the silica contacted with water was used as a baseline result for comparison purposes. 257 11 Additionally, in the hydrate forming region, the equilibrium mole fraction of CO2 in water was 258 reduced as temperature decreased [40]. Thus, highest solubility of CO2 observed in the water at 259 lowest temperature that was due to the existence of CO2 hydrate. 3.3 Effect of driving forces in hydrate forming region 277 [48] studied the formation of hydrate in pure CO2 by using STR with SDS and 301 TBAB) were preferably studied combined-promoters due to their great CO2 uptake ability 281 achieved at 275 K and 36 bar. Then, some additional experiments at 30 bar and 22 bar for T1-5 282 and T3-2 were performed. In each experiment, approximately 0.50 g wet silica was used and the 283 investigations were performed in HPVA for 1200 minutes. Then, the results were compared with 284 the baseline experiment at various driving forces. 285 TBAB) were preferably studied combined-promoters due to their great CO2 uptake ability 281 achieved at 275 K and 36 bar. Then, some additional experiments at 30 bar and 22 bar for T1-5 282 and T3-2 were performed. In each experiment, approximately 0.50 g wet silica was used and the 283 investigations were performed in HPVA for 1200 minutes. Then, the results were compared with 284 the baseline experiment at various driving forces. 285 The comparison of hydrate formation at various driving forces is illustrated in Fig. 3 and Fig. 4. 287 Fig. 3 (a) and Fig. 3(b) shows that T3-2 had a highest water conversion to hydrate and CO2 uptake 288 at 275 K and 30 bar respectively followed by T1-5 and the baseline experiment. However, T1-5 289 demonstrated the best results at 275 K and 22 bar as shown in Fig. 4(a) and Fig. 4(b) with T3-2 290 and baseline experiment obtaining almost identical results. Table 2 summarizes the gas uptake 291 obtained by each sample at various operating pressures. Generally, the gas uptake for all samples 292 increased as the driving force (∆P) increased from 5 to 19 bar with T1-5 demonstrating the best 293 result at all driving force except at ∆P = 5 bar. Combined-promoters designated type T1-5 gives 294 the maximum value of CO2 uptake up to 5.95 ± 0.21 mmol of CO2 per g of H2O as ∆P increased 295 from 5 to 19 bar at constant temperature (275 K) that is in accord with the results reported in the 296 literature [47]. Even though the gas uptake of T3-2 was the highest at this driving force which was 297 almost 0.50 mmol of CO2 per g of H2O higher than T1-5. The total CO2 molecules captured by 298 T1-5 was the highest (0.17 mmol) which was 0.03 mmol higher than T3-2. 3.3 Effect of driving forces in hydrate forming region 277 A study was performed to investigate the effect of driving force (∆P) on hydrate formation. Various 278 operating pressures (36, 30 and 22 bar) in pure CO2 gas were investigated at 275 K by employing 279 silica contacted with different combined-promoters. T1-5 and T3-2 (0.01 mol% SDS + 0.10 mol% 280 12 TBAB) were preferably studied combined-promoters due to their great CO2 uptake ability 281 achieved at 275 K and 36 bar. Then, some additional experiments at 30 bar and 22 bar for T1-5 282 and T3-2 were performed. In each experiment, approximately 0.50 g wet silica was used and the 283 investigations were performed in HPVA for 1200 minutes. Then, the results were compared with 284 the baseline experiment at various driving forces. 285 286 The comparison of hydrate formation at various driving forces is illustrated in Fig. 3 and Fig. 4. 287 Fig. 3 (a) and Fig. 3(b) shows that T3-2 had a highest water conversion to hydrate and CO2 uptake 288 at 275 K and 30 bar respectively followed by T1-5 and the baseline experiment. However, T1-5 289 demonstrated the best results at 275 K and 22 bar as shown in Fig. 4(a) and Fig. 4(b) with T3-2 290 and baseline experiment obtaining almost identical results. Table 2 summarizes the gas uptake 291 obtained by each sample at various operating pressures. Generally, the gas uptake for all samples 292 increased as the driving force (∆P) increased from 5 to 19 bar with T1-5 demonstrating the best 293 result at all driving force except at ∆P = 5 bar. Combined-promoters designated type T1-5 gives 294 the maximum value of CO2 uptake up to 5.95 ± 0.21 mmol of CO2 per g of H2O as ∆P increased 295 from 5 to 19 bar at constant temperature (275 K) that is in accord with the results reported in the 296 literature [47]. Even though the gas uptake of T3-2 was the highest at this driving force which was 297 almost 0.50 mmol of CO2 per g of H2O higher than T1-5. The total CO2 molecules captured by 298 T1-5 was the highest (0.17 mmol) which was 0.03 mmol higher than T3-2. This is expected due 299 to the higher amount of available water molecules attained by T1-5, 1.30 mmol higher than T3-2. 300 In past, Silva et al. 3.3 Effect of driving forces in hydrate forming region 277 Hence, the results showed that 316 high operating pressure enhanced the formation of hydrate due to greater driving force (∆P). In 317 addition, different samples had diverse effects on hydrate formation at different driving forces. In 318 past, Kobayashi et al. [49] said a batch system is assumed to instantaneously keep itself in 319 thermodynamic equilibrium and Mori et al. [50] referenced that the change in gas phase 320 arrangement in batch mode is unavoidably convoyed by a change in the guest molecule 321 composition in an instantaneously formed hydrate. These can be associated with a decrease in 322 driving force in batch mode upon hydrate growth wherein in a pure CO2 system, this effect was 323 only observed when the initial operating pressure was below 30 bar. At high initial operating 324 pressure (36 bar), a massive ratio of CO2 to water molecules was expected to provide an extra 325 driving force, which explained the high CO2 uptake, obtained. 326 In contrast to T1-5, the total CO2 molecules captured by the baseline experiment were lower at all 312 driving forces even though the amount of water molecules available for hydrate formation was 313 higher than T1-5 by almost 0.50 mmol. However, the CO2 molecules captured by the baseline 314 experiment were higher than T3-2 at all driving forces except at ∆P = 13 bar. In addition, at this 315 medium driving force, T3-2 exhibited the closest result to T1-5. Hence, the results showed that 316 high operating pressure enhanced the formation of hydrate due to greater driving force (∆P). In 317 addition, different samples had diverse effects on hydrate formation at different driving forces. In 318 past, Kobayashi et al. [49] said a batch system is assumed to instantaneously keep itself in 319 thermodynamic equilibrium and Mori et al. [50] referenced that the change in gas phase 320 arrangement in batch mode is unavoidably convoyed by a change in the guest molecule 321 composition in an instantaneously formed hydrate. These can be associated with a decrease in 322 driving force in batch mode upon hydrate growth wherein in a pure CO2 system, this effect was 323 only observed when the initial operating pressure was below 30 bar. At high initial operating 324 pressure (36 bar), a massive ratio of CO2 to water molecules was expected to provide an extra 325 driving force, which explained the high CO2 uptake, obtained. 3.3 Effect of driving forces in hydrate forming region 277 This is expected due 299 to the higher amount of available water molecules attained by T1-5, 1.30 mmol higher than T3-2. 300 In past, Silva et al. [48] studied the formation of hydrate in pure CO2 by using STR with SDS and 301 THF as promoters. They inferred that if just SDS was utilized, clathrate hydrate was formed in a 302 traditional manner yet when THF was combined with SDS in an ideal extent, it was possible to 303 13 13 observe crystals of THF hydrate which stabilized the framework and acted as a promoter of CO2 304 hydrate. Moreover, Yang et al. [39] performed a study on phase equilibrium for the THF-CO2- 305 H2O system which showed a drastic decrease in pressure in the presence of 3.00 mol% THF and 306 SDS (at all concentrations). Also, the highest equilibrium temperature obtained was 291.55 K at 307 30 bar in the presence of 3.0 mol% THF and 0 mg/L SDS respectively. The experiments on hydrate 308 formation have indicated that CO2 hydrate forms rapidly at all experimental pressures when the 309 SDS concentration is 1000 ppm which indicates that SDS enhances the hydrate formation rate. 310 311 observe crystals of THF hydrate which stabilized the framework and acted as a promoter of CO2 304 hydrate. Moreover, Yang et al. [39] performed a study on phase equilibrium for the THF-CO2- 305 H2O system which showed a drastic decrease in pressure in the presence of 3.00 mol% THF and 306 SDS (at all concentrations). Also, the highest equilibrium temperature obtained was 291.55 K at 307 30 bar in the presence of 3.0 mol% THF and 0 mg/L SDS respectively. The experiments on hydrate 308 formation have indicated that CO2 hydrate forms rapidly at all experimental pressures when the 309 SDS concentration is 1000 ppm which indicates that SDS enhances the hydrate formation rate. 310 311 In contrast to T1-5, the total CO2 molecules captured by the baseline experiment were lower at all 312 driving forces even though the amount of water molecules available for hydrate formation was 313 higher than T1-5 by almost 0.50 mmol. However, the CO2 molecules captured by the baseline 314 experiment were higher than T3-2 at all driving forces except at ∆P = 13 bar. In addition, at this 315 medium driving force, T3-2 exhibited the closest result to T1-5. 3.3 Effect of driving forces in hydrate forming region 277 326 14 3.3.1 Kinetic additives effect of hydrate formation 327 3.3.1 Kinetic additives effect of hydrate formation 327 Generally, an increase in the driving force increases the gas uptake and kinetic rate of hydrate 328 formation. Fig. 5 illustrates that the initial rate of clathrate formation of T3-2 at 275 K and 30 bar 329 was the fastest that was 13% greater than T1-5 and almost 70% faster than the baseline experiment. 330 However, the initial rate of clathrate formation at 275 K and 22 bar as shown in Fig. 6 was the 331 fastest for T1-5 with the value of 0.012 mmol of CO2 per g of H2O per min followed by T3-2 332 (0.005 mmol of CO2 per g of H2O per min) and baseline experiment (0.004 mmol of CO2 per g of 333 H2O per min). TBAB inhibit the hydrate formation but the combining promoter SDS used in the 334 formation of T3-2 mitigate the inhibition effect of TBAB on hydrate formation only to some extent. 335 Therefore, the rate of hydrate formation and CO2 uptake of T3-2 is lower than that of T1-5. In view 336 of these observations, it was inferred that THF displayed the quickest kinetics when it is joined 337 with SDS of 0.01 mol%, practically more than half (50%) a solitary promoter alone at a similar 338 concentration. In this way, it was affirmed that 0.01 mol% of SDS joined with THF gave the most 339 maximum rate of clathrate formation and also CO2 uptake due to reinforcing combined effect of 340 promoters. Hence, T1-5 was proved to be the best option for hydrate formation at low driving 341 force. These findings are in concurrence with the consequences of Kang et al. [51] who 342 investigated the formation of hydrate in bulk water (cluster of water molecules) at different 343 pressure and found that CO2 uptakes increase as the operating pressure increased. In contrast, 344 Zheng et al. [29] studied CO2 semi clathrate formation under various concentration of promoters 345 in HBGS at a driving temperature and reported that the CO2 uptakes increase as the operating 346 temperature sets up to 4.1 K. Thus, as ∆P increases or as ∆T decreases, the driving force also 347 increases that indicates the successful formation of CO2 hydrate. 348 Generally, an increase in the driving force increases the gas uptake and kinetic rate of hydrate 328 formation. Fig. 3.4 Enhanced hydrate formation in non-hydrate forming region 349 3.4 Enhanced hydrate formation in non-hydrate forming region 349 The use of promoters could enhance hydrate formation as the baseline experiment did not show 350 any hydrate formation at 288 K and 36 bar. Each promoter was extensively investigated by 351 previous researchers where SDS [41] can avoid the development of obstructing hydrate film whilst 352 TBAB [35] and THF [43] can form semi-clathrate and sII hydrates respectively. Both types of 353 hydrate are said to entrap more CO2 molecules in the small cage of sII hydrate and semi-clathrate 354 hydrate cavities correspondingly [52]. Moreover, several researchers [53, 54] have investigated 355 the effect of combining SDS and THF on CO2 hydrate formation and they discovered that the 356 synergic effect improves hydrate formation. 357 358 However, the synergic effect of combining SDS and TBAB has not yet been reported in the 359 literature. Herein, the hydrate formation is investigated in non-hydrate forming region at 36 bar 360 and various operating temperatures by employing pure CO2 gas and novel combined-promoters. 361 Yang et al. [39] plotted the phase equilibrium of hydrate formation in pure CO2 gas system and 362 showed that at 36 bar, the equilibrium temperature was 280 K. In this study, the operating 363 temperature of 288 K led to the driving force of ∆T = 8 K and for 293 K, ∆T = 13 K. Unlike ∆P, 364 the highest value of ∆T was equivalent to the lowest driving force available for the system because 365 the operating conditions could be shifted to the right-hand side of phase equilibrium, also known 366 as the non-hydrate forming region. This study was then used as a basis for the investigation of 367 hydrate formation at IGCC plant operating conditions. 368 3.4.1 Combined promoters effect at various driving forces 369 Further investigation was performed by employing three combined-promoters (T1-5, T3-2 and 370 The use of promoters could enhance hydrate formation as the baseline experiment did not show 350 any hydrate formation at 288 K and 36 bar. Each promoter was extensively investigated by 351 previous researchers where SDS [41] can avoid the development of obstructing hydrate film whilst 352 TBAB [35] and THF [43] can form semi-clathrate and sII hydrates respectively. Both types of 353 hydrate are said to entrap more CO2 molecules in the small cage of sII hydrate and semi-clathrate 354 hydrate cavities correspondingly [52]. 3.4 Enhanced hydrate formation in non-hydrate forming region 349 Moreover, several researchers [53, 54] have investigated 355 the effect of combining SDS and THF on CO2 hydrate formation and they discovered that the 356 synergic effect improves hydrate formation. 357 However, the synergic effect of combining SDS and TBAB has not yet been reported in the 359 literature. Herein, the hydrate formation is investigated in non-hydrate forming region at 36 bar 360 and various operating temperatures by employing pure CO2 gas and novel combined-promoters. 361 Yang et al. [39] plotted the phase equilibrium of hydrate formation in pure CO2 gas system and 362 showed that at 36 bar, the equilibrium temperature was 280 K. In this study, the operating 363 temperature of 288 K led to the driving force of ∆T = 8 K and for 293 K, ∆T = 13 K. Unlike ∆P, 364 the highest value of ∆T was equivalent to the lowest driving force available for the system because 365 the operating conditions could be shifted to the right-hand side of phase equilibrium, also known 366 as the non-hydrate forming region. This study was then used as a basis for the investigation of 367 hydrate formation at IGCC plant operating conditions. 368 3.3.1 Kinetic additives effect of hydrate formation 327 5 illustrates that the initial rate of clathrate formation of T3-2 at 275 K and 30 bar 329 was the fastest that was 13% greater than T1-5 and almost 70% faster than the baseline experiment. 330 However, the initial rate of clathrate formation at 275 K and 22 bar as shown in Fig. 6 was the 331 fastest for T1-5 with the value of 0.012 mmol of CO2 per g of H2O per min followed by T3-2 332 (0.005 mmol of CO2 per g of H2O per min) and baseline experiment (0.004 mmol of CO2 per g of 333 H2O per min). TBAB inhibit the hydrate formation but the combining promoter SDS used in the 334 formation of T3-2 mitigate the inhibition effect of TBAB on hydrate formation only to some extent. 335 Therefore, the rate of hydrate formation and CO2 uptake of T3-2 is lower than that of T1-5. In view 336 of these observations, it was inferred that THF displayed the quickest kinetics when it is joined 337 with SDS of 0.01 mol%, practically more than half (50%) a solitary promoter alone at a similar 338 concentration. In this way, it was affirmed that 0.01 mol% of SDS joined with THF gave the most 339 maximum rate of clathrate formation and also CO2 uptake due to reinforcing combined effect of 340 promoters. Hence, T1-5 was proved to be the best option for hydrate formation at low driving 341 force. These findings are in concurrence with the consequences of Kang et al. [51] who 342 investigated the formation of hydrate in bulk water (cluster of water molecules) at different 343 pressure and found that CO2 uptakes increase as the operating pressure increased. In contrast, 344 Zheng et al. [29] studied CO2 semi clathrate formation under various concentration of promoters 345 in HBGS at a driving temperature and reported that the CO2 uptakes increase as the operating 346 temperature sets up to 4.1 K. Thus, as ∆P increases or as ∆T decreases, the driving force also 347 increases that indicates the successful formation of CO2 hydrate. 348 15 3.4.1 Combined promoters effect at various driving forces 369 Further investigation was performed by employing three combined-promoters (T1-5, T3-2 and 370 T1A-2) at the 288 K and 36 bar operating conditions. Then, T1-5 and T3-2 were employed for the 371 16 investigation at 293 K and 36 bar. All experiments were conducted for 1200 minutes and 0.5 g of 372 silica contacted with combined-promoter was used for each experiment. Fig. 7 (a) illustrates the 373 conversion of water to hydrate at 288 K and 36 bar wherein T3-2 was found to show the best result 374 with around 10 mol% conversion. This was followed by T1-5 and THF with both having a 375 conversion around 9 mol%, followed by T1A-2 and SDS with around 6 mol% for both 376 conversions. The water conversion to hydrate and gas uptake results for SDS and THF reported 377 here are in accordance with the results reported in the literature [47]. Fig. 7 (b) and Table 3 show 378 that the highest gas uptake was observed for T1-5 with the value of 1.25 mmol of CO2 per g of 379 H2O followed by THF (1.15 mmol of CO2 per g of H2O), T3-2 (1.00 mmol of CO2 per g of H2O), 380 T1A-2 (0.68 mmol of CO2 per g of H2O) and SDS (0.66 mmol of CO2 per g of H2O). 381 382 The results showed that by adding THF, TBAB and EGME to SDS, water conversion to the 383 clathrate formation and the maximum gas uptake was increased accordingly. Significant 384 improvement was observed when 5.60 mol% THF was added to 0.01 mol% SDS with almost 385 double gas uptake obtained as compared to SDS (0.01 mol%) alone. In addition, during the study 386 of hydrate phase equilibria of mixed hydrates having CO2 and N2, the gas uptake for 3 mol% THF 387 alone was almost comparable to T1-5 which showed that THF was a very good promoter for 388 hydrate formation at high temperature [55]. The same trend was observed for T3-2 in which 0.10 389 mol% TBAB was added to 0.01 mol% SDS. However, 0.1 mol% EGME only showed a minimal 390 effect on hydrate formation when it was added to 0.01 mol% SDS. Based on the results obtained 391 at these operating conditions, T1-5 and T3-2 were further investigated at 293 K and 36 bar. Fig. 3.4.1 Combined promoters effect at various driving forces 369 8 392 (a) also demonstrates that T3-2 had the best water conversion to water entrapped clathrate with a 393 conversion of around 6 mol% at temperature of 293 K and pressure of 36 bar. This was followed 394 investigation at 293 K and 36 bar. All experiments were conducted for 1200 minutes and 0.5 g of 372 silica contacted with combined-promoter was used for each experiment. Fig. 7 (a) illustrates the 373 conversion of water to hydrate at 288 K and 36 bar wherein T3-2 was found to show the best result 374 with around 10 mol% conversion. This was followed by T1-5 and THF with both having a 375 conversion around 9 mol%, followed by T1A-2 and SDS with around 6 mol% for both 376 conversions. The water conversion to hydrate and gas uptake results for SDS and THF reported 377 here are in accordance with the results reported in the literature [47]. Fig. 7 (b) and Table 3 show 378 that the highest gas uptake was observed for T1-5 with the value of 1.25 mmol of CO2 per g of 379 H2O followed by THF (1.15 mmol of CO2 per g of H2O), T3-2 (1.00 mmol of CO2 per g of H2O), 380 T1A-2 (0.68 mmol of CO2 per g of H2O) and SDS (0.66 mmol of CO2 per g of H2O). 381 investigation at 293 K and 36 bar. All experiments were conducted for 1200 minutes and 0.5 g of 372 silica contacted with combined-promoter was used for each experiment. Fig. 7 (a) illustrates the 373 conversion of water to hydrate at 288 K and 36 bar wherein T3-2 was found to show the best result 374 with around 10 mol% conversion. This was followed by T1-5 and THF with both having a 375 conversion around 9 mol%, followed by T1A-2 and SDS with around 6 mol% for both 376 conversions. The water conversion to hydrate and gas uptake results for SDS and THF reported 377 here are in accordance with the results reported in the literature [47]. Fig. 3.4.1 Combined promoters effect at various driving forces 369 As 402 a result, fewer CO2 molecules were consumed in hydrate formation at 288 K for T3-2, which was 403 0.02 mmol less than T1-5. Moreover, slightly high error bars for T3-2 observed at these operating 404 conditions, were due to regeneration experiment performed by reusing the same sample. However, 405 other regeneration experiments demonstrated quite high regeneration values as shown in Table 3. 406 Finally, the CO2 molecules captured at 293 K were comparable for both samples which showed 407 that THF and TBAB demonstrated the same effect at this operating temperature. 408 by T1-5 being almost 50% lower than T3-2. Though, the maximum gas uptake for T1-5 was 0.03 395 CO2 (mmol)/ H2O (g) CO2 per g of H2O higher than T3-2 as presented in Fig. 8 (b) and Table 3. 396 However, the maximum gas uptake for samples T1-5 and T3-2 reported in Fig. 8 (b) shows 397 consistency within the estimated uncertainties of reported results. 398 by T1-5 being almost 50% lower than T3-2. Though, the maximum gas uptake for T1-5 was 0.03 395 CO2 (mmol)/ H2O (g) CO2 per g of H2O higher than T3-2 as presented in Fig. 8 (b) and Table 3. 396 However, the maximum gas uptake for samples T1-5 and T3-2 reported in Fig. 8 (b) shows 397 consistency within the estimated uncertainties of reported results. 398 The same trend was observed at both operating temperatures due to high equilibrium moisture 400 content in T1-5 which was 50% higher than T3-2. Thus, T3-2 demonstrated the highest water 401 conversion to hydrate as compared to T1-5 due to lower water presence inside silica gel pores. As 402 a result, fewer CO2 molecules were consumed in hydrate formation at 288 K for T3-2, which was 403 0.02 mmol less than T1-5. Moreover, slightly high error bars for T3-2 observed at these operating 404 conditions, were due to regeneration experiment performed by reusing the same sample. However, 405 other regeneration experiments demonstrated quite high regeneration values as shown in Table 3. 406 Finally, the CO2 molecules captured at 293 K were comparable for both samples which showed 407 that THF and TBAB demonstrated the same effect at this operating temperature. 408 3.4.1 Combined promoters effect at various driving forces 369 7 (b) and Table 3 show 378 that the highest gas uptake was observed for T1-5 with the value of 1.25 mmol of CO2 per g of 379 H2O followed by THF (1.15 mmol of CO2 per g of H2O), T3-2 (1.00 mmol of CO2 per g of H2O), 380 T1A-2 (0.68 mmol of CO2 per g of H2O) and SDS (0.66 mmol of CO2 per g of H2O). 381 The results showed that by adding THF, TBAB and EGME to SDS, water conversion to the 383 clathrate formation and the maximum gas uptake was increased accordingly. Significant 384 improvement was observed when 5.60 mol% THF was added to 0.01 mol% SDS with almost 385 double gas uptake obtained as compared to SDS (0.01 mol%) alone. In addition, during the study 386 of hydrate phase equilibria of mixed hydrates having CO2 and N2, the gas uptake for 3 mol% THF 387 alone was almost comparable to T1-5 which showed that THF was a very good promoter for 388 hydrate formation at high temperature [55]. The same trend was observed for T3-2 in which 0.10 389 mol% TBAB was added to 0.01 mol% SDS. However, 0.1 mol% EGME only showed a minimal 390 effect on hydrate formation when it was added to 0.01 mol% SDS. Based on the results obtained 391 at these operating conditions, T1-5 and T3-2 were further investigated at 293 K and 36 bar. Fig. 8 392 (a) also demonstrates that T3-2 had the best water conversion to water entrapped clathrate with a 393 conversion of around 6 mol% at temperature of 293 K and pressure of 36 bar. This was followed 394 17 by T1-5 being almost 50% lower than T3-2. Though, the maximum gas uptake for T1-5 was 0.03 395 CO2 (mmol)/ H2O (g) CO2 per g of H2O higher than T3-2 as presented in Fig. 8 (b) and Table 3. 396 However, the maximum gas uptake for samples T1-5 and T3-2 reported in Fig. 8 (b) shows 397 consistency within the estimated uncertainties of reported results. 398 399 The same trend was observed at both operating temperatures due to high equilibrium moisture 400 content in T1-5 which was 50% higher than T3-2. Thus, T3-2 demonstrated the highest water 401 conversion to hydrate as compared to T1-5 due to lower water presence inside silica gel pores. 3.4.2 Kinetic additives effect of hydrate formation 409 The 432 effect of promoters in mitigating hydrate phase equilibria to the hydrate forming region was 433 explained earlier in which THF and TBAB are known as thermodynamic promoters due to their 434 ability to form sII and semi-clathrate hydrates respectively that attracted more CO2 molecules to 435 get involved in hydrate formation. Thus, this was the reason CO2 uptake was almost 2 mmol of 436 CO2 per g of H2O when T1-5 and T3-2 combined-promoters were employed in FBR. Therefore, 437 at 293 K temperature and pressure condition of 36 bar, T1-5 and T3-2 demonstrated almost 438 comparable rates of hydrate formation as illustrated in Fig. 10. This indicated that at high 439 temperature, TBAB was the best alternative to THF to be employed together with SDS. 440 CO2 molecules for occupancy in small cages. The role of TBAB in T3-2 combined-promoter 418 provided more cavities for the occupancy of CO2 molecules by forming semi-clathrate hydrate. 419 Moreover, the ability of TBAB to readily form semi-clathrate hydrate in hydrate forming 420 conditions caused TBA+ to occupy large cage leaving the small cages empty/partially empty which 421 reduced the formation of CO2 hydrate to 0.29 mol% of TBAB. Another EGME promoter was 422 considered as an alternative to THF due to the ability of EGME molecules to act as structure maker 423 solutes when dissolved in water. However, the gas uptake of EGME containing T1A-2 sample was 424 just 9% lower than T1-5 and the total CO2 molecules consumed was only 0.05 mmol lower. 425 Therefore the initial kinetics of the sample that employed THF alone were faster than T3-2 and 426 T1A-2 and slightly slower than T1-5 which showed that THF was the best promoter to be 427 combined with SDS for enhancing clathrate formation. Even though the hydrate phase equilibrium 428 mitigated the hydrate forming region with the presence of combined-promoters, it significantly 429 affects CO2 uptake and hydrate formation if temperature and pressure conditions changed below 430 or above to their respective optimum range. The hydrate phase equilibria promoting the lower 431 pressure and high temperature regions when the thermodynamic promoters were introduced. 3.4.2 Kinetic additives effect of hydrate formation 409 Fig. 9 illustrates the rate of clathrate formation at 288 K and 36 bar where the addition of 5.60 410 mol% THF to form T1-5 significantly increased the initial kinetics of silica contacted with single 411 SDS (0.01 mol%) from 0.005 to 0.015 mmol of CO2 per g of H2O per min. Moreover, the addition 412 of 0.10 mol% TBAB and 0.10 mol% EGME in 0.01 mol% SDS also doubled the initial rate of 413 hydrate formation for single SDS as illustrated by T3-2 and T1A-2 respectively. These indicated 414 that the combination of other promoters with SDS enhanced the kinetics of hydrate formation 415 known as a synergic effect. The synergic effect of T1-5 was obtained from SDS which avoided 416 the development of obstructing hydrate film whilst THF formed sII hydrate which attracted more 417 18 CO2 molecules for occupancy in small cages. The role of TBAB in T3-2 combined-promoter 418 provided more cavities for the occupancy of CO2 molecules by forming semi-clathrate hydrate. 419 Moreover, the ability of TBAB to readily form semi-clathrate hydrate in hydrate forming 420 conditions caused TBA+ to occupy large cage leaving the small cages empty/partially empty which 421 reduced the formation of CO2 hydrate to 0.29 mol% of TBAB. Another EGME promoter was 422 considered as an alternative to THF due to the ability of EGME molecules to act as structure maker 423 solutes when dissolved in water. However, the gas uptake of EGME containing T1A-2 sample was 424 just 9% lower than T1-5 and the total CO2 molecules consumed was only 0.05 mmol lower. 425 Therefore the initial kinetics of the sample that employed THF alone were faster than T3-2 and 426 T1A-2 and slightly slower than T1-5 which showed that THF was the best promoter to be 427 combined with SDS for enhancing clathrate formation. Even though the hydrate phase equilibrium 428 mitigated the hydrate forming region with the presence of combined-promoters, it significantly 429 affects CO2 uptake and hydrate formation if temperature and pressure conditions changed below 430 or above to their respective optimum range. The hydrate phase equilibria promoting the lower 431 pressure and high temperature regions when the thermodynamic promoters were introduced. 3.4.2 Kinetic additives effect of hydrate formation 409 The 432 effect of promoters in mitigating hydrate phase equilibria to the hydrate forming region was 433 explained earlier in which THF and TBAB are known as thermodynamic promoters due to their 434 ability to form sII and semi-clathrate hydrates respectively that attracted more CO2 molecules to 435 get involved in hydrate formation. Thus, this was the reason CO2 uptake was almost 2 mmol of 436 CO2 per g of H2O when T1-5 and T3-2 combined-promoters were employed in FBR. Therefore, 437 at 293 K temperature and pressure condition of 36 bar, T1-5 and T3-2 demonstrated almost 438 comparable rates of hydrate formation as illustrated in Fig. 10. This indicated that at high 439 temperature, TBAB was the best alternative to THF to be employed together with SDS. 440 19 3.5 Thermodynamically shifted hydrate phase equilibrium in IGCC 441 conditions 442 One of the most important findings in this work was the ability of combined-promoters to shift the 443 hydrate phase equilibrium to a higher operating temperature. Fig. 11 demonstrates the hydrate 444 phase equilibrium for pure CO2. As the use of solid adsorbent for hydrate formation will lead to 445 the use of a fluidized bed reactor (FBR). Previously, some works on the application of FBR by 446 using pure CO2 gas were performed by Yang et al. [39, 52], Mekala et al. [56] and Kumar et al. 447 [37]. Kumar et al. [37] and Mekala et al. [56] investigated FBR (also known as HPVA) in which 448 0.25 mm silica gel and 0.46 mm silica sand (particle sizes) were employed respectively with no 449 improvement in hydrate phase equilibrium compared to bulk water [57] as shown in Fig. 11. 450 451 3.5 Thermodynamically shifted hydrate phase equilibrium in IGCC 441 conditions 442 One of the most important findings in this work was the ability of combined-promoters to shift the 443 hydrate phase equilibrium to a higher operating temperature. Fig. 11 demonstrates the hydrate 444 phase equilibrium for pure CO2. As the use of solid adsorbent for hydrate formation will lead to 445 the use of a fluidized bed reactor (FBR). Previously, some works on the application of FBR by 446 using pure CO2 gas were performed by Yang et al. [39, 52], Mekala et al. [56] and Kumar et al. 447 [37]. Kumar et al. [37] and Mekala et al. 3.4.2 Kinetic additives effect of hydrate formation 409 [56] investigated FBR (also known as HPVA) in which 448 0.25 mm silica gel and 0.46 mm silica sand (particle sizes) were employed respectively with no 449 improvement in hydrate phase equilibrium compared to bulk water [57] as shown in Fig. 11. 450 451 3.5 Thermodynamically shifted hydrate phase equilibrium in IGCC 441 conditions 442 However, Yang et al. [39, 52] managed to prove that the application of combined-promoters at 452 optimum concentrations with 3 mol% of THF + 0.01 mol% SDS and equivalent concentration of 453 THF + TBAB inside glass bead pores shifted the phase equilibrium to a higher temperature region 454 (290 and 291 K respectively). In addition, Yang et al. [52] also discovered that both THF and 455 TBAB showed the same role in thermodynamically shifting the phase equilibrium to a higher 456 temperature region. At the same concentration of TBAB (5 mol%), the temperature increased from 457 286 to 291 K at operating pressure of 35 bar as the concentration of THF increased from 0–5 458 mol%. Also, at the same concentration of THF (5 mol%) and 35 bar, the temperature was observed 459 to increase from 289 to 291 K as the concentration of TBAB increased from 0–5 mol%. 460 Moreover, Joshi et al. [58] reported that the addition of SDS did not mitigate the phase equilibrium 462 of CO2 -TBAB-H2O system while Yang et al. [52] mentioned that SDS is known as a kinetic 463 additive which can change the kinetic properties and has no influence on the hydrate phase 464 Moreover, Joshi et al. [58] reported that the addition of SDS did not mitigate the phase equilibrium 462 of CO2 -TBAB-H2O system while Yang et al. [52] mentioned that SDS is known as a kinetic 463 additive which can change the kinetic properties and has no influence on the hydrate phase 464 20 equilibrium [59]. Thus, the presence of thermodynamic promoters i.e. THF and TBAB in 465 combined type promoters T1-5 and T3-2 respectively inside silica gel in this work (Table 1) 466 promoted the phase equilibrium to 293 K and not the existence of 0.01 mol% SDS. Furthermore, 467 the R square value of this study, interpreting from the fitness of data set, shows more goodness of 468 fit with the value of 0.96 in comparison to the studies reported in the literature (Fig. 11). 469 4 Additives effect for CO2 hydrate formation 470 In past, massive efforts have been done to enhance the driving forces and gas uptake of CO2 471 hydrate formation by adding different thermodynamic and kinetic additives such as THF, SDS, 472 tetra-butyl ammonium salts and Cyclopentane so that it can readily be applied for pre-combustion 473 capture. THF and SDS can be effectively used to mitigate hydrate formation conditions, promote 474 hydrate growth rate and improve separation efficiency. Ricaurte et al. [54] studied the effect of 475 several additives on CO2 hydrate formation in which SDS was paired with one of the 476 thermodynamic promoters (THF, 1,3-dioxolane, 2-methyl-THF and CP) and THF was paired with 477 one of the kinetic promoters (SDS, SDBS and DATCI). The results highlight that the combination 478 of SDS and THF was the best for the formation of CO2 hydrate from natural gas. However, Torre 479 et al. [53] mentioned that the combination of THF and SDS compared to the single promoter was 480 very advantageous in accelerating hydrate. Herslund et al. [60] presented new equilibrium data for 481 the quaternary system H2O-THF-CP-CO2 which lowers equilibrium pressure of the system by 25- 482 30% due to the formation of CP and THF hydrates simultaneously. Li et al. [61] discovered that 483 the addition of CP into a TBAB solution remarkably enhanced the CO2 separation and speed up 484 the hydrate nucleation rate. While Yang et al. [52] performed a hydrate phase equilibrium 485 investigation on various combinations of THF and TBAB concentrations in pure CO2 gas system 486 and found that the THF-TBAB system greatly shifted the hydrate phase equilibrium to the higher 487 21 temperature region around 291 K at an operating pressure of 42 bar. In spite of great advancement 488 in the study of additives, the investigations are limited to the application inside stirred tank reactor. 489 Therefore, some works must have been done to investigate the synergic effect of additives so that 490 the system can readily be applied in IGCC conditions and this study successfully finds a solution 491 and a way forward to utilize novel T1A-2 and T3-2 promoters in IGCC condition. 492 493 5 Conclusions 494 Three novel combined promoters namely T1-5, T3-2 and T1A-2 were investigated. The effect of 495 these combined promoters and various driving forces on the formation of CO2 hydrates were 496 successfully investigated in IGCC conditions. Overall, the gas uptake for all samples in hydrate 497 forming conditions increased as the driving force (∆P) of the pure CO2 system increased. 498 Combined-promoters designated type T1-5 demonstrated the best result with the value of CO2 499 uptake increasing from 0.86 ± 0.09 to 5.95 ± 0.21 mmol of CO2 per g of H2O as ∆P increased 500 from 5 to 19 bar at constant temperature (275 K). In contrast, the gas uptake was reduced from 501 5.95 ± 0.21 to 0.45 ± 0.07 mmol of CO2 per g of H2O as ∆T increased from -5 to 13 K at constant 502 pressure (36 bar). In general, the amount of available water inside silica gel pores determined total 503 number of CO2 molecules captured through hydrate formation. Combined-promoters designated 504 type T3-2 captured the fewest CO2 molecules at all driving forces due to the lowest amount of 505 available moisture content. However, T3-2 achieved an optimum result at CO2 partial pressure of 506 30 bar (identical to the IGCC operating pressure of 70 bar) where the total number of CO2 507 molecules captured were 0.01 mmol higher than the baseline experiment (0.13 mmol) due to 508 synergic effect. Thus, the study on non-hydrate forming region by employing pure CO2 gas led to 509 the selection of 283 K and 36 bar as the operating conditions in IGCC by employing pure CO2 510 22 wherein combined-promoters designated types T3-2 were chosen as an adsorbent to enhance CO2 511 capture by HBGS technique. Conclusively these results recommend that several improvements 512 can be considered to improve hydrate formation in the IGCC conditions by considering different 513 factors that were discussed in this work. In future, the study on the selectivity of CO2 gas molecules 514 towards hydrate formation in fuel gas mixture by gas chromatography (GC) analysis and the 515 improvement of reactor configuration by employing macroporous or mesoporous silicas (silica 516 sand or gel) with combined-promoters are suggested. 517 wherein combined-promoters designated types T3-2 were chosen as an adsorbent to enhance CO2 511 capture by HBGS technique. References 519 [1] H.-W. Schiffer, T. Kober, E. Panos, World Energy Council’s Global Energy Scenarios to 2060, 520 Zeitschrift für Energiewirtschaft, 42 (2018) 91-102. 521 Zeitschrift für Energiewirtschaft, 42 (2018) 91-102. 521 [2] S.P. Mathur, A. Arya, Impact of Emission Trading on Optimal Bidding of Price Takers in a 522 Competitive Energy Market, in: Harmony Search and Nature Inspired Optimization Algorithms, 523 Springer, 2019, pp. 171-180. 524 p g pp [3] A. Antenucci, G. 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Bedecarrats, 1, 3 649 Dioxolane versus tetrahydrofuran as promoters for CO2-hydrate formation: Thermodynamics 650 properties, and kinetics in presence of sodium dodecyl sulfate, Chemical Engineering Science, 126 651 (2015) 688-697. 652 26 [54] M. Ricaurte, C. Dicharry, X. Renaud, J.-P. Torré, Combination of surfactants and organic 653 compounds for boosting CO2 separation from natural gas by clathrate hydrate formation, Fuel, 654 122 (2014) 206-217. 655 [55] S.-P. Kang, H. Lee, C.-S. Lee, W.-M. Sung, Hydrate phase equilibria of the guest mixtures 656 containing CO2, N2 and tetrahydrofuran, Fluid Phase Equilibria, 185 (2001) 101-109. 657 [56] P. Mekala, M. Busch, D. Mech, R.S. Patel, J.S. [61] X.-S. Li, C.-G. Xu, Z.-Y. Chen, J. Cai, Synergic effect of cyclopentane and tetra-n-butyl 672 ammonium bromide on hydrate-based carbon dioxide separation from fuel gas mixture by 673 measurements of gas uptake and X-ray diffraction patterns, international journal of hydrogen 674 energy, 37 (2012) 720-727. 675 References 519 Sangwai, Effect of silica sand size on the 658 formation kinetics of CO2 hydrate in porous media in the presence of pure water and seawater 659 relevant for CO2 sequestration, Journal of Petroleum Science and Engineering, 122 (2014) 1-9. 660 [57] J. Carroll, Natural gas hydrates (a guide for engineers), Second Edition ed., Elsevier Inc USA: 661 Burlington, 2009. 662 [58] A. Joshi, J.S. Sangwai, K. Das, N.A. Sami, Experimental investigations on the phase 663 equilibrium of semiclathrate hydrates of carbon dioxide in TBAB with small amount of surfactant, 664 International Journal of Energy and Environmental Engineering, 4 (2013) 11. 665 [59] A. Kumar, G. Bhattacharjee, B. Kulkarni, R. Kumar, Role of surfactants in promoting gas 666 hydrate formation, Industrial & Engineering Chemistry Research, 54 (2015) 12217-12232. 667 [60] P.J. Herslund, K. Thomsen, J. Abildskov, N. Von Solms, A. Galfré, P. Brântuas, M. 668 Kwaterski, J.-M. Herri, Thermodynamic promotion of carbon dioxide–clathrate hydrate formation 669 by tetrahydrofuran, cyclopentane and their mixtures, International Journal of Greenhouse Gas 670 Control, 17 (2013) 397-410. 671 [61] X.-S. Li, C.-G. Xu, Z.-Y. Chen, J. Cai, Synergic effect of cyclopentane and tetra-n-butyl 672 ammonium bromide on hydrate-based carbon dioxide separation from fuel gas mixture by 673 measurements of gas uptake and X-ray diffraction patterns, international journal of hydrogen 674 energy, 37 (2012) 720-727. 675 27 27 List of Tables List of Tables Table 1. The amount of promoters used to prepare each combined-promoter (brief description of each code T1-5, T3-2 and T1A-2). Table 1. The amount of promoters used to prepare each combined-promoter (brief description of each code T1-5, T3-2 and T1A-2). No. Type of combined- promoter Concentration and mass of promoter Mass of water (g) THF SDS TBAB EGME mol% g mol% g mol% g mol% g 1 T1-5 5.60 9.11 0.01 0.07 - - - - 38.39 2 T3-2 - - 0.01 0.08 0.10 0.84 - - 46.66 3 T1A-2 - - 0.01 0.08 - - 0.10 0.23 47.26 Table 1. The amount of promoters used to prepare each combined-promoter (brief descripti T1-5, T3-2 and T1A-2). nt of promoters used to prepare each combined-promoter (brief description of each code A-2) 28 28 Table 2. Comparison of gas uptake for T1-5, T3-2 and baseline experiment at 275 K and 36, 30 and 22 bar in 1200 minutes. Operating conditions Sample Exp. No. No. r regeneration experiment References 519 of moles of water (mmol) CO2 formed in hydrate (mmol) Mean CO2 formed in hydrate (mmol) CO2 uptake (mmol of CO2/g of H2O) Mean CO2 uptake (mmol of CO2/g of H2O) (90% CI) SD 275 K and 36 bar T1-5 1 3.70 0.39 0.40 5.82 5.95 ± 0.21 0.18 2 3.70 0.41 6.08 T3-2 1 2.40 0.23 0.24 5.36 5.57 ± 0.34 0.29 2 2.40 0.25 5.77 SiG- H2O 1 4.10 0.29 0.31 3.93 4.04 ± 0.17 0.15 2 4.30 0.32 4.14 275 K and 30 bar T1-5 1 3.70 0.15 0.17 2.62 2.81 ± 0.30 0.26 2 3.70 0.18 2.99 T3-2 1 2.40 0.13 0.14 3.09 3.28 ± 0.31 0.27 2 2.40 0.15 3.47 SiG- H2O 1 4.20 0.14 0.13 1.82 1.71 ± 0.19 0.16 2 4.10 0.12 1.60 275 K and 22 bar T1-5 1 3.70 0.05 0.05 0.91 0.86 ± 0.09 0.08 2 3.70 0.04 0.80 T3-2 1 2.40 0.01 0.01 0.35 0.30 ± 0.09 0.08 2 2.40 0.01 0.24 SiG- H2O 1 4.10 0.02 0.03 0.28 0.32 ± 0.06 0.05 2 4.20 0.03 0.35 1-5, T3-2 and baseline experiment at 275 K and 36, 30 and 22 bar in 1200 minutes. 29 Table 3. The comparison of gas uptake at 36 bar and operating temperatures of 288 K and 293 K in 1200 minutes. Operating conditions Sample Exp. No. No. of moles of water (mmol) CO2 formed in hydrate (mmol) Mean CO2 formed in hydrate (mmol) Water conversion to hydrate (mol%) Mean water conversion to hydrate (mol%) CO2 uptake (mmol of CO2/g of H2O) Mean CO2 uptake (mmol of CO2/g of H2O) (90% CI) SD 288 K and 36 bar T1-5 1 3.70 0.07 0.07 1.26 1.25 ± 0.01 0.01 2 r 3.70 0.07 1.24 T3-2 1 2.40 0.05 0.05 1.12 1.00 ± 0.20 0.17 2r 2.40 0.04 0.88 T1A-2 1 3.50 0.05 0.05 0.76 0.68 ± 0.13 0.11 2 r 3.50 0.04 0.60 SiG- THF 1 3.50 0.06 0.07 1.17 1.15 ± 0.03 0.03 2 3.50 0.07 1.13 SiG- SDS 1 3.70 0.04 0.04 0.62 0.66 ± 0.06 0.05 2 3.60 0.04 0.69 293 K and 36 bar T1-5 1 3.70 0.02 0.02 0.41 0.45 ± 0.07 0.06 2 r 3.70 0.02 0.49 T3-2 1 2.40 0.02 0.03 0.41 0.42 ± 0.01 0.01 2 2.30 0.03 0.42 r ti i t Table 3. References 519 The comparison of gas uptake at 36 bar and operating temperatures of 288 K and 293 K in 1200 minutes. 36 bar and operating temperatures of 288 K and 293 K in 1200 minutes. 30 List of Figures Fig. 1. Schematic representation of HPVA for hydrate formation. Fig. 1. Schematic representation of HPVA for hydrate formation. 31 Fig. 2. P-t curves show 2-stage pressure drop in 1200 min for standard silica gel sample. Fig. 2. P-t curves show 2-stage pressure drop in 1200 min for standard silica gel sample. 32 32 32 Fig. 3. Comparison of experiments at 275 K and 30 bar in 1200 min; (a) Water convers hydrate, (b) Gas uptake for T1-5, T3-2 and baseline. Fig. 3. Comparison of experiments at 275 K and 30 bar in 1200 min; (a) Water conversion to hydrate, (b) Gas uptake for T1-5, T3-2 and baseline. 33 Fig. 4. Comparison of experiments at 275 K and 22 bar in 1200 min; (a) Water conversion hydrate, (b) Gas uptake for T1-5, T3-2 and baseline. Fig. 4. Comparison of experiments at 275 K and 22 bar in 1200 min; (a) Water conversion to hydrate, (b) Gas uptake for T1-5, T3-2 and baseline. 34 Fig. 5. Rate of hydrate formation at 275 K and 30 bar for 1200 minutes and inset for the first 150 minutes (T1-5, T3-2 and baseline experiment). Fig. 5. Rate of hydrate formation at 275 K and 30 bar for 1200 minutes and inset for the first 150 minutes (T1-5, T3-2 and baseline experiment). 35 35 35 Fig. 6. Rate of hydrate formation at 275 K and 22 bar for 1200 minutes and inset for the first 150 minutes (T1-5, T3-2 and baseline experiment). Fig. 6. Rate of hydrate formation at 275 K and 22 bar for 1200 minutes and inset for the first 150 minutes (T1-5, T3-2 and baseline experiment). 36 Fig. 7. The comparison of experiments at 288 K and 36 bar in 1200 min; (a) Water conversion hydrate, (b) Gas uptake for T1-5, T3-2, T1-A and baseline. Fig. 7. The comparison of experiments at 288 K and 36 bar in 1200 min; (a) Water conversion to hydrate, (b) Gas uptake for T1-5, T3-2, T1-A and baseline. 37 Fig. 8. The comparison of experiments at 293 K and 36 bar in 1200 min; (a) Water convers hydrate, (b) Gas uptake for T1-5 and T3-2. Fig. 8. References 519 The comparison of experiments at 293 K and 36 bar in 1200 min; (a) Water conversion to hydrate, (b) Gas uptake for T1-5 and T3-2. 38 Fig. 9. Rate of hydrate formation at 288 K and 36 bar for 1200 minutes and inset for the first 150 minutes (T1-5, T3-2, T1A-2 and baseline experiments). Fig. 9. Rate of hydrate formation at 288 K and 36 bar for 1200 minutes and inset for the first 150 minutes (T1-5, T3-2, T1A-2 and baseline experiments). 39 39 Fig. 10. Rate of hydrate formation at 293 K and 36 bar for 1200 minutes and inset for the first 500 minutes (T1-5 and T3-2). Fig. 10. Rate of hydrate formation at 293 K and 36 bar for 1200 minutes and inset for the first 500 minutes (T1-5 and T3-2). 40 Fig. 11. Comparison of hydrate phase equilibrium of pure CO2 gas of this study with Yang et al. [52], Yang et al. [39], Kumar et al. [37], Mekala et al. [56] and Carrol work [57]. Fig. 11. Comparison of hydrate phase equilibrium of pure CO2 gas of this study with Yang et al. [52], Yang et al. [39], Kumar et al. [37], Mekala et al. [56] and Carrol work [57]. 41 41
W264471300.txt
https://journals.iucr.org/e/issues/2009/02/00/at2706/at2706.pdf
en
2-(2-Thienyl)-4,5-dihydro-1<i>H</i>-imidazole
Acta crystallographica. Section E
2,009
cc-by
3,436
addenda and errata Acta Crystallographica Section E Data collection Structure Reports Online Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2005) Tmin = 0.825, Tmax = 0.922 ISSN 1600-5368 2-(2-Thienyl)-4,5-dihydro-1H-imidazole. Corrigendum Reza Kia,a‡ Hoong-Kun Funa*§ and Hadi Kargarb 28316 measured reflections 3100 independent reflections 3040 reflections with I > 2(I) Rint = 0.021 Refinement R[F 2 > 2(F 2)] = 0.027 wR(F 2) = 0.080 S = 1.15 3100 reflections 96 parameters H atoms treated by a mixture of independent and constrained refinement max = 0.52 e Å3 min = 0.24 e Å3 a X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bDepartment of Chemistry, School of Science, Payame Noor University (PNU), Ardakan, Yazd, Iran Correspondence e-mail: hkfun@usm.my Received 5 May 2009; accepted 18 May 2009 Key indicators: single-crystal X-ray study; T = 100 K; mean (C–C) = 0.001 Å; R factor = 0.027; wR factor = 0.080; data-to-parameter ratio = 32.3. Table 1 Hydrogen-bond geometry (Å,  ). D—H  A D—H H  A D  A D—H  A N1—H1  N2i C3—H3A  N2i 0.857 (16) 0.95 2.130 (16) 2.59 2.9803 (10) 3.4815 (11) 171.5 (16) 156 Symmetry code: (i) x; y þ 12; z þ 12. Consideration of a previous unrecognized twinning of the original investigated crystal of the title compound [Kia et al. (2009). Acta Cryst. E65, o301] led to improved reliability factors and to a slightly higher precision for all geometric parameters. The crystal under investigation was twinned by pseudo-merohedry with [100, 010, 001] as the twin matrix and a refined twin domain fraction of 0.9610 (5):0.0390 (5). The results of the new crystal structure refinement are given here. Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009). Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: WM2233). Experimental References Crystal data C7H8N2S Mr = 152.21 Monoclinic, P21 =c a = 6.1321 (2) Å b = 11.5663 (3) Å c = 10.0098 (3) Å  = 90.154 (1) V = 709.95 (4) Å3 Z=4 Mo K radiation  = 0.37 mm1 T = 100 K 0.54  0.28  0.22 mm Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc. Madison, Wisconsin, USA. Kia, R., Fun, H.-K. & Kargar, H. (2009). Acta Cryst. E65, o301. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Spek, A. L. (2009). Acta Cryst. D65, 148–155. ‡ Thomson Reuters ResearcherID: A-5471-2009. § Thomson Reuters ResearcherID: A-3561-2009. Acta Cryst. (2009). E65, e15 doi:10.1107/S1600536809018790 Kia et al. e15 supporting information supporting information Acta Cryst. (2009). E65, e15 [https://doi.org/10.1107/S1600536809018790] 2-(2-Thienyl)-4,5-dihydro-1H-imidazole. Corrigendum Reza Kia, Hoong-Kun Fun and Hadi Kargar 2-(2-Thienyl)-4,5-dihydro-1H-imidazole Crystal data C7H8N2S Mr = 152.21 Monoclinic, P21/c Hall symbol: -P 2ybc a = 6.1321 (2) Å b = 11.5663 (3) Å c = 10.0098 (3) Å β = 90.154 (1)° V = 709.95 (4) Å3 Z=4 F(000) = 320 Dx = 1.424 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 9869 reflections θ = 2.5–34.3° µ = 0.37 mm−1 T = 100 K Block, colourless 0.54 × 0.28 × 0.22 mm Data collection Bruker SMART APEXII CCD area-detector diffractometer Radiation source: fine-focus sealed tube Graphite monochromator φ and ω scans Absorption correction: multi-scan (SADABS; Bruker, 2005) Tmin = 0.825, Tmax = 0.922 28316 measured reflections 3100 independent reflections 3040 reflections with I > 2σ(I) Rint = 0.021 θmax = 35.0°, θmin = 1.8° h = −9→9 k = −18→17 l = −15→15 Refinement Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.027 wR(F2) = 0.080 S = 1.15 3100 reflections 96 parameters 0 restraints Primary atom site location: structure-invariant direct methods Acta Cryst. (2009). E65, e15 Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H atoms treated by a mixture of independent and constrained refinement w = 1/[σ2(Fo2) + (0.0391P)2 + 0.2148P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = 0.001 Δρmax = 0.52 e Å−3 Δρmin = −0.24 e Å−3 sup-1 supporting information Special details Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K. Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) S1 N2 N1 C1 H1A C2 H2A C3 H3A C4 C5 C6 H6A H6B C7 H7A H7B H1 x y z Uiso*/Ueq 0.46976 (3) 0.06708 (11) 0.04589 (11) 0.63940 (14) 0.7552 0.58842 (14) 0.6646 0.40890 (13) 0.3524 0.32621 (12) 0.14267 (12) −0.15422 (13) −0.1723 −0.2848 −0.11001 (13) −0.2425 −0.0643 0.058 (3) 0.141639 (18) 0.29657 (6) 0.30384 (6) 0.05379 (8) 0.0101 0.05399 (7) 0.0100 0.12729 (7) 0.1382 0.18073 (6) 0.26046 (6) 0.36275 (7) 0.4380 0.3144 0.37870 (7) 0.3611 0.4591 0.2686 (14) 0.59512 (2) 0.61145 (7) 0.83752 (7) 0.68566 (9) 0.6480 0.81867 (9) 0.8839 0.84861 (8) 0.9360 0.73587 (7) 0.72548 (7) 0.79460 (8) 0.8404 0.8103 0.64400 (8) 0.5911 0.6248 0.9125 (16) 0.01527 (6) 0.01355 (11) 0.01323 (11) 0.01780 (15) 0.021* 0.01659 (14) 0.020* 0.01337 (13) 0.016* 0.01149 (12) 0.01079 (11) 0.01479 (14) 0.018* 0.018* 0.01491 (13) 0.018* 0.018* 0.025 (4)* Atomic displacement parameters (Å2) S1 N2 N1 C1 C2 C3 C4 C5 C6 C7 U11 U22 U33 U12 U13 U23 0.01701 (9) 0.0150 (3) 0.0146 (3) 0.0174 (3) 0.0188 (3) 0.0164 (3) 0.0132 (3) 0.0119 (3) 0.0138 (3) 0.0147 (3) 0.01822 (10) 0.0168 (3) 0.0166 (3) 0.0179 (3) 0.0151 (3) 0.0128 (3) 0.0117 (3) 0.0114 (3) 0.0178 (3) 0.0179 (3) 0.01059 (9) 0.0088 (2) 0.0084 (2) 0.0181 (4) 0.0159 (3) 0.0109 (3) 0.0096 (3) 0.0090 (3) 0.0127 (3) 0.0121 (3) 0.00444 (6) 0.0027 (2) 0.0032 (2) 0.0052 (3) 0.0033 (3) 0.0005 (2) 0.0006 (2) −0.0006 (2) 0.0027 (2) 0.0035 (2) 0.00195 (6) −0.0001 (2) 0.0013 (2) 0.0000 (3) −0.0028 (3) −0.0005 (2) 0.0003 (2) 0.0006 (2) 0.0021 (2) 0.0001 (2) −0.00027 (6) 0.0007 (2) 0.0004 (2) −0.0017 (3) 0.0004 (2) 0.0004 (2) −0.0002 (2) −0.0005 (2) 0.0005 (2) 0.0020 (2) Acta Cryst. (2009). E65, e15 sup-2 supporting information Geometric parameters (Å, º) S1—C1 S1—C4 N2—C5 N2—C7 N1—C5 N1—C6 N1—H1 C1—C2 C1—H1A C2—C3 1.7120 (9) 1.7236 (8) 1.2996 (10) 1.4798 (11) 1.3657 (10) 1.4669 (11) 0.858 (16) 1.3684 (13) 0.9500 1.4221 (12) C2—H2A C3—C4 C3—H3A C4—C5 C6—C7 C6—H6A C6—H6B C7—H7A C7—H7B 0.9500 1.3819 (11) 0.9500 1.4586 (10) 1.5435 (12) 0.9900 0.9900 0.9900 0.9900 C1—S1—C4 C5—N2—C7 C5—N1—C6 C5—N1—H1 C6—N1—H1 C2—C1—S1 C2—C1—H1A S1—C1—H1A C1—C2—C3 C1—C2—H2A C3—C2—H2A C4—C3—C2 C4—C3—H3A C2—C3—H3A C3—C4—C5 C3—C4—S1 91.94 (4) 105.85 (6) 107.17 (6) 120.4 (11) 123.3 (11) 111.96 (6) 124.0 124.0 112.65 (7) 123.7 123.7 112.15 (7) 123.9 123.9 128.49 (7) 111.29 (6) C5—C4—S1 N2—C5—N1 N2—C5—C4 N1—C5—C4 N1—C6—C7 N1—C6—H6A C7—C6—H6A N1—C6—H6B C7—C6—H6B H6A—C6—H6B N2—C7—C6 N2—C7—H7A C6—C7—H7A N2—C7—H7B C6—C7—H7B H7A—C7—H7B 120.21 (5) 116.64 (7) 122.62 (7) 120.71 (6) 101.10 (6) 111.6 111.6 111.6 111.6 109.4 105.62 (6) 110.6 110.6 110.6 110.6 108.7 C4—S1—C1—C2 S1—C1—C2—C3 C1—C2—C3—C4 C2—C3—C4—C5 C2—C3—C4—S1 C1—S1—C4—C3 C1—S1—C4—C5 C7—N2—C5—N1 C7—N2—C5—C4 0.09 (7) −0.35 (10) 0.50 (11) 179.29 (8) −0.43 (9) 0.20 (7) −179.55 (7) 0.30 (9) −177.67 (7) C6—N1—C5—N2 C6—N1—C5—C4 C3—C4—C5—N2 S1—C4—C5—N2 C3—C4—C5—N1 S1—C4—C5—N1 C5—N1—C6—C7 C5—N2—C7—C6 N1—C6—C7—N2 12.15 (9) −169.84 (7) −173.20 (8) 6.50 (10) 8.92 (12) −171.38 (6) −17.77 (8) −11.91 (9) 17.89 (8) Hydrogen-bond geometry (Å, º) D—H···A i N1—H1···N2 C3—H3A···N2i D—H H···A D···A D—H···A 0.857 (16) 0.95 2.130 (16) 2.59 2.9803 (10) 3.4815 (11) 171.5 (16) 156 Symmetry code: (i) x, −y+1/2, z+1/2. Acta Cryst. (2009). E65, e15 sup-3 organic compounds Acta Crystallographica Section E Data collection Structure Reports Online Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2005) Tmin = 0.825, Tmax = 0.922 ISSN 1600-5368 2-(2-Thienyl)-4,5-dihydro-1H-imidazole Refinement Reza Kia,a Hoong-Kun Funa* and Hadi Kargarb R[F 2 > 2(F 2)] = 0.050 wR(F 2) = 0.128 S = 1.24 3100 reflections a X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bDepartment of Chemistry, School of Science, Payame Noor University (PNU), Ardakan, Yazd, Iran Correspondence e-mail: hkfun@usm.my 27675 measured reflections 3100 independent reflections 3040 reflections with I > 2(I) Rint = 0.021 91 parameters H-atom parameters constrained max = 0.62 e Å3 min = 0.39 e Å3 Table 1 Hydrogen-bond geometry (Å,  ). Received 8 January 2009; accepted 9 January 2009 D—H  A D—H H  A D  A D—H  A 0.75 0.95 0.99 0.99 2.23 2.60 2.89 2.83 2.977 3.482 3.539 3.691 171 155 124 146 Key indicators: single-crystal X-ray study; T = 100 K; mean (C–C) = 0.002 Å; R factor = 0.050; wR factor = 0.128; data-to-parameter ratio = 34.1. N1—H1N1  N2 C3—H3A  N2i C6—H6A  Cg1ii C6—H6B  Cg1iii In title compound, C7H8N2S, the five-membered rings are twisted by a dihedral angle of 5.17 (10) . Two intermolecular N—H  N and C—H  N hydrogen bonds to the same acceptor N atom form seven-membered rings, producing R12(7) ring motifs. These interactions link neighbouring molecules into one-dimensional chains extended along the c axis. The crystal structure is further stabilized by weak intermolecular C—H   interactions. Symmetry codes: (i) x; y þ 12; z þ 12; (ii) x; y þ 12; z þ 32; (iii) x  1; y; z. Cg1 is the centroid of the S1/C1–C4 (thiophen) ring. Related literature For reference geometrical data, see: Allen et al. (1987). For details of hydrogen-bond motifs, see: Bernstein et al. (1995). For a related structure and the synthesis, see, Kia et al. (2008); Stibrany et al. (2004). For the applications of imidazoline derivatives, see, for example: Blancafort (1978); Chan (1993); Vizi (1986); Li et al. (1996); Ueno et al. (1995); Corey & Grogan (1999). i (2) (2) (2) (2) Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003). HKF and RK thanks the Malaysian Government and Universiti Sains Malaysia for the Science Fund grant No. 305/ PFIZIK/613312. RK thanks Universiti Sains Malaysia for a post-doctoral research fellowship. HK thanks PNU for the financial support. HKF also thanks Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/ PFIZIK/811012. Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: AT2706). References Experimental Crystal data C7H8N2S Mr = 152.21 Monoclinic, P21 =c a = 6.1321 (2) Å b = 11.5663 (3) Å c = 10.0098 (3) Å  = 90.154 (1) Acta Cryst. (2009). E65, o301 V = 709.95 (4) Å3 Z=4 Mo K radiation  = 0.37 mm1 T = 100.0 (1) K 0.54  0.28  0.22 mm Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19. Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573. Blancafort, P. (1978). Drugs Future, 3, 592–592. Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Chan, S. (1993). Clin. Sci. 85, 671–677. Corey, E. J. & Grogan, M. J. (1999). Org. Lett. 1, 157–160. Kia, R., Fun, H.-K. & Kargar, H. (2008). Acta Cryst. E64, o2406. Li, H. Y., Drummond, S., De Lucca, I. & Boswell, G. A. (1996). Tetrahedron, 52, 11153–11162. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13. Stibrany, R. T., Schugar, H. J. & Potenza, J. A. (2004). Acta Cryst. E60, o527– o529. Ueno, M., Imaizumi, K., Sugita, T., Takata, I. & Takeshita, M. (1995). Int. J. Immunopharmacol. 17, 597–603. Vizi, E. S. (1986). Med. Res. Rev. 6, 431–449. doi:10.1107/S1600536809001068 Kia et al. o301 supporting information supporting information Acta Cryst. (2009). E65, o301 [doi:10.1107/S1600536809001068] 2-(2-Thienyl)-4,5-dihydro-1H-imidazole Reza Kia, Hoong-Kun Fun and Hadi Kargar S1. Comment Imidazoline derivatives are of great importance because they exhibit significant biological and pharmacological activities including antihypertensive (Blancafort 1978), antihyperglycemic (Chan 1993), antidepressive (Vizi 1986), antihypercholesterolemic (Li et al., 1996) and antiinflammatory properties (Ueno et al., 1995). These compounds are also used as catalysts and synthetic intermediates in some organic reactions (Corey & Grogan 1999). Due to these important applications of imidazolines, here we report the crystal structure of the title compound (I). In the title compound (I) (Fig. 1), bond lengths (Allen et al. 1987) and angles are within the normal ranges and are comparable with the related structures (Stibrany et al. 2004; Kia et al., 2008). The two five-membered rings are not coplanar to each other and twisted by a dihedral angle of 5.17 (10)°. Two intermolecular N—H···N and C—H···N hydrogen bonds involving a nitrogen atom as an acceptor form seven-membered rings, producing, R12(7) ring motifs (Table 1). These interactions link neighbouring molecules into 1-D extended chains along the c axis (, Fig. 2). The crystal structure is further stabilized by weak intermolecular C—H···π interactions [C6—H6A···Cg1i and C6—H6B···Cg1ii: (i) -x, 1/2 + y, 3/2 - z, (ii) -1 + x, y, z; Cg1 is the centroid of the S1/C1–C4 thiophene ring. S2. Experimental The synthetic method was based on the previous work (Stibrany et al. 2004), except that 10 mmol of 2-cyano-thiophene and 40 mmol of ethylenediamine was used. Single crystals suitable for X-ray diffraction were obtained by evaporation of a toluene solution at room temperature. S3. Refinement The hydrogen atom bound to N1 was located from the difference Fourier map and constrained to refine with the respective parent atom, see Table 1. The rest of the hydrogen atoms were positioned gemetrically and refined in a riding model approximation with C—H = 0.95–0.99 Å and Uiso (H) = 1.2 Ueq (C). Acta Cryst. (2009). E65, o301 sup-1 supporting information Figure 1 The molecular structure of (I) with atom labels and 50% probability ellipsoids for non-H atoms. Figure 2 The crystal packing of (I), viewed down the b-axis showing 1-D infinite chain along the c-axis by intermolecular N— H···N and C—H···N interactions. The intermolecular interactions are shown as dashed lines. 2-(2-Thienyl)-4,5-dihydro-1H-imidazole Crystal data C7H8N2S Mr = 152.21 Monoclinic, P21/c Hall symbol: -P 2ybc a = 6.1321 (2) Å b = 11.5663 (3) Å c = 10.0098 (3) Å β = 90.154 (1)° V = 709.95 (4) Å3 Z=4 Acta Cryst. (2009). E65, o301 F(000) = 320 Dx = 1.424 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 9869 reflections θ = 2.5–34.3° µ = 0.37 mm−1 T = 100 K Block, colourless 0.54 × 0.28 × 0.22 mm sup-2 supporting information Data collection Bruker SMART APEXII CCD area-detector diffractometer Radiation source: fine-focus sealed tube Graphite monochromator φ and ω scans Absorption correction: multi-scan (SADABS; Bruker, 2005) Tmin = 0.825, Tmax = 0.922 27675 measured reflections 3100 independent reflections 3040 reflections with I > 2σ(I) Rint = 0.021 θmax = 35.0°, θmin = 2.7° h = −9→9 k = −18→17 l = −15→15 Refinement Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.050 wR(F2) = 0.128 S = 1.24 3100 reflections 91 parameters 0 restraints Primary atom site location: structure-invariant direct methods Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ2(Fo2) + 1.7551P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max < 0.001 Δρmax = 0.62 e Å−3 Δρmin = −0.39 e Å−3 Special details Experimental. The low-temperature data was collected with the Oxford Cyrosystem Cobra low-temperature attachment. Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) S1 N2 N1 H1N1 C1 H1A C2 H2A C3 H3A C4 C5 C6 H6A H6B x y z Uiso*/Ueq 0.46967 (8) 0.0669 (2) 0.0460 (2) 0.0584 0.6387 (3) 0.7542 0.5888 (3) 0.6655 0.4092 (3) 0.3530 0.3260 (3) 0.1427 (3) −0.1543 (3) −0.1724 −0.2849 0.14161 (4) 0.29635 (14) 0.30376 (14) 0.2724 0.05389 (17) 0.0100 0.05418 (16) 0.0103 0.12742 (15) 0.1385 0.18060 (14) 0.26052 (14) 0.36276 (17) 0.4380 0.3144 0.59514 (4) 0.61122 (15) 0.83746 (14) 0.9026 0.6858 (2) 0.6482 0.81838 (19) 0.8835 0.84860 (17) 0.9360 0.73589 (16) 0.72556 (16) 0.79447 (17) 0.8403 0.8101 0.01548 (10) 0.0137 (2) 0.0133 (2) 0.016* 0.0180 (3) 0.022* 0.0169 (3) 0.020* 0.0136 (3) 0.016* 0.0117 (3) 0.0109 (3) 0.0154 (3) 0.018* 0.018* Acta Cryst. (2009). E65, o301 sup-3 supporting information C7 H7A H7B −0.1097 (3) −0.2423 −0.0634 0.37874 (16) 0.3615 0.4591 0.64419 (17) 0.5912 0.6252 0.0151 (3) 0.018* 0.018* Atomic displacement parameters (Å2) S1 N2 N1 C1 C2 C3 C4 C5 C6 C7 U11 U22 U33 U12 U13 U23 0.01727 (19) 0.0153 (6) 0.0148 (6) 0.0166 (7) 0.0186 (7) 0.0164 (7) 0.0131 (6) 0.0120 (6) 0.0143 (7) 0.0152 (7) 0.01847 (19) 0.0161 (6) 0.0170 (6) 0.0181 (8) 0.0155 (7) 0.0129 (7) 0.0120 (6) 0.0113 (6) 0.0186 (7) 0.0181 (7) 0.01071 (17) 0.0098 (6) 0.0080 (5) 0.0192 (8) 0.0167 (7) 0.0113 (6) 0.0100 (6) 0.0094 (6) 0.0132 (7) 0.0120 (7) 0.00446 (15) 0.0027 (5) 0.0029 (5) 0.0057 (6) 0.0029 (6) −0.0001 (5) 0.0005 (5) −0.0011 (5) 0.0030 (6) 0.0035 (6) 0.00185 (13) 0.0003 (4) 0.0016 (4) −0.0001 (6) −0.0034 (6) −0.0002 (5) −0.0003 (5) 0.0005 (5) 0.0019 (5) 0.0000 (5) −0.00026 (14) 0.0009 (5) 0.0004 (5) −0.0015 (6) 0.0009 (6) 0.0004 (5) −0.0005 (5) −0.0004 (5) 0.0007 (6) 0.0018 (5) Geometric parameters (Å, º) S1—C1 S1—C4 N2—C5 N2—C7 N1—C5 N1—C6 N1—H1N1 C1—C2 C1—H1A C2—C3 1.7099 (19) 1.7239 (17) 1.302 (2) 1.480 (2) 1.364 (2) 1.468 (2) 0.7501 1.362 (3) 0.9500 1.423 (3) C2—H2A C3—C4 C3—H3A C4—C5 C6—C7 C6—H6A C6—H6B C7—H7A C7—H7B 0.9500 1.381 (2) 0.9500 1.459 (2) 1.541 (2) 0.9900 0.9900 0.9900 0.9900 C1—S1—C4 C5—N2—C7 C5—N1—C6 C5—N1—H1N1 C6—N1—H1N1 C2—C1—S1 C2—C1—H1A S1—C1—H1A C1—C2—C3 C1—C2—H2A C3—C2—H2A C4—C3—C2 C4—C3—H3A C2—C3—H3A C3—C4—C5 C3—C4—S1 91.82 (9) 105.57 (14) 107.14 (14) 119.6 124.2 112.21 (14) 123.9 123.9 112.63 (16) 123.7 123.7 112.08 (15) 124.0 124.0 128.52 (15) 111.26 (13) C5—C4—S1 N2—C5—N1 N2—C5—C4 N1—C5—C4 N1—C6—C7 N1—C6—H6A C7—C6—H6A N1—C6—H6B C7—C6—H6B H6A—C6—H6B N2—C7—C6 N2—C7—H7A C6—C7—H7A N2—C7—H7B C6—C7—H7B H7A—C7—H7B 120.22 (12) 116.78 (15) 122.49 (15) 120.71 (14) 101.03 (13) 111.6 111.6 111.6 111.6 109.4 105.80 (14) 110.6 110.6 110.6 110.6 108.7 Acta Cryst. (2009). E65, o301 sup-4 supporting information C4—S1—C1—C2 S1—C1—C2—C3 C1—C2—C3—C4 C2—C3—C4—C5 C2—C3—C4—S1 C1—S1—C4—C3 C1—S1—C4—C5 C7—N2—C5—N1 C7—N2—C5—C4 −0.16 (16) −0.2 (2) 0.5 (2) 179.52 (17) −0.60 (19) 0.44 (14) −179.67 (15) 0.6 (2) −177.67 (15) C6—N1—C5—N2 C6—N1—C5—C4 C3—C4—C5—N2 S1—C4—C5—N2 C3—C4—C5—N1 S1—C4—C5—N1 C5—N1—C6—C7 C5—N2—C7—C6 N1—C6—C7—N2 11.9 (2) −169.73 (15) −173.27 (18) 6.9 (2) 8.5 (3) −171.36 (13) −17.79 (18) −12.26 (19) 18.12 (18) Hydrogen-bond geometry (Å, º) D—H···A i N1—H1N1···N2 C3—H3A···N2i C6—H6A···Cg1ii C6—H6B···Cg1iii D—H H···A D···A D—H···A 0.75 0.95 0.99 0.99 2.23 2.60 2.89 2.83 2.977 (2) 3.482 (2) 3.539 (2) 3.691 (2) 171 155 124 146 Symmetry codes: (i) x, −y+1/2, z+1/2; (ii) −x, y+1/2, −z+3/2; (iii) x−1, y, z. Acta Cryst. (2009). E65, o301 sup-5
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A54T polymorphism in the fatty acid binding protein 2 studies in a Saudi population with type 2 diabetes mellitus
Lipids in health and disease
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Abstract Background: Fatty acid-binding protein 2 (FABP2) is an intracellular protein expressed exclusively in the enterocytes of proximal small intestine. FABP2 has a high affinity for saturated and unsaturated long-chain fatty acids and is believed to be involved in the absorption and transport of dietary fatty acids. Methods: This is a case–control study conceded in 438 T2DM cases and 460 subjects with normal glucose levels and non-obese considered as healthy controls. Allelic discrimination was performed using TaqMan single- nucleotide polymorphism was carried out by real time-polymerase chain reaction (RT-PCR) assays using purified DNA. Results: Clinical data and anthropometric measurements except age, glucose levels and lipid profile of the patients were significantly different from those of the controls (p < 0.05). Statistical analyses failed to show any type of significant association of the polymorphism between cases and controls. However logistic regression analyses was suggests that the TT genotype is significantly associated with male patients (p = 0.001). None of the allele or genotypes of FABP2 A54T was associated with T2DM cases versus the controls (AT genotype, OR = 0.85 (0.64-1.12), p = 0.25; TT genotype, OR = 0.66 (0.39-1.11), p = 0.11; T allele, 0.82 (0.67-1.02), p = 0.08). Conclusion: In conclusion, this study suggests that the above named variant in FABP2 gene is not potential contributor to the risk of T2DM and related traits in a Saudi population. However TT genotype is a risk factor for the disease in males. Keywords: A54T polymorphism, FABP2 gene, Type 2 diabetes mellitus, Saudi population © 2014 Alharbi 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/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. Open Access A54T polymorphism in the fatty acid binding protein 2 studies in a Saudi population with type 2 diabetes mellitus Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 A54T polymorphism in the fatty acid binding protein 2 studies in a Saudi population with type 2 diabetes mellitus Khalid Khalaf Alharbi1†, Imran Ali Khan1*†, Mohammad D Bazzi2†, Nasser M Al-Daghri3, Tarique N Hasan4†, May Salem Alnbaheen5,6, Fawiziah Khalaf Alharbi7, Yazeed A Al-Sheikh1, Rabbani Syed1 and Mourad AM Aboul-Soud1 * Correspondence: imkhan@ksu.edu.sa †Equal contributors 1Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh 11433, Kingdom of Saudi Arabia Full list of author information is available at the end of the article Introduction relatives of T2DM patients is 3.62 times that in the com- mon population, so the researchers of various countries make great efforts to explore the T2DM susceptible genes. Once the T2DM susceptible genes are sought out, it means that the T2DM prevention clues have been found. It is an effective measure to screen the T2DM susceptible population and prevent T2DM progress. It is now generally considered that T2DM is not a sole disorder, but a multigenic disorder with extensive her- edity heterogeneous, categorized by high levels of glu- cose and metabolic disorders [3,4]. Obesity is one of the complication for T2DM and the leading cause of pre- ventable deaths and a serious health complications in the Saudi Arabia [5]. Type 2 diabetes mellitus (T2DM) is a chronic degenerative disease, phenotypically and genetically characterized by in- sulin resistance (IR) in insulin-target tissues, and impaired insulin secretion from pancreatic β-cells [1]. T2DM affects nearly 31.6% individuals in the Kingdom of Saudi Arabia [2]. The interaction of genetic and environmental factors is universally acknowledged as the primary underlying T2DM mechanism. The T2DM risk in the first degree * Correspondence: imkhan@ksu.edu.sa †Equal contributors 1Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh 11433, Kingdom of Saudi Arabia Full list of author information is available at the end of the article Page 2 of 6 Page 2 of 6 Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 samples were stored at −80°C. The rs1799883 polymorph- ism was genotyped using a TaqMan® SNP genotyping assay (Assay ID: C_2834835_10) on a 7300HT sequence detection system (Applied Biosystems, USA). Primers and probes were obtained from Applied Biosystems as Assays- by-Design™. Cases and controls were ensured to have even treatment during the assay procedure, and each plate included negative controls (with no DNA). Plates were read on the ABI Prism 7300 using the Sequence Detection Software (Applied Biosystems) using 40 PCR cycles (92°C denaturation for 15 seconds, 60°C annealing/extension for 60 seconds). Measurements were repeated for samples with failed genotypes. Assays that did not show >95% concordance were discarded and replaced with alterna- tive assays with the same tagging properties. Genome Wide Association Studies (GWAS) are power- ful tools to identify genetic variants that are associated with common diseases. So far, GWAS identified at least 50–52 genetic loci robustly associated with T2DM [6]. Statistical analysis ll l l All statistical analysis was carried out using the statistical program i.e. statistical package for social sciences (IBM SPSS 19.0 SPSS Inc., Chicago, USA). The difference of mean age of patients and controls were significantly differ- ent (Table 1). Hence in order to overcome the significance difference of mean age, logistic regression was performed and it was found that patients with ages 35 (1 patient), 72 (2 patients), 77 (2 patients), 84 (2 patients), 85 (2 patients) and 86 (2 patients) years were redundant whereas rest all the patient ages were significantly not different from those The aim of the present study was to investigate the contribution of A54T genetic polymorphism identified by Baier et al [12] in the FABP2 variants to risk of T2DM in a Saudi population, since this polymorphism results in a functionally altered FABP2 protein which confers suscepti- bility to metabolic disorders like T2DM, thereby to con- tribute to the personalized prevention of this condition and A54T polymorphism has been associated with T2DM disease in many but not all studies. Table 1 Demographic characteristics of the study population Controls (n = 460) T2DM (n = 438) p Age (Years) 45.99 ± 7.77 53.5 ± 10.78 <0.0001 Weight (kg) 76.61 ± 14.52 77.37 ± 13.55 0.41 Height (cm) 161.25 ± 8.79 161.10 ± 9.30 0.80 Body mass index (kg/m2) 29.22 ± 5.58 29.9 ± 5.89 0.95 Sex: Male/Female (52.6%)/(47.4%) (56.8%)/(43.2%) 0.0002 SBP (mmHg) 114.80 ± 8.04 125.83 ± 9.96 <0.0001 DBP (mmHg) 75.81 ± 6.20 81.25 ± 4.82 0.0001 Waist (cms) 89.75 ± 14.19 95.3 ± 18.96 <0.0001 Hips (cms) 101.75 ± 14.72 99.64 ± 16.52 0.61 FBS (mmol/L) 5.23 ± 0.61 12.92 ± 4.60 <0.0001 Triglycerides (mmol/L) 1.62 ± 0.86 2.24 ± 1.62 <0.0001 Cholesterol (mmol/L ) 5.04 ± 0.96 5.61 ± 1.26 <0.0001 HDL-C (mmol/L ) 0.64 ± 0.23 0.84 ± 0.37 <0.0001 LDL-C (mmol/L) 3.66 ± 0.85 3.76 ± 1.05 0.0008 Glucose (mmol/L) 5.7 ± 1.2 9.4 ± 1.5 0.0002 Insulin (μU/mL) 12.5 ± 1.8 16.2 ± 2.2 0.0002 HOMA-IR 3.15 ± 1.9 6.8 ± 2.4 0.00008 Note: Data represented as mean ± SD for continuous variables, pValues for independent t-test are given. A p-value significant at <0.05. NA, Not Analyzed/ Not Applicable. Table 1 Demographic characteristics of the study population Introduction Several genetic markers have now been implicated for T2DM development pathways involved in the disease [7,8]. Fatty acid binding protein 2 (FABP2) has been stud- ied as one of the marker, due to its role in the uptake, intracellular metabolism and excretion of long chain fatty acids. This gene is located on 4q28-q31 chromosomal re- gion, consist of approximately 3.4 kbs. Many polymor- phisms in FABP2 gene have already linked with metabolic phenotypes. The most extensively studies polymorphism was Alanine54threnonine (A54T) substitution at codon 54 of exon 2 that results from G to A nucleotide substitution and affects primary protein structure [9,10]. This change affects the ability of the protein to transport dietary fatty acids, which may elevate saturated fatty acids level in the serum which might induce endothelial dysfunction leading to increased cardiovascular mortality [11]. Materials and methods Selection of subjects This is a case–control study carried out in King Saud University, Riyadh, Saudi Arabia. In this study we have collected in about 900 subjects; 438 T2DM cases and 460 healthy controls from the capital city. All the normal controls were selected from the general population based on normal glucose values and non-obese subjects. The details of the collection of patients, inclusion and exclusion criteria were described in the prior publication [1]. Ethical approval for the study was achieved from the ethics committee, King Saud University. Written informed consent was obtained from each patient. Anthropometric and biochemical measurements of the patients involved in this study has been described in the prior publication [1]. DNA extraction and genotyping 5 mL of the venous blood was collected into plain (coagu- lated) and EDTA (anticoaggulated) tubes. Plain vacutainer consist of 3 mL of the serum sample was used to analyze the biochemical parameters and 2 mL of the EDTA sam- ple was used for molecular analysis. Genomic DNA was extracted from peripheral blood leukocytes using Norgen DNA extraction kit (Norgen Biotek corp, Canada). DNA Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 Page 3 of 6 Table 2 Distribution of FABP2 A54T genotypes and alleles of this study Genotype Patients’ n (%) Controls n (%) OR (CI = 95%) P value χ2 1 d. f. AA 220 (51.52) 260 (56.52) 1 (reference) 1 (reference) AT 170 (39.81) 171 (37.17) 0.85 (0.64-1.12) 0.25 1.12 TT 37 (8.66) 29 (6.30) 0.66 ( 0.39-1.11) 0.11 2.43 A 610 (71.42) 691 (75.10) 1 (reference) 1 (reference) T 224 (28.57) 229 (24.89) 0.82 (0.67-1.02) 0.08 3.06 AA + AT vs TT 0.7 (0.42-1.17) 0.18 1.79 TT + AT vs AA 1.22 (0.93-1.59) 0.13 2.22 The genotypic and allelic frequencies and dominant as recessive models of patients are significantly not different from controls. Table 2 Distribution of FABP2 A54T genotypes and alleles of this study The genotypic and allelic frequencies and dominant as recessive models of patients are significantly not different from controls. 0.82 (95% CI = 0.67-1.02); p = 0.08). There were no signifi- cant differences in both the genotypic and allelic frequen- cies between the cases as well as controls. However upon multiple logistic regression analysis TT genotype was found to be associated with male patients (OR = 1.24 95% CI = 0.09-0.60, p = 0.001) (Tables 3 and 4). FABP2 geno- typic frequencies of A54A, A54T, and T54T were 56.5%, 37.2%, and 6.3% in the control group, 51.52%, 39.81% and 8.66% in the T2DM group; allelic frequencies of Ala and Thr were 0.75 and 0.25 for the control group, 0.71 and 0.29 for the T2DM group. The odds ratio for any genotype of A54T SNP was not significantly related with the risk of developing T2DM in this studied population (for AA + AT vs TT; OR-0.7 (95% CI = 0.42-1.17); p = 0.12 and for TT + AT vs AA; OR-1.22 (95% CI = 0.93-1.59); p = 0.25) from the Saudi population. of controls. Hence those patients were excluded from the further calculations if genotypic and allelic analyses. DNA extraction and genotyping The sex ratio of patients and controls were also differ- ent significantly. So, separate multiple analyses after logistic regressions were performed for patient and con- trols. The allele and genotype frequencies of FABP2 gene in patients were compared to controls by chi-square analysis. The distribution of the genotypes deviates from Hardy-Weinberg equilibrium (HWE). Clinical characteris- tics of all the subjects were expressed as mean ± SD. Con- tinuous variables were compared between the groups using two-tailed student t-test. Odds ratios (ORs) and 95% CI, with adjustment for age, sex and BMI were calculated using multiple logistic regression analysis. All tests were conducted at the p < 0.05 level of significance. Clinical characteristics h l FABP2 is an intracellular protein expressed in the villus tips of the small intestine, has a high affinity for saturated and unsaturated long-chain fatty acids and is believed to be involved in the absorption and transport of dietary fatty acids [13]. The association between fatty acid metabolism and IR is well known, and the FABP2 gene has been sug- gested as a possible candidate gene in the development of IR and T2DM [14]. A54T polymorphism in FABP2 was investigated as a possible genetic factor associated with T2DM and Obesity. Studies examining the association of In this case–control study, we have carried out in almost 900 subjects; 438 patients with T2DM (216 females and 244 males, 45.99±7.77 years old) and 460 normal control subjects (200 female and 238 male, 53.5 ± 10.78 years old). The mean age was 60 years for patients and 59 years for the control group. Clinical and anthropometric data are revealed in Table 1 for T2DM patients and control subjects. The results show that T2DM subjects were significantly older than controls but anthropometric measurements and hip were not significant (p > 0.05). T2DM subjects appear to have higher levels of SBP, DBP, fasting glucose, insulin, HOMA-IR and lipid profile and waist (p < 0.05). Table 3 Genotypic distribution according to sex Patients AA AT TT Male 122 95 31 Female 98 86 6 Total 220 181 37 Controls Male 136 95 13 Female 124 76 16 Total 260 171 29 Table 3 Genotypic distribution according to sex Genotype frequencies Canani et al [26] showed that A54T polymorphism confers susceptibility to renal disease in T2DM patients. There are very few reports on the association of this poly- morphism with T2DM. Several studies from non-European ethnic backgrounds have reported a positive association between FABP2 variants and T2DM. A54T polymorphism was carried out in relation to multiple diseases and the re- ports are summarize in Table 5, which shows positive as- sociation with T2DM and a combination of other diseases like chronic kidney disease, Microalbminuria, postprandial fatty acids and with the glyburide therapy. In our study, we have examined only T2DM (n = 438) samples and that have not examined its association with other disease. 0.5 OR, Odds ratio, 95% CI-95% confidence interval; multiple logistic regression calculated by SPSS v.19, AA genotype was set as zero because redundancy A54T polymorphism with IR, T2DM and Obesity are contradictory and inconclusive [10]. The product of T al- lele of FABP2 possesses a greater affinity for long-chain FA than the A allele [15]. In addition, individuals with the T allele of this polymorphism were more insulin resistant than were those with the A allele [12]. The T allele was also shown to be associated with higher plasma levels of LDL-C [16] and dyslipidemia (high plasma concentration of triglycerides and low concentration of HDL-C) [17]. In addition, the T allele of A54T polymorphism has previ- ously been associated with atherothrombotic cerebral in- farction in individuals with metabolic syndrome [18] and a parental history of stroke in the Swedish population [19]. Moreover, it was associated with a 2- to 3.5- fold increase in cardiovascular risk in dyslipidemic men with diabetes There are several studies denote no association of the T allele with T2DM [27-29] and our study is supporting the above mentioned studies. In some studies, subjects were distributed in homozygous for the A allele (AA) and T allele carriers (AT and TT), mainly because there were only few subjects homozygous for the variant [23,30]. We observed the association of A54T polymorphism with Table 5 Association Studies of FABP2 A54T gene polymorphism on different ethnic groups S. Genotype frequencies Results for the genotypic distribution of FABP2 A54T polymorphism and the frequency of A and T alleles in patients and controls have been tabulated in Table 2. The genotype distribution for A54T polymorphism showed no deviation from HWE in both the case and control groups (χ2 = 0.37, p = 0.54). Genotyping of the A54T polymorph- ism in the FABP2 gene revealed that the allelic frequency of T allele was 0.285 in cases and 0.248 in controls (OR- Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 Page 4 of 6 Page 4 of 6 Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 Table 4 Calculation for the association of A54T genotypes with T2DM patients and control in male and female sexes OR 95% CI P Value Patients Genotypes AT Male 1 (reference) Female 1.1 (0.74-1.65) 0.62 TT Male 1 (reference) Female 1.24 (0.09-0.60) 0.001 Controls Genotypes AT Male 1 (reference) Female 0.87 (0.59-1.29) 0.5 TT Male Female 1.35 (0.62-2.91) 0.44 OR, Odds ratio, 95% CI-95% confidence interval; multiple logistic regression calculated by SPSS v.19, AA genotype was set as zero because redundancy Table 4 Calculation for the association of A54T genotypes with T2DM patients and control in male and female sexes Table 4 Calculation for the association of A54T genotypes with T2DM patients and control in male and female sexes OR 95% CI P Value compared with their dyslipidemic nondiabetic counter- parts [20]. We have now shown that A54T polymorphism was not significantly associated with T2DM, with the minor allele representing the risk factor for this condition. In the present study we investigated the association of FABP2 A54T polymorphism with T2DM in a Saudi population. To the best of our knowledge, this is the first study investigating the association of A54T polymorphism in a Saudi population. The frequency of T allele of A54T polymorphism was 0.29 similar to Greek and Caucasian population [21-23]. A54T polymorphism was identified via linkage disequilibrium map, as a haploblock spanning 50 kb that includes 22 SNPs. However, the T54 allele is present in only one of six possibilities among the frequent haplotypes (>2%). It is interesting that in this haploblock, there are no other known or putative genes except for FABP2 [24]. Previous studies of A54T polymorphisms investigated lipid related diseases such as coronary artery disease (CAD) [25]. Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 T2DM according to all possible genetic models (i.e. addi- tive, dominant and recessive). No association of A54T polymorphism was found with T2DM according to any genetic model used, a finding shared by other studies that examined such an association [31]. There are limitations to the study design as it is a case–control observational study rather than cross sectional or prospective study. We have chosen only one SNP (A54T) to study the T2DM disease. with and without type 2 diabetes mellitus. Clin Med Insights Endocrinol Diab 2014, 7:1–6. Diab 2014, 7:1 6. 3. Li YY, Wang LS, Lu XZ, Yang ZJ, Wang XM, Zhou CW, Xu J, Qian Y, Chen AL: CDKAL1 gene rs7756992 A/G polymorphism and type 2 diabetes mellitus: a meta-analysis of 62, 567 subjects. Sci Rep 2013, 4(3):3131. 4. Shen HB, Shen DB: An epidemiological study on genetic agent in type 2 diabetes mellitus. China Public Health 1999, 15:492–494. 5. Al-Daghri NM, Alkharfy KM, Al-Attas OS, Krishnaswamy S, Mohammed AK, Albagha OM, Alenad AM, Chrousos GP, Alokail MS: Association between type 2 diabetes mellitus-related SNP variants and obesity trait in a Saudi population. Mol Bio Rep 2014, 41:1731–1740. p p p 6. Wilson PW, Meigs JB, Sullivan X, Fox CS, Nathan DM, D’Agostino RB: prediction of incident diabetes mellitus in middle-aged adults: the Framingham offspring study. Arch Intern Med 2007, 167:1068–1074. 7. Albuquerque D, Nobrega C, Manco L: Association of FTO polymorphisms with obesity and obesity-related outcomes in Portuguese children. PLoS One 2013, 8(1):e54370. 6. Wilson PW, Meigs JB, Sullivan X, Fox CS, Nathan DM, D’Agostino RB: prediction of incident diabetes mellitus in middle-aged adults: the Framingham offspring study. Arch Intern Med 2007, 167:1068–1074. 7. Albuquerque D, Nobrega C, Manco L: Association of FTO polymorphisms with obesity and obesity-related outcomes in Portuguese children. PLoS One 2013, 8(1):e54370. In conclusion, the present study provides no evidence of any association between A54T polymorphism (rs1799883) in FABP2 gene and T2DM, suggesting that A54T poly- morphism is not a major risk factor for the T2DM. Over- all, this study indicates that A54T polymorphism could not affect directly the presence of T2DM due to the differ- ential absorption of long chain fatty acids in the presence of the T allele. Authors’ contributions AKK and BMD were main investigator of this study. IAK has plan the study protocol, drafted the manuscript, prepared the final version of the manuscript and CA. ANM has confirmed the T2DM samples. HTN has helped in the revision of the manuscript. AMS and AFK helped with the genotyping and interpretation of the data. SR, took care about the sample collection. AYA and AMAM has participated in the study coordination and took part in the statistical analysis. All authors read and approved the final manuscript. 11. Freathy RM, Mook-Kanamori DO, Sovio U, Prokopenko I, Timpson NJ, Berry DJ, Warrington NM, Widen E, Hottenga JJ, Kaakinen M, Lange LA, Bradfield JP, Kerkhof M, Marsh JA, Magi R, Chen CM, Lyon HN, Kirin M, Adair LS, Aulchenko YS, Bennett AJ, Borja JB, Bouatia-Naji N, Charoen P, Coin LJ, Cousminer DL, de Geus EJ, Deloukas P, Elliott P, Early Growth Genetics (EGG) Consortium, McCarthy MI: Variants in ADCY5 and near CCNL1 are associated with fetal growth and birth weight. Nat Genet 2010, 42:430–435. 11. Freathy RM, Mook-Kanamori DO, Sovio U, Prokopenko I, Timpson NJ, Berry DJ, Warrington NM, Widen E, Hottenga JJ, Kaakinen M, Lange LA, Bradfield JP, Kerkhof M, Marsh JA, Magi R, Chen CM, Lyon HN, Kirin M, Adair LS, Aulchenko YS, Bennett AJ, Borja JB, Bouatia-Naji N, Charoen P, Coin LJ, Cousminer DL, de Geus EJ, Deloukas P, Elliott P, Early Growth Genetics (EGG) Consortium, McCarthy MI: Variants in ADCY5 and near CCNL1 are associated with fetal growth and birth weight. Nat Genet 2010, 42:430–435. 12. Baier LJ, Sacchettini JC, Knowler WC, Eads J, Paolisso G, Tataranni PA, Mochizuki H, Bennett PH, Bogardus C, Prochazaka M: An amino acid substitution in the human intestinal fatty acid binding protein is associated with increased fatty acid binding, increased fat oxidation, and insulin resistance. J Clin Invest 1995, 95:1281–1287. Competing interest h h d l h 10. Tavridou A, Arvanitidis KI, Tiptiri-Kourpeti A, Petridis I, Ragia G, Kyroglou S, Christakidis D, Manolopoulos VG: Tha 54 allele of fatty acid binding protein 2 gene is associated with obesity but not type 2 diabetes mellitus in a Caucasian population. Diabetes Res Clin Pract 2009, 84:132–137. 10. Tavridou A, Arvanitidis KI, Tiptiri-Kourpeti A, Petridis I, Ragia G, Kyroglou S, Christakidis D, Manolopoulos VG: Tha 54 allele of fatty acid binding protein 2 gene is associated with obesity but not type 2 diabetes mellitus in a Caucasian population. Diabetes Res Clin Pract 2009, 84:132–137. p g The authors declare that they have no competing interests. Acknowledgement The author would like to extend their sincere appreciation to the Deanship of Scientific Research at King Saud University for its funding of this research through the Research Group Project no RGP-VPP-244. 13. Albala C, Villaroel A, Santos JL, Angel B, Lera L, Liberman C, Sanchez H, Perez-Bravo F: FABPS Ala54Thr polymorphism and diabetes in Chilean elders. Diabetes Res Clin Pract 2007, 77:245–250. Author details 1 1Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh 11433, Kingdom of Saudi Arabia. 2Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia. 3Biomarkers research programme, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia. 4Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia. 5Stem Cell unit, Department of Anatomy, College of Medicine, King Khalid University Hospital, Riyadh 11461, Kingdom of Saudi Arabia. 6Prepratory Year, Saudi Electronic University, Riyadh, Kingdom of Saudi Arabia. 7Department of Biology Science, College of Science and Arts, Al-Qassim University, P.O. Box 1300, Buraidah 51431, Kingdom of Saudi Arabia. 14. Zhao T, Zhao J, Yang W: Association of the fatty acid-binding protein 2 gene Ala54Thr polymorphism with insulin related and blood glucose: a meta-analysis in 13451 subjects. Diabetes Metab Res Rev 2010, 26:357–364. 15. Lowe JB, Sacchettini JC, Laposata M, McQuillan JJ, Gordon JI: Expression of rat intestinal fatty acid-binding protein in Escherichia coli: purification and comparison of ligand binding characteristics with that of Escherichia coli-derived rat liver fatty acid-binding protein. J Biol Chem 1987, 262:5931–5937. 16. Yamada K, Yuan X, Ishiyama S, Koyama K, Ichikawa F, Koyanagi A, Koyama W, Nonaka K: Association between Ala54Thr substitution of the fatty acid-binding protein 2 gene with insulin resistance and intra-abdominal fat thickness in Japanese men. Diabetologia 1997, 40:706–710. 17. Galluzzi JR, Cupples LA, Otvos JD, Wilson PW, Schaefer EJ, Ordovas JM: Association of the A/T54 polymorphism in the intestinal fatty acid binding protein with variations in plasma lipids in the Framingham Offspring Study. Atherosclerosis 2001, 159:417–424. Received: 15 March 2014 Accepted: 26 March 2014 Published: 1 April 2014 18. Guettier JM, Georgopoulos A, Tsai MY, Radha V, Shanthirani S, Deepa R, Gross M, Rao G, Mohan V: Polymorphisms in the fatty acid-binding pro- tein 2 and apolipoprotein C-III genes are associated with the metabolic syndrome and dyslipidemia in a South Indian population. J Clin Endocrinol Metab 2005, 90:1705–1711. Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 This is the first study finding the interaction between FABP2 and T2DM in Saudi population. Further functional studies as well as well-characterized larger mo- lecular epidemiological studies are necessary to confirm our findings. 7. Albuquerque D, Nobrega C, Manco L: Association of FTO polymorphisms with obesity and obesity-related outcomes in Portuguese children. PLoS One 2013, 8(1):e54370. 8. Perry JRB, Vought BF, Yengo L, Amin N, Dupuis J, Ganser M, Grallert H, Navarro P, Li M, Qi L, Steinthorsdottir V, Scott RA, Almgren P, Arking DE, Aulchenko Y, Balkau B, Benediktsson R, Bergman RN, Boerwinkle E, Bonnycastle L, Burtt NP, Campbell H, Charpentier G, Collins FS, Gieger C, Green T, Hadjadj S, Hattersley AT, Herder C, Hofman A: Stratifying type 2 diabetes Cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases. PLoS Genet 2012, 8(5):e1002741. 9. Mansego ML, Martinez F, Martinez-Larrad MT, Zabena C, Rojo G, Morcillio S, Soriquer F, Martin-Escudero JC, Serrano-Rios M, Redon J, Chaves FJ: Common variants of the liver fatty acid binding protein gene influences the risk of type 2 diabetes and insulin resistance in Spanish population. PLoS One 2012, 7(3):e31853. 9. Mansego ML, Martinez F, Martinez-Larrad MT, Zabena C, Rojo G, Morcillio S, Soriquer F, Martin-Escudero JC, Serrano-Rios M, Redon J, Chaves FJ: Common variants of the liver fatty acid binding protein gene influences the risk of type 2 diabetes and insulin resistance in Spanish population. PLoS One 2012, 7(3):e31853. Genotype frequencies No Population Cases Controls Association Disease 1 Germany - 68 No Obesity 2 Japan 228 813 Yes MI + chronic kidney disease 3 Japan 636 1106 Yes Chronic kidney disease + T2DM 4 Japan 313 971 Yes Atherothrombic cerebral infarction 5 Brazil 72 37 Yes T2DM + microalbminuria 6 Mexico - 131 No Lipid metabolism 7 Brazil 513 529 Yes Renal disease + T2DM 8 Brazil 26 529 Yes Postprandial fatty acids + T2DM 9 Spain 108 101 Yes Hypercholesterolemic 10 Present Study 438 460 No T2DM Table 5 Association Studies of FABP2 A54T gene polymorphism on different ethnic groups Table 5 Association Studies of FABP2 A54T gene polymorphism on diff Page 5 of 6 Page 5 of 6 2. Al-Attas O, Al-Daghri NM, Alokail M, Abd-Airahman S, Vinodson B, Sabico S: Metabolic benefits of Six-month Thiamine supplementation in patients Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 Nozawa Y: Association of genetic variants with atherothrombotic cerebral infarction in Japanese individuals with metabolic syndrome. Int J Mol Med 2008, 21:801–188. Nozawa Y: Association of genetic variants with atherothrombotic cerebral infarction in Japanese individuals with metabolic syndrome. Int J Mol Med 2008, 21:801–188. 20. Carlsson M, Orho-Melander M, Hedenbro J, Almgren P, Groop LC: The T 54 allele of the intestinal fatty acid-binding protein 2 is associated with a parental history of stroke. J Clin Endocrinol Metab 2000, 85:2801–2804. 21. Sipilainen R, Uusitupa M, Heikkinen S, Rissanen A, Laakso M: Variants in the human intestinal fatty acid binding protein 2 gene in obese subjects. J Clin Endocrinol Metab 1997, 82:2629–2632. 22. Fisher E, Li Y, Burwinkel B, Kuhr V, Hoffman K, Mohlig M, Spranqer J, Pfeiffer A, Boeing H, Schrezenmeir J, Doring F: Preliminary evidence of FABP2 A54T polymorphism associated with reduced risk of type 2 diabetes and obesity in women from a German cohort. Horm Metab Res 2006, 38:341–345. 23. Pihlajamaki J, Rissanen J, Heikkinen S, Karjalainen L, Laakso M: Codon 54 polymorphism of the human intestinal fatty acid binding protein 2 gene is associated with dyslipidemias but not with insulin resistance in patients with familial combined hyperlipidemia. Arterioscler Thromb Vasc Biol 1997, 17:1039–1044. 24. Tuomi T, Carlsson A, Li H, Isomaa B, Miettinen A, Nilsson A, Nissen M, Ehrnstrom BO, Forsen B, Snickars B, Lahti K, Forsblom C, Saloranta C, Taskinen MR, Groop LC: Clinical and genetic characteristics of type 2 diabetes with and without GAD antibodies. Diabetes 1999, 48:150–157. 25. Ohrvall M, Berglund L, Salminen I, Lithell H, Aro A, Vessby B: The serum cholesterol ester fatty acid composition but not the serum concentration of alpha tocopherol predicts the development of myocardial infarction in 50-year-old men: 19 years follow-up. Atherosclerosis 1996, 127:65–71. 26. Canani LH, Capp C, Ng DP, Choo SG, Maia AL, Nabinger GB, Santos K, Crispim D, Roisemberg I, Krolewski AS, Gross JL: The fatty acid-binding protein-2 A54T polymorphism is associated with renal disease in patients with type 2 diabetes. Diabetes 2005, 54:3326–3330. 27. Lei HH, Coresh J, Shuldiner AR, Boerwinkle E, Brancati FL: Variants of the insulin receptor substrate-1 and fatty acid binding protein 2 genes and the risk of type 2 diabetes, obesity, and hyperinsulinemia in African- Americans: the Atherosclerosis Risk in Communities Study. Diabetes 1999, 48:1868–1872. 28. References 1. Alharbi KK, Khan IA, Munshi A, Alharbi FK, Al-Sheikh Y, Al-Nbaheen MS: Association of the genetic variants of insulin receptor substrate 1 (IRS-1) with type 2 diabetes mellitus in a Saudi population. Endocrine 2014 [Epub ahead of print]. 19. Yamada Y, Kato K, Oguri M, Yoshida T, Yokoi K, Watanabe S, Metoki N, Yoshida H, Satoh K, Ichihara S, Aoyagi Y, Yasunaga A, Park H, Tanaka M, 19. Yamada Y, Kato K, Oguri M, Yoshida T, Yokoi K, Watanabe S, Metoki N, Yoshida H, Satoh K, Ichihara S, Aoyagi Y, Yasunaga A, Park H, Tanaka M, 2. Al-Attas O, Al-Daghri NM, Alokail M, Abd-Airahman S, Vinodson B, Sabico S: Metabolic benefits of Six-month Thiamine supplementation in patients Page 6 of 6 Page 6 of 6 Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 doi:10.1186/1476-511X-13-61 Cite this article as: Alharbi et al.: A54T polymorphism in the fatty acid binding protein 2 studies in a Saudi population with type 2 diabetes mellitus. Lipids in Health and Disease 2014 13:61. Alharbi et al. Lipids in Health and Disease 2014, 13:61 http://www.lipidworld.com/content/13/1/61 Ito K, Nakatani K, Fujii M, Katsuki A, Tsuchihashi K, Murala K, Goto H, Yano Y, Gabazza EC, Sumida Y, Adachi Y: Codon 54 polymorphism of the fatty acid binding protein gene and insulin resistance in the Japanese population. Diabetes Med 1999, 16:119–124. 29. Rissanen J, Pihlajamaki J, Heikkinen S, Kekalainen P, Kuusisto J, Laakso M: The Ala54Thr polymorphism of the fatty acid binding protein 2 gene does not influence insulin sensitivity in Finnish nondiabetic and NIDDM subjects. Diabetes 1997, 46:711–712. 30. Chiu KC, Chuang LM, Yoon C: The A54T polymorphism at the intestinal fatty acid binding protein 2 is associated with insulin resistance in glucose tolerant Caucasians. BMC Genet 2001, 2:7. 31. Weiss EP, Brown MD, Shuldiner AR, Hagberg JM: Fatty acid binding protein-2 gene variants and insulin resistance: gene and gene- environment interaction effects. Physiol Genom 2002, 10:145–157. doi:10.1186/1476-511X-13-61 Cite this article as: Alharbi et al.: A54T polymorphism in the fatty acid binding protein 2 studies in a Saudi population with type 2 diabetes mellitus. Lipids in Health and Disease 2014 13:61. 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 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
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Genetic Polymorphisms in Inflammasome-Dependent Innate Immunity among Pediatric Patients with Severe Renal Parenchymal Infections
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RESEARCH ARTICLE Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: CHC was supported by Ministry of Science and Technology, Taiwan (MOST 103-2314-B-182- 022-MY3; NSC 98-2314-B-182A-007-MY3) and the Chang Gung Memorial Hospital (CMRPG 4A0111, 4A0112, 4A0113) for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Background Inflammasome innate immune response activation has been demonstrated in various inflammatory diseases and microbial infections. However, to our knowledge, no study has examined the inflammasome-dependent pathways in patients with urinary tract infection. Defective or variant genes associated with innate immunity are believed to alter the host’s susceptibility to microbial infection. This study investigated genetic polymorphisms in genes encoding inflammasomes and the subsequent released cytokines in pediatric patients with severe renal parenchymal infections. Editor: Zhanjun Jia, University of Utah School of Medicine, UNITED STATES Medicine, UNITED STATES Received: May 10, 2015 Accepted: September 22, 2015 Published: October 7, 2015 Copyright: © 2015 Cheng 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: May 10, 2015 Accepted: September 22, 2015 Published: October 7, 2015 Copyright: © 2015 Cheng 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. OPEN ACCESS Citation: Cheng C-H, Lee Y-S, Chang C-J, Lin J-C, Lin T-Y (2015) Genetic Polymorphisms in Inflammasome-Dependent Innate Immunity among Pediatric Patients with Severe Renal Parenchymal Infections. PLoS ONE 10(10): e0140128. doi:10.1371/journal.pone.0140128 * pedneph.cheng@msa.hinet.net Chi-Hui Cheng1,2*, Yun-Shien Lee3,4, Chee-Jen Chang5, Jui-Che Lin6, Tzou-Yien Lin2,7 Chi-Hui Cheng1,2*, Yun-Shien Lee3,4, Chee-Jen Chang5, Jui-Che Lin6, Tzou-Yien Lin2,7 1 Division of Pediatric Nephrology, Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Taoyuan, Taiwan, 2 College of Medicine, Chang Gung University, Taoyuan, Taiwan, 3 Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan, 4 Department of Biotechnology, Ming-Chuan University, Taoyuan, Taiwan, 5 Statistical Center for Clinical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan, 6 Institute of Oral Medicine, Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan, 7 Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Taoyuan, Taiwan * pedneph.cheng@msa.hinet.net Methodology This study included patients diagnosed with acute pyelonephritis (APN) and acute lobar nephronia (ALN) who had no underlying disease or structural anomalies other than vesi- coureteral reflux (VUR). Single nucleotide polymorphism (SNP) genotyping was performed in the genes associated with inflammasome formation and activation (NLRP3, CARD8) and subsequent IL–1β cytokine generation (IL–1β). Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Introduction Urinary tract infections (UTIs) are among the most prevalent bacterial infectious diseases among pediatric patients, with morbidity risks of ~3% and ~1% in prepubertal females and males, respectively [1]. The clinical severity of UTIs ranges from uncomplicated lower UTIs, such as asymptomatic bacteriuria (ABU), to acute pyelonephritis (APN), acute lobar nephronia (ALN), and renal abscess formation [2, 3]. Among these UTIs, ALN presents as a localized non-liquefactive inflammatory renal bacterial infection. ALN has been identified as a compli- cated form of acute renal infection, representing progression of the inflammatory process of APN. Our previous studies suggested that ALN might represent a relatively early stage in renal abscess development [2, 3], with a longer duration of antibiotic treatment recommended for patients with ALN compared with those with APN [2]. Nevertheless, APN, ALN, and intrare- nal abscess are considered the most serious forms of UTIs requiring different durations of anti- biotic treatment. Furthermore, in some cases, additional surgical procedures are indicated for proper treatment [2, 4]. Patients’ susceptibility to UTIs and disease severity are determined by complicated interac- tions between the host and pathogenic microbes [4–6]. In addition to certain virulence factors associated with uropathogenic Escherichia coli in specific UTIs [4–8], intra-individual varia- tions play a role in clinical severity. These observations highlight the importance of host fac- tors, such as the presence of vesicoureteral reflux (VUR) or genetic polymorphisms in innate immunity pathway genes, in defending bacterial invasion and infection [9–11]. The innate immune system is considered the first line of defense against microbial infection. In response to microbial invasion, innate immunity is initiated or activated with expression of extracellular or intracellular germline-encoded pattern-recognition receptors (PRRs) [12, 13]. Next, various intracellular signaling cascades are triggered, which ultimately culminate in host defense responses to eliminate the microbial invasions. However, such host responses can also result in various tissue injuries if the host proinflammatory responses are too robust. Previously, we studied pediatric patients with UTIs of differing clinical severity to examine the associations with genetic variations in the innate immunity pathways that were dependent upon Toll-like receptors (TLRs), one of the best-characterized PRRs. We demonstrated that the AA genotype and A allele of the IL–8 SNP were related to patient susceptibility to paren- chymal infection and were correlated with the severity of infection in pediatric patients with APN and ALN, probably due to the upregulation of IL–8 expression [14]. Conclusions This study is the first to suggest that the inflammasome-dependent innate immunity path- way is associated with the pathogenesis of pediatric severe renal parenchymal infections. Further investigation is warranted to clarify its pathogenic mechanism. Principal Findings A total of 40 SNPs were selected for initial genotyping. Analysis of samples from 48 patients each and 96 controls revealed that only nine SNPs (five SNPs in NLRP3; three SNPs in CARD8; one SNP in IL–1β) had heterozygosity rates >0.01. Hardy–Weinberg equilibrium was satisfied for the observed genotype frequencies of these SNPs. Analysis excluding Competing Interests: The authors have declared that no competing interests exist. 1 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs patients with VUR, a well-known risk factor for severe UTIs, revealed a lower frequency of the CC genotype in NLRP3 (rs4612666) in patients with APN and ALN than in controls. Cor- rection for multiple-SNP testing showed that the non-VUR subgroup of the APN+ALN com- bined patient groups remained significantly different from the control group (P < 0.0055). PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 Introduction Additionally, MAL- DI-TOF SNP analyses revealed that the genetic variant in TLR–2 (rs3804100, T1350C) might protect the host from severe UTIs such as ALN [15]. 2 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs Similar to TLRs, the cytosolic nucleotide-binding domain–leucine-rich repeat-containing receptors (NLRs, or NOD-like receptors) have been investigated as PRRs for microbial attacks [13, 16, 17]. In addition to recognizing the pathogen-associated molecular patterns (PAMPs), the highly conserved markers specific to microbes, these PRRs can also sense danger signals or danger-associated molecular patterns (DAMPs) released after cellular damage or stress induced by pathogen attacks [13, 16, 18]. Pathogen recognition activates the host inflamma- some, a complex of cytosolic NLR-containing proteins, including the NLRP3 protein, protease caspase–1, and the adaptor protein ASC (apoptosis associated speck-like protein containing a CARD; the caspase recruitment domain). Activated caspase–1 leads to the cleavage of the pro- IL–1β and pro-IL–18 to produce IL–1β and IL–18 cytokines, respectively, to form an inflam- masome-dependent immune response [17, 19, 20]. Despite of inflammasome-dependent immune response has been reported to be associated with various microbial sensing and reaction to microbial infections [13, 16, 21, 22], none has explored its likely association with urinary tract infections, to our knowledge. Henceforth, to exam inflammasome-dependent innate immunity pathway on pediatric patients with severe renal parenchymal infections might provide supplementary information to our earlier findings based on the TLR-dependent pathway [14, 15]. In this investigation, we attempted to assess the likely variations in genes associated with the inflammasome-dependent innate immunity path- way for pediatric patients with various severe UTIs. The genes selected for initial genotyping involved in inflammasome formation (NLRP3, CARD8) and subsequent activation and IL–1β cytokine generation (IL–1β). Among these, NLRP3 has been implicated to be associated with the tubulointerstitious disease, such as renal infection [19]. These components may play a role in various inflammatory responses and bacterial clearance in pediatric patients with UTIs of differing clinical severity, such as APN and the clinically more severe disease ALN. Addition- ally, as VUR is a well-known risk factor for severe parenchymal infectious disease [9, 23], a sub- group of APN and ALN cases without VUR (non-VUR) was examined to exclude the possible effects of VUR. Ethics statement This investigation was approved by the Institutional Review Board of Chang Gung Memorial Hospital. Written informed consent was obtained from the parents of all participating patients following a full explanation of the study. Introduction This investigation was part of our ongoing effort to explore the pathogenic host and bacte- rial urovirulence factors related to pediatric APN and ALN; as such, it includes patients contin- uously enrolled since our previous studies [5, 14, 15]. Therefore, compared with our previous reports, this study enrolled a greater number of participants, with a total of 138 APN and 222 ALN cases and 225 controls, including those cases in our earlier investigations on SNPs in TLR-dependent innate immunity pathway genes (113 APN and 172 ALN cases and 222 con- trols) [14, 15]. Genotying for the genes associated with the inflammsome-dependent pathway was commenced on the second half of year 2012, while genotyping for genes associated with the TLR-dependent pathway presented in earlier publications [14, 15] has been completed in 2010. Study setting and patient selection criteria This study is part of our ongoing investigation of the pathogenic host and bacterial uroviru- lence factors related to pediatric APN and ALN [5, 14, 15]. Patients were enrolled in the study if they fulfilled the diagnostic criteria for APN and ALN caused by E. coli and lacked any of the 3 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs exclusion criteria. Participants were admitted to Chang Gung Children’s Hospital, a tertiary medical center located near Taipei in northern Taiwan, between January 2004 and December 2008 as well as between January 2012 and December 2013. The controls consisted of patients who visited the outpatient clinic for reasons other than a UTI or severe infection. The controls had no history of UTI or severe infections and no positive urine culture [14, 15]. A detailed diagnostic schematic plan for patients suspected of having APN or ALN was described previously [2, 5, 14, 15]. Briefly, all patients with a suspected UTI due to the presence of pyuria (>5 white blood cells/high-power field) who had fever with symptoms and signs related to UTIs (e.g., pain, dysuria, and frequent urination) or without focus underwent renal ultrasonography on the first or second day after admission. Computed tomography (CT) was performed immediately when the initial ultrasonographic findings showed unilateral or bilat- eral nephromegaly or a focal renal mass. For patients who presented with borderline nephro- megaly on ultrasonography, CT was performed when the patient remained febrile for 72 h after starting the antibiotic therapy. ALN was diagnosed based on positive CT findings. Tech- netium 99m-dimercaptosuccinic acid scintigraphy (99mTc-DMSA) was performed within 3–7 days of admission in patients suspected of having a febrile UTI who did not satisfy the sono- graphic criteria for ALN. APN was defined as focal or diffuse areas of decreased 99mTc-DMSA uptake without evidence of cortical loss. Patients were excluded from this study if they showed evidence of underlying disease such as diabetes; immunodeficiency; or structural anomalies such as neurogenic bladder, posterior urethral valve, urinary diversion, bladder diverticulum, ureterocele, or urinary tract obstruction (other than VUR). PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 Genotyping by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-based mini-sequencing analysis or direct DNA sequencing Genotyping for the genes associated with inflammasome-dependent innate immunity pathway presented here commenced on the second half of year 2012, while genotyping for genes associ- ated with the TLR-dependent pathway presented in earlier publications [14, 15] has been com- pleted in 2010. No further genotyping on the inflammasome-dependent pathway was planned. SNPs in the genes encoding NLRP3, CARD8, and IL–1β, as well as in their respective pro- moter regions, were identified in the NCBI dbSNP database [24]. A total of 40 SNPs (rs35829419, rs10754558, rs4925659, rs12239046, rs10754555, rs35829479, rs10733113, rs1539019, rs4925648, rs4925663, rs10802501, rs2027432, rs76291085, rs4353135, rs4266924, rs55646866, rs6672995, rs4925650, rs3806265, rs4612666, rs10733112, rs12079994, rs12048215, rs10925019, rs4925654, rs10925026, rs12565738, and rs4378247 for NLRP3; rs2043211, rs6509365, rs1965759, rs1062808, rs4389238, rs2288877, rs2288876, and rs1972619 for CARD8; rs1143643, rs1143634, rs1143629, and rs16944, for IL–1β) were selected for initial genotyping based on previous studies on SNPs in inflammasome-dependent pathogenic mech- anisms for various diseases [25–42]. Analysis of samples from 96 controls and 48 patients each revealed that only nine SNPs had heterozygosity rates >0.01. Among these, rs4612666 (NLRP3), rs4925650 (NLRP3), rs10754558 (NLRP3), rs1965759 (CARD8), rs2043211 (CARD8), and rs1143629 (IL–1β) were analyzed by direct DNA sequencing (S1 Table). Three other SNPs, rs1539019 (NLRP3), rs4925663 (NLRP3) and rs1972619 (CARD8), were genotyped by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-based mini- sequencing analysis (S2 Table). Genomic DNA was extracted from peripheral blood lymphocytes using a Nucleospin 1 Blood DNA extraction kit (Macherey-Nagel, Düren, Germany) [15]. For direct DNA Genomic DNA was extracted from peripheral blood lymphocytes using a Nucleospin 1 Blood DNA extraction kit (Macherey-Nagel, Düren, Germany) [15]. For direct DNA 4 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs sequencing, polymerase chain reaction (PCR) was performed in a master mix (50 μL) contain- ing 25 ng of DNA, 25 μL DreamTaq Green PCR Master Mix (2x) (Thermo Scientific), 0.5 μL of each primer (5 pM, Integrated DNA Technologies, IDT) (S1 Table), and 23.5 μL distilled deionized water (dd H2O). PCR was carried out for 35 cycles with initial denaturation at 94°C for 2 min followed by denaturation at 94°C for 30 s, annealing for 30 s, extension at 72°C for 40 s, and final extension at 72°C for 7 min. All PCR products were analyzed on a 1.5% agarose gel to verify the amplification reaction. Genotyping by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-based mini-sequencing analysis or direct DNA sequencing The amplified products were then subjected to direct auto- mated sequencing (ABI Prism 3730 DNA Analyzer). For MALDI-TOF-based mini-sequencing analysis, the SNPs were genotyped as described previously [14, 15] using the primers listed in S2 Table. Briefly, the PCR mix (25 μL) contained 200 ng of genomic DNA, primers (25 pM each), dNTPs (0.2 mM), 1× Fast-Start PCR buffer, 1 M betaine, and 1 U of Fast-Start Taq Polymerase (Roche Diagnostics, Basel, Switzerland). The PCR reaction was initiated at 95°C for 5 min, followed by 40 cycles at 95°C for 45 s, 50°C for 45 s, and 60°C for 45 s, with a final extension at 52°C for 10 min. Unincorporated dNTPs and primers were removed automatically by MAPIIA (GenePure PCR Purification System; Bruker, Bremen, Germany). The purified products were amplified further using the respective mini- sequencing primers (S2 Table) in 20 μL of a solution containing 50 ng of the PCR product, 1 μL (10 pmol) of mini-sequencing primer, 0.5 μL of 1 mM ddNTP/dNTP mixture, 0.5 U of Thermo Sequenase DNA Polymerase (Amersham Biosciences, Piscataway, NJ), and 2 μL of the reaction buffer provided by the manufacturer. The reactions were carried out with initial dena- turation at 96°C for 1 min, followed by 50 cycles of 96°C for 15 s, 50°C for 15 s, 60°C for 100 s, and 96°C for 30 s (Thermo Hybaid, Waltham, MA). The reaction products were purified auto- matically by MAPIIA (Single-Strand DNA Binding Beads; Bruker). The purified samples were then mixed with 0.5 μL of matrix solution (50 mg/mL 3-hydropicolinic acid in a 4:5:1 mixture of water, acetonitrile, and 50 mg/mL diammonium citrate) and spotted onto 384-well Teflon sample plates (PerSeptive Biosystems, Framingham, MA). MALDI-TOF mass spectra were acquired with a Bruker Autoflex MALDI-TOF mass spectrometer (Bruker) and AutoXecute software (Bruker) to validate the genotype data. PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 Results A total of 360 patients (182 males and 178 females) who fulfilled the enrollment criteria for APN and ALN were included in this study. Among these, 138 patients (77 males and 61 females; 2.50 ± 2.98 years old; range, one month to 14.42 years old) were diagnosed with APN and 222 (105 males and 117 females; 3.05 ± 2.78 years old; range, one month to 15 years old) with ALN. The control population consisted of 225 subjects (123 males and 102 females; mean age ± SD, 2.96 ± 3.02 years old; range, one month to 11 years old]). Although more patients were included in this investigation as compared to those reported in earlier studies [14, 15], sta- tistical differences in the demographic and clinical characteristics among these three groups remained similar to those reported earlier [14, 15], with no significant differences detected in the sex ratio and age among the three groups (control, APN and ALN). The observed genotype frequency in all groups met the requirements for HWE. The MAL- DI-TOF mass spectra in NLRP3 (rs1539019) matched with the auto-sequencing results from randomly selected cases (Fig 1), indicating that MALDI-TOF could be used as the direct DNA sequencing method for analyzing the likely SNPs. Genotypic analyses of the nine SNPs revealed that NLRP3 (rs4612666) demonstrated a sig- nificant difference in genotype frequency between the APN and control cases [OR (95% CI): 2.32 (1.66, 3.97)] as well as between the APN and ALN cases [OR (95% CI): 0.50 (0.29, 0.86)] in the dominant model (Table 1). Additionally, NLRP3 (rs4925650), NLRP3 (rs10754558), and CARD8 (rs1965759) showed significant differences among different groups using the recessive model (Table 1). Nevertheless, after correction for multiple-SNP testing (nine SNPs examined), only NLRP3 (rs4612666) showed a significant difference between the APN and control using the dominant model (P < 0.0055). Allele frequency analyses demonstrated that NLRP3 (rs4612666) and NLRP3 (rs10754558) showed significant differences when comparing ALN with APN [OR (95% CI): 1.42 (1.04, 1.93)] and APN with control [OR (95% CI): 1.46 (1.20, 2.01)] (Table 2). As VUR has been indicated as a significant risk factor for upper UTIs [9, 23], further analy- ses were carried out in the subgroups of APN and ALN patients with no VUR. Statistical analysis Hardy–Weinberg equilibrium (HWE) was tested for goodness-of-fit using a χ2 test with one degree of freedom. Comparison of genotype and allele frequencies among the control, APN, and ALN groups were performed by χ2 analysis or two-sided Fisher’s exact test, as appropriate. The association of outcome and SNP genotype was analyzed with recessive and dominant models [10]. For the dominant model, the genotypes of minor homozygotes and heterozygotes were combined and compared with common homozygous genotypes. In a similar manner, the genotypes of common homozygotes and heterozygotes were combined and compared with minor homozygous genotype for recessive model analysis. A P-value <0.05 was considered to indicate statistical significance. As no adjustments were made to correct for multiple compari- sons, the chance of type I errors may have been increased. All statistical analyses were per- formed using SPSS software (Version 17.0, IBM SPSS Statistics). At first, 96 cases (48 APN and 48 ALN) and 96 control samples were analyzed for NLRP3 (rs4612666) SNP. These 192 samples indicated that the probability of exposure among controls is 0.25. Using the dominant model, if the true odds ratio for disease in exposed subjects relative to unexposed subjects is 1.89 as we noted among these 192 samples, we will need to study 196 patients and 196 control patients to be able to reject the null hypothesis that this odds ratio equals 1 with probability (power) of 0.8. The Type I error probability associated with this test of this null hypothesis is 0.05. The samples size estimate was performed with PS Power and PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 5 / 15 SNPs in Inflammasome among Pediatric Patients with Severe UTIs Sample Size Calculations Version 3.1.2 (http://biostat.mc.vanderbilt.edu/PowerSampleSize) [43]. PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 Results VUR was not observed in 65 APN patients (35 males and 30 females; 2.51 ± 2.77 years old) and 133 ALN patients (67 males and 66 females; 2.92 ± 2.63 years old).Our previous report indicated that the number of patients with VUR in the control group needed to be determined based upon the reported prevalence rate because voiding cystourethrography (VCUG) was not medically advised in these control patients [15, 44]. Because the prevalence rate of VUR at the mean age of the control group (2.96 years old) was ~0.3%, the number of patients with VUR in the 225 control cases could be assumed to be zero. Additionally, no differences were found in age and sex ratio among the control and non-VUR subgroup of APN and ALN. Among the nine SNPs examined using the dominant model, only NLRP3 (rs4612666) showed a significant difference in genotypic frequency between the control group and non- VUR in the APN, ALN, and combined (APN+ALN) subgroups. In these analyses, the CC genotype frequency of the non-VUR subgroups of APN, ALN, and APN+ALN cases were sig- nificantly lower than that of the control (Table 3). However, with the correction for multiple- SNP testing, only the non-VUR subgroup of the APN+ALN group remained significantly dif- ferent from the control group (P < 0.0055). Nevertheless, allele frequency analyses showed no significant differences between the control and non-VUR subgroups of APN and ALN (Table 4). 6 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 Discussion A concerted host innate and adaptive immune response is required for defending against bac- terial invasion or infection. For this defense, the host must first recognize the pathogen through A concerted host innate and adaptive immune response is required for defending against bac- terial invasion or infection. For this defense, the host must first recognize the pathogen through Table 1. Genotypic analysis of the SNPs. SNP Group Genotype, n (%) Dominant model Recessive model 00 01 11 (01, 11 vs. 00) (00, 01vs. Discussion 11) CC CT TT OR (95% CI) Pa OR (95% CI) Pa OR (95% CI) Pa OR (95% CI) Pa NLRP3 Control 68 (32.7) 95 (45.7) 45 (21.6) 1.00 1.00 (rs4612666) APN 23 (17.3) 84 (63.2) 26 (19.5) 2.32 (1.66, 3.97) 0.002c 1.00 1.14 (0.66, 1.95) 0.644 1.00 ALN 61 (29.5) 116 (56.0) 30 (14.5) 1.16 (0.77, 1,76) 0.478 0.50 (0.29, 0.86) 0.011 1.63 (0.98, 2.71) 0.059 1.43 (0.81, 2.55) 0.220 Combinedb 84 (24.7) 200 (58.8) 56 (16.5) 1.48 (1.01, 2.17) 0.043 1.40 (0.90, 2.17) 0.133 GG GA AA OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P NLRP3 Control 66 (31.9) 97 (46.9) 44 (21.3) 1.00 1.00 (rs4925650) APN 40 (30.5) 70 (53.4) 21 (16.0) 1.07 (0.66, 1.71) 0.794 1.00 1.41 (0.80, 2.51) 0.235 1.00 ALN 65 (30.4) 89 (41.6) 60 (28.0) 1.07 (0.71, 1.62) 0.738 1.01 (0.63, 1.62) 0.975 0.69 (0.44, 1.08) 0.107 0.49 (0.28, 0.85) 0.011 Combined 105 (30.4) 159 (46.1) 81 (23.5) 1.07 (0.74, 1.55) 0.721 0.88 (0.58, 1.33) 0.546 CC CG GG OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P NLRP3 Control 85 (37.9) 105 (46.9) 34 (15.2) 1.00 1.00 (rs10754558) APN 64 (47.8) 59 (44.0) 11 (8.2) 0.67 (0.43, 1.03) 0.066 1.00 2.03 (0.99, 4.16) 0.049 1.00 ALN 86 (40.0) 102 (47.4) 27 (12.6) 0.92 (0.63, 1.35) 0.659 1.37 (0.89, 2.12) 0.151 1.25 (0.72, 2.15) 0.427 0.61 (0.29, 1.28) 0.189 Combined 150 (43.0) 161 (46.1) 38 (10.9) 0.81 (0.58, 1.14) 0.228 1.47 (0.90, 2.42) 0.124 GG GT TT OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P NLRP3 Control 86 (39.4) 104 (47.7) 28 (12.8) 1.00 1.00 (rs1539019) APN 53 (40.5) 58 (44.3) 20 (15.3) 0.96 (0.62, 1.49) 0.852 1.00 0.82 (0.44, 1.52) 0.524 1.00 ALN 67 (32.2) 104 (50.0) 37 (17.8) 1.37 (0.92, 2.04) 0.120 1.43 (0.91, 2.25) 0.122 0.68 (0.40, 1.16) 0.156 0.83 (0.46, 1.51) 0.546 Combined 120 (35.4) 162 (47.8) 57 (16.8) 1.19 (0.84, 1.69) 0.334 0.73 (0.45, 1.19) 0.203 TT TC CC OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P NLRP3 Control 57 (28.9) 97 (49.2) 43 (21.8) 1.00 1.00 (rs4925663) APN 29 (24.8) 60 (51.3) 28 (23.9) 1.24 (0.73, 2.08) 0.426 1.00 0.89 (0.52, 1.53) 0.666 1.00 ALN 51 (24.8) 101 (49.0) 54 (26.2) 1.24 (0.80, 1.92) 0.344 1.00 (0.59, 1.69) 0.995 0.79 (0.50, 1.24) 0.303 0.89 (0.52, 1.50) 0.651 Combined 80 (24.8) 161 (49.8) 82 (25.4) 1.24 (0.83, 1.84) 0.295 0.82 (0.54, 1.25) 0.357 CC CT TT OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P CARD8 Control 126 (60.6) 71 (34.1) 11 (5.3) 1.00 1.00 (rs1965759) APN 70 (53.8) 59 (45.4) 1 (0.8) 1.32 (0.85, 2.05) 0.223 1.00 7.20 (0.92, 56.5) 0.033 1.00 ALN 116 (54.7) 87 (41.0) 9 (4.2) 1.27 (0.86, 1.87) 0.224 0.97 (0.62, 1.50) 0.875 1.26 (0.51, 3.11) 0.616 1.00 (0.02, 1.42) 0.096 Combined 186 (54.4) 146 (33.9) 10 (2.9) 1.29 (0.91, 1.83) 0.155 1.85 (0.77, 4.44) 0.161 TT TA AA OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P CARD8 Control 65 (29.4) 108 (48.9) 48 (21.7) 1.00 1.00 (rs2043211) APN 37 (28.0) 72 (54.5) 23 (17.4) 1.07 (0.66, 1.73) 0.782 1.00 1.32 (0.76, 2.28) 0.330 1.00 ALN 58 (26.5) 118 (53.9) 43 (19.6) 1.16 (0.77, 1.77) 0.475 1.09 (0.67, 1.77) 0.733 1.14 (0.72, 1.81) 0.573 0.87 (0.50, 1.52) 0.622 Combined 95 (27.1) 190 (54.1) 66 (18.8) 1.13 (0.78, 1.64) 0.529 1.20 (0.79, 1.82) 0.386 GG GA AA OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P CARD8 Control 113 (51.6) 93 (42.5) 13 (5.9) 1.00 1.00 (rs1972619) APN 60 (48.0) 53 (42.4) 12 (9.6) 1.16 (0.74, 1.79) 0.521 1.00 0.59 (0.26, 1.35) 0.208 1.00 ALN 93 (44.5) 97 (46.4) 19 (9.1) 1.33 (0.91, 1.95) 0.142 1.15 (0.74, 1.80) 0.534 0.63 (0.30, 1.31) 0.215 1.06 (0.50, 2.27) 0.877 Combined 153 (45.8) 150 (44.9) 31 (9.3) 1.26 (0.90, 1.77) 0.183 0.62 (0.32, 1.21) 0.155 CC CT TT OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P IL1-β Control 52 (23.7) 122 (55.7) 45 (20.5) 1.00 1.00 (rs1143629) APN 24 (18.0) 71 (53.4) 38 (28.6) 1.43 (0.83, 2.45) 0.196 1.00 0.65 (0.40, 1.08) 0.093 1.00 ALN 52 (24.0) 114 (52.5) 51 (23.5) 1.00 (0.64, 1.55) 1.000 0.70 (0.41, 1.20) 0.196 0.85 (0.54, 1.34) 0.488 1.30 (0.80, 2.13) 0.287 Combined 76 (21.7) 185 (52.4) 89 (25.4) 1.14 (0.76, 1.70) 0.537 0.77 (0.51, 1.15) 0.200 a P-values <0.05 are shown in bold. SNPs in Inflammasome among Pediatric Patients with Severe UTIs b APN + ALN c Statistically significant with correction for multiple-SNP testing (P < 0.0055) SNPs in Inflammasome among Pediatric Patients with Severe UTIs Fig 1. MALDI-TOF mass spectra from the genotyping of NLRP3 (rs1539019) PCR product and its sequencing results. (A) The SNP by MALDI-TOF MS based on the molecular weights of the mini-sequencing products listed in S2 Table. (B) Sequencing results for each of from the G/T, T/T, and G/G genotypes of rs1539019. The SNPs are indicated by arrows. doi:10.1371/journal.pone.0140128.g001 PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 Fig 1. MALDI-TOF mass spectra from the genotyping of NLRP3 (rs1539019) PCR product and its sequencing results. (A) The SNPs were genotyped by MALDI-TOF MS based on the molecular weights of the mini-sequencing products listed in S2 Table. (B) Sequencing results for each of the PCR products from the G/T, T/T, and G/G genotypes of rs1539019. The SNPs are indicated by arrows. doi:10.1371/journal.pone.0140128.g001 PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 7 / 15 c Statistically significant with correction for multiple-SNP testing (P < 0.0055) doi:10.1371/journal.pone.0140128.t001 b APN + ALN c Statistically significant with correction for multiple SNP testing (P < 0 0055) b APN + ALN b APN + ALN a P-values <0.05 are shown in bold. APN Control APN ALN Combinedb OR (95% CI) Pa OR (95% CI) Pa OR (95% CI) Pa OR (95% CI) Pa NLRP3, (rs4612666), C major allele 55.53 48.87 57.49 54.12 0.77 (0.56, 1.04) 0.089 1.08 (0.82, 1.43) 0.569 0.95 (0.74, 1.21) 0.649 1.42 (1.04, 1.93) 0.028 NLRP3, (rs4925650), G major allele 55.31 57.25 51.17 53.48 1.08 (0.79, 1.48) 0.621 0.85 (0.65, 1.11) 0.228 0.93 (0.73, 1.19) 0.553 0.78 (0.57, 1.07) 0.120 NLRP3, (rs10754558), C major allele 61.38 69.78 63.72 66.05 1.46 (1.02, 2.01) 0.021 1.11 (0.84, 1.45) 0.475 1.23 (0.96, 1.57) 0.104 0.76 (0.55, 1.05) 0.095 NLRP3, (rs1539019), G major allele 63.30 62.60 57.21 59.29 0.97 (0.71, 1.33) 0.851 0.78 (0.59, 1.02) 0.069 0.84 (0.66, 1.08) 0.181 0.80 (0.58, 1.10) 0.165 NLRP3, (rs4925663), T major allele 53.55 50.43 49.27 49.69 0.88 (0.64, 1.22) 0.448 0.84 (0.64, 1.11) 0.224 0.86 (0.67, 1.10) 0.227 0.96 (0.69, 1.32) 0.778 CARD8, (rs1965759), C major allele 77.64 76.54 75.24 75.73 0.94 (0.65, 1.36) 0.739 0.88 (0.64, 1.20) 0.411 0.90 (0.69, 1.20) 0.468 0.93 (0.65, 1.34) 0.700 CARD8, (rs2043211), T major allele 53.84 55.30 53.42 54.13 1.06 (0.78, 1.44) 0.707 0.98 (0.75, 1.28) 0.896 1.01 (0.80, 1.29) 0.928 0.93 (0.68, 1.26) 0.625 CARD8, (rs1972619), G major allele 72.83 69.20 67.70 68.26 0.84 (0.60, 1.18) 0.310 0.78 (0.58, 1.05) 0.101 0.80 (0.62, 1.05) 0.105 0.93 (0.67, 1.31) 0.688 IL1-β, (rs1143629), C major allele 51.60 44.74 50.23 48.14 0.76 (0.56, 1.03) 0.078 0.95 (0.73, 1.23) 0.685 0.87 (0.69, 1.11) 0.258 1.25 (0.92, 1.69) 0.159 a P-values <0.05 are shown in bold. b APN + ALN doi:10.1371/journal.pone.0140128.t002 g Table 2. Allele frequency analysis of the SNPs. SNP Major allele frequency (%) APN vs. control ALN vs. control Combined vs. control ALN vs. APN Control APN ALN Combinedb OR (95% CI) Pa OR (95% CI) Pa OR (95% CI) Pa OR (95% CI) Pa NLRP3, (rs4612666), C major allele 55.53 48.87 57.49 54.12 0.77 (0.56, 1.04) 0.089 1.08 (0.82, 1.43) 0.569 0.95 (0.74, 1.21) 0.649 1.42 (1.04, 1.93) 0.028 NLRP3, (rs4925650), G major allele 55.31 57.25 51.17 53.48 1.08 (0.79, 1.48) 0.621 0.85 (0.65, 1.11) 0.228 0.93 (0.73, 1.19) 0.553 0.78 (0.57, 1.07) 0.120 NLRP3, (rs10754558), C major allele 61.38 69.78 63.72 66.05 1.46 (1.02, 2.01) 0.021 1.11 (0.84, 1.45) 0.475 1.23 (0.96, 1.57) 0.104 0.76 (0.55, 1.05) 0.095 NLRP3, (rs1539019), G major allele 63.30 62.60 57.21 59.29 0.97 (0.71, 1.33) 0.851 0.78 (0.59, 1.02) 0.069 0.84 (0.66, 1.08) 0.181 0.80 (0.58, 1.10) 0.165 NLRP3, (rs4925663), T major allele 53.55 50.43 49.27 49.69 0.88 (0.64, 1.22) 0.448 0.84 (0.64, 1.11) 0.224 0.86 (0.67, 1.10) 0.227 0.96 (0.69, 1.32) 0.778 CARD8, (rs1965759), C major allele 77.64 76.54 75.24 75.73 0.94 (0.65, 1.36) 0.739 0.88 (0.64, 1.20) 0.411 0.90 (0.69, 1.20) 0.468 0.93 (0.65, 1.34) 0.700 CARD8, (rs2043211), T major allele 53.84 55.30 53.42 54.13 1.06 (0.78, 1.44) 0.707 0.98 (0.75, 1.28) 0.896 1.01 (0.80, 1.29) 0.928 0.93 (0.68, 1.26) 0.625 CARD8, (rs1972619), G major allele 72.83 69.20 67.70 68.26 0.84 (0.60, 1.18) 0.310 0.78 (0.58, 1.05) 0.101 0.80 (0.62, 1.05) 0.105 0.93 (0.67, 1.31) 0.688 IL1-β, (rs1143629), C major allele 51.60 44.74 50.23 48.14 0.76 (0.56, 1.03) 0.078 0.95 (0.73, 1.23) 0.685 0.87 (0.69, 1.11) 0.258 1.25 (0.92, 1.69) 0.159 a P-values <0.05 are shown in bold. b APN + ALN d i 10 1371/j l 0140128 t002 Table 2. Allele frequency analysis of the SNPs. doi:10.1371/journal.pone.0140128.t002 the expression of various extracellular or intracellular PRRs such as the TLRs and the NOD- like receptors (NLRs). Following this microbial sensing step, consecutive activation of intracel- lular signaling cascades marks the initiation of the immune responses [13]. These responses determine the host health status as well as the clinical severity [9]. Therefore, the risk of bacte- rial infection would be influenced by the signal transmission effectiveness in the immune response pathway. Defective signal transmission caused by a genetic polymorphism in the receptors, adaptors, or cytokines would influence an individual’s risk for infectious diseases [11, 14, 15, 45, 46]. NLRs have been considered important PRRs for various PAMPs, including lipopolysaccha- ride (LPS), bacterial toxins, and viral nucleic acids [19, 22]. Discussion Table 1. Genotypic analysis of the SNPs. PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 8 / 15 SNPs in Inflammasome among Pediatric Patients with Severe UTIs the expression of various extracellular or intracellular PRRs such as the TLRs and the NOD- like receptors (NLRs). Following this microbial sensing step, consecutive activation of intracel- lular signaling cascades marks the initiation of the immune responses [13]. These responses determine the host health status as well as the clinical severity [9]. Therefore, the risk of bacte- rial infection would be influenced by the signal transmission effectiveness in the immune response pathway. Defective signal transmission caused by a genetic polymorphism in the receptors, adaptors, or cytokines would influence an individual’s risk for infectious diseases [11, 14, 15, 45, 46]. NLRs have been considered important PRRs for various PAMPs, including lipopolysaccha- ride (LPS), bacterial toxins, and viral nucleic acids [19, 22]. The NLRs can also sense damage- associated molecular patterns (DAMPs) such as potassium efflux, reactive oxygen species, urate crystals, and extracellular matrix components including hyaluronan and biglycan [13, 16–20]. Following recognition of the signal pattern, the inflammasome consisting of NLRs, adaptor protein ASC, and caspase–1 is activated, and cytokines are released. These signal trans- mission cascades form an inflammasome-dependent innate immunity pathway. In the present study, the most significant finding was the association between NLRP3 (rs4612666) and severe renal parenchymal infections, APN and ALN. After excluding patients with VUR, a well-known risk factor for severe UTI, we found that patients with APN and ALN had a lower genotype frequency of NLRP3 (rs4612666) CC than did controls. This result implies that the CC genotype in NLRP3 (rs4612666) participates in regulating the inflamma- tory responses for pediatric renal parenchymal infections in patients from Taiwan. Genetic variations can modify the extent or severity of disease in susceptible patients. Muta- tions in the NLRP3 gene have been linked to several autoinflammatory disorders including Table 2. Allele frequency analysis of the SNPs. SNP Major allele frequency (%) APN vs. control ALN vs. control Combined vs. control ALN vs. PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs Table 3. Genotypic analysis of the SNPs in the patient subgroup without vesicoureteral reflux (non-VUR). SNP Group Genotype, n (%) Dominant model Recessive model 00 01 11 (01, 11 vs. 00) (00, 01vs. The NLRs can also sense damage- associated molecular patterns (DAMPs) such as potassium efflux, reactive oxygen species, urate crystals, and extracellular matrix components including hyaluronan and biglycan [13, 16–20]. Following recognition of the signal pattern, the inflammasome consisting of NLRs, adaptor protein ASC, and caspase–1 is activated, and cytokines are released. These signal trans- mission cascades form an inflammasome-dependent innate immunity pathway. In the present study, the most significant finding was the association between NLRP3 (rs4612666) and severe renal parenchymal infections, APN and ALN. After excluding patients with VUR, a well-known risk factor for severe UTI, we found that patients with APN and ALN had a lower genotype frequency of NLRP3 (rs4612666) CC than did controls. This result implies that the CC genotype in NLRP3 (rs4612666) participates in regulating the inflamma- tory responses for pediatric renal parenchymal infections in patients from Taiwan. Genetic variations can modify the extent or severity of disease in susceptible patients. Muta- tions in the NLRP3 gene have been linked to several autoinflammatory disorders including PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 9 / 15 11) CC CT TT OR (95% CI) Pa OR (95% CI) Pa OR (95% CI) Pa OR (95% CI) Pa NLRP3 Control 68 (32.7) 95 (45.7) 45 (21.6) 1.00 1.00 (rs4612666) APN 12 (19.0) 40 (63.5) 11 (17.5) 2.06 (1.03, 4.13) 0.038 1.00 1.31 (0.63, 2.71) 0.473 1.00 ALN 26 (20.6) 82 (65.1) 18 (14.3) 1.87 (1.11, 3.14) 0.018 0.91 (0.42, 1.94) 0.797 1.66 (0.91, 3.01) 0.096 1.27 (0.56, 2.88) 0.568 Combinedb 38 (20.1) 122 (64.6) 29 (15.3) 1.93 (1.22, 3.05) 0.005c 1.52 (0.91, 2.55) 0.108 GG GA AA OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P NLRP3 Control 66 (31.9) 97 (46.9) 44 (21.3) 1.00 1.00 (rs4925650) APN 20 (32.8) 34 (55.7) 7 (11.5) 0.96 (0.52, 1.77) 0.894 1.00 2.08 (0.89, 4.90) 0.087 1.00 ALN 43 (33.1) 59 (45.4) 28 (21.5) 0.95 (0.59, 1.51) 0.820 0.99 (0.52, 1.89) 0.968 0.98 (0.58, 1.68) 0.951 0.47 (0.19, 1.15) 0.094 Combined 63 (33.0) 93 (48.7) 35 (18.3) 0.95 (0.63, 1.45) 0.815 1.20 (0.73, 1.97) 0.464 CC CG GG OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P NLRP3 Control 85 (37.9) 105 (46.9) 34 (15.2) 1.00 1.00 (rs10754558) APN 28 (45.9) 25 (41.0) 8 (13.1) 0.72 (0.41, 1.28) 0.260 1.00 1.19 (0.52, 2.71) 0.687 1.00 ALN 45 (34.9) 63 (48.8) 21 (16.3) 1.14 (0.73, 1.79) 0.566 1.58 (0.85, 2.95) 0.145 0.92 (0.51, 1.67) 0.784 0.78 (0.32, 1.87) 0.571 Combined 73 (38.4) 88 (46.3) 29 (15.3) 0.98 (0.66, 1.46) 0.921 0.99 (0.58, 1.70) 0.981 GG GT TT OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P NLRP3 Control 86 (39.4) 104 (47.7) 28 (12.8) 1.00 1.00 (rs1539019) APN 20 (31.7) 33 (52.4) 10 (15.9) 1.40 (0.77, 2.54) 0.267 1.00 0.78 (0.36, 1.71) 0.682 1.00 ALN 46 (35.9) 63 (49.2) 19 (14.8) 1.16 (0.74, 1.83) 0.516 0.83 (0.44, 1.58) 0.567 0.85 (0.45, 1.59) 0.600 1.08 (0.47, 2.49) 0.852 Combined 66 (34.6) 96 (50.3) 29 (15.2) 1.23 (0.82, 1.85) 0.307 0.82 (0.47, 1.44) 0.496 TT TC CC OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P NLRP3 Control 57 (28.9) 97 (49.2) 43 (21.8) 1.00 1.00 (rs4925663) APN 15 (26.8) 27 (48.2) 14 (25.0) 1.11 (0.57, 2.17) 0.753 1.00 0.84 (0.42, 1.68) 0.616 1.00 ALN 35 (27.8) 57 (45.2) 34 (27.0) 1.06 (0.64, 1.74) 0.822 0.95 (0.47, 1.93) 0.890 0.76 (0.45, 1.27) 0.289 0.90 (0.44, 1.86) 0.779 Combined 50 (27.5) 84 (46.2) 48 (26.4) 1.08 (0.69, 1.68) 0.752 0.78 (0.49, 1.25) 0.301 (Continued) Table 3. Genotypic analysis of the SNPs in the patient subgroup without vesicoureteral reflux (non-VUR). Table 3. Genotypic analysis of the SNPs in the patient subgroup without vesicoure PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 10 / 15 SNPs in Inflammasome among Pediatric Patients with Severe UTIs Table 3. (Continued) SNP Group Genotype, n (%) Dominant model Recessive model 00 01 11 (01, 11 vs. 00) (00, 01vs. 11) CC CT TT OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P CARD8 Control 126 (60.6) 71 (34.1) 11 (5.3) 1.00 1.00 (rs1965759) APN 37 (60.7) 23 (37.7) 1 (1.6) 1.00 (0.56, 1.79) 0.991 1.00 3.35 (0.42, 26.5) 0.309 1.00 ALN 72 (55.8) 50 (38.8) 7 (5.4) 1.22 (0.78, 1.90) 0.388 1.22 (0.66, 2.27) 0.529 0.97 (0.37, 2.58) 0.956 0.29 (0.04, 2.44) 0.440 Combined 109 (57.4) 73 (38.4) 8 (4.2) 1.14 (0.77, 1.70) 0.516 1.27 (0.50, 3.23) 0.788 TT TA AA OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P CARD8 Control 65 (29.4) 108 (48.9) 48 (21.7) 1.00 1.00 (rs2043211) APN 17 (26.6) 34 (53.1) 13 (20.3) 1.15 (0.62, 2.15) 0.657 1.00 1.09 (0.55, 2.17) 0.809 1.00 ALN 38 (29.2) 65 (50.0) 27 (20.8) 1.01 (0.63, 1.62) 0.971 0.88 (0.45, 1.71) 0.698 1.06 (0.62, 1.80) 0.834 0.97 (0.46, 2.04) 0.941 Combined 55 (28.4) 99 (51.0) 40 (20.6) 1.05 (0.69, 1.61) 0.812 1.07 (0.67, 1.71) 0.784 GG GA AA OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P CARD8 Control 113 (51.6) 93 (42.5) 13 (5.9) 1.00 1.00 (rs1972619) APN 28 (50.9) 23 (41.8) 4 (7.3) 1.03 (0.57, 1.86) 0.927 1.00 0.81 (0.25, 2.57) 0.713 1.00 ALN 59 (46.8) 56 (44.4) 11 (8.7) 1.21 (0.78, 1.88) 0.393 1.18 (0.63, 2.22) 0.613 0.66 (0.29, 1.52) 0.326 0.82 (0.25, 2.70) 0.744 Combined 87 (48.1) 79 (43.6) 15 (8.3) 1.15 (0.78, 1.71) 0.482 0.70 (0.32, 1.51) 0.359 CC CT TT OR (95% CI) P OR (95% CI) P OR (95% CI) P OR (95% CI) P IL1-β Control 52 (23.7) 122 (55.7) 45 (20.5) 1.00 1.00 (rs1143629) APN 12 (20.0) 34 (56.7) 14 (23.3) 1.25 (0.62, 2.52) 0.541 1.00 0.85 (0.43, 1.68) 0.640 1.00 ALN 33 (25.8) 67 (52.3) 28 (21.9) 0.90 (0.54, 1.48) 0.670 0.72 (0.34, 1.52) 0.387 0.92 (0.54, 1.57) 0.770 1.09 (0.52, 2.26) 0.823 Combined 45 (23.9) 101 (53.7) 42 (22.3) 0.99 (0.63, 1.56) 0.964 0.90 (0.56, 1.45) 0.660 a P values <0 05 are shown in bold APN + ALN c Statistically significant with correction for multiple-SNP testing (P < 0.0055) Muckle–Wells syndrome, familial cold autoinflammatory syndrome, and chronic infantile neurologic cutaneous and articular syndrome [17]. SNPs in Inflammasome among Pediatric Patients with Severe UTIs Table 4. Allele frequency analysis of the SNPs in the non-VUR patient subgroup. SNP Major allele frequency (%) APN vs. control ALN vs. control Combined vs. control ALN vs. APN Control APN ALN Combinedb OR (95% CI) Pa OR (95% CI) Pa OR (95% CI) Pa OR (95% CI) Pa NLRP3, (rs4612666), C major allele 55.53 50.79 53.17 52.38 0.83 (0.56, 1.23) 0.350 0.91 (0.66, 1.25) 0.554 0.88 (0.67, 1.17) 0.374 1.10 (0.72, 1.69) 0.662 NLRP3, (rs4925650), G major allele 55.31 60.66 55.77 57.33 1.25 (0.83, 1.88) 0.296 1.02 (0.75, 1.39) 0.908 1.09 (0.82, 1.44) 0.567 0.82 (0.53, 1.27) 0.368 NLRP3, (rs10754558), C major allele 61.38 66.39 59.30 61.58 1.24 (0.82, 1.89) 0.311 0.92 (0.67, 1.25) 0.586 1.10 (0.76, 1.34) 0.954 0.74 (0.47, 1.16) 0.185 NLRP3, (rs1539019), G major allele 63.30 57.94 60.55 59.69 0.80 (0.53, 1.20) 0.274 0.89 (0.65, 1.22) 0.470 0.86 (0.65, 1.14) 0.289 1.11 (0.72, 1.72) 0.625 NLRP3, (rs4925663), T major allele 53.55 50.89 50.40 50.55 0.90 (0.59, 1.37) 0.619 0.88 (0.64, 1.21) 0.433 0.89 (0.67, 1.18) 0.408 0.98 (0.63, 1.53) 0.930 CARD8, (rs1965759), C major allele 77.64 79.51 75.19 76.58 1.12 (0.68, 1.84) 0.662 0.87 (0.61, 1.26) 0.464 0.94 (0.68, 1.31) 0.721 0.78(0.46, 1.32) 0.354 CARD8, (rs2043211), T major allele 53.84 53.13 54.23 53.87 0.97 (0.66, 1.44) 0.885 1.02 (0.75, 1.38) 0.921 1.00 (0.76, 1.32) 0.995 1.05 (0.68, 1.60) 0.837 CARD8, (rs1972619), G major allele 72.83 71.82 69.05 69.89 0.95 (0.60, 1.51) 0.831 0.83 (0.59, 1.17) 0.89 0.87 (0.64, 1.18) 0.359 0.88 (0.53, 1.43) 0.597 IL1-β, (rs1143629), C major allele 51.60 48.33 51.95 50.80 0.88 (0.59, 1.32) 0.526 1.01 (0.75, 1.38) 0.928 0.97 (0.74, 1.28) 0.820 1.16 (0.75, 1.78) 0.513 a P-values <0.05 are shown in bold. b APN + ALN doi:10 1371/journal pone 0140128 t004 Table 4. Allele frequency analysis of the SNPs in the non-VUR patient subgroup. doi:10.1371/journal.pone.0140128.t004 sensing and reaction to various microbial infections [13, 16, 21, 22]. However, to our knowl- edge, no study has reported the likely association of renal parenchymal infections and the inflammasome-dependent innate immune pathway. This investigation suggested that the NLRP3 polymorphisms could influence the susceptibility of pediatric patients to severe renal parenchymal infections. NLRP3 is in the NLR family of proteins. Other NLR proteins, including NLRP1, NLRC4 and AIM2 are also involved in sensing and activation by various microbes [16, 17, 21, 22]. Additionally, NLRP3 polymorphisms have been associated with susceptibility to a number of different diseases, such as coal workers' pneumoconiosis, Crohn’s disease, sporadic malignant melanoma, psoriasis and many others [27, 28, 30–32, 34, 37, 41, 42, 47]. Inflammasome activation has been associated with microbial PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 11 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 Author Contributions Conceived and designed the experiments: CHC YSL TYL. Performed the experiments: CHC YSL. Analyzed the data: CHC YSL CJC JCL. Contributed reagents/materials/analysis tools: CHC YSL CJC JCL. Wrote the paper: CHC JCL. Conceived and designed the experiments: CHC YSL TYL. Performed the experiments: CHC YSL. Analyzed the data: CHC YSL CJC JCL. Contributed reagents/materials/analysis tools: CHC YSL CJC JCL. Wrote the paper: CHC JCL. Whether polymorphisms in genes encoding other NLR proteins are linked with the severity of pediatric renal parenchymal infections remains to be explored. Similarly, the likely roles of IL– 18 polymorphism, another cytokine indicated in inflammasome-dependent innate immunity pathway in various kidney diseases [17–20], in pediatric renal infectious diseases would also require further investigations. Previous study has shown the CC genotype frequency is higher in the cases with food- induced anaphylaxis than those without [42]. In addition, the NLRP3 rs4162666 C allele has been demonstrated to be associated with higher transcriptional activity in THP–1 cell in vitro [42]. However, the CC genotype is significantly less in the non-VUR subgroup of cases with APN and ALN as compared to the control. This suggests that the finding about the higher tran- scription activity in C allele may not be feasible to explain our results here. More experimental works are warranted to clarify about the possible biological pathway. In summary, this is the first study to show that the inflammasome-dependent innate immu- nity pathway is likely involved in severe renal parenchymal infection. We showed that genetic polymorphisms in NLRP3 (rs4612666) are related to the pediatric patient’s susceptibility to APN and ALN. Further investigations of phenotypes or functional assessment of this SNP is 12 / 15 PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 SNPs in Inflammasome among Pediatric Patients with Severe UTIs warranted to confirm their pathogenic roles. Additionally, as the statistical power to detect sig- nificant associations with genetic variants is determined by sample size, a larger cohort study is recommended to replicate and validate the associations of SNPs with the severe UTIs, includ- ing APN and ALN. S1 File. The supplementary patient data. (XLSX) S1 Table. Primers employed for DNA amplification by direct DNA sequencing analysis of single nucleotide polymorphisms (SNPs). (DOCX) S2 Table. 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Combined polymor- phisms in genes encoding the inflammasome components NALP3 and CARD8 confer susceptibility to Crohn's disease in Swedish men. American Journal of Gastroenterology. 2009; 104(5):1180–8. doi: 10. 1038/ajg.2009.29 PMID: 19319132 42. Hitomi Y, Ebisawa M, Tomikawa M, Imai T, Komata T, Hirota T, et al. Associations of functional NLRP3 polymorphisms with susceptibility to food-induced anaphylaxis and aspirin-induced asthma. Journal of Allergy & Clinical Immunology. 2009; 124(4):779–85.e6. doi: 10.1016/j.jaci.2009.07.044 PMID: 19767079 43. Dupont WD, Plummer WD Jr. Power and sample size calculations for studies involving linear regres- sion. Control Clin Trials. 1998; 19(6):589–601. PMID: 9875838 44. Practice parameter: the diagnosis, treatment, and evaluation of the initial urinary tract infection in febrile infants and young children. American Academy of Pediatrics. Committee on Quality Improvement. Sub- committee on Urinary Tract Infection. Pediatrics. 1999; 103(4 Pt 1):843–52. PMID: 10103321 45. Hawn TR, Scholes D, Wang H, Li SS, Stapleton AE, Janer M, et al. Genetic variation of the human uri- nary tract innate immune response and asymptomatic bacteriuria in women. PLoS One. 2009; 4(12): e8300. doi: 10.1371/journal.pone.0008300 PMID: 20016852 46. Ragnarsdottir B, Lutay N, Gronberg-Hernandez J, Koves B, Svanborg C. PLOS ONE | DOI:10.1371/journal.pone.0140128 October 7, 2015 References Genetics of innate immunity and UTI susceptibility. Nat Rev Urol. 2011; 8(8):449–68. doi: 10.1038/nrurol.2011.100 PMID: 21750501 47. Verma D, Lerm M, Blomgran Julinder R, Eriksson P, Soderkvist P, Sarndahl E. Gene polymorphisms in the NALP3 inflammasome are associated with interleukin–1 production and severe inflammation: rela- tion to common inflammatory diseases? Arthritis & Rheumatism. 2008; 58(3):888–94. doi: 10.1002/art. 23286 PMID: 18311798 15 / 15
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Sustainable and low-cost solutions for thermal and acoustic refurbishment of old buildings
Journal of physics. Conference series
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Sustainable and low-cost solutions for thermal and acoustic refurbishment of old buildings To cite this article: M Neri et al 2021 J. Phys.: Conf. Ser. 1868 012027 View the article online for updates and enhancements. This content was downloaded from IP address 83.42.137.33 on 28/04/2021 at 13:47 Journal of Physics: Conference Series Journal of Physics: Conference Series PAPER • OPEN ACCESS PAPER • OPEN ACCESS M Neri 1, E Levi1, E A Piana1, P Pujadas2, E Cuerva2, A Guardo2, M Pilotelli1 1 University of Brescia, Department of Industrial and Mechanical Engineering, via Branze 38, Brescia, Italy 2 Universitat Politècnica de Catalunya. Avda. Diagonal, Barcelona manuela.neri@unibs.it 2 Universitat Politècnica de Catalunya. Avda. Diagonal, Barcelona manuela.neri@unibs.it Abstract. This paper investigates the possibility to realize solutions for buildings thermal and acoustic refurbishment by using end-of-life household materials, such as cardboard, clothes, and egg-boxes. These solutions can be installed to improve the indoor quality in neighborhoods populated by people below the poverty threshold. The considered end-of-life household materials and their combination have been analyzed from the acoustic and thermal points of view. First of all, the sound insulation and the sound absorption properties have been determined by means of an impedance tube. Then, the summer and the winter thermal performances, when coupled to different wall systems, have been investigated analitically. The results suggest that good thermal and acoustic characteristics can be achieved in a contained thickness by coupling end-of-life household materials. 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. Published under licence by IOP Publishing Ltd 1 This content was downloaded from IP address 83.42.137.33 on 28/04/2021 at 13:47 This content was downloaded from IP address 83.42.137.33 on 28/04/2021 at 13:47 IOP Publishing 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) 1868 (2021) 012027 doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series Sustainable and low-cost solutions for thermal and acoustic refurbishment of old buildings M Neri 1, E Levi1, E A Piana1, P Pujadas2, E Cuerva2, A Guardo2, M Pilotelli1 1 University of Brescia, Department of Industrial and Mechanical Engineering, via Branze 38, Brescia, Italy 2 Universitat Politècnica de Catalunya. Avda. Diagonal, Barcelona l i@ ib it M Neri 1, E Levi1, E A Piana1, P Pujadas2, E Cuerva2, A Guardo2, M Pilotelli1 1 University of Brescia, Department of Industrial and Mechanical Engineering, via Branze 38, Brescia, Italy 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) 020) 1868 (2021) 012027 IOP Publishing doi:10.1088/1742-6596/1868/1/012027 1868 (2021) 012027 doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series This article is part of a project that aims to develop the knowledge towards possible low-cost improvements in thermal and acoustic comfort conditions for people living under the poverty threshold, providing also simple and fast application solutions. However, these solutions not only aim to solve the thermal and acoustic vulnerability, but also to become an instrument for social change and the realization of individuals. In particular, in this paper, the acoustic and thermal performance of a group of end-of-life household materials are investigated with the aim to identify a solution to be installed indoor on vertical walls to guarantee an improvement of the acoustic and thermal conditions. This article is part of a project that aims to develop the knowledge towards possible low-cost improvements in thermal and acoustic comfort conditions for people living under the poverty threshold, providing also simple and fast application solutions. However, these solutions not only aim to solve the thermal and acoustic vulnerability, but also to become an instrument for social change and the realization of individuals. In particular, in this paper, the acoustic and thermal performance of a group of end-of-life household materials are investigated with the aim to identify a solution to be installed indoor on vertical walls to guarantee an improvement of the acoustic and thermal conditions. About acoustic comfort, the two main properties to be considered are the attitude of the material to dissipate acoustic energy, expressed through the sound absorption coefficient α, and the sound insulation capability, represented by the sound transmission loss TL. In this work, to determine these parameters a four-microphone transmission tube has been used in this work. This apparatus is a double standing wave tube equipped with four microphones. By means of this device it is possible to determine the transfer matrix of a material. For this reason, this device is particularly suitable for the acoustic characterization and optimization of complex layered structures [9]. Another advantage is that it requires smaller samples if compared to the 10 m2 necessary to perform measurements in a transmission suite. The only drawback using a transmission tube is that only the “normal incidence” characteristics of the materials can be evaluated, while in real life applications diffuse incidence is the actual condition. 2. Methods In this paper, a group of end-of-life household materials has been analyzed from the acoustic and the thermal points of view. Firstly, end-of-life household materials have been tested acoustically and, then, some of them have been analyzed thermally. 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) Nonetheless, with the experimental tests it has been possible to compare the acoustic performances of several samples when subject to normal incidence. These first results will be refined in future studies. Then, some of the tested configurations have been analyzed also from the thermal point of view. Since the systems are designed for Italy and the Raval neighborhood, that are situated in the Mediterranean area, both the summer and the winter conditions have been considered. Indeed, since in these locations, summer is characterized by a wide daily temperature variation, it is necessary to consider not only the thermal conductivity and thickness of the layers, but also their heat capacity and their position in the wall. 1. Introduction Good structural performance but weak thermal and acoustic insulation performances characterize the most widespread building technologies in Europe. Despite in recent years many buildings have been refurbished from an energetic point of view, this kind of interventions is not reasonably priced for low-income people. Consequently, in these realities, tenants are often forced to live in unhealthy conditions because the heating system is missing, or ventilation is not adequate. This phenomenon of social urban vulnerability is common in many developed countries. In the orbit of urban vulnerability are found concepts such as exclusion, marginality, and poverty which, though not synonymous, may be mutually reinforcing. The correlation between poverty and low indoor air quality (IAQ) has been highlighted in several studies [1,2]. This problem mainly affects elderly people and people forced to stay home for many hours, like long-term unemployed or disabled. The city of Barcelona, like many other cities in the world, suffers strong internal vulnerabilities and inequalities because of differences in the social composition of the population through spatial distribution. The Raval area is the one with the highest concentration of poverty in the whole urban area of Barcelona, and it is characterized by two population groups, that are elderly people and immigrants, both with low incomes. Nowadays, building design embraces many aspects such as environmental, social and sustainability issues [3]. For example, local sustainable construction materials should be chosen, and local workers should be involved as already done in several projects [4]. For this reason, building systems must be cheap, made of materials easy-to-be-found in the vicinity of the building site, safe and easy to be installed during the construction phase also by non-skilled workers. From this point of view, end-of-life household materials are cheap (or even free), easy-to-be-found, safe and, when discharged, they have properties that can still be exploited. The possibility to reuse these materials was investigated by several authors: properties of clothes [5], cardboards [6], and plastic containers [7] were analyzed in several works. The reuse of these materials reduces the amount of produced waste and, consequently, of material discharged in the environment; indeed, only a small percentage of household waste materials is recycled. For example, in 2017, only the 14% of the textile waste was recycled and the rest was addressed to incineration [8]. 1 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) 2.1. Acoustic performances 2.1. Acoustic performances The acoustic characterization has been carried out according to the procedure described in the ASTM E2611 standard [9]. The procedure requires the measurements to be performed using a four- microphone impedance tube. Such device has a loudspeaker, generating a wide-band white noise, mounted at one end and an anechoic termination at the other end. The sample is placed in the central section, between two microphone pairs. A multichannel analyzer measures the microphones signals and computes the transfer functions. Such functions are then post-processed by a MATLAB script based on the ASTM E2611 [10] standard to obtain the acoustic parameters of the sample and its transfer matrix. The single materials and the combinations reported in Table 1 have been tested. For each sample type, three tests have been performed and the results have been averaged. The tests have been organized as follows: the first two sets are made of egg-boxes samples featuring single/double layers (test 02-03-22) and egg-boxes coupled with polyester fiber (test 04-05). In some cases, a steel sphere was embedded inside the polyester fiber and the structure closed using a cardboard layer (test 07-08-17). In order to accommodate the steel element inside the structure, a cylindrical hole was made at the center of the cardboard disks. A third set of samples includes samples mainly made of cardboard (test 13–14). Samples made of clothes of different fabric types represent the fourth experimental set. Several repetitions have been performed for each measurement to assess how the ability of the person assembling the samples can affect its performances. This aspect will be further investigated in future analysis. The fifth (and final) set of measurements has been made on samples obtained by combining egg boxes, clothes and metal elements. In general, to improve the acoustical behavior, disks and egg- 2 020) 1868 (2021) 012027 IOP Publishing doi:10.1088/1742-6596/1868/1/012027 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) 1868 (2021) 012027 doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series boxes exposed to the sound source were perforated to allow the sound to pass through the first layer. The sequences reported in Table 1 start with the material closest to the sound source. The frequency range investigated goes from 100 Hz to 3150 Hz. boxes exposed to the sound source were perforated to allow the sound to pass through the first layer. 2.1. Acoustic performances The sequences reported in Table 1 start with the material closest to the sound source. The frequency range investigated goes from 100 Hz to 3150 Hz. Table 1. Specimens tested in the impedance tube. The diameter of the samples is 46 mm. Table 1. Specimens tested in the impedance tube. The diameter of the samples is 46 mm. 3 3 IOP Publishing 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) 1868 (2021) 012027 doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series Figure 1. Walls configurations (MP, MPF, MLP) and the additional panels (Poli, CDB) considered in the analysis. The additional panels are installed internally. Figure 1. Walls configurations (MP, MPF, MLP) and the additional panels (Poli, CDB) considered in the analysis. The additional panels are installed internally. 3.1. Acoustic performances The absorption coefficient α and the sound transmission loss TL of the samples reported in Table 1 have been determined by means of a 4-microphone impedance tube. When dealing with the acoustic comfort both sound absorption and sound insulation performances are influential. Yet, since the reference walls have good sound insulation basic performances, sound absorption can be considered more interesting. In Figure 2, for the first set of samples the most interesting sound insulation performance is the one given by specimen 22 (reverse double pyramid) with a TL following the mass law up to 800 Hz and then a behavior typical of double walls, with a mass-spring-mass resonance frequency around 1800 Hz. Also the specimen 02 (single egg box) showed an acceptable performance, with a rather flat TL of 12 dB from 100 Hz up to 2000 Hz, while specimen 03 (perforate egg box with polyester) is not able to reach the performances of the other samples. For the same samples, with the exception of sample 02 which is not permeable to air, α is characterized by wide peaks at given frequencies due to holes obtained in the egg cardboard behaving like Helmholtz resonators (sample 03) or quarter wavelengths resonators (sample 22). In the case of sample 03 the peak around 700 Hz is very wide due to the presence of sound absorbing polyester fiber inside the main volume. As concerns the second set of samples, TL curves are all very similar as can be seen in Figure 3. This behavior can be explained by the nature of the samples which are built with the same elements: the egg cardboard, the polyester foam and the steel sphere. The only variables are the orientation of the samples and the presence of a cardboard disk. The TL of samples 04 and 05 are characterized by the typical mass law behavior due to the single egg cardboard, except a dip around 1200 Hz. The samples 07 and 08 have higher values of TL due to the double or triple layer structure which causes an increase of the mass and an increase of the curve slope due to multiple resonances of the layers. In particular, sample 08 exhibits very interesting performances at low frequencies and the higher TL of the group also at high frequencies. For these samples α is characterized by multiple peaks typical of the resonators featured in the cardboard parts. 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) Journal of Physics: Conference Series 1868 (2021) 012027 doi 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) 020) 1868 (2021) 012027 IOP Publishing doi:10.1088/1742-6596/1868/1/012027 1868 (2021) 012027 doi:10.1088/1742-6596/1868/1/012027 3.1. Acoustic performances The breadth of the peaks depends again on the presence of polyester fibers. The best sample is Test 08, having a rather high α also at high frequency, with a maximum of 0.95 at 2 kHz. The third set of samples shown in Figure 4 presents very similar TL curves for all the samples. The performances are very similar and TL at low frequency is the highest among the entire group of tested materials. Such behaviour is due to the density of the stacking, which makes the samples similar to sandwich materials featuring non compressible cores. For this reason the trend is characterised by a linear behaviour followed by the typical coincidence dip. For samples 13 and 14, α is marked out by a maximum around 600 Hz due to the resonance of the Helmholtz resonators featured in the cardboard. For sample 17, α is very similar to the one of sample 08 (having a very similar structure), with three peaks reaching a value of 0.8. The fourth set considers tissues and results are shown in Figure 5. Comparing the different samples, the TL curves are all very similar and are typical for porous materials. The better performances are reached by the thicker samples (sample 26 – 100 mm) and by the sample having the higher density (sample 30 – high density viscose). Also, α curves have a shape typical for porous materials, with an S shape, low values at low frequencies and values approaching 1 at high frequencies. The fifth and last set is a combination of tissues, egg boxes and metal parts. As can be seen in Figure 6, the TL curves have very similar trends. If compared to the TL curves of the fourth set, the values are generally higher at low frequency due to the higher mass per unit area of the samples. Sample 36 has the best performances for this group. As concerns α, the behavior is dominated by the Helmholtz resonator characteristic shape featuring a peak around 400 Hz followed by an increase of the coefficient due to the presence of the tissues. As a general remark, the higher the flow resistivity of the tissue, the lower α in the high frequency region. 3 2 Th l f 2.2. Thermal investigation g The thermal effect of an insulating panel made of end-of-life household materials applied to different walls has been investigated. The aim of the analysis is to understand if the materials at hand exhibit promising characteristics that can justify further investigations. Three basic wall configurations called MP103, MLP01, and MPF01 have been considered. Such configurations have been renamed MP, MLP and MPF in the following part (Section 3.2). These basic types of walls have been extrapolated from the UNI/TR 11552 [11] standard and represent the typical building solutions used for Italian council estate. Since, as stated in [11], the wall thickness is variable, the largest and the smallest thicknesses have been considered. The thermal performances of the walls have been compared with those of the walls equipped with one of the additional insulating panels shown in Figure 1 (Poli or CDB), these latter installed on the internal side of the wall. Indeed, the solutions considered in this paper are designed for historical urban contexts in which the external appearance of the buildings must be preserved and external intervention are not allowed. In the following sections, type and thickness of each configuration are declared in the name. For example, MPmin-Poli50 represents the thinner wall configuration MP coupled to the Poli panel. The variable layer of the Poli panel is 50 mm thick. In particular, the periodic thermal transmittance Y12, the delay, the thermal transmittance U and the decrement factor f have been calculated according to the UNI EN ISO 13786:1999 [12]. The periodic thermal transmittance Y12, an important parameter for the evaluation of the summer comfort conditions, represents the amplitude of the density of heat flow rate on one side when the temperature amplitude on that side is zero and there is unit temperature amplitude on the other side. The decrement factor f describes how well the wall reduces the internal temperature peak. The thermal transmittance, instead, describes the insulating performance in stationary conditions like the ones found during the wintertime. 4 020) 1868 (2021) 012027 IOP Publishing doi:10.1088/1742-6596/1868/1/012027 3.2. Thermal performances Since clothes and cardboard have shown good acoustic performances, they have been evaluated also from the thermal point of view. Given their limited thickness, egg-boxes have not been considered in this section. 5 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) Journal of Physics: Conference Series 1868 (2021) 012027 IOP Publishing doi:10.1088/1742-6596/1868/1/012027 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) IOP Publishing 020) 1868 (2021) 012027 IOP Publishing doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series Figure 2. Acoustic properties of samples made of clothes (one fabric at a time). Figure 5. Acoustic properties of samples made of clothes combined with other household waste materials. Figure 4. Acoustic properties of samples made of egg-box coupled with other household waste materials. Figure 6. Acoustic properties of samples made of cardboard. Figure 3. Acoustic properties of samples made of at least one egg- box. Figure 2. Acoustic properties of samples made of clothes (one fabric at a time). Figure 2. Acoustic properties of samples made of clothes (one fabric at a time). Figure 3. Acoustic properties of samples made of at least one egg- box. Figure 3. Acoustic properties of samples made of at least one egg- box. Figure 3. Acoustic properties of samples made of at least one egg- box. Figure 4. Acoustic properties of samples made of egg-box coupled with other household waste materials. Figure 4. Acoustic properties of samples made of egg-box coupled with other household waste materials. Figure 4. Acoustic properties of samples made of egg-box coupled with other household waste materials. Figure 5. Acoustic properties of samples made of clothes combined with other household waste materials Figure 6. Acoustic properties of samples made of cardboard. Figure 6. Acoustic properties of samples made of cardboard. 6 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) Journal of Physics: Conference Series 1868 (2021) 012027 IOP Publishing doi:10.1088/1742-6596/1868/1/012027 IOP Publishing 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) ) 1868 (2021) 012027 g doi:10.1088/1742-6596/1868/1/012027 Journal of Physics: Conference Series Journal of Physics: Conference Series 1868 (2021) 012027 doi:10.1088/1742-6596/1868/1/012027 Figure 7. Dynamic thermal characteristics of MP, MLP, MPF wall configurations coupled with the POLI additional panels. Figure 7. Dynamic thermal characteristics of MP, MLP, MPF wall configurations coupled with the POLI additional panels. aracteristics of MP, MLP, MPF wall configurations coupled with the Figure 8. Dynamic thermal characteristics of MP, MLP, MPF wall configurations coupled with the CDB additional panels. Figure 8. 3.2. Thermal performances Dynamic thermal characteristics of MP, MLP, MPF wall configurations coupled with the CDB additional panels. The thermal characteristics of MP, MLP and MPF wall configurations with and without the additional insulating panels are shown in Figures 7 and 8. In Figure 7 it can be noted that the addition of the panel Poli (made of clothes and cardboard), determines a reduction of Y12, f, and U, whereas the delay of the dynamic thermal transmittance slightly increases in modulus. In particular, a significant reduction of Y12 has been obtained with the thicker 100POLI panel. A significant reduction of U has been obtained for MPF and MLP wall configurations. For the thicker version of the panel (100POLI), the decrement factor f increases of about 2 hours, and for MP-max and MPF-max the addition of the panel corresponds to a time shift of about 12 hours. Even if the increment of f is limited, the time shift represents a good improvement because the indoor temperature peak takes place when it is possible to cool the indoor ambient naturally, simply opening the windows. In Figure 8 it is shown how the addition of a cardboard layer determines a decrease of Y12, f and U. As regards the time shift f of the dynamic thermal transmittance, the variation is lower than one hour. However, with the same thickness, better performances belong to the panel made of polyester and this is probably due to the fact that this latter has greater density. 2020 UIT Seminar on Heat Transfer (UIT-HTS 2020) Journal of Physics: Conference Series 1868 (2021) 012027 IOP P doi:10.1088/1742-6596/1868/ 020) 1868 (2021) 012027 IOP Publishing doi:10.1088/1742-6596/1868/1/012027 020) 1868 (2021) 012027 IOP Publishing doi:10.1088/1742-6596/1868/1/012027 1868 (2021) 012027 doi:10.1088/1742-6596/1868/1/012027 and transmission loss has been obtained for samples made of cardboard, but interesting results have been obtained also for samples made with two egg-boxes, especially in terms of transmission loss. Moreover, it has been shown that higher density clothes ensure a better acoustic performance. Due to the practical difficulties met when manufacturing the samples, which are often non planar, further analysis will be required to investigate how the operators manual skills affect the acoustic performances of the specimens. From the thermal point of view, the installation of panels made of clothes and cardboard respectively determines a reduction of the periodic thermal transmittance and the thermal transmittance. However, due its greater density, panels made of clothes are more effective. This paper shows that end-of-life household materials have a potential for the refurbishment of old buildings from both the acoustic and the thermal points of view. Future works will investigate how the application of these panels can affect the hygrometric behavior of the walls. Moreover, other configurations will be tested acoustically. Acknowledgements The authors would like thank the Department of Mechanical and Industrial Engineering for funding the research through the MetATer PRD project. 4. Conclusions In this paper the acoustic and thermal performances of several end-of-life household materials have been investigated. From the acoustic point of view, the best compromise between sound absorption 7 References References [1] Fabbri K 2015 Building and fuel poverty, an index to measure fuel poverty: An Italian case study. Energy, 89: 244. doi.org/10.1016/j.energy.2015.07.073. [1] Fabbri K 2015 Building and fuel poverty, an index to measure fuel poverty: An Italian case study. Energy, 89: 244. doi.org/10.1016/j.energy.2015.07.073. [2] Fowler T et al. 2015 Excess winter deaths in Europe: A multi-country descriptive analysis. European Journal of Public Health vol 25, pp 339-345. [3] Agenda 21 for sustainable construction in developing countries: a discussion document, International Council for Research and Innovation in Building and Construction, CIB; United Nations Environment Programme International Environmental Technology Centre, UNEP- IETC. Available at: https://researchspace.csir.co.za/dspace/handle/10204/3511 p p p [4] Burroughs S and Růžička J. 2019 The Use of Natural Materials for Construction Projects – Social Aspects of Sustainable Building: Case Studies from Australia and Europe, IOP Conf. Series: Earth and Environmental Science vol 290. [4] Burroughs S and Růžička J. 2019 The Use of Natural Materials for Construction Projects – Social Aspects of Sustainable Building: Case Studies from Australia and Europe, IOP Conf. Series: Earth and Environmental Science vol 290. [5] Briga-Sá A, Nascimento D, Teixeira N, Pinto J, Caldeira F, Varum H and Paiva A 2013 Textile waste as an alternative thermal insulation building material solution. Construction and Building Materials vol 38, pp 155-160, doi.org/10.1016/j.conbuildmat.2012.08.037. [6] Secchi S, Asdrubali F, Cellai G, Nannipieri E, Rotili A and Vannucchi I 2015 Experimental and environmental analysis of new sound-absorbing and insulating elements in recycled cardboard, Journal of Building Engineering vol 5, pp 1-12, doi:10.1016/j.jobe.2015.10.005 [7] Pons O and Abt T 2020 Evaluation of household waste materials for façade components in primary educational workshops. Mechanical and fire properties, Journal of Building Engineering vol 29, doi.org/10.1016/j.jobe.2020.101202. g g g j j [8] Preferred fiber & materials market report, https://textileexchange.org, Accessed on the 22nd February 2020. [9] Levi E, Neri M, Pilotelli M, Piana E A and Lezzi A M 2019 Numerical and experimental study on metamaterials featuring acoustical and thermal properties, Journal of Physics: Conference Series. [10] ASTM E2611 - 19 Standard Test Method for Normal Incidence Determination of Porous Material Acoustical Properties Based on the Transfer Matrix Method. p [11] UNI/TR 11552:2014 – Opaque envelope components of buildings – Thermo-physical parameters (in Italian). [12] UNI EN ISO 13786:2018- Thermal performance of building components - Dynamic thermal characteristics – Calculation methods. 8 8
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TMD pain: the effect on health related quality of life and the influence of pain duration
Health and quality of life outcomes
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RESEARCH Open Access BioMed Central © 2010 Tjakkes 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 Objectives: As impact of literature concerning this subject is scarce, the objectives of this study were to assess whether the Health Related Quality of Life (HRQoL) is decreased in patients with painful temporomandibular disorders as compared to the HRQoL in the general population, and to evaluate to what extent pain duration affects HRQoL. Methods: Data concerning physical and mental health were retrieved from patients with painful temporomandibular disorders. Assessment tools used were: the Mandibular Function Impairment Questionnaire (MFIQ), the Short-Form-36 (SF-36), the Hospital Anxiety and Depression Schedule (HADS), and the General Health Questionnaire (GHQ). In order to examine the influence of the duration of pain on HRQoL, the total sample was divided into three different subgroups. Subgroup 1 consisted of patients with complaints existing less than one year. Patients with complaints from 1 to 3 years were allocated to the second group. The 3rd subgroup included patients with complaints longer than 3 years. Results: The total sample consisted of 95 patients (90 females and 5 males). On most physical and social functioning items, groups 2 and 3 scored significantly worse than the general population. On the other hand, none of the groups differed from the general population when comparing the mental items. Duration of pain was significantly correlated with SF-36 subscale physical functioning and the mandibular impairment. Conclusion: Patients with TMD pain less than one year score better than compared to the population norm. With a longer duration of pain, mental health scores and role limitations due to emotional problems do not appear to be seriously affected by reduced physical health, while social functioning appears to be considerably affected. * Correspondence: g.h.e.tjakkes@kchir.umcg.nl 1 Department of Oral and Maxillofacial Surgery, University Medical Center Groningen University of Groningen, Groningen, PO Box 30.001, 9700 RB, The Netherlands Full list of author information is available at the end of the article Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46 http://www.hqlo.com/content/8/1/46 * Correspondence: g.h.e.tjakkes@kchir.umcg.nl Background become more obvious and prominent. Even after a decrease of the somatosensory input, suffering and pain behaviour may continue and even increase [6]. Temporomandibular disorders (TMDs) comprise a group of disorders that affect the temporomandibular joint (TMJ), the masticatory muscles, or both. TMDs involve musculoskeletal pain, disturbances in the mandibular movement patterns, and/or impairment in functional movement [1]. Pain is the main characteristic of most TMDs and also the main reason for patients to seek treat- ment [2]. Many TMDs should be considered chronic pain conditions, since they show lot of similarities [3]. Psycho- logical factors have been implicated in the initiation as well in the perpetuation of several TMDs [4]. Stress, somatic distress, and depression may be potential etiolog- ical risk factors for TMD-related pain [5]. When the duration of pain increases, psychological factors may It is generally accepted that quality of life is negatively affected by chronic pain [7,8]. The impact of TMDs (and other types of orofacial pain) on Health Related Quality of Life (HRQoL), however, has scarcely been described. Recently, Naito et al. conducted a systematic review on oral health status and health-related quality of life [9]. They found only one study concerning TMDs. In this study, Reisine and Weber [10] observed a sample of 30 patients with temporomandibular disorders, during 6 months. Different aspects of HRQoL were investigated e.g. anxiety, perceptions and social functioning. It was found that while the pain decreased over time, oral and functional aspects did not improve significantly within the same period of time. This result may be due to a slower response of other parameters to treatment in con- trast to a relatively rapid response of pain. Furthermore, the authors found relatively poor ratings of well-being Page 2 of 8 Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46 http://www.hqlo.com/content/8/1/46 Page 2 of 8 less than one year. Patients with complaints from 1 to 3 years were allocated to the second group. The 3rd sub- group consisted of patients with complaints longer than 3 years. Secondly, the influence of the duration of pain was studied using results of the total sample in regression analysis. During their first visit to the clinic, patients were informed about the study and the content of the ques- tionnaires. When patients were willing to participate, they were requested to fill in an informed consent. HRQoL was measured by the following instruments SF-36 The Medical Outcome Short Form Health Survey, a 36 item health survey, was used to assess the patients' HRQoL [18]. It includes eight health concepts: physical functioning (PF, measuring the physical activities), role limitations due to physical health problems (RP, measur- ing the effect of the physical health on work and daily activities), bodily pain (BP), general health (GH) percep- tions, vitality (VT, measuring energy/fatigue), social functioning (SF), role limitations due to personal or emo- tional problems (RE measuring the effect of the emotions on work and daily activities) and general mental health (MH including anxiety and depression). The scores on every subscale range from 0-100, with higher scores indi- cating better health states. Reference values were used to compare the results of the group in question. The refer- ence values were taken from a Dutch study, which con- sisted of a random Dutch sample of 1742 persons, which is used as the reference group [19]. In this study the mean values for each subscale were for PF 83.0 (sd 22.8), RP 76.4 (sd 36.3), BP 74.9 (sd 23.4), GH 70.7 (sd 20.7) VT 68.8 (sd 19.3), SF 84.0 (sd 22.4), RE 82.3 (sd 32.9), MH 76.8 (sd 17.4) [19]. MFIQ Assessment and Instruments During the second visit to the clinic, patients were instructed how to complete the questionnaires. Subse- quently, patients were left alone to complete the ques- tionnaires. When necessary, unclear test items could be clarified by the interviewer. Only Dutch versions of the questionnaires were used. It is not clear whether and, if so, how (chronic) pain related to TMDs influences HRQoL, and whether pain duration is of influence. It may be hypothesized that when pain has just begun, this will mainly affect physical factors such as physical functioning. When the pain lasts for a longer period, and treatment so far has failed to relieve the pain, it may start to have more impact on the emotional behaviour, social factors and HRQoL. How- ever, whether this is the case is yet not clear. Information concerning the influence of pain and its persistence on HRQoL may guide (the emphasis of) treatment in these patients. Therefore, the aims of this study were to assess whether the HRQoL is decreased in orofacial pain patients as compared to the general population, and to study the effect of duration of pain on HRQoL. Methods and materials Sample Patients were recruited from the department of Oral and Maxillofacial Surgery of the University Medical Center Groningen. The group consisted of 95 patients consecu- tively consulting the TMD/Orofacial Pain section for their orofacial pain problems. The inclusion criteria were age over 16 years, no language barrier, and the presence of a painful temporomandibular disorder as classified according to the RDC/TMD [15,16]. From the axis II information, the duration and impact of the pain were assessed. The influence of the duration of pain on HRQoL was examined by two means. Firstly, the total sample was divided into three different subgroups. Sub- group 1 consisted of patients with complaints existing Background and high levels of anxiety, suggesting that TMD patients are characterized by relatively negative psychological states, and that when pain persist (even when dimin- ished) functional aspects do not improve. Murray et al. [11] described the HRQoL, as measured with the Oral Health Impact Profile (OHIP), of patients referred to a craniofacial pain unit because of TMD and facial pain. With regard to pain-related disability and HRQoL, 29.7% of the sample reported a frequently dis- turbed sleep as a consequence of their oral conditions, and 36.4% reported feelings of depression. Different researchers have found a larger impairment of the oral HRQoL in TMD patients compared with healthy popula- tion, using the OHIP [12,13]. Quality of life has been described by the World Health Organisation as " ... an individual's perception of their position in life in the context of the culture and value sys- tem of which they live with the relation to their goals, expectations, standards and concerns." This concept incorporates different aspects of individuals, including physical health, psychological state, level of indepen- dence, social relationships, personal beliefs and their rela- tionship to salient features of the environment [17]. LeResche et al. [14] studied the facial expression as well as states of anxiety, depression, somatization and daily stress in a group of TMD pain patients, subgrouped into a chronic and non-chronic category. With regard to these four aspects of HRQoL, no differences were found between a group of patients that perceived pain for the first time within the last two months (non chronic group) and a group that suffered from pain for over 6 months (chronic group). Sample size calculation To estimate the a priori sample size, an effect size of 0.4 was chosen. By convention this effect size is considered as a moderate effect size. Sample was calculated on an ANOVA with the parameters α, β, number of groups and effect size. α was set at 5%, β at 10%, number of groups 3, resulting in a critical F of 3.10931. The total calculated sample was 84. To account for possible dropouts, sample size was about 10% increased to 95. Results Patients In total 95 patients (90 females and 5 males) provided their consent to participate in the study. Their average age was 40.3 yrs (sd 13.1, ranging from 17-69). According to the RDC/TMD criteria, patients were diagnosed with a group I diagnosis (myofascial pain), a group II diagnosis (disc displacement) a group III (arthralgia, osteoarthritis and osteoarthrosis). A group I diagnosis was established in 31.9%; a group II diagnosis in 4.4% and a group III in 35.2%. A combined diagnosis was made in 28.7% of all cases (in 7.8% group I and II, in 17.6% group I and III, and in 3.3% group II and III were combined). Furthermore, the participants of the 3 subgroups based on pain dura- tion were calculated: subgroup 1 (pain present for less than one year) consisted of 15 patients (14 females; 1 male, mean age 37.7 yrs, sd 14.4, range 17-69), subgroup 2 (1-3 years pain duration) consisted of 16 patients (13 females, 3 males; mean age 37.5 yrs, sd 14.1, range 20-68), and subgroup 3 (more than 3 years of pain) consisted of 64 patients (63 females, 1 male; mean age 41.6 yrs, sd 12.5, range 17-67). The distribution of the diagnoses, medication use and coinciding chronic pain diseases among the three groups is listed in Table 1. To assess depression and anxiety in a hospital setting, the HADS was used [21]. To screen for anxiety (HADS-A) the odd items were used. For the screening of depression (HADS-D), the even items of questionnaire were used. On each subscale, scores up to 7 indicate no signs of anx- iety or depression, scores between 8 and 10 suggest prob- able anxiety or depression, and scores over 10 indicate the presence of anxiety or depression, respectively [21]. GHQ 28 The general health questionnaire was used to assess dif- ferent types of psychiatric distress. It is a 28 item list which can be divided into four different subscales: somatic symptoms (GHQA), anxiety and insomnia (GHQB), social dysfunction (GHQC) and severe depres- sion (GHQD) [22]. The reference values were for GHQA 6.2, GHQB 5.8, GHQC 7.0, GHQD 1.6 and were retrieved from a general Dutch population of 485 persons [23]. Effects of pain duration: Three groups Results compared with reference values Table 2 shows the mean SF-36 and GHQ scores for the three subgroups. The first ("relatively acute") subgroup scored better on the subscale physical functioning and worse on subscales general health and vitality than the general population, but on the other subscales this sub- group and the general population revealed comparable scores. ( MFIQ The Mandibular Function Impairment Questionnaire was used to obtain information about the function Page 3 of 8 Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46 http://www.hqlo.com/content/8/1/46 Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46 http://www.hqlo.com/content/8/1/46 analysis. Data were analyzed using SPSS 14 (SPSS Inc, USA). The level of significance was set at 0.05. This study was approved by the Medical Ethical Committee of the University Medical Center Groningen. impairment of the jaw. It was developed to provide for a tool, additional to the clinical assessment, for assessment of function impairment in the patients own value system [20]. It comprises 17 items, concerning mandibular func- tions e.g. speaking and eating different types of food. A functional impairment rating score (FIRS) can be retrieved. This is a score ranging from 0 (no function impairment) up to 5 (indicating severe function impair- ment) [20]. HADS impairment of the jaw. It was developed to provide for a tool, additional to the clinical assessment, for assessment of function impairment in the patients own value system [20]. It comprises 17 items, concerning mandibular func- tions e.g. speaking and eating different types of food. A functional impairment rating score (FIRS) can be retrieved. This is a score ranging from 0 (no function impairment) up to 5 (indicating severe function impair- ment) [20]. Statistical analysis Descriptive statistics were performed to summarize sam- ple characteristics. Data were tested for normality using the Kolmogorov-Smirnov test. By means of one sample T-tests, the HRQoL scores of the patients were compared to those of a general population. To test mean differences in HRQoL among subgroups, one-way ANOVA was car- ried out, followed by Scheffe's post hoc multiple compari- son test in case of a significant result. In order to study the association between the duration of pain and the scores on the different SF-36 subscales, HADS scores, GHQ-28 scores, and MFIQ score, respectively, Pearson correlation coefficients were calculated. Outlier analysis with scatter plots was performed to look for possible dif- ference in scores between female and male participants. Data from the total sample was analysed in a regression Compared with the general population, the second sub- group scored worse on four subscales (bodily pain, vital- ity, general health and social functioning) and the third subgroup scored worse on six SF-36 subscales (bodily pain, vitality, general health, social functioning, physical functioning and role emotional). In the first and second group, scores on the GHQ scales did not significantly differ from scores in the general pop- ulation. The third group showed more impairment in somatic symptoms and showed higher social dysfunction, with worse scores on GHQA and the GHQC, compared to those obtained from the general population. g Comparisons between groups No differences were found in age between the three groups. Statistically significant differences were found Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46 http://www.hqlo.com/content/8/1/46 Page 4 of 8 Table 1: Distribution of age, RDC diagnoses medication usage and coinciding chronic pain disorders among the three subgroups. Group 1 2 3 Total 15 16 64 Female/male 1/14 3/13 1/63 Age (sd) 37.6 (14.4) 37.5 (14.1) 41.6 (12.5) RDC/TMD diagnosis: n n n Group I 3 8 20 Group II 0 0 3 Group III 5 7 24 Group I + group II 0 0 4 Group I + group III 5 0 12 Group II + group III 2 1 1 Analgesic usage Paracetamol 0 1 7 NSAID 1 0 3 Tricyclic antidepressant 1 5 6 Tricyclic antidepressant + paracetamol 1 0 0 Tricyclic antidepressant + NSAID 0 0 2 NSAID + opioid 0 0 2 Other chronic pain condition Rheumatoid arthritis 0 2 1 Hernia 0 0 1 Back pain 0 0 1 Group 1: Myofascial pain Group 2: Disc displacement Group 3: Arthralgia/osteoarthritis/osteoarthrosis n of age, RDC diagnoses medication usage and coinciding chronic pain disorders among the three between groups 1 and 3 with regard to the SF-36 subscore on the scales physical functioning and bodily pain (i.e. scores were better in group 1), but not between groups 2 and 3. Other SF-36 scores did not differ significantly between the three groups. between groups 1 and 3 with regard to the SF-36 subscore on the scales physical functioning and bodily pain (i.e. scores were better in group 1), but not between groups 2 and 3. Other SF-36 scores did not differ significantly between the three groups. in these three subgroups (Table 2). No significant differ- ences between the three groups were found in the FIRS. in these three subgroups (Table 2). No significant differ- ences between the three groups were found in the FIRS. Both HADSA and HADSD scores were worse in groups 2 and 3 as compared to group 1 (Table 3). In addition, the HADSD score in group 2 was worse than in group 3. Both HADSA and HADSD scores were worse in groups 2 and 3 as compared to group 1 (Table 3). In addition, the HADSD score in group 2 was worse than in group 3. g Comparisons between groups The third group showed more somatic problems as well as a higher level of social dysfunction compared to the first group, as GHQA and GHQC scales revealed signifi- cant differences between these groups. Effects of pain duration: total sample The social, psychological and part of the physical mea- sures did not show significant correlation with pain dura- tion. Of all calculated correlations, the SF-36 subscale bodily pain and the Function Impairment Rating Scale (FIRS) were significantly correlated with the duration of pain. The patients' impairment in mandibular function, as assessed with the MFIQ and expressed in the function impairment rating scale (FIRS), was 2.4 (sd 1.1) for the first group, 2.6 (sd 2.0) for the second group, and 3.3 (sd 1.6) for the third group, indicating moderate impairment Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46 http://www.hqlo.com/content/8/1/46 Page 5 of 8 Table 2: SF-36 and GHQ scores in three groups of orofacial pain patients and reference values. reference 1 2 3 Scale Mean (SD) Mean (SD) n = 15 Mean (SD) n = 16 Mean (SD) n = 64 SF-36 PFa 83.0 (22.8) 92.1 (8.1)*3 74.2 (33.1) 72.3 (25.7)*1 SF-36 RPa 76.4 (36.3) 54.2 (38.1) 71.2 (3.6) 3 41.2 (39.7)*2 SF-36 BPa 74.9 (23.4) 66.1 (20.4)3 53.2 (27.5)* 48.5 (19.7)*1 SF-36 GHa 70.7 (20.7) 53.0 (23.4)* 55.8 (18.7)* 54.4 (20.6)* SF-36 VTa 68.8 (19.3) 52.9 (14.9)* 49.3 (21.6)* 55.2 (19.4)* SF-36 SFa 84.0 (22.4) 74.0 (22.9) 66.0 (29.2)* 66.7 (23.4)* SF-36 REa 82.3 (32.9) 66.7 (31.8) 81.0 (55.0) 80.9 (34.1) SF-36 MHa 76.8 (17.4) 66.4 (12.5) 60.6 (17.9)3 73.2 (13.0)2 GHQAb 6.2 6.7 (4.1) 6.3 (4.1) 8.2 (4.0)* GHQBb 5.8 2.8 (2.1)2 7.5 (3.6)1 5.9 (4.4) GHQCb 7.0 6.6 (1.8) 3 8.2 (3.3) 8.3 (2.3)*1 GHQDb 1.6 0.8 (1.8) 2.7 (3.5) 1.9 (3.0) Values in mean (standard deviation, * p < 0.05 from reference values, in superscript the group to which the value is statistically different; reference values from a Aaronson et al.[19], b Koeter & Ormel [23]. (PF, physical functioning; RP, Role limitations physical; BP, bodily pain; GH, general health; VT, vitality; SF, social functioning; RE, role limitations emotional; MH, mental health; SD, standard deviation; GHQA, somatic symptoms; GHQB, anxiety and insomnia; GHQC, social dysfunction; GHQD, severe depression; P, P-value) 1. group with complaints of one year or shorter 2. group with complaints within 1 and 3 years 3. group with complaints longer than 3 years. Table 2: SF-36 and GHQ scores in three groups of orofacial pain patients and reference values. Outlier analysis revealed no differences on the sub- scales in any of the assessed subscales between female and male patients. Effects of pain duration: total sample patients classified into different cognitive-behavioural profiles seem to respond differently when the same treat- ment is offered [24]. Thus, not only the physical but also the psychological status may influence the treatment out- come. Discussion The duration of pain is thought to have a significant impact on a patient's psychological status (Figure 1) [6]. To provide more insight into the effect of duration of pain complaints, we compared patients with relatively acute pain (less than 1 year) and patients with chronic pain (1-3 years and > 3 years, respectively). A striking finding was In this study we examined whether the duration of pain in TMD patients seeking treatment affects the HRQoL and psychological well-being. When managing these patients, psychological assessment may lead the clinician to multi- dimensional, biobehavioral therapy modalities rather than to somatically based therapies [2]. Also, TMD Table 3: FIRS, HADSA and HADSD scores (standard deviation) for three groups. Group 1 2 3 score FIRS (sd) 2.4 (1.1) 2.6 (2.0) 3.3 (1.6) HADS A (sd) 3.3 (1.8)2,3 6.4 (4.1)1 5.0 (3.6)1 HADS D (sd) 1.6 (1.1)2,3 6.2 (4.2)1,3 3.5 (3.1)1,2 1.: group with complaints of one year or shorter 2.: group with complaints within 1 and 3 years 3.: group with complaints longer than 3 years. (FIRS; functional impairment rating score, HADSA; anxiety, HADSD; depression. In superscript the group to which the value is statistically different) Table 3: FIRS, HADSA and HADSD scores (standard deviation) for three groups. Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46 http://www.hqlo.com/content/8/1/46 Page 6 of 8 Page 6 of 8 Page 6 of 8 Figure 1 The effect of duration of symptoms on psychosocial fac- tors. From Okeson [6]. Used with permission. Between the different pain duration groups, statistically significant differences were found only on a few scales. Comparing "better" scores from the first group with "worse" scores from the third group, leads in the physical functioning scale to a significant difference between those scores. Although the HADS scores are interpreted using cut-off points, it is striking that the depression scale (HADSD) in group 2 is not only higher compared to group 1, but also compared to group 3. Patients who experience complaints for a short time may not be seri- ously affected, but when pain persists, psychological dis- tress will be more pronounced. Later, when patients are used to the pain or when they are sufficiently reassured about their health status, the psychological distress will return to lower values again. Discussion This is in accordance with the score on the mental health item of the SF-36, which is better in the third group compared to the second group. Figure 1 The effect of duration of symptoms on psychosocial fac- tors. From Okeson [6]. Used with permission. that in all three subgroups the SF-36 scores of the scales role emotional and mental health did not differ signifi- cantly from the reference values. It may be, that patients with a longer experience of complaints tend to get used to their pain and symptoms and incorporate them as a part of their life, thereby leaving their mental health less affected. According to our findings, it may seem that patients with a shorter duration of pain seem to underrate their physical impairment or at least do not consider it to be relevantly impaired, as the scores are "better" compared with a healthy reference group. Patients with longer last- ing pain at least longer than one year, have more pro- nounced physical problems. The role limitations due to emotional problems or the mental health seem to be hardly affected, however. It has been suggested that psy- chological functioning is merely related to patients' beliefs and coping strategies rather than to the physical impairment [25]. On the other hand, the social function- ing scale in the SF-36 as well as the GHQC score suggest that social functioning is affected in the third group. This may be explained by role limitations due to physical limi- tations, which in turn may be the result of the actual dis- order. The first group did score significantly higher ("better") on the scale "physical functioning", compared to the pop- ulation norm. This finding could be explained by possible underestimation of the physical situation, when patients visit a hospital and are allocated to a study group that answers questions about health. Patients with pain or function problems that have arisen within the last year, may tend to focus on these problems in an opposite man- ner than patients who have a longer experience with these problems. In addition, the scale bodily pain was not sig- nificantly different from the reference value. Because of the relatively short existence of pain, patients may under- estimate or underrate the consequences of their disorders on the measured scales. Discussion They may be convinced that (pain) symptoms will be transient and, therefore, patients will not allow them to affect the physical items. Patients may also feel the need to convince the doctor that the symptoms are purely physical, and want to display that statement in the answers of the subscales. In addition to the analysis with three subgroups, we cal- culated Pearson correlation coefficients with data from all patients. This revealed a significant correlation between the whole range duration of pain with the sub- scale physical functioning and the mandibular impair- ment (FIRS). So with a longer duration of pain, the somatic well-being is considered worse. It remains unclear whether the physical discomfort has worsened during its existence or whether the discomfort is only rated worse due to its longer existence. Other subscales and other scores did not show significant correlation with duration of pain, which may be explained by a large range of duration of pain in contrast to the smaller scale range of the scores on other subscales and the other question- naires. By contrast, on SF-36 physical health items ("bodily pain", "general health" and "vitality") the second and third group scored significantly worse than reference values. In addition, in the third group the items physical functioning and role physical were also worse than reference values. This physical impairment was confirmed by the FIRS scores, indicating moderate function impairment. So the mandibular function was lowered in all three groups. The GHQA score, which represents the somatic general health, is significantly lower ("worse") in the third group, which is in accordance with the scores on the SF-36. With significantly lower scores on the physical scales of the SF- 36, the second and third subgroup did not score signifi- cantly lower on the mental scales. One factor that may be of influence on the results is the age. In our sample, no difference was found between the three groups. Besides TMD pain, other pain condition could play a role in HRQoL. Of the studied sample totally five had an accompanying chronic condition. In the sec- Page 7 of 8 Page 7 of 8 Tjakkes et al. References Chigago: Quintessence Publishing; 2005. 6. Okeson JP: Bell's orofacial pains Sixth edition. Chigago: Quintessence Publishing; 2005. 7. Kempen GI, Ormel J, Brilman EI, Relyveld J: Adaptive responses among Dutch elderly: the impact of eight chronic medical conditions on health-related quality of life. Am J Public Health 1997, 87:34-44. 7. Kempen GI, Ormel J, Brilman EI, Relyveld J: Adaptive responses among Dutch elderly: the impact of eight chronic medical conditions on health-related quality of life. Am J Public Health 1997, 87:34-44. 8. Schlenk EA, Erlen JA, Dunbar-Jacob J, McDowell J, Engberg S, Sereika SM: Health related quality of life in chronic disorders: a comparison across studies using the MOS SF-36. Qual Life Res 1998, 7:57-65. 8. Schlenk EA, Erlen JA, Dunbar-Jacob J, McDowell J, Engberg S, Sereika SM: Health related quality of life in chronic disorders: a comparison across studies using the MOS SF-36. Qual Life Res 1998, 7:57-65. Authors' contributions l d d Authors' contributions GHET conceptualized and designed the study, acquired the data and partici- pated in data analysis, and drafted the manuscript; JJR, ETV, BS contributed in data analysis and participated in revising the manu- script critically for important intellectual content. All authors read and approved the final manuscript. 18. Hays RD, Sherbourne CD, Mazel RM: The RAND 36-Item Health Survey 1.0. Health Econ 1993, 2:217-227. 19. Aaronson NK, Muller M, Cohen PDA, Essink-Bot ML, Fekkes M, Sanderman R, Sprangers MAG, Te Velde A, Verrips E: Translation, validation and norming of the Dutch language version of the SF-36 health survey in community and chronic disease populations. J Clin Epidemiol 1998, 51:1055-1068. Conclusion 9. Naito M, Yuasa H, Nomara Y, Nakayama T, Hamajima N, Hanada N: Oral health status and health-related quality of life: a systematic review. J Oral Sci 2006, 48:1-7. In patients with chronic pain conditions, such as most TMD pains, it has been demonstrated that psychological factors are better predictors of treatment outcome on the long-term than physical findings are [2,28]. When TMD patients with pain less than one year are compared to a reference population, it was found that these patients scored better on physical functioning. However, we found that patients with longer lasting problems have more pro- nounced physical problems and limitations and that these limitations have impact on social functioning in this group. The mental health and role limitations due to emotional problems do not seem to be seriously affected by reduced physical activities. Especially in cases of lon- ger duration of pain, where initial treatment has failed to relieve the pain, the social functioning may be consider- ably affected and should therefore be taken into account when managing these conditions. 10. Reisine ST, Weber J: The effects of temporomandibular joint disorders on patients' quality of life. Comm Dent Health 1989, 6:257-270. 11. Murray H, Locker D, Mock D, Tenenbaum HC: Pain and the quality of life in patients referred to a craniofacial pain unit. J Orofac Pain 1996, 10:316-323. 12. Segu M, Collesano V, Lobbia S, Rezzani C: Cross-cultural validation of a short form of the Oral Health Impact Profile for temporomandibular disorders. Comm Dent Oral Epid 2005, 33:123-130. 13. John MT, Reissman DR, Schierz O: Oral health-related quality of life in patients with temporomandibular disorders. J Orofac Pain 2007, 21:46-54. 14. LeResche L, Dworkin DF, Wilson L, Ehrlich KJ: Effect of temporomandibular disorder pain duration on facial expressions and verbal report. Pain 1992, 51:289-295. 15. Dworkin S, LeResche L: Research diagnostic criteria for temporomandibular disorders: review, criteria, examinations and specifications, critique. J Craniomand Disord Fac Oral Pain 1992, 6:301-355. 16. Lobbezoo F, Van Selms MK, John MT, Huggins K, Ohrbach R, Visscher CM, Zaag J Van Der, Meulen MJ Van Der, Naeije M, Dworkin SF: Use of the Research Diagnostic Criteria for Temporomandibular Disorders for multinational research: translation efforts and reliability assessments in The Netherlands. J Orofac Pain 2005, 4:301-308. Competing interests The authors declare that they have no competing interests. 17. The World Health Organization quality of life assessment (WHOQOL): position paper from the World Health Organization. Soc Sci Med 1995, 10:1403-1409. Discussion Health and Quality of Life Outcomes 2010, 8:46 http://www.hqlo.com/content/8/1/46 University of Applied Sciences, Groningen, PO Box 275, 9700 VB, The Netherlands and 4Office for Medical Technology Assessment, University Medical Center Groningen, University of Groningen, Groningen, PO Box 30.001, 9700 RB, The Netherlands ond group, two suffered also from rheumatoid arthritis. In the third group, one patient suffered from rheumatoid arthritis, one from hernia and one from low back pain. These conditions could have influenced the question- naire outcomes, although the number of patients is a slight minority compared to the total sample size, there- fore we argued this to be of negligible influence. References 1. Stegenga B: Temporomandibular joint osteoarthrosis and internal derangement. Diagnostic and therapeutic outcome assessment. In PhD Thesis University of Groningen; Faculty of Medicine; 1991. 1. Stegenga B: Temporomandibular joint osteoarthrosis and internal derangement. Diagnostic and therapeutic outcome assessment. In PhD Thesis University of Groningen; Faculty of Medicine; 1991. A limitation of this study could be the large female pre- dominance, which is than in the general population, which may hamper the generalizability of the results. However, a predominance of female gender in TMDs is also found in epidemiological research [26]. In addition, more female than male patients seek treatment for their pain problems, leading to an increasing female predomi- nance in specialist centers, with a female:male ratio rang- ing from 2:1 to 9:1 [27]. In addition, outlier analysis (to explore possible differences in measurements in our sam- ple between male and female patients) revealed no outli- ers in the assessed subscales. We thus consider sex difference in our sample to be of minor influence and we therefore decided to include both male and female in the total analysis. 2. Dworkin SF: Psychological and psychosocial assessment. In Temporomandibular disorders: an evidence-based approach to diagnosis and treatment Edited by: Laskin DM, Greene CS, Hylander WL. Chigago: Quintessence publishing. Co., Inc; 2006:203-228. 2. Dworkin SF: Psychological and psychosocial assessment. In Temporomandibular disorders: an evidence-based approach to diagnosis and treatment Edited by: Laskin DM, Greene CS, Hylander WL. Chigago: Quintessence publishing. Co., Inc; 2006:203-228. 3. Dworkin SF, Massoth DL: Temporomandibular disorders and chronic pain: disease or illness? J Prosth Dent 1994, 712:29-38. 3. Dworkin SF, Massoth DL: Temporomandibular disorders and chronic pain: disease or illness? J Prosth Dent 1994, 712:29-38. 4. Yap AUJ, Tan KBC, Chua EK, Tan HH: Depression and somatization in patients with temporomandibular disorders. J Prost Dent 2002, 88:479-484. 4. Yap AUJ, Tan KBC, Chua EK, Tan HH: Depression and somatization in patients with temporomandibular disorders. J Prost Dent 2002, 88:479-484. 5. Zakrzewska JM, Harrison SH: Assessment and management of orofacial pain. Pain research and clinical management Amsterdam. Elsevier; 2002. 5. Zakrzewska JM, Harrison SH: Assessment and management of orofacial pain. Pain research and clinical management Amsterdam. Elsevier; 2002. 6. Okeson JP: Bell's orofacial pains Sixth edition. Chigago: Quintessence Publishing; 2005. 5. Zakrzewska JM, Harrison SH: Assessment and management of orofacial pain. Pain research and clinical management Amsterdam. Elsevier; 2002. 6. Okeson JP: Bell's orofacial pains Sixth edition. Competing interests Th h d l h Competing interests The authors declare that they have no competing interests. Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46 http://www.hqlo.com/content/8/1/46 22. Goldberg DP, Hillier VF: A scaled version of the General Health Questionnaire. Psychol Med 1979, 9:139-145. 23. Koeter MWJ, Ormel J: General Health Questionnaire, Nederlandse bewerking; handleiding Lisse: Swets Test services; 1991. 24. Dahlstrom L, Widmark G, Carlsson SG: Cognitive-behavioural profiles among different categories of orofacial pain patients: diagnostic and treatment implications. Eur J Oral Sci 1997, 105:377-383. 25. Turner JA, Dworkin SF, Mancl L, Huggins KH, Truelove E: The roles of beliefs, catastrophizing, and coping in the functioning of patients with temporomandibular disorder. Pain 2001, 92:41-51. 26. LeResche L: Epidemiology of temporomandibular disorders: implications for the investigation of etiological factors. Crit Rev Oral Biol 1997, 8:291-305. 27. Bush FM, Harkins SW, Harrington WG, Price DD: Analysis of gender effects on pain perception and symptom presentation in tempormandibular pain. Pain 1993, 53:73-80. 28. Turk DC, Okifuji A: Psychological factors in chronic pain: evolution and revolution. J Consult Clin Psychol 2002, 70:678-690. doi: 10.1186/1477-7525-8-46 Cite this article as: Tjakkes et al., TMD pain: the effect on health related qual- ity of life and the influence of pain duration Health and Quality of Life Out- comes 2010, 8:46 22. Goldberg DP, Hillier VF: A scaled version of the General Health Questionnaire. Psychol Med 1979, 9:139-145. 22. Goldberg DP, Hillier VF: A scaled version of the General Health Questionnaire. Psychol Med 1979, 9:139-145. 23. Koeter MWJ, Ormel J: General Health Questionnaire, Nederlandse bewerking; handleiding Lisse: Swets Test services; 1991. 23. Koeter MWJ, Ormel J: General Health Questionnaire, Nederlandse bewerking; handleiding Lisse: Swets Test services; 1991. 24. Dahlstrom L, Widmark G, Carlsson SG: Cognitive-behavioural profiles among different categories of orofacial pain patients: diagnostic and treatment implications. Eur J Oral Sci 1997, 105:377-383. 25. Turner JA, Dworkin SF, Mancl L, Huggins KH, Truelove E: The roles of beliefs, catastrophizing, and coping in the functioning of patients with temporomandibular disorder. Pain 2001, 92:41-51. 26. LeResche L: Epidemiology of temporomandibular disorders: implications for the investigation of etiological factors. Crit Rev Oral Biol 1997, 8:291-305. 27. Bush FM, Harkins SW, Harrington WG, Price DD: Analysis of gender effects on pain perception and symptom presentation in tempormandibular pain. Pain 1993, 53:73-80. 28. Turk DC, Okifuji A: Psychological factors in chronic pain: evolution and revolution. J Consult Clin Psychol 2002, 70:678-690. Author Details 1Department of Oral and Maxillofacial Surgery, University Medical Center Groningen University of Groningen, Groningen, PO Box 30.001, 9700 RB, The Netherlands, 2Center for Dentistry and Oral Hygiene, Department of Oral Health Care and Clinical Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, 9700 VB, The Netherlands, 3Research Innovation Group in Health Care and Nursing, Hanze University Groningen, 20. Stegenga B, De Bont LG, De Leeuw R, Boering G: Assessment of mandibular function impairment associated with temporomandibular joint osteoarthrosis and internal derangement. J Orofac Pain 1993, 2:183-195. 21. Zigmond AS, Snaith RP: The Hospital Anxiety and Depression Scale. Acta Psychiatr Scan 1983, 67:361-370. Page 8 of 8 Tjakkes et al. Health and Quality of Life Outcomes 2010, 8:46 http://www.hqlo.com/content/8/1/46 doi: 10.1186/1477-7525-8-46 Cite this article as: Tjakkes et al., TMD pain: the effect on health related qual- ity of life and the influence of pain duration Health and Quality of Life Out- comes 2010, 8:46
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COVID-19: viral–host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection
Journal of translational medicine
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Messina et al. J Transl Med (2020) 18:233 https://doi.org/10.1186/s12967-020-02405-w Messina et al. J Transl Med (2020) 18:233 https://doi.org/10.1186/s12967-020-02405-w Journal of Translational Medicine Open Access COVID‑19: viral–host interactome analyzed by network based‑approach model to study pathogenesis of SARS‑CoV‑2 infection Francesco Messina1†, Emanuela Giombini1†, Chiara Agrati1, Francesco Vairo1, Tommaso Ascoli Bartoli1, Samir Al Moghazi1, Mauro Piacentini1,2, Franco Locatelli3, Gary Kobinger4, Markus Maeurer5,6, Alimuddin Zumla7,8, Maria R. Capobianchi1*  , Francesco Nicola Lauria1†, Giuseppe Ippolito1† and COVID 19 INMI Network Medicine for IDs Study Group Abstract Background:  Epidemiological, virological and pathogenetic characteristics of SARS-CoV-2 infection are under evaluation. A better understanding of the pathophysiology associated with COVID-19 is crucial to improve treatment modalities and to develop effective prevention strategies. Transcriptomic and proteomic data on the host response against SARS-CoV-2 still have anecdotic character; currently available data from other coronavirus infections are there- fore a key source of information. Methods:  We investigated selected molecular aspects of three human coronavirus (HCoV) infections, namely SARS- CoV, MERS-CoV and HCoV-229E, through a network based-approach. A functional analysis of HCoV–host interactome was carried out in order to provide a theoretic host–pathogen interaction model for HCoV infections and in order to translate the results in prediction for SARS-CoV-2 pathogenesis. The 3D model of S-glycoprotein of SARS-CoV-2 was compared to the structure of the corresponding SARS-CoV, HCoV-229E and MERS-CoV S-glycoprotein. SARS-CoV, MERS-CoV, HCoV-229E and the host interactome were inferred through published protein–protein interactions (PPI) as well as gene co-expression, triggered by HCoV S-glycoprotein in host cells. Results:  Although the amino acid sequences of the S-glycoprotein were found to be different between the various HCoV, the structures showed high similarity, but the best 3D structural overlap shared by SARS-CoV and SARS-CoV-2, consistent with the shared ACE2 predicted receptor. The host interactome, linked to the S-glycoprotein of SARS-CoV and MERS-CoV, mainly highlighted innate immunity pathway components, such as Toll Like receptors, cytokines and chemokines. Conclusions:  In this paper, we developed a network-based model with the aim to define molecular aspects of pathogenic phenotypes in HCoV infections. The resulting pattern may facilitate the process of structure-guided phar- maceutical and diagnostic research with the prospect to identify potential new biological targets. Keywords:  Coronavirus infection, Virus–host interactome, Spike glycoprotein Background In December 2019, a novel coronavirus (SARS-CoV-2) was first identified as a zoonotic pathogen of humans in Wuhan, China, causing a respiratory infection with associated bilateral interstitial pneumonia. The *Correspondence: maria.capobianchi@inmi.it †Francesco Messina, Emanuela Giombini, Francesco Nicola Lauria and Giuseppe Ippolito contributed equally to this work 1 National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy © The Author(s) 2020. 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 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. © The Author(s) 2020. 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 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. Messina et al. J Transl Med (2020) 18:233 Messina et al. J Transl Med (2020) 18:233 Page 2 of 10 Page 2 of 10 disease caused by SARS-CoV-2 was named by the World Health Organization as COVID-19 and it has been classified as a global pandemic since it has spread rapidly to all continents. As of May 20, 2020, there have been 4.889.287 confirmed COVID-19 cases worldwide with 322.457 deaths reported to the WHO [1]. Whilst clinical and epidemiological data on COVID-19 have become readily available, information on the pathogen- esis of the SARS-CoV-2 infection has not been forth- coming [2]. The transcriptomic and proteomic data on host response against SARS-CoV-2 is scanty and not effective therapeutics and vaccines for COVID-19 are available yet.f We investigated here biologically and clinically relevant molecular targets of three human coronaviruses (HCoV) infections using a network based approach. A functional analysis of HCoV–host interactome was carried out in order to provide a theoretic host–pathogen interaction model for HCoV infections, and to predict viable mod- els for SARS-CoV-2 pathogenesis. Three HCoV caus- ing respiratory diseases were used as the model targets, namely: SARS-CoV, that shares with SARS-CoV-2 a strong genetic similarity, including MERS-CoV, and HCoV-229E. Comparative reconstruction of S‑glycoprotein in HCoVsh Comparative reconstruction of S‑glycoprotein in HCoVsh Comparative reconstruction of S‑glycoprotein in HCoVs The reconstruction of virus–host interactome was car- ried out using the RWR algorithm to explore the human PPI network and the multilayer PPI platform enriched with gene expression data sets. 259 sequences of CoVs, infecting different animal hosts (Additional file  1: Table S1), were downloaded by GSAID and NCBI data- base in order to evaluate the variability in the S gene. SARS-CoV, HCoV-229E and MERS-CoV and other CoV full genome sequence groups were aligned with MAFFT [14], synonymous and non-synonymous mutations, and amino acid similarity were calculated using the SSE pro- gram with a sliding windows of 250 nucleotides and a pass of 25 nu [15]. A homology model was built for the amino acid sequences of the S-glycoprotein, derived from the full genome sequence obtained at “SARS-CoV-2/ INMI1/human/2020/ITA” (MT066156.1). The Swiss pdb server was used to construct three-dimensional mod- els for the S-glycoprotein of SARS-CoV-2 [16]. Among proteins with a 3D structure, the best match with the “SARS-CoV-2/INMI1/human/2020/ITA” sequence was the 6VSB.1, that was evaluated considering the iden- tity of two amino acid sequences and the QMEN value included in Swiss pdb server. The model of a single chain was overlapped with the three-dimensional structure of S-glycoprotein single chain belonging to SARS-CoV (5WRG), HCoV-229E (6U7H.1) and MERS-CoV (5X59), using Chimera 1.14 [17]. In order to better evaluate the conservation of the sequence in each site, all sequences were aligned with MAFFT and the topology of all struc- tures were compared. The detailed description of the reconstruction of S-glycoprotein structure is reported in Additional file 2. The investigation of structural genomics and inter- actomics of SARS-CoV-2 can be implemented through systematical mapping of protein–protein interactions (PPI) between SARS-CoV-2 and human host, and an integrated bioinformatics approach [12, 13]. Structural analysis of specific SARS-CoV-2 proteins, in particular Spike glycoproteins (S-glycoproteins), and their interac- tions with human proteins, can guide the identification of the putative functional sites and help to better define the pathologic phenotype of the infection. This functional interaction analysis between the host and other HCoVs, combined with an evolutionary sequence analysis of SARS-CoV-2, can be used to guide new treatment and prevention interventions. Methods Coronaviruses (CoVs) typically affect the respiratory tract of mammals, including humans, and lead to mild to severe respiratory tract infections [3]. Many emerg- ing HCoV infections have spilled-over from animal res- ervoirs, such as HCoV-OC43 and HCoV-229E which cause mild diseases such as common colds [4, 5]. During the past 2 decades, two highly pathogenic HCoVs, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS- CoV), have led to global epidemics with high morbid- ity and mortality [6]. In this period, a large amount of experimental data associated with the two infections has allowed to better understand molecular mechanism(s) of coronavirus infection, and enhance pathways for devel- oping new drugs, diagnostics and vaccines and identi- fication of host factors stimulating (proviral factors) or restricting (antiviral factors) infection remains poorly understood [7]. Structures of many proteins of SARS- CoV and MERS-CoV, and biological interactions with other viral and host proteins have been widely explored; through experimental testing of small molecule inhibi- tors with anti-viral effects [8, 9]. ACE2, expressed in type 2 alveolar cells in the lung, has been identified as recep- tor of SARS-CoV and SARS-CoV-2, while dipeptidyl peptidase DPP4 was identified as the specific receptor for MERS-CoV [10, 11]. PPI and gene co‑expression network Network analysis, based on protein–protein interactions and gene expression data, was performed in order to view all possible virus–host protein interactions during the HCoV infections. Since the SARS-CoV-2 genome exhibits substantial similarity to the SARS-CoV genome [18] and Messina et al. J Transl Med (2020) 18:233 Page 3 of 10 subsequently also the proteome [19], we hypothesized that several molecular interactions that were observed in the SARS-CoV interactome will be preserved in the SARS-CoV-2 interactome. Virus–host interactomes (SARS-CoV, MERS-CoV, HCoV-229E) were inferred through published PPI data, using two publicly accessi- ble databases (STRING Viruses and VirHostNet), as well as published scientific reports with a focus on virus–host interactions [20–22]. As a next step, the virus–host PPI list, extracted in this first step, was merged with addi- tional PPI databases, i.e. BioGrid, InnateDB-All, IMEx, IntAct, MatrixDB, MBInfo, MINT, Reactome, Reactome- FIs, UniProt, VirHostNet, BioData, CCSB Interactome Database, using R packages PSICQUIC and biomaRt [23, 24]. In total, a large PPI interaction database was assem- bled, including 13,020 nodes and 71,496 interactions.h sequence obtained at Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, using Swiss pdb viewer server (Additional file 2: Figure S2a, b). The SARS-CoV-2 S-glycoprotein structure was then compared to other HCoVs as shown in Additional file  2: Figure S2. The S-glycoprotein structures of the various HCoV were very similar overall. In particular, a strong similarity was shown in the RBD (nCov: residues 319–591) [30], and this was most evident for the compar- ison between SARS-CoV-2 and SARS-CoV, which share the same cell receptor (ACE2). The amino acid differ- ences among the S-glycoproteins of the selected HCoVs (SARS-CoV-2, MERS-CoV, SARS-CoV, HCoV-229E) are shown in Additional file 2: Figure S3, where a lower topology similarity was observed with HCoV-229E S-gly- coprotein, which binds a different host receptor. The gene expression data set was built from the Pro- tein Atlas database, using tissue and cell line data [25]. To identify the most likely interactions, and to obtain func- tional information, Random walk with restart (RWR), a state-of-the-art guilt-by-association approach by R pack- age RandomWalkRestartMH [26] was used. It allows to establish a proximity network from a given protein (seed), to study its functions, based on the premise that nodes related to similar functions tend to lie close to each other in the network. For each node, a score was computed as measure of proximity to the seed protein. Human CoV and host interactome An interactome map was built to highlight biological connections among S-glycoprotein and the human pro- teome. Using the analysis pipeline described in the meth- ods, a large PPI interaction database was assembled, including 13,020 nodes and 71,496 interactions between human host and the three selected viruses (SARS-CoV, MERS-CoV and HCoV-229E).h The interactome reconstruction was obtained with the RWR analysis, finding 200 closest proteins to seed, or S-glycoproteins of HCoV-229E, SARS-CoV and MERS- CoV (Additional file  2: Figures  S4–S6). In Additional file 1: Tables S2–S4, lists of genes selected by RWR algo- rithm for HCoV-229E, SARS-CoV and MERS-CoV, along with proximity score were reported. In order to further dissect the S-glycoprotein-host interactions, enrichment analysis was carried out with Reactome and KEGG data- bases. Reactome pathway enrichment analysis revealed biological pathways of DNA repair, transcription and gene regulation for the HCoV-229E S-glycoprotein, with high significance (FDR < 0.01%). KEGG pathway enrich- ment analysis revealed ubiquitin mediated proteolysis as the most significant pathway (FDR < 0.01%), as well as cellular proliferation pathways, associated with other viral infections (Hepatitis B, measles, Epstein–Barr virus infection and Human T-cell leukemia virus 1 infection) as well as with carcinogenesis (Fig. 1). Next, the RWR algorithm was applied to a multilayer network built on the PPI interactome and on the Gene Coexpression (COEX) network, again with S-glycoprotein of HCoV- 229E as seed. The results highlighted a set of genes that are connected in both PPI and COEX analysis, including ANPEP, RAD18, APEX, POLH, APEX1, TERF2, RAD51, Functional enrichment analysis To evaluate functional pathways of proteins involved in host response, gene enrichment analysis was performed, using Kyoto Encyclopedia of Genes and Genomes (KEGG) human pathways and Gene Ontology databases. Network representation from the gene enrichment anal- ysis was performed using ShinyGO v0.61 [27]. The sta- tistical significance was obtained, calculating the False Discovery Rate (FDR). PPI and gene co‑expression network S-glycoproteins of SARS-CoV, MERS-CoV and HCoV-229E were used as seed in the application of the RWR algorithm. f Overall, the pattern arising from such comparison was consistent with specific host receptors, as well as with different host reservoirs and ancestry [31]. Structure of S‑glycoprotein CoVs To evaluate the diversity along the full genome, pairwise distance was calculated on 259 HCoV genomes. Diversity was distributed along the entire CoV genome, with the most conserved region located in Orf1ab, as expected, while the spike gene region exhibited a rather high diver- sity (Additional file 2: Figure S1), due to key role of the S-glycoprotein during viral entry in specific hosts [28]. i Consequently, the analysis was focused on the S-gly- coprotein, as a key virus component involved in host interaction [29]. A 3D model of S-glycoprotein of the SARS-CoV-2 sequence (MT066156.1) was built on the Messina et al. J Transl Med (2020) 18:233 Page 4 of 10 Fig. 1  KEGG human pathway and Reactome pathways enrichment analysis for 200 proteins identified by RWR algorithm using S-glycoprotein of HCoV-229E an pathway and Reactome pathways enrichment analysis for 200 proteins identified by RWR algorithm using S-glycoprotein Fig. 1  KEGG human pathway and Reactome pathways enrichment analysis for 200 proteins identified by RWR algorithm using S-glycoprotein of HCoV-229E proliferation, TGF-β and other infection-related path- ways (FDR < 0.0001%) (Fig. 3). The PPI-COEX multilayer analysis highlighted a set of genes that are connected in both PPI and COEX analysis, i.e.CLEC4G, CLEC4M, CD209, ACE2, RPSA, all associated to the GO biologi- cal process category of SARS-CoV entry into host cell (FDR < 0.01%) (Fig. 4). In MERS-CoV, the Reactome pathway enrichment analysis showed a strong associa- tion with membrane signals activated by GPCR ligand binding (FDR < 0.0001%), and chemokine/chemokine receptor pathways. Consistent results were obtained with KEGG pathway enrichment, that highlighted cytokine– cytokine receptor and chemokine signalling pathways (FDR < 0.0001%) (Fig. 5). Finally, PPI-COEX multilayer analysis evidenced, for both PPI and COEX, CCR4, CXCL2, CXCL10, CXCL9, PF4, PF4V1, CCL11, CXCL11, XCL1, CXCR4 and CXCL14, all genes identified by the GO biological processes involved in the chemokine cas- cade (FDR < 0.0001%), in line with the results obtained with enrichment analyses (Fig. 6). Fig. 2  PPI-COEX multilayer analysis, based on human PPI interactome and COEX network, with top 50 closest proteins/genes identified by RWR, using S-glycoprotein of HCoV-229E. Edges in blue represent protein-protein interactions, while red edges are coexpressions Fig. 2  PPI-COEX multilayer analysis, based on human PPI interactome and COEX network, with top 50 closest proteins/genes identified by RWR, using S-glycoprotein of HCoV-229E. Edges in blue represent protein-protein interactions, while red edges are coexpressions Discussion In‑depth comparative analysis of S‑glycoprotein l d k l b d CDC7, USP7, XRCC5, RAD18, FEN1, PCNA, all associ- ated to the GO biological process category of DNA repair (FDR < 0.0001%) (Fig. 2). The same analyses were con- ducted for SARS-CoV and MERS-CoV. In‑depth comparative analysis of S‑glycoprotein l d k l b d In‑depth comparative analysis of S‑glycoprotein We applied network analysis, based on protein–pro- tein interactions and gene expression data, in order to describe the interactome of the coronavirus S-glycopro- tein and host proteins, with the aim to better understand SARS-CoV-2 pathogenesis. A preliminary structural analysis was conducted on the S-glycoprotein of SARS- CoV-2 as compared to the other 3 HCoV, using the S-glycoprotein as a model to shed light on the host–path- ogen interaction in the dynamic process of SARS-CoV-2 The Reactome pathway enrichment analysis for the SARS-CoV revealed S-glycoprotein connection with early activation of innate immune system, such as the Toll Like Receptor Cascade and TGF-β, with a strong significance (FDR < 0.0001%), while the KEGG pathway enrichment analysis revealed an association with cellular Messina et al. J Transl Med (2020) 18:233 Page 5 of 10 Fig. 3  KEGG human pathway and Reactome pathways enrichment analyses for 200 proteins identified by RWR algorithm using S-glycoprotein of SARS-CoV ig. 3  KEGG human pathway and Reactome pathways enrichment analyses for 200 proteins identified by RWR algorithm usin ARS C V pathway and Reactome pathways enrichment analyses for 200 proteins identified by RWR algorithm using S-glycoprotein of Fig. 4  PPI-COEX multilayer analysis based on human PPI interactome and COEX network, with top 50 closest proteins/genes identified by RWR, using S-glycoprotein of SARS-CoV. Edges in blue represent protein-protein interactions, while red edges are coexpressions and SARS-CoV-2, consistent with the shared ACE2 pre- dicted receptor. Of note, the newly discovered SARS-CoV-2 genome has revealed differences between SARS-CoV-2 and SARS or SARS-like coronaviruses [31]. Although no amino acid substitutions were present in the recep- tor-binding motifs, that directly interact with human receptor ACE2 protein in SARS-CoV, six mutations occurred in the other region of the RBD [31, 32] were identified. On the other hand, the genomic comparative analysis highlighted the strong diversity in the S gene among CoV in different hosts, confirming the biologi- cally vital role of the S-glycoprotein as a key factor in viral entry in cross-species transmission events [28]. y In addition, the comparative 3D structural data may facilitate the definition of already known antibody epitopes in the S-glycoprotein of other coronaviruses, it will also be useful in rational vaccine design and in gauging anti-virus directed immune responses after vaccination [30]. In‑depth comparative analysis of S‑glycoprotein l d k l b d In fact, S-glycoprotein remains an important target for vaccines and drugs previously evaluated in SARS and MERS, while a neutralizing antibody targeting the S-glycoprotein protein could provide passive immunity. The host interactome, linked to S-glycoprotein of SARS-CoV and MERS-CoV, mainly highlighted innate immunity pathway com- ponents, such as Toll Like receptors, cytokines and chemokines. The 3D structural analysis confirmed that Fig. 4  PPI-COEX multilayer analysis based on human PPI interactome and COEX network, with top 50 closest proteins/genes identified by RWR, using S-glycoprotein of SARS-CoV. Edges in blue represent protein-protein interactions, while red edges are coexpressions infection. Although the amino acid sequences of the S-glycoprotein were different between the various HCoVs, the structural analysis exhibited high similarity; the best 3D structural overlap was found for SARS-CoV Messina et al. J Transl Med (2020) 18:233 Page 6 of 10 Fig. 5  KEGG human pathway and Reactome pathways enrichment for 200 proteins identified by RWR algorithm using S-glycoprotein of MERS-CoV GG human pathway and Reactome pathways enrichment for 200 proteins identified by RWR algorithm using S-glycoprotein Fig. 6  PPI-COEX multilayer analysis based on human PPI interactome and COEX network, with top 50 closest proteins/genes identified by RWR, using S-glycoprotein of MERS-CoV. Edges in blue represent protein-protein interactions, while red edges indicate coexpressions infections indicated the presence of several hub proteins. In the HCoV-229E–host interactome hub position was hold by RAD18 and APEX, which play an important role in DNA repair due to UV damage in phase S [33]. For the SARS-CoV interactome, the gene hubs were identified in ACE2, CLEC4G and CD209, which are known interactors with S-glycoprotein of SARS-CoV [34, 35]. In fact, two independent mechanisms were described as trigger of SARS-CoV infection: proteolytic cleavage of ACE2 and cleavage of S-glycoprotein. The latter activates the glycoprotein for cathepsin L-independent host cell entry. Activated the S-glycoprotein by cathepsin L mech- anism in host cell entry was reported in many infections of CoV, such as HCoV-229E and SARS-CoV [36, 37]. A recent study speculated that this interaction will be pre- served in SARS-CoV-2 [19], but might be disrupted of a substantial number of mutations in the receptor binding site of S gene will occur. Likewise, the S-glycoprotein in SARS-CoV-2 is expected to interact with type II trans- membrane protease (TMPRSS2) and probably is involved in inhibition of antibody-mediated neutralization [38, 39]. In‑depth comparative analysis of S‑glycoprotein l d k l b d It is rather unexpected that, for this virus, no intra- cellular pathways were highlighted by the multilayer analysis, suggesting that this field is still open to further investigation. Fig. 6  PPI-COEX multilayer analysis based on human PPI interactome and COEX network, with top 50 closest proteins/genes identified by RWR, using S-glycoprotein of MERS-CoV. Edges in blue represent protein-protein interactions, while red edges indicate coexpressions Fig. 6  PPI-COEX multilayer analysis based on human PPI interactome and COEX network, with top 50 closest proteins/genes identified by RWR, using S-glycoprotein of MERS-CoV. Edges in blue represent protein-protein interactions, while red edges indicate coexpressions we established that S-glycoprotein of SARS-CoV-2 has strong similarity in the 3D structure with SARS-CoV [18]. In MERS-CoV infection a gene hub role was described for DPP4, which is known to regulate cytokine levels through catalytic cleavage [40]. Immune cell—recruit- ing chemokines and cytokines, such as IP-10/CXCL- 10, MCP-1/CCL-2, MIP-1α/CCL-3, RANTES/CCL-5, can be strongly induced by MERS-CoV, showing higher inducibility in human monocyte—derived macrophages Host interactome in all three HCoV infectionsh The reconstruction of virus–host interactome was car- ried out using RWR algorithm to explore the human PPI network and studying PPI and COEX multilayer. The PPI network topology of host interactome in all three Messina et al. J Transl Med (2020) 18:233 Page 7 of 10 aid to design a ‘blue print’ for SARS-CoV-2 associated pathogenicity. by MERS-CoV as compared to than SARS-CoV infec- tion [41]. The cellular proliferation pathways, involved immediately after virus entry, were described in all three models, resulting consistent with inhibiting activity on cell proliferation and cytotoxic effect due to HCoV infec- tions [42, 43]. Finally, biological pathways, revealed by enrichment analysis in over all models, supported early activation of innate immune system, as Toll Like recep- tor Cascade and TGF-β for SARS-CoV, or chemokine and cytokine pathways and infection-related pathways for MERS-CoV, with a strong significance for both. The severity and the clinical picture of SARS-CoV and MERS-CoV infections could be related to the activation of exaggerated immune mechanism, causing uncon- trolled inflammation [47]; however, the role of strong immune response in SARS-CoV-2 infection severity is still uncertain. However, we may consider that host kinases link mul- tiple signalling pathways in response to a broad array of stimuli, including viral infections. TGF-β, produced during the inflammatory phase by macrophages, is an important mediator of fibroblast activation and tissue repair. High levels of systemic inflammatory cytokines/ chemokines has been widely reported for MERS-CoV infections [48–50], correlating with immunopathology and massive pulmonary infiltration into the lungs [51]. Also the HCoV-229E infection can be described with this distance model, although this infection was not asso- ciated with a severe respiratory disease. In fact, HCoV- 229E is responsible for mild upper respiratory tract infections, such as common colds, with only occasional spreading to the lower respiratory tract, but it interacts with dendritic cells in the upper respiratory tract, induc- ing a cytopathic effect [52]. Conclusions I l i In conclusion, we developed a network-based model, which could be the framework for structure-guided research process and for the pathogenetic evaluation of specific clinical outcome. Accurate structural 3D protein models and their interaction with host receptor proteins can allow to build a more detailed theoretical disease model for each HCoV infection, and support the drawing of a disease model for COVID-19. Our analyses suggests it is important to carry out in silico experiments and sim- ulations through specific algorithms. Second, Mitogen activated protein kinase (MAPK) is a major cell signalling pathway that is known to be acti- vated by diverse groups of viruses, and plays an impor- tant role in cellular response to viral infections. MAPK interacting kinase 1 (MNK1) has been shown to regulate both cap-dependent and internal ribosomal entry sites (IRES)-mediated mRNA translation; Third, The identification of the MAPK pathway in SARS-CoV model is highly consistent with in vivo model, where P38 MAPK was found increased in the lungs of mice infected with SARS-CoV [44];hi Pathogenic model for HCoV infections We constructed a host molecular interactome with SARS- CoV, MERS-CoV and HCoV-229E in patients with can- cer, assuming that most of these interactions, especially for SARS-CoV, are shared with SARS-CoV-2. A network- based methodology, along with guilt-by-association algo- rithm (RWR), was applied to define the pathological model of COVID-19 and provide a treatment of SARS-CoV-2, using existing transcriptomic and proteomic information.i Based on the main pathways identified by the network- based interactome analysis, the following issues require focus further study: First, The predicted receptor for SARS-CoV-2 has been inferred to be ACE-2, i.e. the same used by SARS-CoV, based on the high similarity of the S-glycoprotein of the two viruses, and this is the basis for hypothesizing to use SARS-CoV as a model for virus–host interactome in COVID-19; Funding INMI authors are supported by the Italian Ministry of Health (Ricerca Corrente Linea 1). G. Ippolito and A. Zumla are co-principal investigator of the Pan-Afri- can Network on Emerging and Re-emerging Infections (PANDORA-ID-NET), funded by the European & Developing Countries Clinical Trials Partnership, supported under Horizon 2020. Sir Zumla is in receipt of a National Institutes of Health Research senior investigator award. M. Maeurer is a member of the innate immunity advisory group of the Bill & Melinda Gates Foundation, and is funded by the Champalimaud Foundation. Supplementary information accompanies this paper at https​://doi. org/10.1186/s1296​7-020-02405​-w. Supplementary information acco org/10.1186/s1296​7-020-02405​-w. Supplementary information accompanies this paper at https​://doi. org/10.1186/s1296​7-020-02405​-w. pp y org/10.1186/s1296​7-020-02405​-w. Additional file 1: Table S1. List of accession numbers of H-CoV. Table S2. List of genes selected by RWR algorithm for HCoV-229E, along with proximity score. Table S3. List of genes selected by RWR algorithm for SARS-CoV, along with proximity score. Table S4. List of genes selected by RWR algorithm for MERS-CoV, along with proximity score. Limitations to our study A single protein, namely S-glycoprotein was used as seed, therefore the highlighted interactions were limited to those connected with this unique viral protein. However, this is a proof of concept study, from which it appears that a similar approach may be used to study other viral proteins interacting with host cell pathways. Fourth, The identification of the TGF-β pathway in S-glycoprotein-induced interactome for SARS-CoV of particular interest, due to the previous evidence that this virus, and in particular its protease, triggered the TGF-β through the p38 MAPK/STAT3 pathway in alveolar basal epithelial cells [45, 46];i Another limitation is that the pathway analysis did not consider tissue and cell type diversity. Finally, the low threshold established for the number of nodes found by RWR (200) limited the reconstruction of the entire pathways. However, this was a software-imposed threshold. Fifth, Innate immune pathways were identified in S-gly- coprotein-induced models of SARS-CoV and MERS-CoV, as Toll Like receptor, cytokine and chemokine. Every described pathway can be matched with clinical aspects, the data presented in this report may therefore Messina et al. J Transl Med (2020) 18:233 Messina et al. J Transl Med (2020) 18:233 Page 8 of 10 Page 8 of 10 In summary, the interactome analysis aided to guide the design of novel models of SARS-CoV pathogenicity. Author details 1 National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy. 2 Department of Biology, University of Rome “Tor Vergata”, Rome, Italy. 3 Department of Pediatric Hematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesu, Rome, Italy. 4 Département de Microbiologie‑Infec- tiologie et d’Immunologie, Université Laval, Quebec, QC, Canada. 5 Immu- noSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal. 6 I. Medizinische Klinik Johannes Gutenberg-Universität, University of Mainz, Mainz, Germany. 7 Department of Infection, Division of Infection and Immu- nity, University College London, London, UK. 8 National Institute for Health Research Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, UK. Acknowledgements We gratefully acknowledge: Collaborators Members of INMI COVID-19 Study Group; COVID 19 INMI Network Medicine for IDs Study Group: We gratefully acknowledge: Collaborators Members of INMI COVID-19 Study Group; COVID 19 INMI Network Medicine for IDs Study Group: Isabella Abbate, Chiara Agrati, Samir Al Moghazi, Tommaso Ascoli Bartoli, Barbara Bartolini, Maria R. Capobianchi , Alessandro Capone, Delia Goletti, Gabriella Rozera, Carla Nisii, Roberta Gagliardini, Fabiola Ciccosanti, Gian Maria Fimia, Emanuele Nicastri, Emanuela Giombini, Simone Lanini, Alessandra D’Abramo, Gabriele Rinonapoli, Enrico Girardi, Chiara Montaldo, Raffaella Mar- coni, Antonio Addis, Bradley Maron, Ginestra Bianconi, Bertrand De Meulder, Jason Kennedy, Shabaana Abdul Khader, Francesca Luca, Markus Maeurer, Mauro Piacentini, Stefano Merler, Giuseppe Pantaleo, Rafick-Pierre Sekaly, Serena Sanna, Nicola Segata, Alimuddin Zumla, Francesco Messina, Francesco Abbreviations CoVs: Coronaviruses; HCoV: Human coronavirus; PPI: Protein–protein interac- tions; COEX: Gene coexpression data; SARS-CoV: Severe acute respiratory syn- drome coronavirus; MERS-CoV: Middle East respiratory syndrome coronavirus; S-glycoprotein: Spike glycoprotein; RWR​: Random walk with restart; FDR: False Discovery Rate. Received: 25 April 2020 Accepted: 4 June 2020 Received: 25 April 2020 Accepted: 4 June 2020 References 1. Johns Hopkins University. Global-cases-covid-19. 2020. https​://www.gisai​ d.org/epifl​u-appli​catio​ns/globa​l-cases​-covid​-19/. 2. Jernigan DB. Update: public health response to the coronavirus disease 2019 outbreak—United States, February 24, 2020. MMWR Morb Mortal Wkly Rep. 2020;69(8):216–9. https​://doi.org/10.15585​/mmwr.mm690​8e1. 3. Paules CI, Marston HD, Fauci AS. Coronavirus infections-more than just the common cold. JAMA. 2020. https​://doi.org/10.1001/jama.2020.0757. ppi y Serena Sanna, Nicola Segata, Alimuddin Zumla, Francesco Messina, Francesco Vairo, Francesco Nicola Lauria, Giuseppe Ippolito. 4. Walsh EE, Shin JH, Falsey AR. Clinical impact of human coronaviruses 229E and OC43 infection in diverse adult populations. J Infect Dis. 2013;208(10):1634–42. https​://doi.org/10.1093/infdi​s/jit39​3. Consent for publication Not applicable. Consent for publication Not applicable. 7. de Wilde AH, Wannee KF, Scholte FE, Goeman JJ, Ten Dijke P, Snijder EJ, et al. A kinome-wide small interfering rna screen identifies proviral and antiviral host factors in severe acute respiratory syndrome coronavirus replication, including double-stranded RNA-activated protein kinase and 1. Johns Hopkins University. Global-cases-covid-19. 2020. https​://www.gisai​ d.org/epifl​u-appli​catio​ns/globa​l-cases​-covid​-19/. 2. Jernigan DB. Update: public health response to the coronavirus disease 2019 outbreak—United States, February 24, 2020. MMWR Morb Mortal Wkly Rep. 2020;69(8):216–9. https​://doi.org/10.15585​/mmwr.mm690​8e1. 3. Paules CI, Marston HD, Fauci AS. Coronavirus infections-more than just the common cold. JAMA. 2020. https​://doi.org/10.1001/jama.2020.0757. 4. Walsh EE, Shin JH, Falsey AR. Clinical impact of human coronaviruses 229E and OC43 infection in diverse adult populations. J Infect Dis. 2013;208(10):1634–42. https​://doi.org/10.1093/infdi​s/jit39​3. 5. Hendley JO, Fishburne HB, Gwaltney JM Jr. Coronavirus infections in working adults. Eight-year study with 229 E and OC 43. Am Rev Respir Dis. 1972;105(5):805–11. https​://doi.org/10.1164/arrd.1972.105.5.805. 6. de Wit E, van Doremalen N, Falzarano D, Munster VJ. SARS and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol. 2016;14(8):523–34. https​://doi.org/10.1038/nrmic​ro.2016.81. 7. de Wilde AH, Wannee KF, Scholte FE, Goeman JJ, Ten Dijke P, Snijder EJ, et al. A kinome-wide small interfering rna screen identifies proviral and antiviral host factors in severe acute respiratory syndrome coronavirus replication, including double-stranded RNA-activated protein kinase and Received: 25 April 2020 Accepted: 4 June 2020 Ethics approval and consent to participate Ethics approval and consent to participate Availability of data and materials PPI data of SARS-CoV, MERS-CoV, HCoV-229E S-glycoprotein were inferred through published PPI data, using STRING Viruses (http://virus​es.strin​g-db. org/) and VirHostNet (http://virho​stnet​.prabi​.fr/), as well as published scientific reports with a focus on virus-host interactions [20–22]. Human PPI databases (BioGrid, InnateDB-All, IMEx, IntAct, MatrixDB, MBInfo, MINT, Reactome, Reactome-FIs, UniProt, VirHostNet, BioData, CCSB Interactome Database), using R packages PSICQUIC (https​://bioco​nduct​or.org/packa​ges/relea​se/bioc/ html/PSICQ​UIC.html) and biomaRt (https​://bioco​nduct​or.org/packa​ges/relea​ se/bioc/html/bioma​Rt.html) [23, 24]. The gene expression data set was built from the Protein Atlas database (https​://www.prote​inatl​as.org/) [25]. Additional file 2: Figure S1. Pairwise distances along 259 full length CoV genomes. In the bottom of picture, indicative gene positioning along CoVs genomes is reported. The list of all considered genomes is reported in Additional file 1: Table S1. Figure S2. 3D structure of S-glycoprotein of SARS-CoV-2 and comparison with the ortholog from HCoV-229E, SARS-CoV, and MERS-CoV. Lateral (a) and superior (b) representation of SARS-CoV-2 S-glycoprotein, deducted for the sequence of patient INMI1 (MT066156.1). Each subunit chain has a different color. Structure com- parison of S-glycoprotein subunit between: HCoV-229E and SARS-CoV-2, in purple and blue respectively (c); SARS-CoV and SARS-CoV-2, in red and blue, respectively (d); MERS-CoV and SARS-CoV-2, in green and blue, respectively (e). Figure S3. Amino acid alignment and secondary motifs in the receptor binding domain (RBD) of S-glycoprotein of HCoV-229E, SARS-CoV, MERS-CoV and SARS-CoV-2 are shown. Legend of secondary motifs identifiers: H = α Helix, E = β Sheet, X = Random coil. Figure S4. HCoV-229E–host interactome resulting from RWR applied to the top 200 closest proteins identified by RWR, using S-glycoprotein of HCoV-229E. Figure S5. SARS-CoV–host interactome resulting from RWR applied to the top 200 closest proteins identified by RWR, using S-glycoprotein of SARS- CoV. Figure S6. MERS-CoV–host interactome resulting from RWR applied to the top 200 closest proteins identified by RWR, using S-glycoprotein of MERS-CoV. 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Ankle Motion Is Associated With Soft Tissue Displacement in the Dorsal Thigh: An in vivo Investigation Suggesting Myofascial Force Transmission Across the Knee Joint
Frontiers in physiology
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ORIGINAL RESEARCH published: 06 March 2020 doi: 10.3389/fphys.2020.00180 Keywords: myofascial force transmission, ultrasound, range of motion, fascia, myofascial chains Citation: Wilke J, Debelle H, Tenberg S, Dilley A and Maganaris C (2020) Ankle Motion Is Associated With Soft Tissue Displacement in the Dorsal Thigh: An in vivo Investigation Suggesting Myofascial Force Transmission Across the Knee Joint. *Correspondence: Jan Wilke *Correspondence: Jan Wilke wilke@sport.uni-frankfurt.de Specialty section: This article was submitted to Striated Muscle Physiology, a section of the journal Frontiers in Physiology Received: 18 December 2019 Accepted: 17 February 2020 Published: 06 March 2020 Ankle Motion Is Associated With Soft Tissue Displacement in the Dorsal Thigh: An in vivo Investigation Suggesting Myofascial Force Transmission Across the Knee Joint Jan Wilke1*, Heloise Debelle2, Sarah Tenberg1, Andrew Dilley3 and Constantinos Maganaris2 1 Department of Sports Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany, 2 School of Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom, 3 Department of Neuroscience, University of Sussex, Brighton, United Kingdom Experiments in cadavers have demonstrated significant mechanical interactions between constituents of myofascial chains. However, evidence for such force transmission effects is scarce under in vivo conditions. The purpose of this trial was to examine the impact of ankle motion on soft tissue displacement of the dorsal thigh. Eleven healthy active individuals (26.8 ± 4.3 years, six males), in prone position and with the knee extended, underwent passive calf stretches (ankle dorsal extension) imposed by an isokinetic dynamometer. High-resolution ultrasound was used to simultaneously capture the displacement of the semimembranosus muscle, which was quantified by means of cross-correlation analysis. Inactivity of the leg muscles was controlled using surface electromyography (EMG). One participant had to be excluded due to major EMG activity during the experiment. According to a one-sample t test testing the difference to the neutral zero position, ankle dorsal extension induced substantial caudal muscle displacements (5.76 ± 2.67 mm, p < 0.0001). Correlation analysis (Spearman), furthermore, revealed a strong association between maximal dorsal extension and semimembranosus motion (rho = 0.76, p = 0.02). In conclusion, the present trial provides initial in vivo evidence for a mechanical force transmission between serially connected skeletal muscles. This means that local alterations of the mechanical tissue properties may modify flexibility in neighboring (superior or inferior) joints. Edited by: Can A. Yucesoy, Bo ˘gaziçi University, Turkey Reviewed by: Filiz Ates, Mayo Clinic, United States Dieter Blottner, Charité - Medical University Berlin, Germany *Correspondence: Jan Wilke wilke@sport.uni-frankfurt.de Edited by: Can A. Yucesoy, Bo ˘gaziçi University, Turkey Reviewed by: Filiz Ates, Mayo Clinic, United States Dieter Blottner, Charité - Medical University Berlin, Germany g ç y, y Reviewed by: Filiz Ates, Mayo Clinic, United States Dieter Blottner, Charité - Medical University Berlin, Germany *Correspondence: Jan Wilke wilke@sport.uni-frankfurt.de INTRODUCTION As a consequence of intermuscular continuity (Yucesoy, 2010; Wilke et al., 2016a; Wilke and Krause, 2019) it has been hypothesized that the modification of local tissue properties can affect adjacent structures (Wilke et al., 2019a): if the linkages connecting two muscles are stiffenough, they may transmit force. In fact, experimental trials made such observation, showing that length changes of lower leg muscles induced mechanical strains in neighboring synergists and antagonists (Huijing and Baan, 2001; Huijing et al., 2011). Since removing the fibrous linkages between the muscles reduced this effect (Huijing and Baan, 2001), the previously produced strains seem to stem from a mechanical force transmission (Yucesoy, 2010). In their systematic review of cadaveric studies, Krause et al. (2016) aimed to answer the question as to whether mutual interactions would also occur between serially connected muscles. According to their findings, substantial forces can be transmitted, particularly in the posterior myofascial chain (plantar aponeurosis, gastrocnemius, hamstring muscles, lumbar fascia/erector spinae muscle). For instance, traction applied to the biceps femoris leads to a force transmission to the lumbar fascia (Vleeming et al., 1995). However, as cadavers (a) frequently exhibit alterations of mechanical tissue properties (e.g., due to fixation in solutions like formalin) and (b) do not produce neuromuscular activity, the findings of most studies investigating in-series mechanical force transmission cannot be extrapolated to in vivo conditions. INTRODUCTION Fascia, the collagenous connective tissue surrounding the skeletal muscles, has long been regarded as a passive packing organ with limited significance for the locomotor system (van der Wal, 2009). However, recent research unveiled a far more complex role. Firstly, histological studies have demonstrated the intrafascial existence of myofibroblasts (e.g., in the gastrocnemius fascia; Front. Physiol. 11:180. doi: 10.3389/fphys.2020.00180 Front. Physiol. 11:180. doi: 10.3389/fphys.2020.00180 March 2020 | Volume 11 | Article 180 Frontiers in Physiology | www.frontiersin.org Dorsal Myofascial Force Transmission Wilke et al. Bhattacharya et al., 2010). Their contraction, most probably mediated by the vegetative nervous system, can produce substantial increases of tissue stiffness in the long-term (Schleip et al., 2019). Secondly, already within minutes or hours, alterations of the water content, e.g., induced by isometric stretching, have been shown to significantly impact viscoelastic tissue properties (Schleip et al., 2012). The capacity of fascia to soften or harden in response to mechanical stimuli may be of particular importance due to another newly discovered feature. In contrast to prior assumptions, the surrounding fasciae do not separate, but connect the skeletal muscles. This architecture can be found between synergists and antagonists located parallel to each other (Yucesoy, 2010) as well as between muscles arranged in-series (Wilke et al., 2016a; Wilke and Krause, 2019). through the linkage, a visible displacement of the non-stretched tissue should occur. Using a simple experimental approach (Cruz-Montecinos et al., 2015) showed that an anterior pelvic tilt leads to a recognizable displacement of the gastrocnemius fascia. Their sonographic examination provides first indications for a cranial- caudal force transmission effect originating at the hip joint. However, in many movements of daily life and sports (e.g., walking, sprinting, jumping, squatting), forces are generated in the legs and hypothetically transmitted in direction of the trunk. In addition to this, all above described available in vivo trials examining the functional relevance of myofascial chains were (1) based on caudal-cranial force transmission and (2) mainly focused treatments around the ankle joint (plantar fascia massage, calf stretching). The present proof-of-principle study, therefore, aimed to elucidate for the first time, if a dorsal extension movement (also often referred to as dorsal flexion) of the ankle leads to a myofascial force transmission to the posterior thigh under in vivo conditions. Ethical Standard The experimental ultrasound study was approved by the local ethics committee and conducted according to the Declaration of Helsinki as well as the guidelines of Good Clinical Practice. All enrolled participants provided written informed consent. Sample Eleven healthy active individuals (26.8 ± 4.3 years, 6♂, 5♀) volunteered to participate. Exclusion criteria included severe orthopedic, cardiovascular, neurological, endocrine and psychiatric diseases, acute inflammation or history of surgery in the lower limb, intake of drugs that modify pain perception and proprioception, muscle soreness and pregnancy or nursing period. Recruitment was performed by word of mouth. Outcome To reveal the spatial relations in the area of interest of the United States image, the thickness of the subcutaneous tissue and the deep fascia of the semimembranosus muscle were determined using ImageJ (NIH, Bethesda, MD, United States). Five equidistant measurements were taken at rest and averaged. FIGURE 1 | Schematic illustration of the experimental set-up. In the prone position and with the knee extended, the ankle joint was passively moved between plantar flexion and dorsal extension (arrow shows way into dorsal extension). Maximal dorsal extension was calculated as the distance from a calibrated neutral zero position (dashed line). Ultrasound recordings were made over the semimembranosus muscle in order to estimate tissue displacement induced by the ankle motion. EMG (not depicted here) used as biofeedback ensured that no voluntary muscle activity occurred. Pelvic fixation with a strap was required to prevent body motion induced by the dynamometer action. As the belt was not in contact with the Hamstrings, it did not affect tissue displacement. FIGURE 1 | Schematic illustration of the experimental set-up. In the prone position and with the knee extended, the ankle joint was passively moved between plantar flexion and dorsal extension (arrow shows way into dorsal extension). Maximal dorsal extension was calculated as the distance from a calibrated neutral zero position (dashed line). Ultrasound recordings were made over the semimembranosus muscle in order to estimate tissue displacement induced by the ankle motion. EMG (not depicted here) used as biofeedback ensured that no voluntary muscle activity occurred. Pelvic fixation with a strap was required to prevent body motion induced by the dynamometer action. As the belt was not in contact with the Hamstrings, it did not affect tissue displacement. The maximal horizontal displacement of the semimembranosus muscle [mm distance from resting position] during maximal passive ankle dorsal extension represented the primary outcome. It was quantified using a frame-by- frame cross-correlation analysis of the obtained ultrasound videos, which reveals the maximum displacement of the muscle relative to the zero position without ankle movement (see Figure 2). The employed algorithm, created in MATLAB (The MathWorks, Inc., Natick, MA, United States), was developed by Dilley et al. (2001) and has been shown to represent a highly reliable method to quantify tissue displacement (ICC: 0.77 to 0.99). Experimental Approach EMG (not depicted here) used as biofeedback ensured that no voluntary muscle activity occurred. Pelvic fixation with a strap was required to prevent body motion induced by the dynamometer action. As the belt was not in contact with the Hamstrings, it did not affect tissue displacement. prevent artifacts induced by variations in pressure to the skin, a custom made template consisting of thermoplastic polymer was used for fixation (Cruz-Montecinos et al., 2015). To detect potential probe movement over the skin, acoustically reflective markers (thin stripes of micropore tape) which are clearly visible in the ultrasound image, were placed on the skin (Morse et al., 2008). Frontiers in Physiology | www.frontiersin.org Outcome Briefly, the software calculates the correlation coefficient between the pixel gray levels of successive frames within previously defined, rectangle-shaped regions of interest (ROI) of the successive frames. The pixel shift revealing the highest coefficient represents the relative movement between two frames. In video recorded in this trial, six equidistant ROIs (approximate size: 5 × 1 mm) were placed within the semimembranosus. Mean maximal horizontal displacement of the ROIs was calculated and analyzed as quantification of muscle displacement. Excellent reliability of this approach (use of the described software and six ROIs including interpretation procedure) has been demonstrated in a previous trial of our workgroup, which also examined fascial displacement in the thigh (Krause et al., 2019). surface electromyography (Biopac MP 160, Biopac Systems Inc., Goleta, CA, United States) was used to monitor muscle activity, providing the participants with live biofeedback. After preparation of the skin (shaving and alcohol cleansing), Ag- AgCl electrodes (8 mm diameter) were positioned over the muscle bellies of the m. semimembranosus, m. gastrocnemius, m. quadriceps femoris and m. tibialis anterior as well as over the lateral malleolus and the lateral femur condyle with the latter two being reference electrodes. Sensor placement was determined according to the SENIAM (surface EMG for non-invasive assessment of muscles) recommendations (Hermens et al., 2000). Electrodes were placed at 1/3 of the distance between the ischial tuberosity and the knee’s medial joint line (semimembranosus), on the most prominent bulge of the gastrocnemius muscle, at 50% of the distance between the anterior spina iliaca superior and the superior part of the patella (quadriceps femoris) and at 1/3 of the way between the tips of the fibula and the medial malleolus (tibialis anterior). Data were sampled at a rate of 1.600 kHz and filtered with a high- and low-pass filter of 10 and 500 Hz, respectively. Experimental Approach A schematic depiction of the experimental approach is shown in Figure 1. All experiments were conducted in the same room and at constant temperature and daytime. The participants were positioned in a standardized prone position on an isokinetic dynamometer (Cybex Norm, Cybex, Ronkonkoma, New York, United States), having their ankle joint axis aligned with the rotational axis of the device. A fixation belt was attached over dorsal pelvis (thus not compressing the Hamstring muscles) to prevent body movement. In the experiment, the ankle (tested leg chosen randomly) was moved passively between plantar flexion and maximal achievable dorsal extension by means of the dynamometer’s continuous passive motion function. During the measurements, ankle joint angle [◦], relative to the neutral zero position, was constantly recorded by the device. Three repetitions, averaged for analysis, were performed at an angular velocity of 5◦/s (Krause et al., 2019). The participants were instructed to remain completely passive, avoiding any voluntary muscle activity. To confirm this, As indicated, to date, only few trials have examined the relevance of myofascial chains in the living organism. A couple of studies demonstrated remote flexibility increases following local exercise treatments (Grieve et al., 2015; Wilke et al., 2016b, 2017, 2019b; Joshi et al., 2018). These findings are intriguing, seemingly verifying the observations made in vitro. It seems plausible that a decrease in tissue stiffness, induced by the local interventions, can be transmitted to more cranial structures (e.g., from Hamstrings and to the neck muscles). However, as the measured outcome (range of motion) represents a functional parameter, the registration of non-local exercise effects does not provide a definite proof for myofascial force transmission under living conditions. The use of high-resolution ultrasound imaging can resolve this research deficit as it is able to visualize a non-stretched tissue during elongation of a neighboring, connected structure: If substantial forces would be transmitted March 2020 | Volume 11 | Article 180 Frontiers in Physiology | www.frontiersin.org 2 Dorsal Myofascial Force Transmission Wilke et al. FIGURE 1 | Schematic illustration of the experimental set-up. In the prone position and with the knee extended, the ankle joint was passively moved between plantar flexion and dorsal extension (arrow shows way into dorsal extension). Maximal dorsal extension was calculated as the distance from a calibrated neutral zero position (dashed line). Ultrasound recordings were made over the semimembranosus muscle in order to estimate tissue displacement induced by the ankle motion. Hamstring Displacement Calculating tissue displacement was highly reliable, revealing almost perfect agreement between the five repetitions (ICC = 0.81, 95%CI: 0.66 to 0.97, p < 0.0001). Corrected for probe movement over the skin, which was negligible (0.09 ± 0.10 mm), passive ankle dorsal extension induced a significant caudal semimembranosus displacement of 5.76 ± 2.67 mm (95%CI: 3.86 to 7.68, p < 0.0001, d = 2.16). The highest value (10.87 ± 1.57 mm) was registered in a 22-year old female while the lowest displacement was found in a 24-year old male (1.22 ± 0.64 mm). In sum, higher values (6.74 ± 3.03 mm) occurred in women when compared to men (5.12 ± 2.46 mm), however, despite a moderate effect size (d = 0.60), this difference did not reach statistical significance (p = 0.38). Regarding the kinematic data indicating maximal ankle dorsal extension (◦) and horizontal tissue displacement (mm), mean values were calculated for the three movement cycles in each condition. To answer the question as to whether ankle movement leads to cranial displacement of the semimembranosus myofascial soft tissue, a twofold approach was chosen. Firstly, the one-sample t test and 95% confidence intervals (95% CI) were used in order to examine whether movement of the semimembranosus occurred (systematic difference to zero). Potential discrepancies between men and women were detected using the t test for independent samples. Effect sizes of both tests were calculated and interpreted according to Cohen (1992) as small (d = 0.2), medium (0.5) or large (0.8). Secondly, to identify significant associations between ankle dorsal extension and semimembranosus displacement, Spearman’s rank correlation was used. According to Evans (1996), resulting coefficients were graded as poor (<0.2), weak (0.2 to 0.4), moderate (0.4 to 0.6), strong (0.6 to 0.8) or optimal (>0.8). Finally, to demonstrate the reliability of the software algorithm for tissue displacement, the intraclass correlation coefficient was used (Bland and Altman, 1996). Based on the suggestions of Fleiss (1986), resulting reliability values were classified as poor (<0.4), moderate (0.4 to 0.75), or excellent (>0.75). All calculations were made with BiAS for Windows 11.2 (Goethe-University, Germany); the significance level was set to α = 0.05. Correlation With Ankle Dorsal Extension Maximal ankle dorsal extension, per average, was 19.8 ± 5.0 degrees. Spearman analysis revealed a strong positive FIGURE 3 | Scatter plot showing the relation between maximal ankle dorsal extension and dorsal thigh soft tissue displacement. Data Processing and Statistics g The recorded ultrasound, dynamometer and EMG data were synchronized using a common electrical impulse delivered through an external trigger to the interface of the employed software (Acqknowledge, Biopac Systems Inc., Goleta, CA, United States). Besides providing biofeedback, EMG data were used to detect involuntary muscle activity with two approaches implemented in the software package: The first was based on a normalization against maximum voluntary contraction (MVC), which was determined by means of isometric contractions of the included muscles. Here, muscle activity was defined as any root mean square values (0.03 s) >5% MVC. The second was based on the algorithm of Hodges and Bui (1996). Briefly, it determines the mean and standard deviation of the signal during a period of 0.25 s under resting conditions and creates a filtered average rectified value In order to familiarize the participants with the device and measurement conditions and to practice keeping the lower leg muscles inactive, a warm-up of three flexion-extension cycles was performed prior to the actual measurements. This approach has already been used successfully in a previous, similar study (Krause et al., 2019). A high-resolution ultrasonography device (My Lab 70, Esaote Biomedica, Genoa, Italy) was used to assess tissue displacement upon ankle joint movement. Video recordings, depicting the soft tissue of the dorsal thigh, were made with a linear array transducer (custom-made, 100 mm × 8 mm, 7.5 Hz) positioned over the belly of the semimembranosus muscle. To March 2020 | Volume 11 | Article 180 3 Wilke et al. Dorsal Myofascial Force Transmission FIGURE 2 | Exemplary visualization of ultrasound-based cross-correlation analysis. Equidistant ROIs (red rectangles) are selected at rest (left image). In this example, five ROIs have been positioned: three within the fascia and one in each, the subcutaneous tissue (SCT) and the muscle. Upon movement (right image), pixel displacements relative to the center of the non-moving ROIs (small yellow square inside the red rectangles in left picture) are tracked (yellow line in right picture). The end of the line indicates the maximal displacement, which is computed by the software algorithm. FIGURE 2 | Exemplary visualization of ultrasound-based cross-correlation analysis. Equidistant ROIs (red rectangles) are selected at rest (left image). In this example, five ROIs have been positioned: three within the fascia and one in each, the subcutaneous tissue (SCT) and the muscle. Hamstring Displacement Black circles represent males, open circles represent females. Data Processing and Statistics Upon movement (right image), pixel displacements relative to the center of the non-moving ROIs (small yellow square inside the red rectangles in left picture) are tracked (yellow line in right picture). The end of the line indicates the maximal displacement, which is computed by the software algorithm. the corresponding data were not included in the inferential statistics. The subcutaneous tissue, per average, had a thickness of 3.80 ± 2.17 mm. With 1.32 ± 0.49 mm, the deep fascia was about two thirds smaller. (ARV). It then extracts the variance with regard to the noise by means of dividing the difference between the ARV and the mean by the standard deviation. For the resulting signal, the median is calculated for the entire waveform. Any activity exceeding this median for at least 0.1 s is considered as muscle activity. Once one of the two methods described detected muscle activity, the corresponding trials were discarded from analysis. DISCUSSION The mechanical role of the soft tissue has been a recent focus of fascia research (Zügel et al., 2018). However, despite compelling evidence from cadaver experiments, pointing toward the occurrence of in-series force transmission effects across myofascial continuities (Krause et al., 2016), there has been a lack of in vivo studies regarding this topic, hitherto (Zügel et al., 2018). Our trial shows that maximal ankle dorsal extension is associated with significant caudal displacements of the semimembranosus muscle and its encapsulating fascia. This finding may explain the remote exercise effects detected in previous studies: It had been shown that stretching or self-myofascial release treatments induced flexibility increases in neighboring or even more distant cranial joints (Grieve et al., 2015; Wilke et al., 2016b, 2017, 2019a; Joshi et al., 2018). Although representing an intriguing observation, the occurrence of non-local changes in such functional outcome could not only be related to a force transmission across myofascial continuity but also be due to other factors such as systemic neural adaptations, i.e., altered stretch tolerance. Against this background, the remote soft tissue displacements established here may, in fact, demonstrate that mechanically relevant amounts of force are transferred to serially connected skeletal muscles in the living organism. When interpreting the novel findings, some noteworthy methodological considerations need to be made. Firstly, the measured soft tissue displacement represents a highly plausible surrogate but not a direct measure of transferred force. While this represents a rather theoretical concern, the effects observed must not only stem from a serial force transmission. Ankle movement has been demonstrated to modify the stiffness of the sciatic nerve. As it crosses the knee joint, it may have an impact on the mechanics of the thigh (Andrade et al., 2016). In addition, the fascial bands spanning from the gastrocnemius muscle to the dorsal thigh do not only attach to the semimembranosus but also to the other parts of the Hamstrings. Previous research revealed substantial mutual interaction between muscles located in parallel (Huijing and Baan, 2001). If force was hence transmitted from the calf it is tenable to assume that it also reached the biceps femoris and the semitendinosus. As a consequence, particularly the forces acting on the latter (pulling it in the caudal direction in the same way as occurring with the semimembranosus), could have induced a (minor) part of the muscle displacement. Another issue relates to the sample size of our investigation. DISCUSSION Evidently, it was sufficient to reveal the presence of semimembranosus motion and its correlation to ankle movement. However, our study may have been underpowered with regard to the influence of sex: female participants had higher displacements but the significance threshold was failed for this observation. Future studies, further delineating the role of sex on serial force transmission are therefore warranted. Finally, a couple of additional outcomes may be of particular value for upcoming research. Besides visualizing other muscles (e.g., those located in parallel and the calf muscles), it would be intriguing to measure the pennation angle in order to complement the displacement data. From a mechanical point of view, our experimental set-up did not allow for a judgment of tissue stiffness which could be another relevant effect modifier. It may be argued that higher stiffness of the implicated transmitting structures (in this case the gastrocnemius) would allow for a higher degree of force transmission. One possibility to assess this outcome would be using the isokinetic dynamometer to calculate the passive resistive torque produced during ankle movement. As a supplement, elastography, which has recently been used to study the mechanical properties of the lower leg muscles (Ates et al., 2017), could be added to gain further insight the mechanical properties of the leg muscles. Particularly, it would allow the measurement of stiffness changes in the entire Hamstring group As indicated, this is one of the first studies examining serial myofascial force transmission under in vivo conditions. The only similar trial conducted by Cruz-Montecinos et al. (2015) demonstrated a coupling of pelvic movement and displacement of the gastrocnemius fascia. The absolute magnitude of fascial displacement was higher in our data (5.8 mm vs. 1.5 mm). This difference may be explained by various factors, including differences in the imaged muscle (semimembranosus vs. gastrocnemius), the moved joint (ankle vs. pelvis) and the direction of force transmission (caudal-cranial vs. cranial-caudal). Notwithstanding, a common finding of both studies was the strong correlation of local ROM alterations and consecutive remote tissue displacements. The practical implications of our research span from sports performance to musculoskeletal disorders. Coaches and exercise professionals should be aware that stretching treatments do affect both the targeted tissue but also morphologically linked skeletal muscles. The relevance of the exercise position, for instance having the knee extended or not when targeting the calf, thus extends beyond the question of mono- or bi-articularity of muscles. RESULTS FIGURE 3 | Scatter plot showing the relation between maximal ankle dorsal extension and dorsal thigh soft tissue displacement. Black circles represent males, open circles represent females. FIGURE 3 | Scatter plot showing the relation between maximal ankle dorsal extension and dorsal thigh soft tissue displacement. Black circles represent males, open circles represent females. All participants completed the experiment. However, while the analyses of the EMG confirmed absence of muscle activity in 10 individuals, one showed above-threshold values and hence, March 2020 | Volume 11 | Article 180 Frontiers in Physiology | www.frontiersin.org 4 Dorsal Myofascial Force Transmission Wilke et al. accordance with previous data (Wilke et al., 2018). Besides its potential relevance under normal conditions, myofascial force transmission could also play a role in the development of overuse disorders. It had been speculated that the occurrence of non-local abnormalities (e.g., increased hamstring stiffness in patients with plantar fasciitis) stems from a pathologically altered/excessive degree of myofascial force transmission (Wilke et al., 2019a). In order to further substantiate this assumption, it seems of interest to conduct similar experiments in both healthy individuals and patients with musculoskeletal disorders. correlation between the extent of caudal semimembranosus displacement and dorsal extension (p = 0.02, rho = 0.76), which suggests that higher ankle movement amplitudes were associated with larger displacements of the semimembranosus muscle (Figure 3). Frontiers in Physiology | www.frontiersin.org REFERENCES Huijing, P. A., and Baan, G. C. (2001). Myofascial force transmission causes interaction between adjacent muscles and connective tissue: effects of blunt dissection and compartmental fasciotomy on length force characteristics of rat extensor digitorum longus muscle. Arch. Physiol. Biochem. 2, 97–109. doi: 10.1076/apab.109.2.97.4269 Andrade, R. J., Nordez, A., Hug, F., Ates, F., Coppieters, M. W., Pezarat-Correia, P., et al. (2016). Non-invasive assessment of sciatic nerve stiffness during human ankle motion using ultrasound shear wave elastography. J. Biomech. 49, 326–331. doi: 10.1016/j.jbiomech.2015.12.017 Huijing, P. A., Yaman, A., Ozturk, C., and Yucesoy, C. A. (2011). Effects of knee joint angle on global and local strains within human triceps surae muscle: MRI analysis indicating in vivo myofascial force transmission between synergistic muscles. Surg. Radiol. Anat. 33, 869–879. doi: 10.1007/s00276-011- 0863-1 Ates, F., Andrade, R. J., Freitas, S. R., Hug, F., Lacourpaille, L., Gross, R., et al. (2017). Passive stiffness of monoarticular lower leg muscles is influenced by knee joint angle. Eur. J. Appl. Physiol. 118, 585–593. doi: 10.1007/s00421-018- 3798-y Joshi, D. G., Balthillaya, G., and Prabhu, A. (2018). Effect of remote myofascial release on hamstring flexibility in asymptomatic individuals – a randomized, controlled trial. J. Bodyw. Mov. Ther. 22, 832–837. doi: 10.1016/j.jbmt.2018. 01.008 Bhattacharya, V., Barooah, P. S., Nag, T. C., Chaudhuri, G. R., and Bhattacharya, S. (2010). Detail microscopic analysis of deep fascia of lower limb and its surgical implication. Ind. J. Plast. Surg. 43, 135–140. doi: 10.4103/0970-0358.73424 Bland, J. M., and Altman, D. G. (1996). Measurement error and correlation coefficients. Br. Med. J. 313, 744–746. Krause, F., Wilke, J., Niederer, D., Vogt, L., and Banzer, W. (2019). Acute effects of foam rolling on passive stiffness, stretch sensation and fascial sliding: a randomized controlled trial. Hum. Mov. Sci. 67:102514. doi: 10.1016/j.humov. 2019.102514 Cohen, J. (1992). A power primer. Psychol. Bull. 112, 155–159 Cruz-Montecinos, C., González Blanche, A., López Sánchez, D., Cerda, M., Sanzana-Cuhce, R., and Cuesta-Vargas, A. (2015). In vivo relationship between pelvis motion and deep fascia displacement of the medial gastrocnemius: anatomical and functional implications. J. Anat. 227, 665–672. doi: 10.1111/joa. 12370 Krause, F., Wilke, J., Vogt, L., and Banzer, W. (2016). Intermuscular force transmission along myofascial chains: a systematic review. J. Anat. 228, 910– 918. doi: 10.1111/joa.12464 Morse, C. I., Degens, H., Seynnes, O. R., Maganaris, C. N., and Jones, D. A. (2008). The acute effect of stretching on the passive stiffness of the human gastrocnemius muscle tendon unit. Exp. AUTHOR CONTRIBUTIONS JW contributed to the concept, design, data acquisition, analysis and interpretation, drafting and critical revision of the manuscript, and final approval of the manuscript. HD contributed to the data acquisition, critical revision of the manuscript, and final approval of the manuscript. ST contributed to the analysis and interpretation, critical revision of the manuscript, and final approval of the manuscript. AD contributed to the analysis and interpretation, and final approval of the manuscript. CM contributed to the concept, design, critical revision of the manuscript, and final approval of the manuscript. CONCLUSION Our study demonstrated under in vivo conditions that mechanical force is transmitted between the ankle and the dorsal thigh upon passive stretching of the gastrocnemius. This finding may represent the morphological substrate of remote exercise effects occurring after treatments based on myofascial chains. The correlation of semimembranosus displacement and ankle dorsal extension, furthermore, may suggest that fascial tissue can restrict flexibility. Future research should elucidate the functional implications of the observed transmission effects in sports and disease. DATA AVAILABILITY STATEMENT The datasets generated for this study are available on request to the corresponding author. DISCUSSION In essence, it may be argued that fascial tissues represent a potential contributor to restrictions in flexibility, which would be in March 2020 | Volume 11 | Article 180 5 Dorsal Myofascial Force Transmission Wilke et al. ETHICS STATEMENT in order to quantify the degree of myofascial force transmission from muscle arranged in parallel. in order to quantify the degree of myofascial force transmission from muscle arranged in parallel. The studies involving human participants were reviewed and approved by the University Research Ethics Committee of Liverpool John Moores University. The patients/participants provided their written informed consent to participate in this study. REFERENCES Physiol. 586, 97–106. doi: 10.1113/ jphysiol.2007.140434 Dilley, A., Greening, J., Lynn, B., Leary, R., and Morris, V. (2001). The use of cross- correlation analysis between high-frequency ultrasound images to measure longitudinal median nerve movement. Ultrasound Med. Biol. 27, 1211–1218. doi: 10.1016/s0301-5629(01)00413-6 Evans, J. D. (1996). Straightforward Statistics for the Behavioral Sciences. Pacific Grove: Brooks/Cole Publishing. Schleip, R., Duerselen, L., Vleeming, A., Naylor, I. L., Lehmann-Horn, F., Zorn, A., et al. (2012). Strain hardening of fascia: static stretching of dense fibrous connective tissues can induce a temporary stiffness increase accompanied by enhanced matrix hydration. J. Bodyw. Mov. Ther. 16, 94–100. doi: 10.1016/j. jbmt.2011.09.003 g Fleiss, J. L. (1986). The Design and Analysis of Clinical Experiments. New York, NY: John Wiley & Sons. Grieve, R., Goodwin, F., Alfaki, M., Bourton, A. J., Jeffries, C., and Scott, H. (2015). The immediate effect of bilateral self myofascial release on the plantar surface of the feet on hamstring and lumbar spine flexibility: a pilot randomised controlled trial. J. Bodyw. Mov. Ther. 19, 544–552. doi: 10.1016/j.jbmt.2014.12.004 Schleip, R., Gabbiani, G., Wilke, J., Naylor, I., Hinz, B., Zorn, A., et al. (2019). Fascia is able to actively contract and may thereby influence musculoskeletal dynamics: a histochemical and mechanographic investigation. Front. Physiol. 10:336. doi: 10.3389/fphys.2019.00336 Hermens, H. J., Freriks, B., Disselhorst-Klug, C., and Rau, G. (2000). Development of recommendations for SEMG sensors and sensor placement procedures. J. Electromyogr. Kinesiol. 10, 361–374. doi: 10.1016/s1050-6411(00)00027-4 van der Wal, J. (2009). The architecture of the connective tissue in the musculoskeletal system. an often overlooked functional parameter as to proprioception in the locomotor apparatus. Int. J. Ther. Massage Bodyw. 2, 9–23. Hodges, P. W., and Bui, B. H. (1996). A comparison of computer-based methods for the determination of onset of muscle contraction using electromyography. Electroencephalogr. Clin. Neurophysiol. 101, 511–519. doi: 10.1016/s0013- 4694(96)95190-5 Vleeming, A., Pool-Goudzwaard, A., Stoeckart, R., Van Wingerden, J. P., and Snijders, C. (1995). The posterior layer of the thoracolumbar fasciaIts function March 2020 | Volume 11 | Article 180 Frontiers in Physiology | www.frontiersin.org 6 Dorsal Myofascial Force Transmission Wilke et al. in load transfer from spine to legs. Spine 20, 753–758. doi: 10.1097/00007632- 199504000-00001 controlled trial. J. Sport Sci. 35, 2021–2027. doi: 10.1080/02640414.2016.125 1606 in load transfer from spine to legs. Spine 20, 753–758. doi: 10.1097/00007632- 199504000-00001 Yucesoy, C. A. (2010). Epimuscular myofascial force transmission implies novel principles for muscular mechanics. Exerc. Sport Sci. Rev. 38, 128–134. Frontiers in Physiology | www.frontiersin.org REFERENCES doi: 10.1097/JES.0b013e3181e372ef Wilke, J., Kalo, K., Niederer, D., Vogt, L., and Banzer, W. (2019b). Gathering hints for myofascial force transmission under in vivo conditions: are remote exercise effects age dependent? J. Sport Rehabil. 28, 758–763. doi: 10.1123/jsr.2018- 0184 Zügel, M., Maganaris, C. M., Wilke, J., Rott, K. J., Klingler, W., and Wearing, S. C. (2018). Fascial tissue research in sports medicine: from molecules to tissue adaptation, injury and diagnostics: consensus statement. Br. J. Sports Med. 52:1497. doi: 10.1136/bjsports-2018-099308 Wilke, J., and Krause, F. (2019). Myofascial chains of the upper limb: a systematic review of anatomical studies. Clin. Anat. 32, 934–940. doi: 10.1002/ca.23424 Wilke, J., Krause, F., Vogt, L., and Banzer, W. (2016a). What is evidence-based about myofascial chains: a systematic review. Arch. Phys. Med. Rehabil. 97, 454–461. doi: 10.1016/j.apmr.2015.07.023 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. Wilke, J., Macchi, V., De Caro, R., and Stecco, C. (2018). Fascia thickness, aging and flexibility: is there an association? J. Anat. 234, 43–49. doi: 10.1111/joa.12902 Wilke, J., Niederer, D., Vogt, L., and Banzer, W. (2016b). Remote effects of lower limb stretching: preliminary evidence for myofascial continuity? J. Sport Sci. 34, 2145–2148. doi: 10.1080/02640414.2016.1179776 Copyright © 2020 Wilke, Debelle, Tenberg, Dilley and Maganaris. 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. limb stretching: preliminary evidence for myofascial continuity? J. Sport Sci. 34, 2145–2148. doi: 10.1080/02640414.2016.1179776 Wilke, J., Vleeming, A., and Wearing, S. (2019a). Overuse injury: the result of pathologically altered myofascial force transmission? Exerc. Sport Sci. Rev. 47, 230–236. doi: 10.1249/JES.0000000000000205 Wilke, J., Vogt, L., Niederer, D., and Banzer, W. (2017). Is remote stretching based on myofascial chains as effective as local exercise? A randomised, March 2020 | Volume 11 | Article 180 Frontiers in Physiology | www.frontiersin.org 7
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Robot-assisted Treatment Contributes to Regaining Upper Limb Motility in Stroke Patients:a Randomized-controlled Trial Based on Functional Near Infrared Spectroscopy
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Jiayue Xu Department of Rehabilitation Medicine, the Second Affiliated Hospital,School of Medicine, South China University of Technology Guiyuan Cai Department of Rehabilitation Medicine, the Second Affiliated Hospital,School of Medicine, South China University of Technology Junbo Jiang Page 1/19 Department of Rehabilitation Medicine, the Second Affiliated Hospital,School of Medicine, South China University of Technology Research Article Keywords: Stroke, Robot-assisted treatment, Upper extremity motor rehabilitation, Functional near infrared spectroscopy Posted Date: April 19th, 2024 Posted Date: April 19th, 2024 DOI: https://doi.org/10.21203/rs.3.rs-4232249/v1 DOI: https://doi.org/10.21203/rs.3.rs-4232249/v1 License:   This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Additional Declarations: No competing interests reported. Page 2/19 Objective This study concentrated on the treatment effect and brain functional responses to RAT obtained with functional near infrared spectroscopy (fNIRS) in individuals having experienced a stroke with upper limb mobility impairment to direct the application of clinical therapy. Methods Eighteen stroke patients were randomly distributed to the robotics group (RG) to receive RAT and the control group (CG) to receive motor training without robot-assistance. Therapies were administered five days per week, for one month, and the outcome indicators were assessed at baseline and 30 days after treatment onset. The clinical evaluations included administration of the Fugl-Meyer assessment for upper-extremity(FMA-UE), action research arm test(ARAT), together with fNIRS recordings.The relative variations in oxyhemoglobin (OxyHb) concentrations measured by fNIRS were used to determine cortical activity levels. Results After four weeks of rehabilitation training, the FMA-UE and ARAT points of both groups considerably increased. The FMA-UE and ARAT points of the RG improved more than those of the CG. In comparison to the CG, fNIRS recordings showed enhanced cortical activation of the primary motor cortex in the ipsilateral hemisphere (i-M1) in the RG. Correlation analysis demonstrated a significant positive correlation between FMA-UE points improvements and therapy-evoked increases in the OxyHb of i-M1 in both the RG(r = 0.88, p < 0.001) and CG (r = 0.71, p = 0.03).It also showed a substantial positive association of the ARAT score changes and therapy-evoked increases in the OxyHb of M1 in the RG (r =  0.92, p < 0.001) and CG(r = 0.87, p < 0.002). Background Robot-assisted treatment(RAT) has drawn a lot of interest in stroke motor rehabilitation. Theoretically, the best protocol for a patient should be selected based on features of the brain's functional reactions associated with RAT. However, due to a paucity of techniques for dynamic brain functional testing, the cortical reaction response to RAT has yet to be thoroughly understood. Conclusion Page 3/19 Our findings suggest that RAT performed as well or better than classic therapy methods that could help patients with stroke with upper extremity motor dysfunction and activate M1. This activation may promote reorganization of brain function. Our findings suggest that RAT performed as well or better than classic therapy methods that could help patients with stroke with upper extremity motor dysfunction and activate M1. This activation may promote reorganization of brain function. ChiCTR, ChiCTR1800019783. Registered 28 November 2018, https://www.chictr.org.cn/ ChiCTR1800019783 ChiCTR, ChiCTR1800019783. Registered 28 November 2018, https://www.chictr.org.cn/ ChiCTR1800019783 ChiCTR, ChiCTR1800019783. Registered 28 November 2018, https://www.chictr.org.cn/ ChiCTR1800019783 Introduction Prior research has shown that increases in neuroplasticity in the adult human brain are associated with upper extremity motor recovery[1]. Many investigations have demonstrated the close relationship between activation of particular cortical area activation and upper extremity motor recovery following stroke[2]. It is vital for stroke patients to undergo rehabilitation to restore the movement capabilities of their paralyzed limbs for the purpose of maintaining their social engagement and quality of life [3]. According to previous research, the prognosis of motor function can be accurately assessed between four to five weeks following a stroke [3, 4]. Therefore, it is crucial for physical therapists to offer effective treatment after stroke. Repetitive task-specific training for poststroke patients can promote neuroplasticity and improve motor function[5] .Traditional rehabilitation techniques are mainly performed under the guidance of a physical therapist, thus, these techniques are time-consuming and laborious.Rehabilitation robots have the advantages of being fatigue-free, quantitative, and individualized, and can administer high-dose, high- repetition exercise training, while also providing objective and immediate training data and assessment data; these robots are expected to be useful tools for promoting patients' functional recovery[6, 7]. Robot-assisted therapy (RAT) for the upper extremities has recently become a well-regarded stroke recovery method.Numerous investigations have confirmed the clinical efficacy of RAT based on clinical evaluation[8] and biomechanical characteristics[9, 10]. Moreover, recent investigations have documented the variable results of RAT among stroke patients[11, 12]. Some studies have shown that RAT does not more substantially enhance motor performance in sufferers with poststroke upper extremity dyskinesia or improve chronic poststroke upper limb impairment compared to other assistive therapies[13, 14].There are not enough clinically useful evaluation methods available to allow physical therapists provide the most appropriate therapeutic therapies based on each patient's unique needs. Therefore, it is important to specifically assess the unique functional responses to RAT of stroke patients with upper extremity motor impairment. The adaptation of adequate training protocols to achieve a significant improvement over current clinical practices depends heavily on the actual assessment of brain function in response to particular kinds of interventions. However, the treatment efficacy of RAT in promoting brain plasticity is unclear. Introduction Repetitive task-specific training for poststroke patients can promote neuroplasticity and improve motor function[5] .Traditional rehabilitation techniques are mainly performed under the guidance of a physical therapist, thus, these techniques are time-consuming and laborious.Rehabilitation robots have the advantages of being fatigue-free, quantitative, and individualized, and can administer high-dose, high- repetition exercise training, while also providing objective and immediate training data and assessment data; these robots are expected to be useful tools for promoting patients' functional recovery[6, 7]. Robot-assisted therapy (RAT) for the upper extremities has recently become a well-regarded stroke recovery method.Numerous investigations have confirmed the clinical efficacy of RAT based on clinical evaluation[8] and biomechanical characteristics[9, 10]. Moreover, recent investigations have documented the variable results of RAT among stroke patients[11, 12]. Some studies have shown that RAT does not more substantially enhance motor performance in sufferers with poststroke upper extremity dyskinesia or improve chronic poststroke upper limb impairment compared to other assistive therapies[13, 14].There are not enough clinically useful evaluation methods available to allow physical therapists provide the most appropriate therapeutic therapies based on each patient's unique needs Therefore it is 14].There are not enough clinically useful evaluation methods available to allow physical therapists provide the most appropriate therapeutic therapies based on each patient's unique needs. Therefore, it is important to specifically assess the unique functional responses to RAT of stroke patients with upper extremity motor impairment. The adaptation of adequate training protocols to achieve a significant improvement over current clinical practices depends heavily on the actual assessment of brain function in response to particular kinds of interventions. However, the treatment efficacy of RAT in promoting brain plasticity is unclear. Page 4/19 Page 4/19 Due to the recent major advancements in functional near infrared spectroscopy (fNIRS) technology, fNIRS has received significant attention in both research and clinical contexts[15]. Because several types of imaging devices, for example, functional magnetic resonance imaging (fMRI) and electroencephalography (EEG) have a low tolerance for motion artifacts, monitoring cortex responses during exercise interventions in real time is still challenging[16]. As a noninvasive technique that measures cortical hemodynamics, fNIRS has benefits like mobility, safety, and the capacity to tolerate motion artifacts[17]. FNIRS can not only be used to deliver tailored neurological modulation with a closed loop control approach ultimately accomplishing individualized brain disease treatment, but also provide knowledge of the mechanisms underpinning neuroregulation in neurological rehabilitation[18]. Furthermore, a thorough review detailing fNIRS-related applications for stroke indicated that fNIRS is a technology with a future monitoring cerebrum activity in the period of particular rehabilitative interventions [19]. In particular, fNIRS technology has been extensively used for recovery studies of persons who had suffered a stroke [20, 21]. By sensing variations in the consistency of oxyhemoglobin (OxyHb) and deoxygenated hemoglobin (DeoxyHb) in the target cerebral cortices,fNIRS evaluates both neuronal activity and neurovascularization[22]. Therefore, our study used an fNIRS system to assess the mechanisms behind the helpful role of robot-assisted recuperation. Accordingly, the main objectives of this research were to verify the effectiveness of robot coaching for upper extremity recovery and brain function remodeling by evaluating the functional improvement after RAT of patients with upper extremity motor impairment after stroke and the particular corticostriatal response pattern of these patients to RAT on the basis of the Fugl-Meyer assessment for upper- extremity (FMA-UE), action research arm test (ARAT) and OxyHb fNIRS analysis.Assessment of functional brain reactions in real time can offer a rationale for patient selection of proper protocols to back up the decision making in the clinic. Participants During their first week of hospitalization, we screened every patient with a first- time stroke who checked into our department of rehabilitation. Patients who had been enrolled in the study were randomized and assessed immediately. At the time of hospital discharge, a second evaluation took place. The First People's Hospital in Guangzhou's ethical committee accepted this study (approval No. K-2021-020-01), and ChiCTR1800019783 is the register number in the China Clinical Trial Registry. Additionally, the trials were conducted in the rehabilitation department's clinical laboratory at the First People's Hospital in Guangzhou, Guangdong, China. All subjects signed an informed consent form. Figure 1 depicts the flowchart for this study(see Fig. 1). llowing were the inclusion criteria for stroke patients:(1) subacute stage The following were the inclusion criteria for stroke patients:(1) subacute stage hemiparesis/hemiplegia(see Table 1) with severe movement disorders due to the first stroke;(2) lesion locations recognized by computed tomography or magnetic resonance imaging;(3) between 30 and 80 hemiparesis/hemiplegia(see Table 1) with severe movement disorders due to the first stroke;(2) lesion locations recognized by computed tomography or magnetic resonance imaging;(3) between 30 and 80 Page 5/19 Page 5/19 years of age ; (4) being able to agree to be involved in research and follow protocol requirements. The following were the exclusion criteria: (1) existence of sequelae of cerebrovascular accident or any other chronically disabling condition with subarachnoid hemorrhage;(2)arthritic impairments,or arm skin lesions that may affect movement; (3)a Mini-Mental State Examination (MMSE) score < 24[23];(5) hemilateral neglect. Table 1 Clinical characteristics of patients in the study. Participants No Age Gender Type Lesion site Duration(days) MMSE ARAT FMA-UE 1 63 M Infarction R-NC 45 28 13 17 2 72 M Infarction L-FL,NC 37 25 9 8 3 62 F Infarction R-FL 71 27 17 11 4 63 M Infarction R-TL,NC 65 26 21 20 5 68 F Infarction R-TL,FL 58 29 14 16 6 75 M Infarction R-TL,PL 27 28 19 35 7 47 M Hemorrhage L-NC 86 29 22 27 8 67 F Infarction L-FL,PL 121 29 25 46 9 54 M Infarction R-NC 78 27 16 38 10 79 F Infarction R-PL,NC 76 26 23 13 11 60 M Infarction R-FL 92 27 21 25 12 43 F Infarction L-FL,NC 56 29 17 10 13 68 M Hemorrhage L-TL,PL 126 28 22 33 14 64 M Infarction R-NC 47 28 13 44 15 64 F Infarction L-FL 78 25 10 16 16 58 M Infarction L-FL 35 29 16 10 17 66 M Infarction L-TL,FL,PL 69 28 18 36 18 71 F Infarction R-FL,PL 25 26 15 28 S i d b li l ti RAT work and fNIRS data acquisition Patients were required to sit in a resting state for 5 minutes during the fNIRS experiment.For this investigation, patients' hemiparetic forearms were placed on a robot-aided upper body workout device (a type of terminal effects device) during the task state, with armature fastening around their forearm and a handle on the paralyzed hand. With an "aided as needed" control method, the robotization delivered target oriented, flat shoulder and elbow extensions at an identical velocity (5.0 cm/s) and movement extent about the center object (Y-axis = 20 cm, X-axis = 30 cm). The patients were instructed to restrict their movements to those required for their motor tasks while in the task state. To assure the participants' safety, a licensed therapist was involved in every step of the trial. A continuum wave fNIRS system (Nirscan, Danyang Huichuang Mechanical Instrument Co.Ltd., China) configured with 24 sources and 24 detectors and a sample rate of 11 Hz was used to continually measure cerebral hemodynamics during each session. In accordance with the universal 10–20 electrochemical positioning technique, 63 channels were distributed across both the left and right prefrontal cortex (symmetrically with FpZ as standard reference), motor cortex (corresponding to zones C3 and C4), and occipital lobe (symmetrical with OZ as standard reference). On the basis of the amended Beer-Lambert law, the optical density variation was used to determine the comparative variation in the levels of OxyHb. We used the OxyHb measurement, which is known to be more susceptible to mission-relevant hematologic variations than other fNIRS measures, i.e.,deoxygenated hemoglobin (DeoxyHb), and total hemoglobin (TotalHb), to produce corticostriatal activation maps; the OxyHb in every region of interest (ROI) was then considered, to analyze the cortical activation pattern. OxyHb indirectly measures brain activity by identifying changes in the cerebral cortex's underlying hemodynamics. Based on the physical placements of the brain's regions and Brodmann's area (BA), three ROIs and their corresponding subsets of the total number of channels were chosen to study corticostriatal activity: the somatosensory cortex(SC), primary motor cortex (M1), and the premotor cortex(PMC)(see Fig. 2). The selected channels for every ROI were chosen based on their anatomical placement in accordance with Brodmann's domain areas, and the OxyHb was estimated from each channel. By reversing the fNIRS channels from right to left across the middle sagittal line for individuals with a right-sided pathology during analysis, the pathological side was consistently considered to be the left hemisphere. Screening and baseline evaluation The baseline assessment was conducted by our study center coordinator if patients met the criteria for inclusion and exclusion. Baseline data such as age, sex, the length of time after the stroke, the site of the lesion, and clinical evaluations such as the FMA-UE[24], MMSE and current upper limb rehabilitation therapies were collected(see Table 1). Page 6/19 Table 1 Clinical characteristics of patients in the study. Table 1 M:Male; F:Female; L:Left; R:Right; FL:Frontal Lobe, PL:Parietal Lobe, TL:Temporal Lobe, OL: Occipital Lobe, NC:Nucleocapsular). MMSE: Mini-mental State Examination; ARAT: Action Research Arm Test; FMA-UE: Fugl-Meyer assessment for upper-extremity. Table 1 M:Male; F:Female; L:Left; R:Right; FL:Frontal Lobe, PL:Parietal Lobe, TL:Temporal Lobe, OL: Occipital Lobe, NC:Nucleocapsular). MMSE: Mini-mental State Examination; ARAT: Action Research Arm Test; FMA-UE: Fugl-Meyer assessment for upper-extremity. Preprocessing of fNIRS data Using the revised Beer-Lambert law and the assumption of constant scattering[25], variations in measured light intensities were used to determine variations in the concentrations of ΔOxyHb and Page 7/19 ΔDeoxyHb. After obtaining the ΔOxyHb and ΔDeoxyHb signals, data preprocessing was carried out. Movement artifacts were subsequently eliminated using a shifting normal bias and cubic spline interpolation processing technique[26]. Finally, we filtered the signal to improve its signal-to-noise(SNR) ratio using a 0.021-2 Hz 6th order Butterworth Bandpass Filter. For the remaining analyses, we focused on the ΔOxyHb signal since it has a superior SNR and a larger association with the oxygen level dependent signaling detected by fMRI.[27, 28] Statistical Analysis Variables are provided as the mean and standard deviation (SD), All statistical analyses were done utilizing SPSS 20.0 (IBM SPSS, Inc., Armonk, NY, USA). The Kolmogorov–Smirnov test was utilized to identify whether the assessed values were normally distributed. Certain demographic variables, including sex and category of stroke were compared between groups by applying a chi-square test. Age, stroke duration, and performance evaluation (MMSE, FMA-UE and ARAT) were compared by employing two independent sample t tests. On the basis of this grouping, notable intra and intergroup disparities in increases in oxyhemoglobin, FMA-UE and ARAT were evaluated using paired sample t tests and independent two sample t tests. We further evaluated the correlation between changes in OxyHb and the FMA-UE and ARAT points for each group of stroke patients to determine the correlations of the cerebrum responses to RAT and the virtual state of the upper limb. Statistical significance was considered for p <  0.05. Demographic information Along with routine rehabilitation procedures, 21 patients who were evaluated between May 2021 and November 2022 were allocated to robotic or classical therapies. One patient allocated to classical therapies and two patients allocated to robotic therapies both dropped out of the research.Finally the robotics group(RG) included 9 individuals and the CG(control group) included 9 individuals. The Table 1 shows that baseline patient characteristics were not substantially different between groups. Age, sex, poststroke length, stroke category, and MMSE, ARAT, and FMA-UE scores for baseline patient identity were not much of a difference across groups (p > 0.05)(see Table 2). Page 8/19 Table 2 Comparison of the fundamental data between the two patient groups. Characteristics Robotic group(n = 9) Control group(n = 9) Statistical result Sex (M/F) 6/3 5/4 χ2 = 0.234 p = 0.629 Age (years) 63.44 ± 8.68 63.67 ± 9.91 t=-0.051     p = 0.960 Duration (days) 65.33 ± 28.41 67.11 ± 30.86 t=-0.127     p = 0.900 MMSE 27.56 ± 1.42 27.33 ± 1.41 t = 0.332     p = 0.744 FMA-UE 24.22 ± 13.06 23.89 ± 12.34 t = 0.560     p = 0.956 ARAT 17.33 ± 4.97 17.22 ± 4.29 t = 0.510     p = 0.960 Comparisons of basic information of two groups of patients. Data are presented as mean ± Mi i t l St t E i ti ARAT A ti R h A T t FMA UE F l M Table 2 omparison of the fundamental data between the two patient groups. Table 2 Comparisons of basic information of two groups of patients. Data are presented as mean ± SD. MMSE: Mini-mental State Examination; ARAT: Action Research Arm Test; FMA-UE: Fugl-Meyer assessment for upper-extremity. Table 2 Comparisons of basic information of two groups of patients. Data are presented as mean ± SD. MMSE: Mini-mental State Examination; ARAT: Action Research Arm Test; FMA-UE: Fugl-Meyer assessment for upper-extremity. Table 2 Comparison of the fundamental data between the two patient groups. Table 2 Comparison of the fundamental data between the two patient groups. Table 2 Comparison of the fundamental data between the two patient grou Effectiveness The changes in FMA-UE, ARAT points from baseline to completion of treatment for the two groups are reported in Fig. 3(see Fig. 3). There was no remarkable difference in FMA-UE and ARAT scores among the two groups at baseline (p = 0.956 and p = 0.960 respectively), no obvious difference in FMA-UE and ARAT points in both groups after the intervention (p = 0.372 and p = 0.054, respectively), and a significant difference between the two groups in the change in FMA-UE and ARAT points from baseline to completion of treatment (p = 0.015 and p = 0.044). There was a noticeable improvement in FMA-UE (p =  0.002) and ARAT (p = 0.003) scores before and after RAT training in the robotic group, and a significant increase in the FMA-UE points (p = 0.038) and nonsignificant improvement in ARAT scores (p = 0.149) before and after conventional treatment in the control group. The hemodynamic findings demonstrated an enhancement in OxyHb concentration in the left and right hemispheres after the RAT. Figure 4 displays the topographic map of the OxyHb averaged across all subjects after training. Significant activation in the ipsilesional M1 was observed in the robotic group(p = Page 9/19 0.048) but not in the control group( p = 0.158). There was a nominal but insignificant increase in OxyHb in the contralateral M1 in both the robotic and control groups( p > 0.05)(see Fig. 4). Correlation analysis revealed a distinct positive correlation between FMA-UE points and changes in intraregional OxyHb in the robotic group ipsilesional M1(i-M1) (r = 0.88, p < 0.001) and control group i-M1 (r = 0.71, p = 0.03), It also revealed a distinct positive correlation between ARAT scores and changes in intraregional OxyHb in the robotic group i-M1 (r = 0.92, p < 0.001) and control group i-M1 (r = 0.87, p =  0.002), as shown in Fig. 5(see Fig. 5).Figure 5 The relationships between the ΔHBO of i-M1 and ΔFMA- UE score, and ΔARAT score.A represents the correlation of ΔHBO and ΔFMA-UE score in RG,B represents the correlation of ΔHBO and ΔARAT score in RG,C represents the correlation of ΔHBO and ΔFMA-UE score in CG,D represents the correlation of ΔHBO and ΔARAT score in CG. Discussion The objective of this experiment was to examine the viability of RAT as a treatment and investigate its impact on upper extremity motor deficits and brain functional capacity following subacute stroke. Our results showed that the 4-week RAT program for upper extremity rehab following stroke was acceptable and practical. No subject reported any trouble complying with study therapeutic guidelines, and no serious adverse events took place. Additionally, we showed that RAT enhanced kinematic performance and improved ARAT points over the improvements achieved with conventional therapy; moreover, RAT reduced upper extremity dyskinesia, as evidenced by the FMA-UE points. Finally, the fNIRS assessment revealed substantial improvements in cerebral excitability. The effectiveness of RAT in the rehab of upper extremity locomotor activity after stroke remains somewhat controversial, some studies have shown that RAT is effective, while others have shown that there is no significant difference between RAT and conventional rehabilitation techniques. Our study showed that RAT is beneficial for the rehab of upper extremity locomotor function after stroke. Numerous studies have demonstrated the effectiveness of usage-dependent neuroplasticity rehabilitation programs e.g., constraint-induced movement therapy and robot treatment[29–32]. In this situation, RAT may promote neuroplasticity of brain regions related to upper extremity motor skill learning in patients who are still recovering from a stroke. In terms of the processes leveraged by RAT, the robot aids the user's voluntary movements by producing a potent proprioceptive sensation that is then transmitted to the brain to increase the strength of the upper extremity motor output signals[33]. All of the above studies support the application of RAT in upper extremity motor rehabilitation after stroke. The effectiveness of RAT in the rehab of upper extremity locomotor activity after stroke remains somewhat controversial, some studies have shown that RAT is effective, while others have shown that there is no significant difference between RAT and conventional rehabilitation techniques. Our study showed that RAT is beneficial for the rehab of upper extremity locomotor function after stroke. y Numerous studies have demonstrated the effectiveness of usage-dependent neuroplasticity rehabilitation programs e.g., constraint-induced movement therapy and robot treatment[29–32]. In this situation, RAT may promote neuroplasticity of brain regions related to upper extremity motor skill learning in patients who are still recovering from a stroke. Discussion In terms of the processes leveraged by RAT, the robot aids the user's voluntary movements by producing a potent proprioceptive sensation that is then transmitted to the brain to increase the strength of the upper extremity motor output signals[33]. All of the above studies support the application of RAT in upper extremity motor rehabilitation after stroke. Additionally, correlation analysis demonstrated a substantial link between the OxyHb alterations in the functional network of the i-M1 zone and the status of patients' upper-limb motion capability. This finding suggests that the ipsilesional M1 region in the brain functional network is more active during RAT of the afflicted upper limb in motility-disabled patients. It was proposed that cortical function and structural remodeling related to the lesion and its peripheral tissue[34] are linked to motor improvement in stroke patients. An enlarged i-M1 area has been found to be related with functional recovery of restricted Page 10/19 evoked locomotion of the afflicted upper limb following stroke, according to a prior study[35]. All of the evidence points to the fact that during aided mode RAT, patients with motor dysfunction show dramatically increased involvement of the M1 regions on the ipsilesional side. This result was consistent with earlier studies that indicated that high-intensity upper limb training can increase the activity of the locomotive regions in the ipsilesional hemisphere and strengthen neuroplasticity[36] during the early stages of recovery. Through task-directed training, the upper limb rehab robot can direct the recruitment of the ipsilateral (ipsilateral to the hemiplegic limb) cortex and the expansion of the contralateral (the opposite side of the hemiplegic limb) cortical locomotive area, thereby promoting the functional reorganization of the functional cortex and the functional recovery of the upper limb[37]. Our findings suggest that neuroplasticity is induced by RAT therapy for upper limb locomotor function in stroke patients. Additionally, the current fNIRS results demonstrated greater locomotor cortex activation in the pathological hemisphere, suggesting that RAT treatment may have increased cortical activity in the i-M1 with a considerable advancement in behavioral states in subacute stroke patients. RAT may speed up upper extremity functional recovery compared to traditional rehabilitation, according to some prior research on acute stroke cases[38]; moreover ,the current study may support this explanation. Limitations The study has several limitations. A small sample size was used, and the follow-up period was insufficient. The lack of tracking patients over time means that this study may not accurately represent the effectiveness of RAT for stroke survivors. The timing of the evaluations, which spanned from 25 to 126 days after the stroke, should be noted as this may have influenced the findings because prior research revealed that the quantity of ipsilesional cortico-cortical activity is reportedly distinct between acutely and chronically phases[40]. The study could be enhanced in numerous ways. To determine any differences in rehabilitation results, the sample size might be enlarged and patients could be further separated into subacute and chronic phases, with mid-term assessment and longer term follow-up. Discussion In a randomized controlled trial that did not show a robotic advantage after treatment based on the Functional Independence Measure (FIM)[10], it was argued that it was not possible to tell whether locomotor manifestations improved or independence was due solely to the fact that the sufferers learned to compensate for the handicap because of numerous shortcomings of the FIM[39], including the sequential nature of the measurements, the absence of a particular trials for the limb involved, and the paucity of discrimination. The difference with our experiment is that we found significan t gains in upper extremity motor functionality in poststroke individuals upper extremity motor deficits after RAT compared to controls by considering FMA and ARAT scores. Fundings This work is supported by the Guangzhou Municipal Science and Technology Program [Grant Number 202206010197 (YL)]; National Science Foundation of China [Grant Number 81772438 (YL), 81974357(YL), 82072548 (GX)]; Author Contribution Jiayue Xu: designed the work and let to the submission, acquired data, analyzed data, drafted and revised the manuscript. Cailing Zhang: performed the experiments, analyzed data, edited and reviewed paper. Wanqi Li: curated data, conducted the research and investigation process. Tuo Lin: Managed and coordinated responsibility for the research activity planning and execution. Guiyuan Cai: conducted the research and investigation process or.performing research, methodology. Junbo Jiang: performed the experiments,curated data. Gengbin Chen: performed the data collection. Jialin Chen: recruited participants. Quan Liu: annotated and maintained research data. Guangqing Xu: acquired financial support. Yue Lan:designed research, edited and reviewed paper, acquired financial support. We sincerely thank all the subjects for their support and cooperation in this study We sincerely thank all the subjects for their support and cooperation in this study Conclusion In summary, this preliminary study showed that RAT is helpful for the restoration of upper extremity locomotor function in stroke patients, as evidenced by significantly improved activation of the motor cortex brain network and FMA-UE, and ARAT points of patients with stroke. In this study, fNIRS was used Page 11/19 Page 11/19 to assess variations in OxyHb linked with motor rehabilitation tasks in stroke survivors. Stroke survivors demonstrated greater activation in ipsilateral motor areas than in contralateral motor areas throughout the motor rehabilitation test, demonstrating that stroke survivors have asymmetrical cortical activation patterns. After RAT, OxyHb in the ipsilateral M1 dramatically rose, indicating that stroke patients use plastic restructuring of motor resources to compensate for reduced function during a rehabilitation activities. To obtain an ideal therapeutic effect and exact rehabilitation treatment, RAT plans should be customized in accordance with the brain functional network activation state of the patient. Conflict of Interest Statement: None of the authors have potential conflicts of interest to be disclosed Conflict of Interest Statement: None of the authors have potential conflicts of interest to be disclosed References 1. Wander, J. D., et al. (2013). Distributed cortical adaptation during learning of a brain-computer interface task. Proc Natl Acad Sci U S A, 110(26), 10818–10823. 1. Wander, J. D., et al. (2013). Distributed cortical adaptation during learning of a brain-computer interface task. Proc Natl Acad Sci U S A, 110(26), 10818–10823. 2. Grefkes, C., et al. (2008). Cortical connectivity after subcortical stroke assessed with functional magnetic resonance imaging. Annals Of Neurology, 63(2), 236–246. 2. Grefkes, C., et al. (2008). Cortical connectivity after subcortical stroke assessed with functional magnetic resonance imaging. Annals Of Neurology, 63(2), 236–246. 3. Winstein, C. J., et al. (2016). Guidelines for Adult Stroke Rehabilitation and Recovery: A Guideline for Healthcare Professionals From the American Heart Association/American Stroke Association. Stroke, 47(6), e98–e169. 4. Kwakkel, G., et al. (2003). Probability of regaining dexterity in the flaccid upper limb: impact of severity of paresis and time since onset in acute stroke. Stroke, 34(9), 2181–2186. 4. Kwakkel, G., et al. (2003). Probability of regaining dexterity in the flaccid upper limb: impact of severity of paresis and time since onset in acute stroke. Stroke, 34(9), 2181–2186. 5. Basteris, A., et al. (2014). Training modalities in robot-mediated upper limb rehabilitation in stroke: a framework for classification based on a systematic review. Journal Of Neuroengineering And Rehabilitation, 11, 111. 6. Lo, A. C., et al. (2010). Robot-assisted therapy for long-term upper-limb impairment after stroke. New England Journal Of Medicine, 362(19), 1772–1783. 7. Kwakkel, G., Kollen, B. J., & Krebs, H. I. (2008). Effects of robot-assisted therapy on upper limb recovery after stroke: a systematic review. Neurorehabil Neural Repair, 22(2), 111–121. 8. Sale, P., et al. (2014). Effects of upper limb robot-assisted therapy on motor recovery in subacute stroke patients. Journal Of Neuroengineering And Rehabilitation, 11, 104. 8. Sale, P., et al. (2014). Effects of upper limb robot-assisted therapy on motor recovery in subacute stroke patients. Journal Of Neuroengineering And Rehabilitation, 11, 104. 9. Mazzoleni, S., et al. (2014). Mechanisms of motor recovery in chronic and subacute stroke patients following a robot-aided training. Ieee Transactions On Haptics, 7(2), 175–180. 10. Lum, P. S., et al. (2002). Robot-assisted movement training compared with conventional therapy techniques for the rehabilitation of upper-limb motor function after stroke. Archives Of Physical Medicine And Rehabilitation, 83(7), 952–959. 11. Veerbeek, J. M., et al. (2017). Effects of Robot-Assisted Therapy for the Upper Limb After Stroke. Neurorehabil Neural Repair, 31(2), 107–121. 11. The datasets are available by request from the corresponding author. The datasets are available by request from the corresponding author. The datasets are available by request from the corresponding author. CRediT authorship contribution statement Jiayue Xu: designed the work and let to the submission, acquired data, analyzed data, drafted and revised the manuscript. Guiyuan Cai: performed the experiments, analyzed data, edited and reviewed paper. Wanqi Li: curated data, conducted the research and investigation process. Tuo Lin: Managed and coordinated responsibility for the research activity planning and execution. Cailing Zhang: conducted the research and investigation process or.performing research, methodology. Junbo Jiang: performed the experiments,curated data. Gengbin Chen: performed the data collection. Jialin Chen: recruited participants. Quan Liu: annotated and maintained research data. Guangqing Xu: acquired financial support. Yue Lan:designed research, edited and reviewed paper, acquired financial support. Page 12/19 Data Availability Statement Data Availability Statement Data Availability Statement Page 12/19 References Veerbeek, J. M., et al. (2017). Effects of Robot-Assisted Therapy for the Upper Limb After Stroke. Neurorehabil Neural Repair, 31(2), 107–121. 12. Mehrholz, J. (2018). 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Motor assessment scale for stroke patients: concurrent validity and interrater reliability. Archives Of Physical Medicine And Rehabilitation, 69(3 Pt 1), 195–197. 24. Poole, J. L., & Whitney, S. L. (1988). Motor assessment scale for stroke patients: concurrent validity and interrater reliability. Archives Of Physical Medicine And Rehabilitation, 69(3 Pt 1), 195–197. 25. Sakatani, K., et al. (2006). Changes of cerebral blood oxygenation and optical pathlength during activation and deactivation in the prefrontal cortex measured by time-resolved near infrared spectroscopy. Life Sciences, 78(23), 2734–2741. 25. Sakatani, K., et al. (2006). Changes of cerebral blood oxygenation and optical pathlength during activation and deactivation in the prefrontal cortex measured by time-resolved near infrared spectroscopy. Life Sciences, 78(23), 2734–2741. 26. Scholkmann, F., et al. (2010). How to detect and reduce movement artifacts in near-infrared imaging using moving standard deviation and spline interpolation. Physiological Measurement, 31(5), 649– 662. 26. Scholkmann, F., et al. (2010). How to detect and reduce movement artifacts in near-infrared imaging using moving standard deviation and spline interpolation. Physiological Measurement, 31(5), 649– 662. 27. Anwar, A. R. (2013). Comparison of causality analysis on simultaneously measured fMRI and NIRS signals during motor tasks. Annu Int Conf IEEE Eng Med Biol Soc, 2013: pp. 2628-31. 27. Anwar, A. R. (2013). Comparison of causality analysis on simultaneously measured fMRI and NIRS signals during motor tasks. Annu Int Conf IEEE Eng Med Biol Soc, 2013: pp. 2628-31. 28. Visani, E., et al. (2015). Hemodynamic and EEG Time-Courses During Unilateral Hand Movement in Patients with Cortical Myoclonus. An EEG-fMRI and EEG-TD-fNIRS Study. Brain Topography, 28(6), 915–925. 28. Visani, E., et al. (2015). Hemodynamic and EEG Time-Courses During Unilateral Hand Movement in Patients with Cortical Myoclonus. An EEG-fMRI and EEG-TD-fNIRS Study. Brain Topography, 28(6), 915–925. Page 14/19 29. Takebayashi, T., et al. (2015). A one-year follow-up after modified constraint-induced movement therapy for chronic stroke patients with paretic arm: a prospective case series study. Topics In Stroke Rehabilitation, 22(1), 18–25. 30. Taub, E., Uswatte, G., & Elbert, T. (2002). New treatments in neurorehabilitation founded on basic research. Nature Reviews Neuroscience, 3(3), 228–236. 31. Wahl, A. S., & Schwab, M. E. (2014). Finding an optimal rehabilitation paradigm after stroke: enhancing fiber growth and training of the brain at the right moment. Frontiers In Human Neuroscience, 8, 381. 32. Wolf, S. L., et al. (2008). References Retention of upper limb function in stroke survivors who have received constraint-induced movement therapy: the EXCITE randomised trial. Lancet Neurology, 7(1), 33–40. 33. Morishita, T., & Inoue, T. (2016). Interactive Bio-feedback Therapy Using Hybrid Assistive Limbs for Motor Recovery after Stroke: Current Practice and Future Perspectives. Neurol Med Chir (Tokyo), 56(10), 605–612. 34. Buch, E. R., et al. (2016). Predicting motor improvement after stroke with clinical assessment and diffusion tensor imaging. Neurology, 86(20), 1924–1925. 34. Buch, E. R., et al. (2016). Predicting motor improvement after stroke with clinical assessment and diffusion tensor imaging. Neurology, 86(20), 1924–1925. 35. Sawaki, L., et al. (2008). Constraint-induced movement therapy results in increased motor map area in subjects 3 to 9 months after stroke. Neurorehabil Neural Repair, 22(5), 505–513. 35. Sawaki, L., et al. (2008). Constraint-induced movement therapy results in increased motor map area in subjects 3 to 9 months after stroke. Neurorehabil Neural Repair, 22(5), 505–513. 36. Zhang, C., Li-Tsang, C. W., & Au, R. K. (2017). Robotic approaches for the rehabilitation of upper limb recovery after stroke: a systematic review and meta-analysis. International Journal Of Rehabilitation Research, 40(1), 19–28. 37. Singh, N., et al. (2021). Evidence of neuroplasticity with robotic hand exoskeleton for post-stroke rehabilitation: a randomized controlled trial. Journal Of Neuroengineering And Rehabilitation, 18(1), 76. 38. Fukuda, H., et al. (2016). Tailor-made rehabilitation approach using multiple types of hybrid assistive limb robots for acute stroke patients: A pilot study. Assistive Technology : The Official Journal Of Resna, 28(1), 53–56. 39. Daly, J. J., et al. (2005). Response to upper-limb robotics and functional neuromuscular stimulation following stroke. Journal Of Rehabilitation Research And Development, 42(6), 723–736. 39. Daly, J. J., et al. (2005). Response to upper-limb robotics and functional neuromuscular stimulation following stroke. Journal Of Rehabilitation Research And Development, 42(6), 723–736. 40. Ward, N. S., et al. (2003). Neural correlates of motor recovery after stroke: a longitudinal fMRI study. Brain, 126(Pt 11), 2476–2496. 40. Ward, N. S., et al. (2003). Neural correlates of motor recovery after stroke: a longitudinal fMRI study. Brain, 126(Pt 11), 2476–2496. Figures Page 15/19 Figure 1 Figure 2 Fnirs multichannael configurations in 10–20 systems and associated brain areas of interest.A represents the serial number and distribution of channels and B represents the distribution of brain Figure 2 Figure 2 Fnirs multichannael configurations in 10–20 systems and associated brain areas of interest.A represents the serial number and distribution of channels and B represents the distribution of brain Page 16/19 Page 16/19 regions.cluster{1} = [1 2 48]cluster{2} = [3 18 20 34 35];cluster{3} = [4 19];cluster{4} = [5 6 7 22];cluster{5} = [44 45];cluster{6} = [1617];cluster{7} = [31 33 46 47 50];cluster{8} = [30 32];cluster{9} = [51];cluster{10} = [42 43 58 59];cluster{11} = [13 52];cluster{12} = [11 24 25 29 39];cluster{13} = [12 26];cluster{14} = [8 9 10 23];cluster{15} = [14 15];cluster{16} = [53 56];cluster{17} = [27 36 38 40];cluster{18} = [28 54 55 57];cluster{19} = [37 41];cluster{20} = [60 61 62 63]. regions.cluster{1} = [1 2 48]cluster{2} = [3 18 20 34 35];cluster{3} = [4 19];cluster{4} = [5 6 7 22];cluster{5} = [44 45];cluster{6} = [1617];cluster{7} = [31 33 46 47 50];cluster{8} = [30 32];cluster{9} = [51];cluster{10} = [42 43 58 59];cluster{11} = [13 52];cluster{12} = [11 24 25 29 39];cluster{13} = [12 26];cluster{14} = [8 9 10 23];cluster{15} = [14 15];cluster{16} = [53 56];cluster{17} = [27 36 38 40];cluster{18} = [28 54 55 57];cluster{19} = [37 41];cluster{20} = [60 61 62 63]. Figure 3 Page 17/19 Figure 3 Figure 3 Figure 3 Page 17/19 FMA-UE:Fugl-Meyer assessment for upper-extremity; ARAT: Action Research Arm Test; RAT: Robot- assisted treatment; RG:Robotic group; CG:Control group; *p<0.05. A indicates the change in FMA-UE of RG and CG before and after treatment. B indicates the change in ARAT of RG and CG before and after treatment. treatment. Figure 4 The blood oxygen concentration in the brain changes before and after training, the redder the color means the higher the blood oxygen concentration. The graph shows that the blood oxygen concentration in the primary motor cortex of the affected hemisphere increased significantly after robot training, but there was no significant change in the control group.i:ipsilesional;c:contralesional. A indicates the change in OxyHb of RG before and after treatment. B indicates the change in OxyHb of CG before and after treatment. Figure 4 The blood oxygen concentration in the brain changes before and after training, the redder the color means the higher the blood oxygen concentration. The graph shows that the blood oxygen concentration in the primary motor cortex of the affected hemisphere increased significantly after robot training, but there was no significant change in the control group.i:ipsilesional;c:contralesional. A indicates the change in OxyHb of RG before and after treatment. B indicates the change in OxyHb of CG before and after treatment. The blood oxygen concentration in the brain changes before and after training, the redder the color means the higher the blood oxygen concentration. The graph shows that the blood oxygen concentration in the primary motor cortex of the affected hemisphere increased significantly after robot training, but there was no significant change in the control group.i:ipsilesional;c:contralesional. A indicates the change in OxyHb of RG before and after treatment. B indicates the change in OxyHb of CG before and after treatment. Page 18/19 igure 5 The relationships between the ΔHBO of i-M1 and ΔFMA-UE score, and ΔARAT score.A represents the orrelation of ΔHBO and ΔFMA-UE score in RG,B represents the correlation of ΔHBO and ΔARAT score RG,C represents the correlation of ΔHBO and ΔFMA-UE score in CG,D represents the correlation of ΔHB nd ΔARAT score in CG. Figure 5 The relationships between the ΔHBO of i-M1 and ΔFMA-UE score, and ΔARAT score.A represents the correlation of ΔHBO and ΔFMA-UE score in RG,B represents the correlation of ΔHBO and ΔARAT score in RG,C represents the correlation of ΔHBO and ΔFMA-UE score in CG,D represents the correlation of ΔHBO and ΔARAT score in CG. Page 19/19
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Supplementary Figure S3 from [&lt;sup&gt;89&lt;/sup&gt;Zr]Zr-DFO-girentuximab and [&lt;sup&gt;18&lt;/sup&gt;F]FDG PET/CT to Predict Watchful Waiting Duration in Patients with Metastatic Clear-cell Renal Cell Carcinoma
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Comparison of next-generation sequencing samples using compression-based distances and its application to phylogenetic reconstruction
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RESEARCH ARTICLE Open Access © 2014 Tran and Chen; 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/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. Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 *Correspondence: nhtran@ntu.edu.sg School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore Abstract Background: Enormous volumes of short read data from next-generation sequencing (NGS) technologies have posed new challenges to the area of genomic sequence comparison. The multiple sequence alignment approach is hardly applicable to NGS data due to the challenging problem of short read assembly. Thus alignment-free methods are needed for the comparison of NGS samples of short reads. Results: Recently several k-mer based distance measures such as CVTree, dS 2, and co-phylog have been proposed or enhanced to address this problem. However, how to choose an optimal k value for those distance measures is not trivial since it may depend on different aspects of the sequence data. In this paper, we considered an alternative parameter-free approach: compression-based distance measures. These measures have shown good performance for the comparison of long genomic sequences, but they have not yet been tested on NGS short reads. Hence, we performed extensive validation in this study and showed that the compression-based distances are highly consistent with those distances obtained from the k-mer based methods, from the multiple sequence alignment approach, and from existing benchmarks in the literature. Moreover, as the compression-based distance measures are parameter-free, no parameter optimization is required and these measures still perform consistently well on multiple types of sequence data, for different kinds of species and taxonomy levels. g , p parameter-free, no parameter optimization is required and these measures still perform consistently well on multiple types of sequence data, for different kinds of species and taxonomy levels. Conclusions: The compression-based distance measures are assembly-free, alignment-free, parameter-free, and thus represent useful tools for the comparison of long genomic sequences as well as the comparison of NGS samples of short reads. Keywords: Alignment-free sequence comparison, Sequence distance, Sequence compression, Next-generation sequencing Ngoc Hieu Tran* and Xin Chen Ngoc Hieu Tran* and Xin Chen Background Sequence distance measures are often applied to compare long genomic sequences such as 16S rRNA sequences, mtDNA sequences, gene encoding sequences, or even whole genome sequences [2-4]. The obtained distances are then used for sequence clustering and classification, for phylogenetic tree reconstruction, for inference of the evolution and relationship of species, etc. Recent advances in next-generation sequencing (NGS) technologies have produced massive amounts of short read data, bringing up promising opportunities in many biomedical research areas such as RNA-seq, ChIP- seq, de novo whole genome sequencing, metagenome sequencing, etc [1]. The short read data also poses new challenges to the field of genomic sequence anal- ysis, including the problem of sequence comparison. However, with the development of NGS technologies, a new type of sequence data emerges: NGS short reads are orders of magnitudes shorter than long genomic sequences while being generated at unprecedented high throughput. Hence, it is highly desirable to go beyond the Page 2 of 13 Page 2 of 13 Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 have been successfully applied to many clustering and classification problems with data of various types, includ- ing DNA sequences, texts and languages, time series, images, sound, video [16-19,21,22]. However, they have not been tested on NGS short reads yet. comparison of long genomic sequences to develop new methods for the comparison of NGS samples of millions of short reads [5]. The multiple sequence alignment (MSA) approach is hardly applicable to large data sets of NGS short reads due to its prohibitive computational cost and the chal- lenging problem of short read assembly, especially for species without any reference genomes (de novo assem- bly). Alignment-free methods [4] could overcome these limitations of the alignment-based approach. They are assembly-free and scalable to large data sets. Most exist- ing alignment-free methods use k-mers (k-tuples or k-words) as sequence signatures to measure sequence distances [6-10]. Markov models were also proposed for DNA sequence comparison [11], and could be incorpo- rated with k-mer distributions to achieve more accurate distances [12,13]. y In this study we demonstrate that the compression- based distance measures can be successfully applied not only to long genomic sequences (including 16S rRNA, mtDNA, and whole genome sequences) but also to NGS samples of short reads. Background Extensive validation was conducted to assess the accuracy of the compression- based and k-mer based distances on four data sets: 29 mammalian mtDNA sequences, 29 Escherichia/Shigella genomes, 70 Gammaproteobacteria genomes, and 39 mammalian gut metagenomic samples. The data sets include various types of genomic sequences, in silico and real NGS short reads, different species and taxonomy levels. The validation results show that the compression- based distances are highly consistent with those distances obtained from the k-mer based methods, from the MSA approach, and from existing benchmarks in the litera- ture. Our results also show that the k-mer based distance measures depend critically on the choice of k, and the optimal k varies across different data sets. In contrast, the compression-based distance measures are parameter-free and thus perform consistently well on all data sets without any optimization of parameters. The details are presented in the following sections. Recently several studies have further refined existing techniques or developed new ones for better applications to NGS short read data. In particular, the following three measures have shown impressive performance on both NGS short reads and long genomic sequences: CVTree [6,7], dS 2 [14,15] and co-phylog [10]. For a given k, CVTree and dS 2 measure the distance between two NGS samples (or two DNA sequences) based on the normalized k-mer frequencies. co-phylog, on the other hand, computes the distance from the average nucleotide substitution rate in the observed k-mers. The k-mer based measures, however, depend consider- ably on the parameter k. A non-optimal choice of k could lead to a dramatically worse result in some cases. In gen- eral, a larger value of k allows the measures to use more parameters to better capture the full characteristics of the input sequences (or NGS samples). However, there might not be sufficient data available for an accurate estimation of a large number of parameters. Moreover, the optimal k value may depend on the types of sequence data, the species of interest, and even the taxonomy level. When the measures are applied to NGS data, we need to consider even more factors such as the NGS platform, the sequenc- ing depth, the read length, etc. Thus, how to choose an optimal k is a very challenging task. Data sets We examined the above six alignment-free distance mea- sures dNCD, d, dCDM, CVTree, dS 2, and co-phylog on both NGS short reads and long genomic sequences (including 16S rRNA, mtDNA, and whole genome sequences). The sequences and short reads were retrieved or simulated from four data sets: 29 mammalian mtDNA sequences [13,17,19,24], 29 Escherichia/Shigella genomes [10], 70 Gammaproteobacteria genomes [10], and 39 metage- nomic mammalian gut samples [14,25]. The authors further refined the distance d and proposed the following in [17] which they referred to as normalized compression-based distance (NCD): dNCD(x, y) = max{C(x|y), C(y|x)} max{C(x), C(y)} . (3) (3) Moreover, they have shown that the dNCD distance is a proper metric, satisfying the non-negativity, identity, symmetry, and triangle inequality axioms. Readers are referred to [16,17,19,20] for more formal theory about sequence complexity, compression and distance metrics. The tool MetaSim [26] was used to simulate short reads from genomic sequences. It offers four error models: 454, Sanger, Empirical (Illumina), and Exact, corresponding to three different NGS platforms and the non-error case, respectively. We set the read length to be 100 and used default settings for other parameters. Short reads were simulated at four sampling depths: 1×, 5×, 10×, and 30×. For applications to real NGS data sets, we recommend that the sequencing coverage should be 5× or higher. In order to ensure a fair comparison, it is also desirable that the samples are produced from the same NGS platforms, with similar experimental conditions, sequencing cover- age, read lengths, etc. Strictly identical numbers of reads or identical read lengths, however, are not necessary. For example, the real NGS data set of 39 metagenomic sam- ples analyzed in our study was produced from the 454 FLX platform, with a total of 2,163,286 reads (an aver- age of 55,469 ± 28,724 (standard deviation, SD) reads per sample, 261 ± 83 nucleotides per read) [25]. The tool MetaSim [26] was used to simulate short reads from genomic sequences. It offers four error models: 454, Sanger, Empirical (Illumina), and Exact, corresponding to three different NGS platforms and the non-error case, respectively. We set the read length to be 100 and used default settings for other parameters. Short reads were simulated at four sampling depths: 1×, 5×, 10×, and 30×. q p y p In principle, any sequence compression tool can be used to compute the above distances. Compression-based distance measures Let x and y denote the two sequences (or NGS samples) to be compared and xy denote their concatenation. Let C(x) denote the size (that is, the number of bytes) of x after being compressed by a sequence compression tool. Data compression is aimed at reducing as much redundant information in the given data as possible. Hence, if x and y share similar patterns, compressing them together should use less storage space than compressing them separately, that is, C(xy) ≤C(x) + C(y). Specifically, if x and y are identical, one could expect that C(xy) ≃C(x) = C(y). On the other hand, if x and y share no information, one could expect that C(xy) ≃C(x)+C(y). These observations sug- gest that one could measure the similarity/dissimilarity between x and y based on their compressed sizes. In this paper, we consider an alternative parameter-free approach: compression-based distance measures [16-18]. Roughly speaking, data compression is aimed at reducing as much redundant information in the given data as pos- sible. Hence, if two NGS samples share similar patterns, compressing them together should be more efficient, that is, should use less storage space, than compressing them separately. The distance between the two NGS samples can then be calculated based on the sizes of the reduced storage space. Readers are referred to [16,17,19,20] for more formal theory about sequence complexity, compres- sion and distance metrics. Compression-based distances In particular, the following distance measure called compression-based dissimilarity measure (CDM) was proposed in [18]: dCDM(x, y) = C(xy) C(x) + C(y). (1) (1) This dCDM distance ranges from 1 2 (when x and y are identical) to 1 (when x and y share no information). This dCDM distance ranges from 1 2 (when x and y are identical) to 1 (when x and y share no information). Page 3 of 13 Page 3 of 13 Page 3 of 13 Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 A more mathematically precise distance was proposed in [16] using the notation of conditional compression: We used the implementations provided by the authors. The tools CVTree and dS 2 have options to input the param- eter k. For CVTree, we tried k from 3 to 32 as allowed by the tool. Compression-based distance measures For dS 2, we were not able to run it for k > 9 due to some “segmentation fault” error, which seems to be a problem of handling dynamic memory in the tool. There is no input option for co-phylog, thus we simply used its default settings. d(x, y) = C(x|y) + C(y|x) C(xy) . (2) (2) Here C(x|y) denotes the compressed size of sequence x conditioning on sequence y. C(x|y) ≃0 indicates that x and y are identical, while C(x|y) ≃C(x) indicates that x and y share no information and thus they are expected to be independent sequences. This distance ranges from 0 to 1 and satisfies the triangle inequality [16]. Data sets More efficient compres- sion should lead to more accurate distance estimates, but may require longer compression time. In this study, we used the tool GenCompress [23] since it can per- form conditional compression on x|y. We used the same compression tool for both long genomic sequences and NGS short reads to ensure a consistent and fair compari- son. When applying GenCompress to an NGS sample, we first concatenated all short reads together to form a sin- gle sequence and then compressed it. Our experiment results show that the compression-based distances are quite robust against different orders of concatenating the short reads. For applications to real NGS data sets, we recommend that the sequencing coverage should be 5× or higher. In order to ensure a fair comparison, it is also desirable that the samples are produced from the same NGS platforms, with similar experimental conditions, sequencing cover- age, read lengths, etc. Strictly identical numbers of reads or identical read lengths, however, are not necessary. For example, the real NGS data set of 39 metagenomic sam- ples analyzed in our study was produced from the 454 FLX platform, with a total of 2,163,286 reads (an aver- age of 55,469 ± 28,724 (standard deviation, SD) reads per sample, 261 ± 83 nucleotides per read) [25]. Accuracy assessment One possible explanation is that co-phylog may be only suitable for closely related species, as the authors mentioned in [10]. We also noted that the CVTree and dS 2 distances varied remarkably with respect to k (Additional file 1: Table S2). For instance, the smallest symmetric difference between the CVTree tree and the MSA tree is 6 (k = 10), but the largest is up to 48 (k = 16, 17). Similarly, the highest cor- relation between the dS 2 distance and the MSA distance is 0.88 (k = 8), but the lowest is down to 0.41 (k = 3). We also assessed the alignment-free distances by exam- ining their corresponding phylogenetic trees. For each distance matrix, the tool neighbor in the package PHYLIP was used to construct a phylogenetic tree using the neighbor joining method [29]. Subsequently, the tool treedist in the package PHYLIP was used to calculate the symmetric difference [30] between the resulting tree from each alignment-free distance and the corresponding MSA/benchmark tree. Each internal node in a phyloge- netic tree corresponds to a subset of clustered leaf nodes. Given two phylogenetic trees with the same set of leaf nodes, the symmetric difference between them is the number of internal nodes that are present in one tree but not in the other. Finally, to assess the clustering and classification abil- ity of the alignment-free distances, we used the parsi- mony score to measure how different a clustering tree is from the true classification (using tools TreeClimber [31], mothur [32]). The parsimony score of a clustering tree is calculated by the tool TreeClimber as follows. First, the parsimony score is set to 0 and the leaf nodes are labeled according to their groups in the true classifica- tion. The algorithm traverses from the leaf nodes to the root and determine the labels of the internal nodes. The labels of each internal node depend on the labels of its two immediate child nodes. If they share common labels then these common labels are assigned to the internal node. If the two child nodes share no label, a penalty of 1 is added to the parsimony score and the internal node is assigned with the union of the label sets of its two child nodes. If a clustering tree is perfect, its parsimony score is equal to the number of groups in the true clas- sification minus one. Accuracy assessment In this study, we considered three k-mer based distance measures: CVTree [6,7], dS 2 [14,15] and co-phylog [10]. Given two DNA sequences (or two NGS samples), CVTree measures the correlation distance between their com- position vectors, where each composition vector is the collection of the normalized frequencies of k-mers. The dS 2 distance is an NGS-extension of the D2, D∗ 2, and DS 2 statistics which were proposed in [8,9] for the comparison of long genomic sequences. The main difference between dS 2 and CVTree lies in the normalization of the frequencies of k-mers. The co-phylog distance is also based on k-mers but not in the frequency context. It measures the distance as the average nucleotide substitution rate in the observed k-mers of the two sequences (or samples). To assess the accuracy of the alignment-free distances, we compared them with those obtained from the MSA approach if applicable and with existing benchmarks in the literature. The tool Clustal Omega [27] was used to perform MSA and then the tool dnadist in the package PHYLIP [28] was used to calculate the distance matrix from the MSA. Following [10,14], we used distance correlation, tree symmetric difference, and parsimony score to measure the accuracy of the alignment-free distances. In particular, we computed the correlation between each alignment-free distance and the MSA/benchmark distance to evaluate their consistency. The correlation between two distance matrices was calculated as follows. We first converted Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 Page 4 of 13 Page 4 of 13 each matrix into a single vector by concatenating all of its rows side by side and then calculated the Pearson correlation between the two vectors. Performance on mtDNA sequences Performance on mtDNA sequences First, we applied the six alignment-free distance measures dNCD, d, dCDM, CVTree, dS 2, co-phylog to the mtDNA sequences and compared the results with those obtained from the MSA method and from existing benchmarks. Additional file 1: Table S1 shows that both compression- based distances dNCD, d, dCDM and k-mer based distances CVTree, dS 2 (for optimal choices of k) are in good agree- ment with the MSA distance. The dS 2 distance has the highest correlation with the MSA distance, whereas the CVTree tree has the smallest symmetric difference from the MSA tree. The compression-based distances, lead- ing by dCDM, performed slightly worse. The co-phylog measure, however, failed for this data set. Accuracy assessment The higher the parsimony score is, the more different the clustering tree is from the true classification. ( ) ( ) The MSA tree (Additional file 2: Figure S1a) is highly consistent with existing benchmarks in the literature [13,17,19,24]. In particular, the MSA tree is nearly iden- tical to those reported in [13,19], except for two minor differences in the branches of dog, cat and the branches of non-murid rodents (fat dormouse, squirrel, guinea pig). Additional file 2: Figures S1a and S1b show that the main difference between the MSA tree and the dCDM tree also lies in the group Rodents. In addition, the dCDM tree indi- cates that pig is closer to cow and sheep than to other species in the group Ferungulates. The branches of dog, cat in the dCDM tree are slightly different from those in the MSA tree, but consistent with previously reported trees in [13,19]. The trees reported by CVTree and dS 2 (Additional file 2: Figures S1c and S1d, respectively) also show differ- ent results for the group Rodents. The phylogeny of the group Rodents is actually still a controversial question, as mentioned in previous studies [13,19]. The position of the cluster of dog, cat, and seals in the group Ferungulates reported by CVTree is not consistent with the other trees and the benchmarks. Overall, all four trees support the hypothesis of (Rodents, (Ferungulates, Primates)), as sug- gested in [13,17,19,24], and have identical phylogeny of the group Primates. The main differences among them include the phylogeny of the group Rodents, the positions of pig and hippo, and the subtree of dog, cat and seals in the group Ferungulates. The tool TreeGraph 2 [33] was used to plot phylogenetic trees. Results and discussion Alignment-free comparison of mammalian mtDNA sequences or their NGS short reads reconfirms the hypothesis (Rodents, (Ferungulates, Primates)) Alignment-free comparison of mammalian mtDNA sequences or their NGS short reads reconfirms the hypothesis (Rodents, (Ferungulates, Primates)) One of the key advantages of the alignment-free distance measures over the alignment-based approach is their scal- ability to large data sets of whole genome sequences or NGS short reads. However, in this section we first want to assess their accuracy on a small, but very well- studied data set of 29 mammalian mtDNA sequences. This data set has been widely used for validation in exist- ing literatures and hence reliable benchmarks are available [13,17,19,24]. Performance on NGS short reads Next, we ask if similar results could be obtained from the comparison of NGS samples of short reads. We used Page 5 of 13 Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 the tool MetaSim [26] to simulate short reads from the mtDNA sequences with four error models 454, Exact, Empirical (Illumina), Sanger, and four different sampling depths 1×, 5×, 10×, and 30×. The read length was set at 100 bp. We used k = 10 for the CVTree distance and k = 8 for the dS 2 distance as suggested by their optimal perfor- mance on the mtDNA sequences in the previous section. Since the MSA method is difficult to apply to NGS short reads, we still kept the MSA distance and tree obtained from the mtDNA sequences as benchmark. At the 1× sampling depth, we found that the alignment-free results were considerably different from the MSA benchmark due to the low coverage. However, at the 5× sampling depth, all five measures dNCD, d, dCDM, CVTree, and dS 2 produced comparably accurate results as when they were applied to the mtDNA sequences. Further increasing the sampling depth to 10× and 30× did not significantly improve the accuracy of the distances. identical to the MSA tree (Additional file 2: Figure S1a) and existing benchmarks in the literature [13,17,19,24], supporting the hypothesis (Rodents, (Ferungulates, Primates)). The dS 2 tree, however, has more inconsistent branches in the group Ferungulates, although it has the highest cor- relation with the MSA distance. Last but not least, we also noted that the alignment-free results obtained from the simulated NGS short reads were consistent with their corresponding counterparts obtained from the mtDNA sequences in the previous section, especially for the non- error (Exact) model (Table 2). When applying GenCompress to an NGS sample, we concatenated all short reads of the sample to form a sin- gle sequence and then compressed it. Hence, it is also important to examine if the compression-based distances are robust against different ways of concatenation. We repeated the experiment with the Empirical (Illumina) samples for 10 different runs in each of which the reads from each sample were concatenated in a random order. Additional file 1: Table S8a shows that the compression- based distances obtained from those runs are highly consistent with each other. Performance on NGS short reads We also compared those dis- tances with the MSA distance and the performance results (Additional file 1: Table S8b) are similar to those reported earlier in Table 1. Table 1 summarizes the results for the 5× sampling depth, similar results for 1×, 10×, and 30× can be found in Additional file 1: Table S2. We highlighted in boldface both the best and the second best of the tree symmet- ric difference and the distance correlation for each error model because they are usually not very different. As shown in Table 1, the dS 2 distance achieved the highest cor- relation with the MSA distance, followed by the CVTree distance. In summary, we have shown that all five alignment- free distance measures dNCD, d, dCDM, CVTree, and dS 2 can be successfully applied to both mtDNA sequences and their NGS short reads. The distances obtained from the NGS short reads were consistent with those obtained from the mtDNA sequences, and they were all in good agreement with the MSA distance as well as with exist- ing benchmarks in the literature. The compression-based measures dNCD, d and dCDM produced comparably accu- rate distances as those optimal results obtained from the k-mer based measures CVTree and dS 2. The compression- based distances were also shown to be quite robust against different concatenations of short reads. In terms of the symmetric difference from the MSA tree, the dCDM distance performed consistently well for all four error models, followed by the dS 2 and dNCD distances. Figure 1 shows the phylogenetic trees recon- structed from the dCDM, CVTree, and dS 2 distances for the NGS short reads simulated using the Empirical (Illumina) error model. The dCDM and CVTree trees are almost Table 1 Comparison of the alignment-free distances and the MSA distance for NGS short reads of the mtDNA sequences dNCD d dCDM CVTree (k = 10) dS 2(k = 8) 454 14 16 10 10 6 Exact 8 8 8 8 8 Empirical 6 8 4 8 12 Sanger 10 14 8 14 8 454 0.68 0.66 0.68 0.75 0.88 Exact 0.69 0.68 0.68 0.71 0.88 Empirical 0.69 0.69 0.66 0.69 0.81 Sanger 0.67 0.67 0.65 0.74 0.87 The short reads were simulated from the mtDNA sequences using four error models 454, Exact, Empirical, and Sanger of the tool MetaSim at 5× sampling depth. Performance on NGS short reads The two smallest tree symmetric differences and the two highest distance correlation coefficients for each error model are highlighted in boldface. Similar results for 1×, 10×, and 30× sampling depths can be found in Additional file 1: Table S2. Table 1 Comparison of the alignment-free distances and the MSA distance for NGS short reads of the mtDNA sequences The CVTree and dS 2 distances varied remarkably with respect to k, and the optimal k was selected according to the MSA benchmark. This may pose a challenging problem when there is no benchmark available for vali- dation. In contrast, the compression-based measures are parameter-free and hence no optimization of any param- eter is required. Phylogeny of closely related Escherichia/Shigella genomes In this section we assess the accuracy of the alignment- free distances on a data set of 29 Escherichia/Shigella genomes. Two main differences between this data set and the previous one are: (i) it consists of whole genome sequences and (ii) the species are closely related bacte- ria in the genus Escherichia and the genus Shigella. This Page 6 of 13 Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 Figure 1 Phylogenetic trees reconstructed from NGS short reads of 29 mtDNA sequences using: (A) dCDM, (B) CVTree (k = 10), (C) dS 2(k = 8). The short reads were simulated from the tool MetaSim using the Empirical model and 5× sampling depth. The group of three species platypus, opossum, and wallaroo was used as the outgroup to root the tree. Figure 1 Phylogenetic trees reconstructed from NGS short reads of 29 mtDNA sequences using: (A) dCDM, (B) CVTree (k = 10), (C) dS 2(k = 8). The short reads were simulated from the tool MetaSim using the Empirical model and 5× sampling depth. The group of three species platypus, opossum, and wallaroo was used as the outgroup to root the tree. the co-phylog measure. Table 3 shows that the dCDM dis- tance performed the best in terms of both tree symmetric difference and distance correlation. The results of dNCD and d are also better than the best results of CVTree and dS 2, especially with the remarkably high correlation with the benchmark co-phylog distance. The dS 2 distance failed for this data set and its correlation with the benchmark co-phylog distance is much lower than that of the other measures. Table 2 Comparison of the phylogenetic trees reconstructed from the mtDNA sequences and from their NGS short reads Table 2 Comparison of the phylogenetic trees reconstructed from the mtDNA sequences and from their NGS short reads p p y g reconstructed from the mtDNA sequences and from their NGS short reads dNCD d dCDM CVTree (k = 10) dS 2(k = 8) 454 10 14 8 8 4 Exact 2 0 4 2 2 Empirical 8 6 6 6 10 Sanger 12 10 8 10 8 The short reads were simulated from the mtDNA sequences using four error models 454, Exact, Empirical, and Sanger of the tool MetaSim at 5× sampling depth. The two smallest tree symmetric differences for each error model are highlighted in boldface. Similar results for 1×, 10×, and 30× sampling depths can be found in Additional file 1: Table S2. dNCD d dCDM CVTree (k = 10) dS 2(k = 8) 454 10 14 8 8 4 Exact 2 0 4 2 2 Empirical 8 6 6 6 10 Sanger 12 10 8 10 8 Performance on whole genome sequences g q We first applied the five measures dNCD, d, dCDM, CVTree, and dS 2 to the whole genome sequences and compared the results with the benchmark obtained from Performance on NGS short reads The phylogenetic trees produced by the CVTree distance are inconsistent for different values of k: it is not clear whether the genus Shigella violates the mono- phyleticity of the genus Escherichia (k = 15) or the mono- phyleticity of the E.coli strains (k = 9, 21) (Additional file 2: Figure S2). This was also mentioned previously in [10]. data set has been studied previously in [10,34] and the authors have shown that the co-phylog distance was highly consistent with the MSA distance in terms of both tree symmetric difference and distance correlation. Hence, to avoid the time-consuming MSA, we used the co-phylog distance as benchmark. Performance on NGS short reads Next, we tested the measures on the data sets of NGS short reads which were simulated from the whole genome sequences. We used MetaSim with four error models and different sampling depths as described earlier. Interest- ingly, even at the lowest 1× sampling depth, we already obtained accurate results from the three compression- based distances dNCD, d, and dCDM. Figure 2 shows the case of the dCDM distance in which the phylogenetic tree The short reads were simulated from the mtDNA sequences using four error models 454, Exact, Empirical, and Sanger of the tool MetaSim at 5× sampling depth. The two smallest tree symmetric differences for each error model are highlighted in boldface. Similar results for 1×, 10×, and 30× sampling depths can be found in Additional file 1: Table S2. Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 Page 7 of 13 Table 3 Comparison of the alignment-free distances and the benchmark co-phylog distance for 29 Escherichia/Shigella genomes dNCD d dCDM CVTree (k = 9) CVTree (k = 15) CVTree (k = 21) dS 2(k = 8) Symmetric difference 16 14 12 20 20 16 24 Distance correlation 0.97 0.95 0.99 0.80 0.79 0.80 0.20 The two smallest tree symmetric differences and the two highest correlation coefficients are highlighted in boldface. Table 3 Comparison of the alignment-free distances and the benchmark co-phylog distance for 29 Escherichia/Shigella genomes dNCD d dCDM CVTree (k = 9) CVTree (k = 15) CVTree (k = 21) dS 2(k = 8) Symmetric difference 16 14 12 20 20 16 24 Distance correlation 0.97 0.95 0.99 0.80 0.79 0.80 0.20 The two smallest tree symmetric differences and the two highest correlation coefficients are highlighted in boldface. Table 3 Comparison of the alignment-free distances and the benchmark co-phylog distance for 29 Escherichia/Shigella genomes dNCD d dCDM CVTree (k = 9) CVTree (k = 15) CVTree (k = 21) dS 2(k = 8) Symmetric difference 16 14 12 20 20 16 24 Distance correlation 0.97 0.95 0.99 0.80 0.79 0.80 0.20 The two smallest tree symmetric differences and the two highest correlation coefficients are highlighted in boldface. In summary, the compression-based distances dNCD, d, and dCDM were consistent with the benchmark co-phylog distance on both types of data, whole genome sequences and NGS short reads of 29 Escherichia/Shigella bacte- ria. Performance on NGS short reads They outperformed the two k-mer based distances CVTree and dS 2, which either failed or produced incon- sistent results for different values of k. The results in this section further emphasize the wide applicability and the consistency of the compression-based distances. They represent useful measures for accurate comparison of dif- ferent types of long genomic sequences and NGS short read data, for both mammalian and bacteria species. reconstructed from the NGS short reads (Exact model) is almost identical to the tree reconstructed from the whole genome sequences. Moreover, both trees are very similar to the benchmark co-phylog tree. The main difference is that in the benchmark co-phylog tree the group of S.boydii and S.sonnei is clustered with E.coli first, whereas in the dCDM trees this group is clustered with S.flexneri first. Table 4 clearly shows that the compression-based dis- tances dNCD, d, and dCDM outperformed the CVTree and dS 2 distances for all NGS data sets, in terms of both tree symmetric difference and distance correlation. We also noted that while the results of the compression- based distances for the whole genome sequences (Table 3) and for the NGS short reads (Table 4) were comparable, the performance of the CVTree and dS 2 distances became worse when they were applied to the NGS short reads. Similar results for the NGS data sets obtained from the 5× sampling depth can be found in Additional file 1: Table S3. Classification of 70 genomes in the class Gammaproteobacteria into their correct orders Table 4 Comparison of the alignment-free distances and the benchmark co-phylog distance for NGS short reads of 29 Escherichia/Shigella genomes son of the alignment-free distances and the benchmark co-phylog distance for NGS short reads of 2 ella genomes Table 4 Comparison of the alignment-free distances and the benchmark co-phylog distance for N Escherichia/Shigella genomes n of the alignment-free distances and the benchmark co-phylog distance for NGS short reads of 29 e Escherichia/Shigella genomes using four error models 454, Exact, Empirical, and Sanger of the tool MetaSim at 1× sampling differences and the two highest correlation coefficients for each error model are highlighted in boldface. Similar results for 5× nal file 1: Table S3. The short reads were simulated from the Escherichia/Shigella genomes using four error models 454, Exact, Empirical, and Sanger of the tool MetaSim at 1× sampling depth. The two smallest tree symmetric differences and the two highest correlation coefficients for each error model are highlighted in boldface. Similar results for 5× sampling depth can be found in Additional file 1: Table S3. 16S rRNA sequences. Table 5 shows that the alignment- free distances are highly correlated with the MSA dis- tance and they all have similar parsimony scores (17-18), except for the co-phylog distance. Overall, the dNCD dis- tance performed slightly better than the others in terms of parsimony score, tree symmetric difference, and dis- tance correlation. Its clustering tree in Figure 3 shows that the genomes of six orders Aeromonadales, Enter- obacteriales, Legionellales, Pasteurellales, Vibrionales, and Xanthomonadales are all correctly classified into their groups. Most of the genomes in the remaining orders are also well clustered. of 70 genomes that were randomly chosen from 15 orders of the class Gammaproteobacteria (Additional file 1: Table S4). As the number of genomes is large and they come from different groups, it is interesting to ask if the dis- tance measures can cluster and classify those genomes into their correct orders. We used the parsimony score to measure the difference between a clustering tree and the true classification [31,32]. As the number of groups is 15, the optimal parsimony score is 14. The higher the parsimony score is, the more different the clustering tree is from the true classification. This data set has been studied previously in [10] and the authors found that the co-phylog distance did not perform well because the bacteria of interest are not closely related. Performance on 16S rRNA sequences Then, we applied the alignment-free distance measures to the 70 whole genome sequences and their simulated NGS short reads. As it is challenging to perform MSA of 70 whole genome sequences, we applied the MSA method to 16S rRNA sequences of those 70 genomes to obtain the benchmark distance and clustering tree (Additional file 2: Figure S3, parsimony score = 18). The clustering results obtained from the NGS short reads are comparable to those obtained from the whole genome sequences, and both are worse than those obtained from the 16S rRNA sequences (Table 5). Since this experiment was conducted at a high taxonomy level We then applied all six alignment-free distance mea- sures dNCD, d, dCDM, CVTree, dS 2, and co-phylog to the Table 5 Comparison of the alignment-free distances and the benchmark MSA distance for 70 Gammaproteobacteria genomes dNCD d dCDM CVTree dS 2 co-phylog parsimony score 17 18 18 17 18 25 16s rRNA sequences tree symmetric difference 50 52 52 50 62 108 distance correlation 0.93 0.90 0.93 0.92 0.92 0.65 parsimony score 22 22 21 21 31 26 Genome sequences tree symmetric difference 80 78 76 84 110 110 distance correlation 0.47 0.46 0.47 0.67 0.50 0.45 parsimony score 21 19 23 24 32 28 NGS short reads tree symmetric difference 90 70 84 88 114 116 distance correlation 0.60 0.58 0.53 0.63 0.48 0.42 The NGS short reads were simulated from the whole genome sequences using the Exact model of MetaSim at 1× sampling depth . The two smallest parsimony scores, the two smallest tree symmetric differences and the two highest correlation coefficients are highlighted in boldface. For CVTree, we used k = 7 for the 16S rRNA data set and k = 12 for the whole genome and NGS data sets. For dS 2, we used k = 6 for the 16S rRNA data set and k = 8 for the whole genome and NGS data sets. Table 5 Comparison of the alignment-free distances and the benchmark MSA distance for 70 Gammaproteobacteria genomes Table 5 Comparison of the alignment-free distances and the benchmark MSA distance for 70 Gamm n of the alignment-free distances and the benchmark MSA distance for 70 Gammaproteobacteria The NGS short reads were simulated from the whole genome sequences using the Exact model of MetaSim at 1× sampling depth . Classification of 70 genomes in the class Gammaproteobacteria into their correct orders The previous section has focused on closely related bac- teria at the genus level. We next applied the MSA and the alignment-free distance measures to a larger data set at a higher taxonomy level. In particular, the data set consists Figure 2 Phylogenetic trees reconstructed from 29 Escherichia/Shigella genomes using (A) co-phylog, (B) dCDM, and from NGS short reads using (C) dCDM. The short reads were simulated from the tool MetaSim using the Exact model and 1× sampling depth. Escherichia Fergusonii was used as the outgroup to root the tree. f 29 E h i hi /Shi ll i (A) h l Figure 2 Phylogenetic trees reconstructed from 29 Escherichia/Shigella genomes using (A) co-phylog, (B) dCDM, and from NGS short reads using (C) dCDM. The short reads were simulated from the tool MetaSim using the Exact model and 1× sampling depth. Escherichia Fergusonii was used as the outgroup to root the tree. Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 Page 8 of 13 Table 4 Comparison of the alignment-free distances and the benchmark co-phylog distance for NGS short reads of 29 Escherichia/Shigella genomes dNCD d dCDM CVTree (k = 9) CVTree (k = 15) CVTree (k = 21) dS 2(k = 8) 454 16 14 12 22 22 54 50 Exact 12 10 10 22 24 36 50 Empirical 16 12 14 24 18 42 54 Sanger 12 10 10 28 24 40 50 454 0.96 0.96 0.97 0.74 0.87 0.31 0.04 Exact 0.97 0.97 0.98 0.82 0.82 0.61 0.05 Empirical 0.96 0.96 0.96 0.77 0.85 0.38 0.01 Sanger 0.97 0.97 0.97 0.78 0.86 0.36 0.04 The short reads were simulated from the Escherichia/Shigella genomes using four error models 454, Exact, Empirical, and Sanger of the tool MetaSim at 1× sampling depth. The two smallest tree symmetric differences and the two highest correlation coefficients for each error model are highlighted in boldface. Similar results for 5× sampling depth can be found in Additional file 1: Table S3. Performance on 16S rRNA sequences The two smallest parsimony scores, the two smallest tree symmetric differences and the two highest correlation coefficients are highlighted in boldface. For CVTree, we used k = 7 for the 16S rRNA data set and k = 12 for the whole genome and NGS data sets. For dS 2, we used k = 6 for the 16S rRNA data set and k = 8 for the whole genome and NGS data sets. Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 Page 9 of 13 Acidithiobacillales Aeromonadales Alteromonadales Cardiobacteriales Chromaales Enterobacteriales Legionellales Methylococcales Oceanospirillales Pasteurellales Pseudomonadales Thiotrichales Vibrionales Xanthomonadales Outgroup Figure 3 Clustering tree reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the dNCD distance. Those 70 genomes belong to 15 orders which are indicated by different colors in the figure. and the species were selected from different orders of the class Gammaproteobacteria, one could expect that the 16S rRNA sequences should be more reliable for the especially for the whole genome sequences and NGS short reads. Last but not least, we noted that the optimal k of CVTree and dS 2 for the whole genome sequences were dif- Figure 3 Clustering tree reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the dNCD distance. Those 70 genomes belong to 15 orders which are indicated by different colors in the figure. and the species were selected from different orders of the class Gammaproteobacteria, one could expect that the 16S rRNA sequences should be more reliable for the classification than the whole genome sequences and their short reads. It can also be seen from Table 5 that the four distances dNCD, d, dCDM, and CVTree performed slightly better than the other two distances, dS 2 and co-phylog, especially for the whole genome sequences and NGS short reads. Last but not least, we noted that the optimal k of CVTree and dS 2 for the whole genome sequences were dif- ferent from those for the 16S rRNA sequences (Additional file 1: Table S5). The optimal k was selected to opti- mize the parsimony score of the clustering trees. This will not be possible if we have no prior knowledge about Page 10 of 13 Page 10 of 13 Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 classified to the group of hindgut-fermenting herbivores. Performance on 16S rRNA sequences Although the optimal tree obtained from the CVTree distance (k = 4) also has the same parsimony score of 3, it seems to have a serious mistake when classifying the two carnivores Polar Bear and Lion to the groups of her- bivores (Additional file 2: Figure S7). The clustering tree obtained from the dCDM distance (parsimony score = 5) is shown in Additional file 2: Figure S8. It correctly distin- guished carnivores from herbivores. However, it wrongly classified Rock Hyraxes, Colobus and Visayam Warty Pig to the group of hindgut-fermenting herbivores. the true classification, which is usually the case in real applications. Performance on the full data set Then, we added back the 11 omnivore samples and repeated the experiment with the full data set. As there are now four groups in the true classification, the optimal parsimony score is 3. We found that the best parsimony score was obtained from the dNCD distance, followed by CVTree (k = 6) and dS 2 (k = 7) (Table 6). It should be noted that the optimal k of the CVTree and dS 2 distances for the sub-data set and for the full data set are different (Table 6, Additional file 1: Table S7). Performance on the sub-data set with 11 omnivore samples excluded The clustering tree of the dNCD distance is shown in Figure 4. The samples from foregut-fermenting herbivores were well clustered together, except for Rock Hyraxes, Colobus, and Visayam Warty Pig, which were classified to the group of hindgut-fermenting herbivores. This is similar to the earlier observation when the 11 omni- vore samples were excluded. Figure 4 also shows that the carnivore samples were grouped together. The omnivore samples, however, were scattered throughout the groups of herbivores and carnivores. This indicates the diversity of the gut microbial communities of omnivores, as men- tioned previously in [14,25]. Another important observa- tion from Figure 4 is that the primates samples, including Baboon 1 and 2, Chimpanzee 1 and 2, Orangutan, Gorilla, Callimicos, Saki, Black Lemur, were clustered together into one group. This may suggest that those primates share common features in their gut microbial environ- ments. Finally, it can be seen that two samples of the same host species were often clustered close to each other such as Chimpanzee 1 and 2, Lion 1 and 2, Okapi 1 and 2, Bighorn Sheep 1 and 2, supporting the accuracy of the classification and the dNCD distance. Following [14,25], we first excluded 11 omnivore sam- ples due to their complicated microbial compositions. The remaining 28 samples belong to three groups: foregut- fermenting herbivores, hindgut-fermenting herbivores, and carnivores. Since there is no benchmark tree for this clustering problem, we only used the parsimony score to evaluate the clustering trees. The optimal parsimony score is 2 as there are only three groups in the true classification. Table 6 shows that the parsimony scores of the CVTree and dS 2 distances for the optimal k are better than those of the compression-based distances dNCD, d, and dCDM. We also noted that the parsimony score of the CVTree distance varied considerably (up to 11), while that of the dS 2 distance was more stable (Additional file 1: Table S7). The optimal tree obtained from the dS 2 distance (k = 5, parsimony score = 3) is shown in Additional file 2: Figure S6. Classification of metagenomic samples from mammalian gut reveals the diet and gut physiology of the host species In this section we consider a real metagenomic data set that includes NGS short reads of 39 fecal samples from 33 mammalian host species. The host species can be clas- sified into four groups according to their diet and gut physiology: foregut-fermenting herbivores (13 samples), hindgut-fermenting herbivores (8 samples), carnivores (7 samples), and omnivores (11 samples) (Additional file 1: Table S6). This data set has been studied previously in [14,25]. In [14] the authors applied the CVTree and dS 2 distances to these 39 metagenomic samples and found that the sequence signatures (that is, the k-mers) of the samples were strongly associated with the diet and gut physiology of the host species. Hence we want to test if the compression-based distance measures dNCD, d and dCDM can also reveal any interesting results from this metagenomic data set. Performance on the sub-data set with 11 omnivore samples excluded Only two samples Rock Hyrax 1 and 2 were wrongly Table 6 Parsimony score for the classificationof 39 metagenomic samples using the alignment-free distances dNCD d dCDM CVTree dS 2 Sub-data set 6 7 5 3 3 (omnivore samples excluded) Full data set 9 12 12 10 10 For CVTree, we used k = 6 for the full data set and k = 4 for the sub-data set in which the omnivore samples were excluded. For dS 2, we used k = 7 for the full data set and k = 5 for the sub-data set. The two smallest parsimony scores for each data set are highlighted in boldface. The results obtained in this section have demon- strated another application of the alignment-free mea- sures of sequence distance: comparison and classification of metagenomic samples of NGS short reads. This task is of critical importance for the understanding of micro- bial communities. Both k-mer based and compression- based distance measures have revealed interesting results about the microbial communities of mammalian gut from their metagenomic samples. In particular, the information For CVTree, we used k = 6 for the full data set and k = 4 for the sub-data set in which the omnivore samples were excluded. For dS 2, we used k = 7 for the full data set and k = 5 for the sub-data set. The two smallest parsimony scores for each data set are highlighted in boldface. Page 11 of 13 Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 Herbivore Foregut Herbivore Hindgut Carnivore Omnivore Figure 4 Clustering tree reconstructed from 39 metagenomic samples using the dNCD distance. The host species’ colors indicate their diet and gut physiology: foregut-fermenting herbivores (green), hindgut-fermenting herbivores (yellow), carnivores (red) and omnivores (blue). Herbivore Hindgut Herbivore Foregut Carnivore Omnivore Figure 4 Clustering tree reconstructed from 39 metagenomic samples using the dNCD distance. The host species’ colors indicate their diet and gut physiology: foregut-fermenting herbivores (green), hindgut-fermenting herbivores (yellow), carnivores (red) and omnivores (blue). Figure 4 Clustering tree reconstructed from 39 metagenomic samples using the dNCD distance. The host species’ c and gut physiology: foregut-fermenting herbivores (green), hindgut-fermenting herbivores (yellow), carnivores (red) and o Conclusions contained in the samples was found to be strongly asso- ciated with the diet and gut physiology of herbivores, carnivores, and omnivores. This agrees well with previous studies in [14,25]. Moreover, our results obtained from the compression-based distance measures also discovered a strong similarity between the gut microbial communi- ties of the primates. This interesting finding has not been observed in previous studies. In this paper we studied the application of compression- based distance measures for the problem of sequence comparison, with a special focus on NGS short read data. Their key advantages are assembly-free, alignment-free, and parameter-free. We conducted extensive validation on various types of sequence data: NGS short reads, 16S rRNA sequences, mtDNA sequences, and whole genome Page 12 of 13 Page 12 of 13 Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 sequences. The sequence data was obtained from several mammalian and bacteria genomes at different taxonomy levels, as well as from microbial metagenomic samples. The results show that the compression-based distance measures produced comparably accurate results as the k- mer based methods, and both were in good agreement with the alignment-based approach and with existing benchmarks in the literature. compression tools should be more efficient and hence provide more accurate distances. Our future research will focus on reducing the running time and studying the effects of different compression tools. In this study we have demonstrated the accuracy and the consistency of the compression-based distance measures on both NGS short reads and long genomic sequences. Those findings underscore the advantages of the compression-based distance measures, suggest- ing that these measures represent useful tools for the alignment-free sequence comparison. An implementation of the compression-based distance measures is provided in the attached Perl scripts (Additional file 3). The k-mer based distance measures, however, may pro- duce inconsistent results depending on the parameter k, the type of sequence data, or the species under con- sideration. For example, the co-phylog measure was not applicable to species with far evolutionary distances from each other (data set of 29 mammalian, data set of 70 Gammaproteobacteria, data set of 39 metagenomic sam- ples). The dS 2 measure failed for the data set of 29 closely related Escherichia/Shigella bacteria. The CVTree mea- sure produced inconsistent results for the data set of 29 Escherichia/Shigella bacteria. Additional files Clustering tree reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the distance dS 2 (k = 6). Figure S6. Clustering tree reconstructed from the metagenomic samples (omnivore samples excluded) using the distance dS 2(k = 5). Figure S7. Clustering tree reconstructed from the metagenomic samples (omnivore samples excluded) using the distance CVTree (k = 4). Figure S8. Clustering tree reconstructed from the metagenomic samples (omnivore samples excluded) using the distance dCDM. Additional file 2: Figure S1. Phylogenetic trees reconstructed from 29 mtDNA sequences using: (a) MSA, (b) dCDM, (c) CVTree (k = 10), (d) dS 2(k = 8). Figure S2. Phylogenetic trees reconstructed from 29 Escherichia/Shigella genomes using: (a) co-phylog, (b) CVTree (k = 9), (c) CVTree (k = 15), (d) CVTree (k = 21). Figure S3. Clustering tree reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the MSA distance. Figure S4. Clustering tree reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the distance CVTree (k = 7). Figure S5. Clustering tree reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the distance dS 2 (k = 6). Figure S6. Clustering tree reconstructed from the metagenomic samples (omnivore samples excluded) using the distance dS 2(k = 5). Figure S7. Clustering tree reconstructed from the metagenomic samples (omnivore samples excluded) using the distance CVTree (k = 4). Figure S8. Clustering tree reconstructed from the metagenomic samples (omnivore samples excluded) using the distance dCDM. One possible drawback when using the compression- based distance measures is the running time. Obviously, compressing a DNA sequence (or an NGS sample) takes longer time than counting its k-mers. Moreover, the compression-based methods need to perform pairwise compression of the input sequences, whereas the k-mer methods only need to calculate one frequency vector for each input sequence. However, in general one may also need to test a wide range of k to find the optimal results when using the k-mer methods. As an example, for the data set of 39 metagenomic sam- ples in our study, the running time of the CVTree measure was ∼1-7 minutes for each k = 2, 3, . . ., 10, and ∼10-60 minutes for each k = 11, 12, . . ., 20. Thus, a test cov- ering all values of k = 2, 3, . . Additional files Additional file 1: Table S1. Comparison of alignment-free distances and the benchmark MSA distance for 29 mtDNA sequences. Table S2. Comparison of alignment-free distances and the benchmark MSA distance for 29 mtDNA sequences and their short reads. Table S3. Comparison of alignment-free distances and the benchmark co-phylog distance for 29 Escherichia/Shigella genomes and their short reads. Table S4. The list of 70 genomes in the class Gammaproteobacteria, their orders, and their accession numbers. Table S5. Comparison of alignment-free distances and the benchmark MSA distance for 70 Gammaproteobacteria genomes and their short reads. Table S6. The list of 39 metagenomic samples and their host species’ diet and gut physiology. Table S7. The parsimony score of the clustering trees for 39 metagenomic samples. Table S8. Performance of the compression-based distances on 10 different random concatenations of the NGS short reads simulated from the mtDNA sequences using the Empirical (Illumina) model. Additional file 1: Table S1. Comparison of alignment-free distances and the benchmark MSA distance for 29 mtDNA sequences. Table S2. Comparison of alignment-free distances and the benchmark MSA distance for 29 mtDNA sequences and their short reads. Table S3. Comparison of alignment-free distances and the benchmark co-phylog distance for 29 Escherichia/Shigella genomes and their short reads. Table S4. The list of 70 genomes in the class Gammaproteobacteria, their orders, and their accession numbers. Table S5. Comparison of alignment-free distances and the benchmark MSA distance for 70 Gammaproteobacteria genomes and their short reads. Table S6. The list of 39 metagenomic samples and their host species’ diet and gut physiology. Table S7. The parsimony score of the clustering trees for 39 metagenomic samples. Table S8. Performance of the compression-based distances on 10 different random concatenations of the NGS short reads simulated from the mtDNA sequences using the Empirical (Illumina) model. Additional file 2: Figure S1. Phylogenetic trees reconstructed from 29 mtDNA sequences using: (a) MSA, (b) dCDM, (c) CVTree (k = 10), (d) dS 2(k = 8). Figure S2. Phylogenetic trees reconstructed from 29 Escherichia/Shigella genomes using: (a) co-phylog, (b) CVTree (k = 9), (c) CVTree (k = 15), (d) CVTree (k = 21). Figure S3. Clustering tree reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the MSA distance. Figure S4. Clustering tree reconstructed from 16S rRNA sequences of 70 Gammaproteobacteria genomes using the distance CVTree (k = 7). Figure S5. Authors’ contributions The running time when using GenCompress to cal- culate the compression-based measures for this data set was ∼25 hours, about 3 times longer than that of CVTree. Compression tools developed specifically for NGS short reads such as BEETL [35] and SCALCE [36] can be applied to reduce the running time. We also expect that such NGS Conclusions The compression-based measures, although not always producing the best dis- tances, performed consistently well across all data sets in the study without any optimization required. We believe such a consistent performance is due to their parameter-free feature. On the other hand, choosing an optimal parameter k for each data set is of criti- cal importance for using the k-mer based methods. This task would become daunting when there is no bench- mark (e.g., true phylogenetic trees or true classifica- tions) available to guide the analysis and the selection of k. Additional files ., 10 only took less than 20 minutes, but if all the values of k = 11, 12, . . ., 20 were included, the running time increased up to ∼8 hours. Additional file 3: Perl scripts and the example data set of 29 mtDNA sequences. 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Page 13 of 13 Tran and Chen BMC Research Notes 2014, 7:320 http://www.biomedcentral.com/1756-0500/7/320 Received: 11 February 2014 Accepted: 16 May 2014 Published: 29 May 2014 Received: 11 February 2014 Accepted: 16 May 2014 Published: 29 May 2014 Received: 11 February 2014 Accepted: 16 May 2014 Published: 29 May 2014 References 1. Metzker ML: Sequence technologies - the next generation. Nat Rev Genet 2010, 11:31–46. 2. Waterman MS: Introduction to Computational Biology: Maps, Sequences, and Genomes. Boca Raton, FL: Chapman and Hall/CRC; 1995. 3. Durbin R, Eddy S, Krogh A, Mitchison G: Biological Sequence Analysis. Cambridge: Cambridge University Press; 1999. 4. Vinga S, Almeida J: Alignment-free sequence comparison-a review. Bioinformatics 2003, 19:513–523. 5. Chan CX, Ragan MA: Next-generation phylogenomics. Biol Direct 2013, 8:3. 6. Qi J, Luo H, Hao B: CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res 2004, 32:W45–W47. 7. 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Biol Direct 2013, 8:3. 6. Qi J, Luo H, Hao B: CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res 2004, 32:W45–W47. 7. Xu Z, Hao B: CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes. Nucleic Acids Res 2009, 37:W174–W178. 8. Reinert G, Chew D, Sun F, Waterman MS: Alignment-free sequence comparison (I): statistics and power. J Comput Biol 2009, 16:1615–1634. 9. Wan L, Reinert G, Sun F, Waterman MS: Alignment-free sequence comparison (II): theoretical power of comparison statistics. J Comput Biol 2010, 17:1467–1490. 10. Yi H, Jin L: Co-phylog: an assembly-free phylogenomic approach for closely related organisms. Nucleic Acid Res 2013, 41:e75. 11. Pham TD, Zuegg J: A probabilistic measure for alignment-free sequence comparison. Bioinformatics 2004, 20:3455–3461. 12. Kantorovitz MR, Robinson GE, Sinha S: A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics 2007, 23:i249–i255. 13. Dai Q, Yang Y, Wang T: Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison. Bioinformatics 2008, 24:2296–2302. 14. Jiang B, Song K, Ren J, Deng M, Sun F, Zhang X: Comparison of metagenomic samples using sequence signatures. BMC Genomics 2012, 13:730. 15. Song K, Ren J, Zhai Z, Liu X, Deng M, Sun F: Alignment-free sequence comparison based on next-generation sequencing reads. J Comput Biol 2013, 20:64–79. 16. Li M, Badger JH, Chen X, Kwong S, Kearney P, Zhang H: An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 2001, 17:149–154. 17. Li M, Chen X, Li X, Ma B, Vitanyi PMB: The similarity metric. IEEE Trans Inform Theory 2004, 50:3250–3264. 18. Keogh E, Lonardi S, Ratanamahatana CA: Towards parameter-free data mining. In Proceedings of the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 22-25 August 2004. Seattle, WA, USA; 2004:206–215. 19. Otu HH, Sayood K: A new sequence distance measure for phylogenetic tree construction. Bioinformatics 2003, 19:2122–2130. 20. Li M, Vitanyi PMB: An introduction to Kolmogorov complexity and its applications: Springer; 2008. [http://www.springer.com/computer/ theoretical+computer+science/book/978-0-387-33998-6] 21. 1. Metzker ML: Sequence technologies - the next generation. Nat Rev Genet 2010, 11:31–46. Kantorovitz MR, Robinson GE, Sinha S: A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics 2007, 23:i249–i255. 13. Dai Q, Yang Y, Wang T: Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison. Bioinformatics 2008, 24:2296–2302. 36. Hach F, Numaganic I, Alkan C, Sahinalp SC: SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinformatics 2012, 28:3051–3057. 14. Jiang B, Song K, Ren J, Deng M, Sun F, Zhang X: Comparison of metagenomic samples using sequence signatures. BMC Genomics 2012, 13:730. doi:10.1186/1756-0500-7-320 Cite this article as: Tran and Chen: Comparison of next-generation sequencing samples using compression-based distances and its application to phylogenetic reconstruction. BMC Research Notes 2014 7:320. 15. Song K, Ren J, Zhai Z, Liu X, Deng M, Sun F: Alignment-free sequence comparison based on next-generation sequencing reads. J Comput Biol 2013, 20:64–79. 16. Li M, Badger JH, Chen X, Kwong S, Kearney P, Zhang H: An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 2001, 17:149–154. y information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 2001, 17:149–154. 17. Li M, Chen X, Li X, Ma B, Vitanyi PMB: The similarity metric. IEEE Trans Inform Theory 2004, 50:3250–3264. 18. Keogh E, Lonardi S, Ratanamahatana CA: Towards parameter-free data mining. In Proceedings of the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 22-25 August 2004. Seattle, WA, USA; 2004:206–215. 19. Otu HH, Sayood K: A new sequence distance measure for phylogenetic tree construction. Bioinformatics 2003, 19:2122–2130. 20. Li M, Vitanyi PMB: An introduction to Kolmogorov complexity and its applications: Springer; 2008. [http://www.springer.com/computer/ theoretical+computer+science/book/978-0-387-33998-6] 21. Benedetto D, Caglioti E, Loreto V: Language tree and zipping. Phys Rev Lett 2002, 88:048702. 1. Metzker ML: Sequence technologies - the next generation. Nat Rev Genet 2010, 11:31–46. 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 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: 22. Ito K, Zuegmann T, Zhu Y: Recent experiences parameter-free data mining. In Proceedings of the 25th International Symposium on Computer and Information Sciences. 22-24 September 2010. London, UK; 2010:365–371. 23. Chen X, Kwong S, Li M: A compression algorithm for DNA sequences and its applications in genome comparison. In Proceedings of the Tenth Workshop on Genome Informatics. 14-15 December 1999. Tokyo, Japan; 1999:51–61. 24. Cao Y, Janke A, Waddell PJ, Westerman M, Takenaka O, Murata S, Okada N, Paabo S, Hasegawa M: Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J Mol Evol 1998, 47:307–322. 25. Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, Fontana L, Henrissat B, Knight R, Gordon JI: Diet drives convergence in gut 25. Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, Fontana L, Henrissat B, Knight R, Gordon JI: Diet drives convergence in gut
https://openalex.org/W3112721604
https://europepmc.org/articles/pmc7794138?pdf=render
English
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Characteristics of healthcare workers who died during the fight against COVID-19 in China
Pakistan journal of medical sciences
2,020
cc-by
2,163
ABSTRACT Coronavirus disease 2019 (COVID-19), first reported in December 2019 in Wuhan, China, has progressed to a pandemic associated with substantial morbidity and mortality. Little is known about the healthcare workers who died fighting the disease in China. This paper analyzed the data of 78 Chinese healthcare workers who died in the fight against COVID-19 between 23 January and 2 June, 2020, and revealed the following characteristics. First, compared to the number of deaths directly attributable to COVID-19, more healthcare workers died from pre-existing disease attack induced by excessive fatigue or died from accidents. Second, the median age of the healthcare workers who died directly from COVID-19 was younger than that of the Wuhan non- healthcare workers who died of COVID 19. Third, although more women than men were involved in fighting the pandemic, more men died. Fourth, more healthcare workers died in Hubei than in other provinces. Fifth, most of the healthcare workers who died directly from COVID-19 were non-professionals. KEYWORDS: Characteristics, healthcare workers, Fatality, COVID-19, China. doi: https://doi.org/10.12669/pjms.37.1.3384 How to cite this: Wang Y, Ji Y, Wang Y. Characteristics of healthcare workers who died during the fight against COVID-19 in China. Pak J Med Sci. 2021;37(1):292-294. doi: https://doi.org/10.12669/pjms.37.1.3384 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. doi: https://doi.org/10.12669/pjms.37.1.3384 How to cite this: Wang Y, Ji Y, Wang Y. Characteristics of healthcare workers who died during the fight against COVID-19 in China. Pak J Med Sci. 2021;37(1):292-294. doi: https://doi.org/10.12669/pjms.37.1.3384 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Short Communication Short Communication Characteristics of healthcare workers who died during the fight against COVID-19 in China Yujun Wang1, Yun Ji2, Yuedong Wang3 Yujun Wang1, Yun Ji2, Yuedong Wang3 ABSTRACT Coronavirus disease 2019 (COVID-19), first reported in December 2019 in Wuhan, Hubei province, China, has progressed to a pandemic associated with substantial morbidity and mortality.1 By June 13, 2020, 83132 confirmed cases had been reported in China, causing 4634 deaths.2 Responding to the pandemic, China focused on traditional public health outbreak response tactics-isolation, quarantine, social distancing, and community containment,3 which have never before been implemented on such a large scale.4,5 Further, a total of 42,600 healthcare workers (28,000 women) from other provinces were sent to Hubei to fight the disease.6 i g Although the disease has been controlled, the whole country has paid a high price. Asides from more than 116.9 billion RMB (approximately 16.5 billion USD) allocated for pandemic prevention and control,7 there were public health interventions and sacrifices that cannot be estimated in monetary terms. On March 5, the Chinese government announced a commendation list of advanced collectives and individuals of the national health system who had contributed to the prevention and control of COVID-19 pandemic. A total of 506 healthcare workers were honored, but 34 of them had died.8 Little is known about the healthcare workers who died fighting the disease. This paper analyzed the characteristics of 78 Chinese healthcare workers who died in the fight against COVID-19. Pak J Med Sci January - February 2021 Vol. 37 No. 1 www.pjms.org.pk 292 1. Yujun Wang, PhD. School of Humanities and International Education, Zhejiang University of Science and Technology, Hangzhou, China; Zhejiang Institute of New Media for Government Affairs, Hangzhou, China. 2. Yun Ji, MD. Department of Surgical Intensive Care Unit, 3. Yuedong Wang, MD. Department of General Surgery, 2,3: Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China. Correspondence: Yuedong Wang, MD. Department of General Surgery, Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou 310009, China. E-mail: wydong2003@hotmail.com * Received for Publication: July 28, 2020 * Accepted for Publication: October 5, 2020 Although the disease has been controlled, the whole country has paid a high price. Asides from more than 116.9 billion RMB (approximately 16.5 billion USD) allocated for pandemic prevention and control,7 there were public health interventions and sacrifices that cannot be estimated in monetary terms. On March 5, the Chinese government announced a commendation list of advanced collectives and individuals of the national health system who had contributed to the prevention and control of COVID-19 pandemic. ABSTRACT A total of 506 healthcare workers were honored, but 34 of them had died.8 Little is known about the healthcare workers who died fighting the disease. This paper analyzed the characteristics of 78 Chinese healthcare workers who died in the fight against COVID-19. doi: https://doi.org/10.12669/pjms.37.1.3384 How to cite this: Wang Y, Ji Y, Wang Y. Characteristics of healthcare workers who died during the fight against COVID-19 in China. Pak J Med Sci. 2021;37(1):292-294. doi: https://doi.org/10.12669/pjms.37.1.3384 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Correspondence: * Accepted for Publication: 292 Pak J Med Sci January - February 2021 Vol. 37 No. 1 www.pjms.org.pk 292 Pak J Med Sci January - February 2021 Vol. 37 No. 1 www.pjms.org.pk 292 Yujun Wang et al. Based on official reports from government agencies9 and reports from news websites, we searched for information on the deaths of 78 Chinese medical workers during the pandemic between 23 January and 2 June, 2020. The following public access data were collected: age, gender, cause of death, professional or not, and their location. Continuous variables are described as medians and interquartile ranges (IQRs) and categorical variables were described as numbers (proportions). The Mann-Whitney U test was applied to compare continuous variables and the χ2 test or Fisher’s exact test was used for categorical variables. respiratory medicine and intensive care, respiratory medicine, gastroenterology, and traditional Chi- nese medicine. Nine were from tertiary hospitals (32.1%), including an otolaryngologist, three oph- thalmologists and five surgeons (Fig.1). gi g ( g ) An analysis of the 78 healthcare workers revealed the following characteristics. First, compared to the number of deaths directly attributable to COVID-19, more healthcare workers died from pre-existing disease attack induced by excessive fatigue or died from accidents. This means that people with underlying morbidities such as heart disease and encephalopathy are more at risk when they are overtired or stressed. Second, the median age of the 28 healthcare workers who died directly from COVID-19 in the study was younger than that of the Wuhan 44 non- healthcare workers who died of COVID 19 as reported by Wu et al (55 versus 69 years).10 Not only were healthcare workers mostly in employment who were younger than 60 years11, but they were also under enormous physical and psychological pressure during the pandemic. Third, although more women than men were involved in fighting the pandemic, more men died. This may be because the female healthcare workers, mostly nurses, were generally younger; the older male healthcare workers may have had more chronic diseases. In addition, the more difficult and dangerous jobs are usually held by men. Fourth, more healthcare workers died in Hubei than in other provinces. This is likely because the outbreak g Of the 78 deaths, 14 were female (17.9%) and 64 were male (82.1%), with a median age of 50 (IQR, 41-56) years. Forty-four came from Hubei province (56.4%) and 34 from other provinces (43.6%). Pak J Med Sci January - February 2021 Vol. 37 No. 1 www.pjms.org.pk 293 a Professionals refer to healthcare workers that worked in emergency departments, infectious diseases departments, respiratory departments, or critical care departments. Correspondence: Twen- ty-eight (35.9% ) died directly from COVID-19, and the rest (64.1%) died from heart attacks, cerebrovas- cular accidents, traffic or hotel collapse accidents, fatigue and sudden unexplained death (Table-I). g p ( ) Of the 28 healthcare workers who died directly from COVID-19, six were women (21.4%) and 22 were men (78.6%), with a median age of 55 (IQR, 43-62) years. Twenty-seven were from Hubei prov- ince (96.4%) and one from Hainan province (3.6%). Fifteen of the healthcare workers (53.6%) were from community or primary hospitals, all but a 59-year- old female nurse were general practitioners (includ- ing the one from Hainan province). Four (14.3%) were from secondary hospitals, with specialties in stics of healthcare workers who died during the fight against COVID-19 in China. Table-I: Characteristics of healthcare workers who died during the fight against COVID-19 in China. Characteristic Patients, No. (%) Total (n = 78) Died of COVID-19 infection (n = 28) Died of other diseases (n = 50) P value Age, median (interquartile range), y 50 (41-56) 55 (43-62) 49 (36-52) 0.005 Sex 0.549 Female 14 (17.9) 6 (21.4) 8 (16.0) Male 64 (82.1) 22 (78.6) 42 (84.0) Professionalsa Yes 7 (9.0) 2 (7.1) 5 (10.0) 0.992 No 71 (91.0) 26 (92.9) 45 (90.0) Died in Hubei province Yes 44 (56.4) 27 (96.4) 17 (34.0) < 0.001 No 34 (43.6) 1 (3.6) 33 (66.0) a Professionals refer to healthcare workers that worked in emergency departments, infectious diseases departments, respiratory departments, or critical care departments. a Professionals refer to healthcare workers that worked in emergency departments, infectious diseases departments, respiratory departments, or critical care departments. Yujun Wang et al. Fi 1 Fig.1 was first and most severe in Hubei province, and the whole society was unprepared and with a critical shortage of personal protective equipment and healthcare workers. Finally, most of the healthcare workers who died directly from COVID-19 were non-professionals. Non-professionals may not have understood the severity of COVID-19 and likely had not received relevant professional training or received appropriate protection measures. 3. Wilder-Smith A, Freedman DO. Isolation, quarantine, social distancing and community containment: pivotal role for old-style public health measures in the novel coronavirus (2019-nCoV) outbreak. J Travel Med. 2020:1-4 doi: 10.1093/jtm/taaa020 /j / 4. Xiao Y, Torok ME. Taking the right measures to control COVID-19. Lancet Infect Dis 2020 Published Online March 5, 2020. doi: 10.1016/ S1473-3099(20)30152-3 5. Wu Z, McGoogan JM. Conflict of interests: Authors state no conflict of interest. Conflict of interests: Authors state no conflict of interest. Conflict of interests: Authors state no conflict of interest. Correspondence: Characteristics of and Important Lessons from the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72 314 Cases from the Chinese Center for Disease Control and Prevention. JAMA. 2020;323:1239–1242. doi:10.1001/jama.2020.2648 j 6. Feng H. Medical, Political, and Medical Bureau: National support to the Hubei medical team exceeds 42,000 female medical staff accounts for 2/3, Gmw.cn http://www.gmw.cn/, 2020-03-08, retrieved from economy.gmw.cn http://economy.gmw.cn/, 2020-03-29. Therefore, rapid and transparent communication is paramount when infectious diseases emerge12, which can relieve people’s tension and anxiety. There must be enough healthcare workers who know how to prevent and treat infectious diseases, and they must be provided with adequate personal protective equipment. y g p y g 7. The central people’s government of the People’s Republic of China, The government at all levels allocated 116.9 billion yuan for epidemic prevention and control, http://www.gov.cn/xinwen/2020-03/15/ content_5491446.htm. 2020-03-15 8. National Health Commission, Ministry of Human Resources and Social Security, State Administration of Traditional Chinese Medicine. Decision to commend advanced collectives and individuals of the national health system for the prevention and control of COVID-19 epidemic. 2020-03-05; http://fg.nujiang.cn/ html/2020/yaowen_0305_33323.htmli Funding: This work was supported by Zhejiang University of Science and Technology basic science research and special fund project (grant number 2019QN41). Funding: This work was supported by Zhejiang University of Science and Technology basic science research and special fund project (grant number 2019QN41). Funding: This work was supported by Zhejiang University of Science and Technology basic science research and special fund project (grant number 2019QN41). y 9. The State Council Information Office of the People’s Republic of China. Fighting COVID-19: China in Action. http://www.scio.gov. cn/zfbps/ndhf/42312/Document/1682142/1682142.htm 10. Wu C, Chen X, Cai Y, Xia J, Zhou X, Xu S, et al. Risk Factors Associated With Acute Respiratory Distress Syndrome and Death in Patients With Coronavirus Disease 2019 Pneumonia in Wuhan, China. JAMA Intern Med. Published online March 13, 2020; doi: 10.1001/jamainternmed.2020.0994 Conflict of interests: Authors state no conflict of interest. REFERENCES /j 11. Wei Li , Jie Zhang , Shifu Xiao , Lin Sun , Characteristics of health worker fatality in China during the outbreak of COVID-19 infection, J Infect. 2020. doi: 10.1016/j.jinf.2020.03.030 1. Zou L, Ruan F, Huang M, Liang L, Huang H, Hong Z, et al. SARS- CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients. N Engl J Med. 2020;382:1177-1179 12. Petersen E, Hui D, Hamer DH, Blumberg L, Madoff LC, Pollack M, et al. Li Wenliang, a face to the frontline healthcare worker. The first doctor to notify the emergence of the SARS-CoV-2, (COVID-19), outbreak. Int J Infect Dis. 2020;93:205-207. g 2. National Health Commission of the People’s Republic of China. Updates on the epidemic. June 14, 2020. http://www.nhc.gov.cn/ xcs/yqtb/list_gzbd. shtml (accessed June 14, 2020 [in Chinese]). 294 Pak J Med Sci January - February 2021 Vol. 37 No. 1 www.pjms.org.pk 294
https://openalex.org/W4392168962
https://www.mdpi.com/1996-1073/17/5/1113/pdf?version=1708951983
English
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Sintered Wick Heat Pipes with Excellent Heat Transfer Capabilities—Case Study
Energies
2,024
cc-by
11,636
energies energies Article Im-Nam Jang and Yong-Sik Ahn * Department of Materials Science and Engineering, Pukyong National University, Busan 48547, Republic of Korea; imnam12@naver.com * Correspondence: ysahn@pknu.ac.kr; Tel.: +82-51-629-6361 Abstract: A sintered wick was formed in a heat pipe through the process of sintering a mixture of copper powder with particle sizes of 100 µm and 200 µm, mixed with a pore-forming agent. The heat pipe’s thermal resistance, which affects its heat transfer efficiency, is determined during manufacturing according to the powder type, thickness of the sintered wick, and filling rate of the working fluid. Heat transfer efficiency was then tested at various inclination angles (0◦, 45◦, and 90◦) to evaluate the performance of heat pipes. Regardless of the filling amount and test angle, the 200 µm copper powder type exhibited superior heat transfer efficiency compared to the 100 µm type. After analyzing heat transfer performance at various filling rates between 20% and 50%, it was determined that the heat pipe’s optimal heat transfer capability occurred at a working fluid filling rate of 30%. The width of the wick was directly related to the heat transfer performance. Keywords: heat pipe; heat transfer performance; effective pore radius; capillary force; sintered wick; working fluid filling ratio 1. Introduction https://doi.org/ 10.3390/en17051113 Academic Editor: Marco Marengo Received: 22 December 2023 Revised: 20 February 2024 Accepted: 23 February 2024 Published: 26 February 2024 1. Introduction The rapid development of the IT and electronics industries has recently complicated the functional requirements for the performance of electronic equipment, and the high- power consumption of this equipment has resulted in a shorter lifetime [1]. Due to the limited space available, the heat dissipation system of aviation components experiences high acceleration. Hence, the designer must take into account safety and operational performance in dynamic conditions and various external environments, covering a wide range of frigid temperatures (−30 ◦C to 45 ◦C). Therefore, it is important to ensure the preservation of a specific standard of performance. Cylindrical copper heat pipes are ideal for heat dissipation in aircraft electrical components due to their exceptional thermal conductivity and efficient use of space. The heat pipes effectively maintain a consistent temperature for the heating element. Originally designed to control satellite temperatures, they are now widely used in different industries and applications in the electronics sector. These applications provide phase-change heat transfer with high thermal conductivity, and a number of automatic temperature characteristics for lifetime and cost-effectiveness, among other benefits [2]. The heat pipe utilizes copper wicks mounted on the inner wall of the copper pipes to circulate the working fluid from the condensing portion to the evaporation section and back again [3]. Heat is transferred to the working fluid in the evaporator through conduction, causing vaporization at the wick surface. This increases the local pressure inside the evaporator and enables the vapor to move towards the condenser. Heat is extracted at the condenser, causing the vapor to condense on the wick surface and release latent heat. Heat pipes have a significant advantage over traditional devices due to their high thermal conductance in a steady state [4]. Citation: Jang, I.-N.; Ahn, Y.-S. Sintered Wick Heat Pipes with Excellent Heat Transfer Capabilities—Case Study. Energies 2024, 17, 1113. https://doi.org/ 10.3390/en17051113 Academic Editor: Marco Marengo Received: 22 December 2023 Revised: 20 February 2024 Accepted: 23 February 2024 Published: 26 February 2024 Citation: Jang, I.-N.; Ahn, Y.-S. Sintered Wick Heat Pipes with Excellent Heat Transfer Capabilities—Case Study. Energies 2024, 17, 1113. https://doi.org/ 10.3390/en17051113 Academic Editor: Marco Marengo Received: 22 December 2023 Revised: 20 February 2024 Accepted: 23 February 2024 Published: 26 February 2024 Citation: Jang, I.-N.; Ahn, Y.-S. Sintered Wick Heat Pipes with Excellent Heat Transfer Capabilities—Case Study. Energies 2024, 17, 1113. Of these requirements, achieving high porosity and permeabil- ity through sintering technology is especially important for the production of heat pipe wicks. Hence, this study applies the wick production parameters—porosity, permeability, and capillary force—which have a notable influence on the heat pipes’ performance, using the data obtained from previous research [5]. The heat transfer efficiency of heat pipes was evaluated under various conditions, including different tilting angles, copper powder sizes, wick thicknesses, and working fluid filling ratios. gli g Figure 1 shows the operational boundaries of a sintered wick heat pipe [6]. It defines the limits of heat pipe performance. Each of these limitations is distinct, independent, and not interconnected. By applying individual analysis techniques for each limitation, it is possible to calculate the heat transport capacity based on the mean operating temperature (adiabatic vapor temperature). The distinct performance limits define an operational range, which is represented by the region enclosed by the combination of these individual limits. The operational range of the heat pipe is essentially the specific region or combination of temperatures and maximum transfer capacity within which it is designed to operate. Therefore, it is possible to either improve the design or ensure that the heat pipe can effectively transfer the necessary thermal load. Also, it is important to keep in mind that the determination of the average operating temperature is essential for the calculation of the heat transport capacity. The operating temperature of a standard heat pipe is generally determined by the heat input. Therefore, the heat transfer and operating temperature are interrelated. The transfer capacity of a heat pipe is influenced by several factors, including the working fluid, the wick structure, the dimensions of the heat pipe, and the operating temperature [7]. Figure 1 shows the operational boundaries of a sintered wick heat pipe [6]. It defines the limits of heat pipe performance. Each of these limitations is distinct, independent, and not interconnected. By applying individual analysis techniques for each limitation, it is possible to calculate the heat transport capacity based on the mean operating temperature (adiabatic vapor temperature). The distinct performance limits define an operational range, which is represented by the region enclosed by the combination of these individual limits. The operational range of the heat pipe is essentially the specific region or combina- tion of temperatures and maximum transfer capacity within which it is designed to oper- ate. Copyright: © 2024 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/). The main factors affecting heat pipe performance include the maximum heat transfer capacity, heat conduction coefficient, heat transfer limit, and thermal resistance. Specifically, https://www.mdpi.com/journal/energies Energies 2024, 17, 1113. https://doi.org/10.3390/en17051113 Energies 2024, 17, 1113 Energies 2024, 17, x FOR 2 of 12 2 of 12 the capillary limit of copper wick is the most important variable that determines the temperature range and heat transfer limits of ground-based heat pipes, out of all the different factors that affect heat transfer. Specifically, the capillary limit of copper wick is the most important variable that deter- mines the temperature range and heat transfer limits of ground-based heat pipes, out of all the different factors that affect heat transfer. Th ill li i i l i d i k h i i i fl d b l f the capillary limit of copper wick is the most important variable that determines the temperature range and heat transfer limits of ground-based heat pipes, out of all the different factors that affect heat transfer. Specifically, the capillary limit of copper wick is the most important variable that deter- mines the temperature range and heat transfer limits of ground-based heat pipes, out of all the different factors that affect heat transfer. Th ill li i i l i d i k h i i i fl d b l f The capillary limit in metal sintered wick heat pipes is influenced by several factors, including the diameter and shape of pores, as well as the porosity, permeability, and thick- ness of the sintered body. Of these requirements, achieving high porosity and permeability through sintering technology is especially important for the production of heat pipe wicks. Hence, this study applies the wick production parameters—porosity, permeability, and capillary force—which have a notable influence on the heat pipes’ performance, using the data obtained from previous research [5]. The heat transfer efficiency of heat pipes was evaluated under various conditions, including different tilting angles, copper powder sizes, wick thicknesses, and working fluid filling ratios. The capillary limit in metal sintered wick heat pipes is influenced by several factors, including the diameter and shape of pores, as well as the porosity, permeability, and thick- ness of the sintered body. Therefore, it is possible to either improve the design or ensure that the heat pipe can effectively transfer the necessary thermal load. Also, it is important to keep in mind that the determination of the average operating temperature is essential for the calculation of the heat transport capacity. The operating temperature of a standard heat pipe is generally determined by the heat input. Therefore, the heat transfer and operating temperature are interrelated. The transfer capacity of a heat pipe is influenced by several factors, including the working fluid, the wick structure, the dimensions of the heat pipe, and the operating temperature [7]. Figure 1. Limitations to heat transport in a heat pipe. Capillary Limitation Each operating limit of a sintered wick heat pipe can be considered independently. The heat pipe requires the maximum capillary pumping pressure (△𝑃௖,௠௔௫) to exceed the overall pressure drop within the pipe for it to operate effectively. This pressure drop con- sists of three components, namely the pressure drop (△𝑃௟) necessary for the liquid to be transferred from the condenser back to the evaporator, the pressure differential (△𝑃௩) re- quired for the vapor to move from the evaporator to the condenser, and the gravitational head, which varies based on the heat pipe’s inclination, determines the pressure (△𝑃௚), and can be zero, positive, or negative. In order for the heat pipe to operate correctly, it is Figure 1. Limitations to heat transport in a heat pipe. Capillary Limitation Each operating limit of a sintered wick heat pipe can be considered independently. The heat pipe requires the maximum capillary pumping pressure (△Pc,max) to exceed the overall pressure drop within the pipe for it to operate effectively. This pressure drop consists of three components, namely the pressure drop (△Pl) necessary for the liquid to be transferred from the condenser back to the evaporator, the pressure differential (△Pv) required for the vapor to move from the evaporator to the condenser, and the gravitational head, which varies based on the heat pipe’s inclination, determines the pressure (△Pg), and can be zero, positive, or negative. In order for the heat pipe to operate correctly, it is essential that this condition is fulfilled; otherwise, the wick in the evaporator section Figure 1. Limitations to heat transport in a heat pipe. C ill Li it ti Figure 1. Limitations to heat transport in a heat pipe. Capillary Limitation Figure 1. Limitations to heat transport in a heat pipe. Figure 1. Limitations to heat transport in a heat pipe. Capillary Limitation Capillary Limitation p y Each operating limit of a sintered wick heat pipe can be considered independently. The heat pipe requires the maximum capillary pumping pressure (△𝑃௖,௠௔௫) to exceed the overall pressure drop within the pipe for it to operate effectively. This pressure drop con- sists of three components, namely the pressure drop (△𝑃௟) necessary for the liquid to be transferred from the condenser back to the evaporator, the pressure differential (△𝑃௩) re- quired for the vapor to move from the evaporator to the condenser, and the gravitational head, which varies based on the heat pipe’s inclination, determines the pressure (△𝑃௚), and can be zero, positive, or negative. In order for the heat pipe to operate correctly, it is Each operating limit of a sintered wick heat pipe can be considered independently. The heat pipe requires the maximum capillary pumping pressure (△Pc,max) to exceed the overall pressure drop within the pipe for it to operate effectively. This pressure drop consists of three components, namely the pressure drop (△Pl) necessary for the liquid to be transferred from the condenser back to the evaporator, the pressure differential (△Pv) required for the vapor to move from the evaporator to the condenser, and the gravitational head, which varies based on the heat pipe’s inclination, determines the pressure (△Pg), and can be zero, positive, or negative. In order for the heat pipe to operate correctly, it is essential that this condition is fulfilled; otherwise, the wick in the evaporator section Energies 2024, 17, 1113 3 of 12 will become depleted of moisture (dried out). The capillary limit refers to the maximum allowable heat flux at which Equation (1) [8] maintains valid. The Laplace–Young equation, represented by Equation (2), determines the highest capillary pressure (△Pc) generated within the wick structure of a heat pipe [8]. △Pc,max ≥△Pl + △Pv + △Pg (1) △Pc = 2σl re f f ·cos(θ) (2) (1) (2) where σl is the free surface energy of the working fluid and re f f corresponds the effective pores radius of the wick, which can be determined for different wick structures, while θ is the contact angle between the fluid and the wick. The contact angle refers to the extent to which a liquid can spread or wet the surface of a wick structure. When a liquid wets a surface, the contact angle θ will be between 0 and π/2 radians. Capillary Limitation Capillary Limitation However, for liquids that do not wet the surface, the contact angle θ will be greater than π/2. The capillary limitation in heat pipes occurs when the combined capillary forces produced by the vapor–liquid interfaces in the evaporator and condenser are insufficient to compensate for the pressure losses caused by fluid movement. Consequently, the heat pipe evaporator becomes dried out, causing a stoppage of thermal energy transfer from the evaporator to the condenser. 2.1. Experimental Set Up The opposite end was linked to a vacuum pump in order to eliminate air and non-condensable gas from the tube. p g p p p p y g weld pinch-off device to seal the opposite end in a similar manner. Each heat pipe was manufactured with the same dimensions for each filling ratio of the working fluid: 20 (0.2 g), 30 (0.3 g), 40 (0.4 g), and 50 (0.5 g) % volume. After the heat pipes were processed, a basic test was conducted to prevent any leakage or improper sealing, which could result in a decline in the heat pipe’s efficiency. y g g p p four hours. Subsequently, the temperature was increased to 950 °C and then held for two and a half hours. Following thorough ultrasonic cleaning with distilled water and ethanol, one of the pipe ends was completely sealed using specialized equipment. The opposite end was linked to a vacuum pump in order to eliminate air and non-condensable gas from the tube. reducing atmosphere, with the temperature raised to 850 ◦C and maintained for four hours. Subsequently, the temperature was increased to 950 ◦C and then held for two and a half hours. Following thorough ultrasonic cleaning with distilled water and ethanol, one of the pipe ends was completely sealed using specialized equipment. The opposite end was linked to a vacuum pump in order to eliminate air and non-condensable gas from the tube. p g p p p p y g weld pinch-off device to seal the opposite end in a similar manner. Each heat pipe was manufactured with the same dimensions for each filling ratio of the working fluid: 20 (0.2 g), 30 (0.3 g), 40 (0.4 g), and 50 (0.5 g) % volume. After the heat pipes were processed, a basic test was conducted to prevent any leakage or improper sealing, which could result in a decline in the heat pipe’s efficiency. y g g p p four hours. Subsequently, the temperature was increased to 950 °C and then held for two and a half hours. Following thorough ultrasonic cleaning with distilled water and ethanol, one of the pipe ends was completely sealed using specialized equipment. The opposite end was linked to a vacuum pump in order to eliminate air and non-condensable gas from the tube. Figure 2. Schematic illustration of the internal layout of a pipe before the sintering. Figure 2. 2.1. Experimental Set Up Schematic illustration of the internal layout of a pipe before the sintering. The working fluid, made up of distilled water, was filled after the vacuu set up. The manufacturing process of a sintered heat pipe was completed by weld pinch-off device to seal the opposite end in a similar manner. Each h manufactured with the same dimensions for each filling ratio of the working g), 30 (0.3 g), 40 (0.4 g), and 50 (0.5 g) % volume. After the heat pipes were basic test was conducted to prevent any leakage or improper sealing, which in a decline in the heat pipe’s efficiency. o preve e’s effic Figure 2. Schematic illustration of the internal layout of a pipe before the sintering. Figure 2. Schematic illustration of the internal layout of a pipe before the sintering. 2.2. Experimental Apparatus and Procedure In order to measure the thermal efficiency of a heat pipe, a standardized testing ap- paratus was set up. This apparatus included an experimental sector, a heating section, a cooling section, a movable apparatus with adjustable angle, a data logger (YOKOGAWA, DA100), and a computer unit, as shown in Figure 3. Typically, a water-cooler circulating system is usually used to evaluate the efficiency of heat pipes. This method is similar to natural convection evaluation techniques except for the use of water cooling The temper The working fluid, made up of distilled water, was filled after the vacuum pump was set up. The manufacturing process of a sintered heat pipe was completed by using a cold weld pinch-off device to seal the opposite end in a similar manner. Each heat pipe was manufactured with the same dimensions for each filling ratio of the working fluid: 20 (0.2 g), 30 (0.3 g), 40 (0.4 g), and 50 (0.5 g) % volume. After the heat pipes were processed, a basic test was conducted to prevent any leakage or improper sealing, which could result in a decline in the heat pipe’s efficiency. Figure 2. Schematic illustration of the internal layout of a pipe before the sintering. 2.1. Experimental Set Up The experimental parameter is shown in Table 1. A copper tube sized 160 mm in length was used in the manufacturing of sintered heat pipes. All heat pipes had an outer diameter of 4 mm and an inner diameter of 3.6 mm. For the manufacturing of sintered heat pipes, two distinct copper powders were used. The first type had an average particle size of 100 µm and showed a relatively consistent size distribution. On the other hand, the second type of powder had an average particle size of 200 µm and showed a varied particle size distribution. The experiment used potassium carbonate (K2CO3) as the pore-forming agent, which exhibited a spherical morphology with an average diameter of 35 µm. A mixture was prepared by combining copper powder with a pore-forming agent, which was present at a concentration of 40%. Table 1. Experimental parameters of heat pipes with wick. Parameters Value Pipe material Copper Outer diameter of pipe, Dwall/mm 4 Inner diameter of pipe, Di/mm 3.6 Total length, L/mm 160 Evaporator length, Le/mm 23 Adiabatic length, La/mm 87 Condenser length, Lc/mm 50 Wick material Copper powder Spherical copper power size, d/µm 100 (uniformity), 200 (diversity) Wick thickness [µm] 902, 534, 179 Working fluid Distilled water Filling ratio [% vol.] 20 (0.2 g), 30 (0.3 g), 40 (0.4 g), 50 (0.5 g) Table 1. Experimental parameters of heat pipes with wick. The heat pipe’s sintered wick was manufactured using a solid-state sintering method. Figure 2 represents a schematic of the heat pipe with wick before the process of sintering. A ceramic bar, with diameters of 1.5 mm, 2 mm, and 2.5 mm, was inserted into the pipe as the inner mandrel after the swaging process, which had caused one end of the pipe to shrink [9]. According to the study conducted by Jang et al. [5], the vertically positioned pipes containing powdered substances were subjected to the predetermined temperature schedule for sintering within the furnace. The sintering process was carried out under a hydrogen Energies 2024, 17, 1113 4 of 12 erature d reducing atmosphere, with the temperature raised to 850 ◦C and maintained for four hours. Subsequently, the temperature was increased to 950 ◦C and then held for two and a half hours. Following thorough ultrasonic cleaning with distilled water and ethanol, one of the pipe ends was completely sealed using specialized equipment. q ature of each component was measured us l d d h h h l 2.2. Experimental Apparatus and Procedure 2.2. Experimental Apparatus and Procedure I d t th th l ffi The thermocouples were placed at distances of Le = 23 mm, La = 87 mm, and Lc = 50 mm from the starting point of the evaporator section. Each thermocouple was affixed to its respective center within each division using heat-resistant polyimide tape (Kapton). Thermal grease was sprayed to the heat block and cooling plate in order to enhance thermal conductivity where they were in contact with the heat pipe. Each test sector was covered with an insulation block to reduce the heat loss from the evaporator, adiabatic, and condenser sections, all of which were fastened with jointers. The heat pipe inclination angle was adjusted from 0◦to 90◦for the tilting angle test, using a variable angle holding table. The DC power supply is employed for setting the heat power input for the evaporator section. Furthermore, the temperature data in a stable state were recorded using a data logger, with an interval of approximately 60 min between each input heating load. The computer also stored steady-state temperature data for the purpose of data reduction and analysis [10]. been divided into two groups for the evaporator, with one group for the adiabatic section and the other group for the condenser section. The thermocouples were placed at dis- tances of Le = 23 mm, La = 87 mm, and Lc = 50 mm from the starting point of the evaporator section. Each thermocouple was affixed to its respective center within each division using heat-resistant polyimide tape (Kapton). Thermal grease was sprayed to the heat block and cooling plate in order to enhance thermal conductivity where they were in contact with the heat pipe. Each test sector was covered with an insulation block to reduce the heat loss from the evaporator, adiabatic, and condenser sections, all of which were fastened with jointers. The heat pipe inclination angle was adjusted from 0° to 90° for the tilting angle test, using a variable angle holding table. The DC power supply is employed for setting the heat power input for the evaporator section. Furthermore, the temperature data in a stable state were recorded using a data logger, with an interval of approximately 60 min between each input heating load. The computer also stored steady-state temperature data for the purpose of data reduction and analysis [10]. Figure 4. Schematic illustration of the configuration of the test device and the locations of thermo- couples. Figure 4. q ature of each component was measured us l d d h h h l 2.2. Experimental Apparatus and Procedure 2.2. Experimental Apparatus and Procedure I d t th th l ffi ply provided heat to the evaporator, while the chiller was used to cool the condenser with water. In order to measure the thermal efficiency of a heat pipe, a standardized testing apparatus was set up. This apparatus included an experimental sector, a heating section, a cooling section, a movable apparatus with adjustable angle, a data logger (YOKOGAWA, DA100), and a computer unit, as shown in Figure 3. Typically, a water-cooler circulating system is usually used to evaluate the efficiency of heat pipes. This method is similar to natural convection evaluation techniques, except for the use of water cooling. The temperature of each component was measured using K-type thermocouples. The DC power supply provided heat to the evaporator, while the chiller was used to cool the condenser with water. In order to measure the thermal efficiency of a heat pipe, a standardized testing ap- paratus was set up. This apparatus included an experimental sector, a heating section, a cooling section, a movable apparatus with adjustable angle, a data logger (YOKOGAWA, DA100), and a computer unit, as shown in Figure 3. Typically, a water-cooler circulating system is usually used to evaluate the efficiency of heat pipes. This method is similar to natural convection evaluation techniques, except for the use of water cooling. The temper- ature of each component was measured using K-type thermocouples. The DC power sup- ply provided heat to the evaporator, while the chiller was used to cool the condenser with water. Figure 3. Schematic illustration of the experimental test apparatus. Figure 3. Schematic illustration of the experimental test apparatus. Figure 3. Schematic illustration of the experimental test apparatus. ematic il Figure 3. Schematic illustration of the experimental test apparatus. Figure 3. Schematic illustration of the experimental test apparatus. The experimental procedure for conducting the temperature rise test at each tilting angle was as follows: At first, the samples were fastened onto the test bench. Secondly, as shown in Figure 4, six thermocouples were positioned on the wall surfaces of the heat tubes, cartridge heater, cooling plate, and ambient temperature. The thermocouples have Energies 2024, 17, 1113 5 of 12 ndly, as he heat 5 of 12 ndly, as he heat been divided into two groups for the evaporator, with one group for the adiabatic section and the other group for the condenser section. q ature of each component was measured us l d d h h h l 2.2. Experimental Apparatus and Procedure 2.2. Experimental Apparatus and Procedure I d t th th l ffi Schematic illustration of the configuration of the test device and the locations of thermocouples. Th ll th l i t f h t i d fi d b th f ll i E ti (3) [11] Figure 4. Schematic illustration of the configuration of the test device and the locations of thermo- Figure 4. Schematic illustration of the configuration of the test device and the locations of thermocouples. Figure 4. Schematic illustration of the configuration of the test device and the locations of thermo- couples. Figure 4. Schematic illustration of the configuration of the test device and the locations of thermocouples. Th ll th l i t f h t i d fi d b th f ll i E ti (3) [11] uples. The overall thermal resistance of a heat pipe defined by the following Equation (3) [11]: e of a heat pipe defined by the following Equation (3) 𝑇 𝑇 R = Teva. −Tcon. . Q (3) n (3) (3) . Q 𝑅= ௘௩௔. ௖௢௡. 𝑄ሶ (3) where 𝑇௘௩௔. and 𝑇௖௢௡. are the temperature of the evaporator and condenser sections, re- spectively. The heat input power, denoted as Q ̇, is controlled by the voltage (V) and am- perage (I). The occurrence of heat pipe dry-out has been attributed to a rapid increase in thermal resistance If an abrupt change occurs the test is stopped and the sample is ex where Teva. and Tcon. are the temperature of the evaporator and condenser sections, respec- tively. The heat input power, denoted as . Q, is controlled by the voltage (V) and amperage (I). The occurrence of heat pipe dry-out has been attributed to a rapid increase in thermal resistance. If an abrupt change occurs, the test is stopped, and the sample is extracted from the device. Conversely, the input power gradually increases once more. 3.1. The Comparison of Heat Transfer Performance According to Cu Powder Type Figure 5c,d shows that the heat pipe encountered operational challenges and showed a notable initial thermal resistance when the filling ratios were set at 40% and 50%. Therefore, even after subjecting the heat block to a rise in temperature of 120 °C, it was not possible to determine the dry out point Figure 5a shows the thermal resistance values of the 100 U and 200 D samples when the working fluid filling level is at 20%. When the test is conducted at angles of 45◦and 90◦, the 100 U sample exhibits dry-out at a heat input of 3.5 W. However, the 200 D sample has a higher Qmax value of 10 W or more. At a 30% filling ratio of the working fluid, the thermal resistance of 100 U is higher than that of 200 D, as shown in Figure 5b. The specimens showed comparable drying out points at both 45◦and 90◦, with few differences. Nevertheless, the thermal resistance of the 200 D specimen was determined to be lower than 100 U. Figure 5c,d shows that the heat pipe encountered operational challenges and showed a notable initial thermal resistance when the filling ratios were set at 40% and 50%. Therefore, even after subjecting the heat block to a rise in temperature of 120 ◦C, it was not possible to determine the dry-out point. was not possible to determine the dry-out point. Based on the previous capillary force test results, it is evident that the capillary force (△𝑃௖) is influenced by a complex correlation with both the porosity and the effective ra- dius of the wick’s pores (𝑟௘௙௙). The 100 U sample had the largest 𝑟௘௙௙ value of 241.31 µm, and the 200 D sample had the lowest one of 155.73 µm. Furthermore, the porosity value of 100 U was found to be 59.07%, which was higher than the porosity value of 200 D, which was estimated to be 56.47% [5]. Nevertheless, the 200 D sample exhibited stronger capil- lary forces. This could be attributed to the smaller effective radius (𝑟௘௙௙) value, which in- dicates that the capillary force is mainly affected by the 𝑟௘௙௙ value. Moreover, empirical p y p Based on the previous capillary force test results, it is evident that the capillary force (△Pc) is influenced by a complex correlation with both the porosity and the effective radius of the wick’s pores (re f f ). 3.1. The Comparison of Heat Transfer Performance According to Cu Powder Type 3.1. The Comparison of Heat Transfer Performance According to Cu Powder Type Figure 5 shows the thermal resistance results for samples 100 U and 200 D. The test angles of 0◦, 45◦, and 90◦are included, as well as the working fluid filling ratio, which ranges from 20% to 50%. The sintering process used a mandrel of 2 mm in diameter, resulting in the formation of a wick with a thickness of 534.7 µm. For heat inputs of 12 W or less, the overall thermal resistance of the 200 D sample was lower than that of the 100 U sample. Energies 2024, 17, 1113 6 of 12 100 U Figure 5. Thermal performance of a heat pipe according to the Cu powder size, the tilting angle, and filling ratios of the working fluid of (a) 20%, (b) 30%, (c) 40%, and (d) 50% (mandrel: 2 mm diameter). Figure 5. Thermal performance of a heat pipe according to the Cu powder size, the tilting angle, and filling ratios of the working fluid of (a) 20%, (b) 30%, (c) 40%, and (d) 50% (mandrel: 2 mm diameter). Figure 5. Thermal performance of a heat pipe according to the Cu powder size, the tilting angle, and filling ratios of the working fluid of (a) 20%, (b) 30%, (c) 40%, and (d) 50% (mandrel: 2 mm diameter). Figure 5. Thermal performance of a heat pipe according to the Cu powder size, the tilting angle, and filling ratios of the working fluid of (a) 20%, (b) 30%, (c) 40%, and (d) 50% (mandrel: 2 mm diameter). Figure 5a shows the thermal resistance values of the 100 U and 200 D samples when the working fluid filling level is at 20%. When the test is conducted at angles of 45° and 90°, the 100 U sample exhibits dry-out at a heat input of 3.5 W. However, the 200 D sample has a higher Qmax value of 10 W or more. At a 30% filling ratio of the working fluid, the thermal resistance of 100 U is higher than that of 200 D, as shown in Figure 5b. The speci- mens showed comparable drying out points at both 45°and 90°, with few differences. Nev- ertheless, the thermal resistance of the 200 D specimen was determined to be lower than 100 U. 3.1. The Comparison of Heat Transfer Performance According to Cu Powder Type The 100 U sample had the largest re f f value of 241.31 µm, and the 200 D sample had the lowest one of 155.73 µm. Furthermore, the porosity value of 100 U was found to be 59.07%, which was higher than the porosity value of 200 D, which was estimated to be 56.47% [5]. Nevertheless, the 200 D sample exhibited stronger capillary forces. This could be attributed to the smaller effective radius (re f f ) value, which indicates that the capillary force is mainly affected by the re f f value. Moreover, empirical evidence suggests that the powder filling density of 200 D is higher than that of 100 U, primarily because it covers a wider range of particle sizes. Therefore, applying a 200 D powder-based wick has significant advantages in creating small, efficient pore sizes. This corresponds to the observation that 200 D has superior thermal conductivity compared to 100 U. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle The average thickness of the wick structure was measured to 534.7 µm, and 179.1 µm for mandrel diameters of 1.5, 2, and 2.5 mm, respectiv 4, 17, x FOR PEER REVIEW ing the wick to become wet in m amount of working fluid that h wick is excessively thick. Moreo e in the cross-sectional area avail uently, the friction coefficient of v onstraint on the maximum heat ough, the passage becomes too s section is contr directions. As a transported to cessive thickne the passage of the vapor flow capacity. Conv olled by the capillary force, cau result, there is a decrease in the he evaporation section when the s of the wick leads to a decreas vapor through the pipe. Consequ passage rises, thus serving as a c rsely, if the wick is not thick en lled b ng th Figure 6. SEM images of the cross-section of a sintered heat pipe according to the th wick. (a) 902 µm (mandrel: 1.5 mm𝜙), (b) 534.7 µm (mandrel: 2 mm𝜙), and (c) 179.1 2.5 mm𝜙). Figure 6. SEM images of the cross-section of a sintered heat pipe according to the thickness of the wick. (a) 902 µm (mandrel: 1.5 mmϕ), (b) 534.7 µm (mandrel: 2 mmϕ), and (c) 179.1 µm (mandrel: 2.5 mmϕ). the condensed working fluid in the condensation sector to be transported to th sector by capillary force. The experimental results in this study coincide with the theory mentioned indicating that the optimal thermal transfer performance was attained by empl Figure 7 shows the thermal resistance measured in the 100 U sample wh the mandrel diameters and tilt angles. The thermal resistance primarily dep surface area of the interface between the liquid and vapor phases, as indicated ical analysis [12]. The sample with the smallest wick thickness (tw) of 179.1 µ diameter: 1.5 mm) showed the highest thermal resistance, indicating the low transfer capability in comparison to all other tested samples. Furthermore, the mal resistance of this sample exhibited a notable difference compared to the sistance of the other samples. In addition, the temperature at the evaporator creased quickly in response to the heat input, ultimately reaching a maximum a heat input of 5 W. The substantial rise in temperature caused difficulties fo determining the final Qmax value. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle The present problems come from the inade ness of the sintered wick, hindering the effective transfer of the condensed w from the condenser section to the evaporator section via capillary force. Th pipe with the thinnest wick exhibited a comparatively lower heat transfer effi the pipe with a thicker wick. The heat resistance remained consistently low for both the 902 µm and 534 Figure 7 shows the thermal resistance measured in the 100 U sample while varying the mandrel diameters and tilt angles. The thermal resistance primarily depends on the surface area of the interface between the liquid and vapor phases, as indicated by theoretical analysis [12]. The sample with the smallest wick thickness (tw) of 179.1 µm (mandrel diameter: 1.5 mm) showed the highest thermal resistance, indicating the lowest thermal transfer capability in comparison to all other tested samples. Furthermore, the initial thermal resistance of this sample exhibited a notable difference compared to the thermal resistance of the other samples. In addition, the temperature at the evaporator section increased quickly in response to the heat input, ultimately reaching a maximum of 70 ◦C at a heat input of 5 W. The substantial rise in temperature caused difficulties for accurately determining the final Qmax value. The present problems come from the inadequate thickness of the sintered wick, hindering the effective transfer of the condensed working fluid from the condenser section to the evaporator section via capillary force. Therefore, the pipe with the thinnest wick exhibited a comparatively lower heat transfer efficiency than the pipe with a thicker wick. medium-sized wick thickness of 534.7 µm, which was produced using a mandrel diameter of 2 mm. When the angle is 0°, it is observed that the thermal resistance of the wick thickness of 902 µm is relatively lower than that of the wick with a thickness of 53 This difference can be attributed to the preferential movement of the working fluid the heat pipe towards one side, caused by the force of gravity. This bias results fr basic assumption that the wick on one side initiates its operation at relatively low peratures. Reducing the thickness of the wick causes the absorbed working fluid t mulate mostly on the lower side of the heat pipe. The formation of a bubble barrier as a result of the large amount of working fluid, even at lower temperatures, whi ders the vapor’s movement. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle ickness of the wick increases, the surface area of liquid that ca so increases. This leads to a reduction in the pressure drop be e easily through the wick. However, Li, Y et al. [13] observed eased in direct proportion to the increase in the thickness of thicknesses, re with a wick th pipe with a th the heat pipe w fer capability. por passage as surface area th As the thi by the wick als can flow more hrough the w direct propor p p wick. They explained that the movement of the working fluid towards the Figure 7. Thermal performance of heat pipe in relation to heat input for various mandrel d and tilt angles: (a) 0°, (b) 45°, and (c) 90°. The wick was made with 100 U powder and fill was 30%. Figure 7. Thermal performance of heat pipe in relation to heat input for various mandrel diameters and tilt angles: (a) 0◦, (b) 45◦, and (c) 90◦. The wick was made with 100 U powder and filling ratio was 30%. 3.3. Comparison of Heat Transfer Performance According to the Working Fluid Filling Ra Figure 8 shows the heat transfer performance of the heat pipe in relation to the ratio (Rf) of the working fluid at various tilting angles. The heat pipes in the experi setup used a wick with the same wick thickness of 534.7 µm (mandrel diameter: which was made by employing 200 D copper powder. Samples were prepared by in 0.2 g (Rf = 20%), 0.3 g (Rf = 30%), 0.4 g (Rf = 40%), and 0.5 g (Rf = 50%) of the workin into the heat pipe, giving a total filling amount of 1 g. At a filling ratio (Rf) of 50%, the thermal resistance exhibited the highest valu test angles. In addition, the thermal resistance showed a tendency to decrease as th The heat resistance remained consistently low for both the 902 µm and 534.7 µm wick thicknesses, regardless of the test angle. Furthermore, it can be observed that the heat pipe with a wick thickness of 534.7 µm has a higher dry-out temperature compared to the heat pipe with a thickness of 902 µm at all tilting angles. Therefore, it can be concluded that the heat pipe with a medium-sized wick thickness of 534.7 µm has the superior heat transfer capability. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle The heat pipe wicks were fabricated by sintering copper powders, with the inclusion of ceramic inner mandrels sized 1.5, 2, and 2.5 mm in diameter. Figure 6 exhibits cross- sectional SEM images of a heat pipe with a wick that has been installed subsequent to the Energies 2024, 17, 1113 7 of 12 , with th sintering process. The average thickness of the wick structure was measured to be 902 µm, 534.7 µm, and 179.1 µm for mandrel diameters of 1.5, 2, and 2.5 mm, respectively. sectional SEM images of a heat pipe with a wick that has been installed subseq sintering process. The average thickness of the wick structure was measured to 534.7 µm, and 179.1 µm for mandrel diameters of 1.5, 2, and 2.5 mm, respectiv Figure 6. SEM images of the cross-section of a sintered heat pipe according to the thi wick. (a) 902 µm (mandrel: 1.5 mm𝜙), (b) 534.7 µm (mandrel: 2 mm𝜙), and (c) 179.1 µ 2.5 mm𝜙). Figure 6. SEM images of the cross-section of a sintered heat pipe according to the thickness of the wick. (a) 902 µm (mandrel: 1.5 mmϕ), (b) 534.7 µm (mandrel: 2 mmϕ), and (c) 179.1 µm (mandrel: 2.5 mmϕ). 4, 17, x FOR PEER REVIEW section is controlled by the capillary force, causing the wick to become wet in m directions. As a result, there is a decrease in the amount of working fluid that ha transported to the evaporation section when the wick is excessively thick. Moreov cessive thickness of the wick leads to a decrease in the cross-sectional area availa the passage of vapor through the pipe. Consequently, the friction coefficient of v the vapor flow passage rises, thus serving as a constraint on the maximum heat t capacity. Conversely, if the wick is not thick enough, the passage becomes too sm the condensed working fluid in the condensation sector to be transported to the sector by capillary force. The experimental results in this study coincide with the theory mentioned indicating that the optimal thermal transfer performance was attained by emplo sintering process. The average thickness of the wick structure was measured to be 902 µm, 534.7 µm, and 179.1 µm for mandrel diameters of 1.5, 2, and 2.5 mm, respectively. g p p q sintering process. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle Consequently, it has been determined that the initial t resistance exhibited a significant value [14]. Therefore, it is important to take into account two factors when determin thickness of the wick. Firstly, the wick should be thick enough to enable the transfe condensed internal working fluid from the condenser section to the vapor section capillary force. Furthermore, it is also necessary that the internal space of the pipe ficiently large to ensure a proper pathway for the flow of vapor. thicknesses, regardless of the test angle. Furthermore, it can be observed that th with a wick thickness of 534.7 µm has a higher dry-out temperature compared pipe with a thickness of 902 µm at all tilting angles. Therefore, it can be con the heat pipe with a medium-sized wick thickness of 534.7 µm has the superior fer capability. This phenomenon can be explained by the decrease in the widt por passage as the wick thickness increases, along with the corresponding inc surface area that comes into contact with the working fluid. As the thickness of the wick increases, the surface area of liquid that can b by the wick also increases. This leads to a reduction in the pressure drop becau can flow more easily through the wick. However, Li, Y et al. [13] observed th sure loss increased in direct proportion to the increase in the thickness of th wick. They explained that the movement of the working fluid towards the e Figure 7. Thermal performance of heat pipe in relation to heat input for various mandrel di and tilt angles: (a) 0°, (b) 45°, and (c) 90°. The wick was made with 100 U powder and filli was 30%. Figure 7. Thermal performance of heat pipe in relation to heat input for various mandrel diameters and tilt angles: (a) 0◦, (b) 45◦, and (c) 90◦. The wick was made with 100 U powder and filling ratio was 30%. egardless of the test angle. Furthermore, it can be observed tha hickness of 534.7 µm has a higher dry-out temperature compa hickness of 902 µm at all tilting angles. Therefore, it can be c with a medium-sized wick thickness of 534.7 µm has the supe This phenomenon can be explained by the decrease in the w s the wick thickness increases, along with the corresponding hat comes into contact with the working fluid. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle This phenomenon can be explained by the decrease in the width of the vapor passage as the wick thickness increases, along with the corresponding increase in the surface area that comes into contact with the working fluid. test angles. In addition, the thermal resistance showed a tendency to decrease as th input increased. The initial thermal resistance is very high due to the excessive am As the thickness of the wick increases, the surface area of liquid that can be absorbed by the wick also increases. This leads to a reduction in the pressure drop because the fluid Energies 2024, 17, 1113 8 of 12 can flow more easily through the wick. However, Li, Y et al. [13] observed that the pressure loss increased in direct proportion to the increase in the thickness of the heat pipe wick. They explained that the movement of the working fluid towards the evaporation section is controlled by the capillary force, causing the wick to become wet in multiple directions. As a result, there is a decrease in the amount of working fluid that has to be transported to the evaporation section when the wick is excessively thick. Moreover, excessive thickness of the wick leads to a decrease in the cross-sectional area available for the passage of vapor through the pipe. Consequently, the friction coefficient of vapor in the vapor flow passage rises, thus serving as a constraint on the maximum heat transfer capacity. Conversely, if the wick is not thick enough, the passage becomes too small for the condensed working fluid in the condensation sector to be transported to the vapor sector by capillary force. 9 orking fluid, which requires more heat input to produce the latent heat of evapora p p y p y The experimental results in this study coincide with the theory mentioned above, indicating that the optimal thermal transfer performance was attained by employing a medium-sized wick thickness of 534.7 µm, which was produced using a mandrel with a diameter of 2 mm. g q p p p he maximum permissible temperature for general electronic products employing s onductors is 125 °C [15]. The dry-out temperature could not be determined, even w he heat block temperature was raised to 130 °C or higher. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle Thus, when the heat pi wick has a thickness of 534 7 µm it is evident that the heat transfer capacity significa When the angle is 0◦, it is observed that the thermal resistance of the wick with a thick- ness of 902 µm is relatively lower than that of the wick with a thickness of 534.7 µm. This difference can be attributed to the preferential movement of the work- ing fluid within the heat pipe towards one side, caused by the force of gravity. This bias results from the basic assumption that the wick on one side initiates its operation at rela- tively lower temperatures. Reducing the thickness of the wick causes the absorbed working fluid to accumulate mostly on the lower side of the heat pipe. The formation of a bubble barrier occurs as a result of the large amount of working fluid, even at lower temperatures, which hinders the vapor’s movement. Consequently, it has been determined that the initial thermal resistance exhibited a significant value [14]. ick has a thickness of 534.7 µm, it is evident that the heat transfer capacity significa ecreases when it is filled to a rate of 50% due to excessive filling. On the other hand, lling ratio (Rf) of 20%, the thermal resistance values consistently show the lowest lev ndicating superior thermal transfer capability regardless of the tested angles. Howe he dry-out point is relatively low, meaning that the pipe cannot effectively perform ansfer at high temperatures. The samples with Rf = 30% and 40% exhibit the same esistance values at angles of 45° and 90°, as shown in Figure 8b,c. Nevertheless, w ubjected to a power exceeding 13 W, the sample with the Rf of 40% exhibits a slig igher thermal resistance compared to the sample with the Rf of 30%. Two key requ ments for an efficient heat pipe are low thermal resistance and a moderately high dry Therefore, it is important to take into account two factors when determining the thickness of the wick. Firstly, the wick should be thick enough to enable the transfer of the condensed internal working fluid from the condenser section to the vapor section using capillary force. Furthermore, it is also necessary that the internal space of the pipe is sufficiently large to ensure a proper pathway for the flow of vapor. 3.2. Comparison of Heat Transfer Performance According to Sintered Wick Thickness and Test Angle ments for an efficient heat pipe are low thermal resistance and a moderately high dry oint. According to these criteria, it can be concluded that this heat pipe exhibits optim eat transfer properties when the filling ratio (Rf) of the working fluid is 30%. As the filling ratio (Rf) of the working fluid rises, there is a proportional increa he amount of fluid that undergoes a phase transition into vapor, as well as an increa 3.3. Comparison of Heat Transfer Performance According to the Working Fluid Filling Ratio e quantity of fluid that returns back to a liquid state in the condenser section. Th itial thermal resistance observed in the condenser section may be attributed to Figure 8 shows the heat transfer performance of the heat pipe in relation to the filling ratio (Rf) of the working fluid at various tilting angles. The heat pipes in the experimental setup used a wick with the same wick thickness of 534.7 µm (mandrel diameter: 2 mm), which was made by employing 200 D copper powder. Samples were prepared by injecting 0.2 g (Rf = 20%), 0.3 g (Rf = 30%), 0.4 g (Rf = 40%), and 0.5 g (Rf = 50%) of the working fluid into the heat pipe, giving a total filling amount of 1 g. nitial thermal resistance observed in the condenser section may be attributed to the p nce of residual working fluid, which acts as a liquid barrier. Furthermore, when the n extensive amount of fluid, the heat input required to convert the working fluid apor also increases. In this case, the thermal resistance remains high at lower temp ures. As the temperature rises, the liquid block reduces gradually, resulting in an incr n heat transfer capacity. As it improves, the corresponding value of Qmax increases. Figure 8. Thermal performance of the heat pipe according to the working fluid filling ratio at di ent test angles of (a) 0°, (b) 45°, and (c) 90°. Figure 8. Thermal performance of the heat pipe according to the working fluid filling ratio at different test angles of (a) 0◦, (b) 45◦, and (c) 90◦. gure 8. Thermal performance of the heat pipe according to the working fluid filling ratio at d nt test angles of (a) 0°, (b) 45°, and (c) 90°. Figure 8. Thermal performance of the heat pipe according to the working fluid filling ratio at different test angles of (a) 0◦, (b) 45◦, and (c) 90◦. Energies 2024, 17, 1113 9 of 12 At a filling ratio (Rf) of 50%, the thermal resistance exhibited the highest value at all test angles. In addition, the thermal resistance showed a tendency to decrease as the heat input increased. The initial thermal resistance is very high due to the excessive amount of working fluid, which requires more heat input to produce the latent heat of evaporation. The maximum permissible temperature for general electronic products employing semicon- ductors is 125 ◦C [15]. The dry-out temperature could not be determined, even when the heat block temperature was raised to 130 ◦C or higher. 3.3. Comparison of Heat Transfer Performance According to the Working Fluid Filling Ratio e quantity of fluid that returns back to a liquid state in the condenser section. Th itial thermal resistance observed in the condenser section may be attributed to Thus, when the heat pipe’s wick has a thickness of 534.7 µm, it is evident that the heat transfer capacity significantly decreases when it is filled to a rate of 50% due to excessive filling. On the other hand, at a filling ratio (Rf) of 20%, the thermal resistance values consistently show the lowest levels, indicating superior thermal transfer capability regardless of the tested angles. However, the dry-out point is relatively low, meaning that the pipe cannot effectively perform heat transfer at high temperatures. The samples with Rf = 30% and 40% exhibit the same heat resistance values at angles of 45◦and 90◦, as shown in Figure 8b,c. Nevertheless, when subjected to a power exceeding 13 W, the sample with the Rf of 40% exhibits a slightly higher thermal resistance compared to the sample with the Rf of 30%. Two key requirements for an effi- cient heat pipe are low thermal resistance and a moderately high dry-out point. According to these criteria, it can be concluded that this heat pipe exhibits optimum heat transfer properties when the filling ratio (Rf) of the working fluid is 30%.il As the filling ratio (Rf) of the working fluid rises, there is a proportional increase in the amount of fluid that undergoes a phase transition into vapor, as well as an increase in the quantity of fluid that returns back to a liquid state in the condenser section. The higher initial thermal resistance observed in the condenser section may be attributed to the presence of residual working fluid, which acts as a liquid barrier. Furthermore, when there is an extensive amount of fluid, the heat input required to convert the working fluid into vapor also increases. In this case, the thermal resistance remains high at lower temperatures. As the temperature rises, the liquid block reduces gradually, resulting in an increase in heat transfer capacity. As it improves, the corresponding value of Qmax increases. EW 10 of 12 Figure 9 shows a schematic diagram illustrating the progressive change in a liquid- vapor state in a heat pipe. The heat pipe contains a wick with a thickness of 534.7 µm, which is made of 200 D powder. This transition proceeds as the temperature rises. During the initial stage, when the evaporation sector is being heated, the heat pipe exhibits a significant level of thermal resistance until the vapor is generated. 3.3. Comparison of Heat Transfer Performance According to the Working Fluid Filling Ratio e quantity of fluid that returns back to a liquid state in the condenser section. Th itial thermal resistance observed in the condenser section may be attributed to Subsequently, despite a rise in temperature and the resulting generation of vapor in the evaporation sector, the presence of bubble blocks hinders the movement of vapor [16]. As the temperature rises, these bubble blocks disappear, thereby enabling the possibility of heat transfer. With an increase in the amount of working fluid, it is expected that the dry-out tem- perature will eventually increase. On the contrary, in order to achieve a low thermal re- sistance, it is essential to minimize the occurrence of initial bubble blockage caused by an excessive amount of working fluid. Therefore, it is necessary to maintain the working fluid at an appropriate level. The study observed that the optimal heat transfer capability was achieved when the level of working fluid was between 30–40%, which corresponds to re- sults from previous studies [17–20]. Figure 9. Thermal resistance variation at different heating power input (tilting angle: 45°). 3.4. Effect of the Tilling Angle on Heat Transfer Performance Figure 9. Thermal resistance variation at different heating power input (tilting angle: 45◦). Figure 9. Thermal resistance variation at different heating power input (tilting angle: 45°). Figure 9. Thermal resistance variation at different heating power input (tilting angle: 45◦). Energies 2024, 17, 1113 10 of 12 10 of 12 Afterwards, at a higher temperature, there is an increase in the amount of vapor accumulated in the condensation sector, while the amount of working fluid that need to be transported back to the evaporation sector through capillary force gradually decreases. In the case of a sustained rise in temperature, the working fluid in the evaporation sector becomes exhausted and the generation of evaporation-latent heat becomes impossible, leading to a dry-out state. g y With an increase in the amount of working fluid, it is expected that the dry-out temperature will eventually increase. On the contrary, in order to achieve a low thermal resistance, it is essential to minimize the occurrence of initial bubble blockage caused by an excessive amount of working fluid. Therefore, it is necessary to maintain the working fluid at an appropriate level. The study observed that the optimal heat transfer capability was achieved when the level of working fluid was between 30–40%, which corresponds to results from previous studies [17–20]. 3.4. Effect of the Tilling Angle on Heat Transfer Performance The comprehensive test results showed that there was an enhancement in heat transfer capability as the test angle (θ) increased from 0◦to 90◦, regardless of variations in powder type and wick thickness. This phenomenon can be attributed to the enhanced thermal distribution enabled by the gravity force, as well as the increased surface area of heat transfer, leading to higher cooling and heating capabilities. Figure 10 shows a schematic illustration of the phenomenon of capillary rise in a cylindrical tube, wherein the tilling angles are denoted by θ. The mathematical representation of the tilting angle requires the calculation of the cosine of the angle(θ) produced between two vectors. Hence, when the test angle reaches 90◦, the alignment of capillary force and gravity occurs, leading to the enhanced movement of the liquid working fluid due to the resultant force. As the test angle approaches 0◦, the relative alignment of capillary force and gravity undergoes a transition leading to a decrease in the value of cosθ and a reduction in the rate of the working fluid’s returning to the evaporator. In the situation of a horizontal orientation, the force of gravity is negated, thus enabling the controlled flow of the working fluid towards the evaporation unit. The decrease in pumping capacity causes a decrease in the ultimate operational threshold [21]. EW 11 of 12 Figure 10. A schematic of capillary rise in a cylindrical tube with tilling angles. Figure 10. A schematic of capillary rise in a cylindrical tube with tilling angles. Figure 10. A schematic of capillary rise in a cylindrical tube with tilling angles. Figure 10. A schematic of capillary rise in a cylindrical tube with tilling angles. 4 Conclusions 4. Conclusions 4. Conclusions 4. Conclusions This can be attributed to the enhanced thermal distribu- tion by the gravity force, as well as the expansion of the surface area for heat transfer due to the enlarged cooling and heating surfaces. Consequently, the heat resistance exhibits a low value, whereas the Qmax exhibits a high value. Author Contributions: Methodology, I.-N.J.; Formal analysis, I.-N.J. and Y.-S.A.; Investigation, I.-N.J. and Y.-S.A.; Resources, Y.-S.A.; Data curation, I.-N.J.; Writing—original draft, I.-N.J. and Y.-S.A.; Writing—review & editing, Y.-S.A.; Visualization, I.-N.J.; Supervision, Y.-S.A.; Project administration, Y.-S.A.; Funding acquisition, Y.-S.A. All authors have read and agreed to the published version of the manuscript. Funding: This research was financially supported by the Ministry of Trade, Industry, and Energy (MOTIE), Korea, under the “Development of a Cooling module for the Aircraft Data Transfer System (DTS)” program (reference number P150200002), supervised by the Korea Institute for Advancement of Technology (KIAT). Data Availability Statement: All data are contained in the paper. Data Availability Statement: All data are contained in the paper. Data Availability Statement: All data are contained in the paper. Conflicts of Interest: The authors declare no conflicts of interest. Conflicts of Interest: The authors declare no conflicts of interest. References 1. Kim, S.-D.; Kang, H.-K.; Sung, B.-H.; Kim, C.-J. In A Study on a Sintered Metal Wick Heat Pipe; Manufacturing and Inspection. In Proceedings of the KSME Conference, The Korean Society of Mechanical Engineers, Seoul, Republic of Korea, 20–22 April 2004; pp. 1487–1492. pp 2. Lee, W.H.; Lee, K.W.; Park, K.H.; Lee, K.J.; Noh, S.Y. In Study on a Operating Characteristics of Loop Heat Pipe Using a Brass Sintered Metal Wick-Water. In Proceedings of the KSME Conference, The Korean Society of Mechanical Engineers, Seoul, Republic of Korea, 20–22 April 2004; pp. 1528–1533. p pp 3. Yun, H.G.; Moon, S.H.; Ko, S.C.; Hwang, G.; Choy, T.G. Manufacturing and operating performance of the heat pipe with sintered wick. Trans. Korean Soc. Mech. Eng. B 2002, 26, 1260–1266. [CrossRef] g 4. Jose, J.; Kumar Hotta, T. A comprehensive review of heat pipe: Its types, incorporation techniques, methods of analysis and applications. Therm. Sci. Eng. Prog. 2023, 42, 101860. [CrossRef] g 4. Jose, J.; Kumar Hotta, T. A comprehensive review of heat pipe: Its types, incorporation techniques, methods of analysis and applications. Therm. Sci. Eng. Prog. 2023, 42, 101860. [CrossRef] pp g g 5. Jang, I.-N.; Ahn, Y.-S. The Study of Copper Powder Sintering for Porous Wick Structures with High Capillary Force. Materials 2023, 16, 4231. [CrossRef] [PubMed] pp g g 5. Jang, I.-N.; Ahn, Y.-S. The Study of Copper Powder Sintering for Porous Wick Structures with High Capillary Force. Materials 2023, 16, 4231. [CrossRef] [PubMed] 6. Nezam, Z.Z.; Zohuri, B. Heat pipe as a passive cooling system driving new generation of nuclear power plants. Edelweiss Chem. Sci. J. 2020, 3, 326. [CrossRef] 6. Nezam, Z.Z.; Zohuri, B. Heat pipe as a passive cooling system driving new generation of nuclear power plants. Edelweiss Chem. Sci. J. 2020, 3, 326. [CrossRef] J 7. Nemec, P.; ˇCaja, A.; Malcho, M. Mathematical model for heat transfer limitations of heat pipe. Math. Comput. Model. 2013, 57, 126–136. [CrossRef] 7. Nemec, P.; ˇCaja, A.; Malcho, M. Mathematical model for heat transfer limitations of heat pipe. Math. Comput. Model. 2013, 57, 126–136. [CrossRef] n, R.; Kew, P. Heat Pipes: Theory, Design and Applications; Butterworth-Heinemann: Oxford, UK, 2013. 9. Jiang, L.-l.; Yong, T.; Wei, Z.; Jiang, L.-z.; Tan, X.; Yan, L.; Gao, J.-w. Design and fabrication of sintered wick for miniature cylindrical heat pipe. Trans. Nonferrous Met. Soc. China 2014, 24, 292–301. [CrossRef] y p p f 10. 4. Conclusions 4. Conclusions 4. Conclusions (1) The heat pipe, which was equipped with a sintered wick made from 200 D powder, exhibited a smaller effective pore radius in comparison to 100 U. As a result, the uti- lization of 200 D powder resulted in an enhanced capillary force and exhibited im- proved efficacy in heat transfer. (1) The heat pipe, which was equipped with a sintered wick made from 200 D powder, exhibited a smaller effective pore radius in comparison to 100 U. As a result, the utilization of 200 D powder resulted in an enhanced capillary force and exhibited improved efficacy in heat transfer. Energies 2024, 17, 1113 11 of 12 11 of 12 (2) The heat pipes’ wick thicknesses were measured as 902 µm, 534.7 µm, and 179.1 µm, which correspond to mandrel diameters of 1.5 mm, 2 mm, and 2.5 mm, respectively. The heat pipe with a wick thickness of 534.7 µm exhibited the most efficient heat transfer performance. The presence of a sufficient thickness of the wick ensures that an appropriate amount of working fluid is available to reach the region where evaporation takes place. Conversely, reducing the thickness of the wick results in a decrease in the amount of working fluid that can be retained in the wick, which can lead to dry-out, even when operating at low temperatures.i y p g p (3) The initial thermal resistance value showed an increase as the filling ratio of the working fluid increased from 20 wt.% to 50 wt.%. Additionally, it was observed that the Qmax value exhibited a positive correlation with increasing temperature. (3) The initial thermal resistance value showed an increase as the filling ratio of the working fluid increased from 20 wt.% to 50 wt.%. Additionally, it was observed that the Qmax value exhibited a positive correlation with increasing temperature. (4) The heat transfer performance showed an enhancement as the tilting angles increased within the range of 0◦to 90◦. This can be attributed to the enhanced thermal distribu- tion by the gravity force, as well as the expansion of the surface area for heat transfer due to the enlarged cooling and heating surfaces. Consequently, the heat resistance exhibits a low value, whereas the Qmax exhibits a high value. (4) The heat transfer performance showed an enhancement as the tilting angles increased within the range of 0◦to 90◦. References Esmaeilzadeh, A.; Silakhori, M.; Nik Ghazali, N.N.; Metselaar, H.S.C.; Bin Mamat, A.; Naghavi Sanjani, M.S.; Iranmanesh, S. Thermal performance and numerical simulation of the 1-pyrene carboxylic-acid functionalized graphene nanofluids in a sintered wick heat pipe. Energies 2020, 13, 6542. [CrossRef] p p g [ ] 11. Park, S.-Y.; Boo, J.-H. An Experimental Study on the Heat Transfer Characteristics of High-Temperature Cylindrical Heat Pipes. Korean J. Air Cond. Refrig. Eng. 2004, 16, 70–76. f g g 12. Vasiliev, L. Micro and miniature heat pipes–Electronic component coolers. J Appl. Therm. Eng. 2008, 28 Energies 2024, 17, 1113 12 of 12 13. Li, Y.; He, J.; He, H.; Yan, Y.; Zeng, Z.; Li, B. Investigation of ultra-thin flattened heat pipes with sintered wick structure. Appl. Therm. Eng. 2015, 86, 106–118. [CrossRef] 13. Li, Y.; He, J.; He, H.; Yan, Y.; Zeng, Z.; Li, B. Investigation of ultra-thin flattened heat pipes with sintered wick structure. Appl. Therm. Eng. 2015, 86, 106–118. [CrossRef] g 14. Liao, X.; Jian, Q.; Zu, S.; Li, D.; Huang, Z. Visualization study and analysis on the heat transfer performance of an ultra-thin flat-plate heat pipe. Int. Commun. Heat Mass Transf. 2021, 126, 105464. [CrossRef] g 14. Liao, X.; Jian, Q.; Zu, S.; Li, D.; Huang, Z. Visualization study and analysis on the heat transfer performance of an ultra-thin flat-plate heat pipe. Int. Commun. Heat Mass Transf. 2021, 126, 105464. [CrossRef] 15. STM32H743 Datasheet. STM32H742xI/G STM32H743xI/G. 2019. Available online: https://www.alldatasheet.com/datasheet- pdf/pdf/1179094/STMICROELECTRONICS/STM32H743.html (accessed on 1 December 2023). 15. STM32H743 Datasheet. STM32H742xI/G STM32H743xI/G. 2019. Available online: https://www.alldatasheet.com/datasheet- pdf/pdf/1179094/STMICROELECTRONICS/STM32H743.html (accessed on 1 December 2023). 17. Chang, C.; Han, Z.; He, X.; Wang, Z.; Ji, Y. 3D printed aluminum flat heat pipes with micro grooves for efficient thermal management of high power LEDs. Sci. Rep. 2021, 11, 8255. [CrossRef] [PubMed] 17. Chang, C.; Han, Z.; He, X.; Wang, Z.; Ji, Y. 3D printed aluminum flat heat pipes with micro grooves for efficient thermal management of high power LEDs. Sci. Rep. 2021, 11, 8255. [CrossRef] [PubMed] g g p p , , [ ] [ ] 18. Manimaran, R.; Palaniradja, K.; Alagumurthi, N.; Velmurugan, K. An investigation of thermal performance of heat pipe using Di-water. Sci. Technol. 2012, 2, 77–80. [CrossRef] g g p p 18. Manimaran, R.; Palaniradja, K.; Alagumurthi, N.; Velmurugan, K. An investigation of thermal performance of heat pipe using Di-water. Sci. Technol. 2012, 2, 77–80. [CrossRef] 19. References Wang, G.; Quan, Z.; Zhao, Y.; Wang, H. Performance of a flat-plate micro heat pipe at different filling ratios and working fluids. Appl. Therm. Eng. 2019, 146, 459–468. [CrossRef] 19. Wang, G.; Quan, Z.; Zhao, Y.; Wang, H. Performance of a flat-plate micro heat pipe at different filling ratios and working fluids. Appl. Therm. Eng. 2019, 146, 459–468. [CrossRef] pp g 20. Zhou, J.; Liu, L.; Yang, X.; Zhang, Y.; Wei, J. Visualization research on influencing factors of flat heat pipes. Appl. Therm. Eng. 2022, 207, 118193. [CrossRef] pp g 20. Zhou, J.; Liu, L.; Yang, X.; Zhang, Y.; Wei, J. Visualization research on influencing factors of flat heat pipes. Appl. Therm. Eng. 2022, 207, 118193. [CrossRef] 21. Bamorovat Abadi, G.; Bahrami, M. A general form of capillary rise equation in micro-grooves. Sci. Rep. 2020, 10, 19709. [CrossRef] [PubMed] Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.
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The legend of Sardanapalus: From ancient Assyria to European stages and screens
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1. Introduction ted M The teaching of engineering and the performance of their schools is a way to analyse the transmission of scientific knowledge and the production of an academic elite, an intelligentsia responsible for innovation and the circulation of knowledge. One of the materials that would progressively expand in utilisation throughout construction, was Portland cement and over the course of the 20th- century the use of reinforced concrete: this new material had the advantage of fire resistance; the possibility of realizing large spans; economy, speed; and improved quality in the construction (Póvoas, 2015). Accepte We focus on the Engineering Faculty of Porto University, through the work of professor Antão de Almeida Garrett, in order to analyse the introduction of reinforced concrete in the decade of 1930, and we concluded that he belongs to a generation of engineering professors that improved the use of concrete and disseminated technical knowledge within the models created by education policies since 1911, under the republican government. Since the second half of the 19th-century progress in transport and communications onwards ensured the next century began with a better understanding of the functioning of materials especially the scope for concrete and its respective typologies. This development interlinked with the registering of numerous patents and other successful applications that brought about its adoption for facades, beams and other structural features. The development of this new material arose from various contributions and experiences, especially those of: Abstract: ript Through the teaching of engineering, the introduction of new materials into civil construction gained a privileged mean of circulating knowledge and stimulating the new construction experiences that shaped a technical intelligence within the scope of which there stood out the professor of the Faculty of Engineering of the University of Porto, including Francisco Xavier Esteves, Francisco Correia de Araújo and Antão Almeida Garrett. nuscrip This chapter’s objective is to analyse the introduction of reinforcing cement and its interconnections with the study plans for engineering teaching at the University of Porto in the 1920s and 1930s, which were first structured around the Technical Faculty that later became the Engineering Faculty of Porto University. We correspondingly opted to identify some of the specific experiences and theoretical reflections around the application of this new construction material and highlighting the role of Antão Almeida Garrett and his purposes for advancing with the utilisation of reinforced cement in civil construction, especially in industrial buildings in Porto. Man Keywords: engineering, intelligence, construction methods, reinforced concrete, affordable Man Keywords: engineering, intelligence, construction methods, reinforced concrete, affordable Man Keywords: engineering, intelligence, construction methods, reinforced concrete, affordable d Ma nce on prefer resistant stonemasonry walls, floors and roofs in wooden structures, varying in their quality in accordance with the economic resources available. The introduction of new construction materials and the teaching of engineering based on technical intelligence: the role of Antão Almeida Garrett Maria da Luz SAMPAIO IHC - Faculdade de Ciências Sociais e Humanas da Universidade Nova de Lisboa, Lisboa, Portugal E-mail : mluzsampaio@fsch.unl.pt ORCID: 0000-0002-9231-4757 Maria da Luz SAMPAIO IHC - Faculdade de Ciências Sociais e Humanas da Universidade Nova de Lisboa, Lisboa, Portugal E-mail : mluzsampaio@fsch.unl.pt ORCID: 0000-0002-9231-4757 rip e Araújo and A t ti A 2. The utilisation of reinforced cement in civil construction in the early decades of the 20th century This process stemmed from the scientific progress that enabled the provision of different construction technologies coupled with experiences associated with the building of large manufacturing facilities, bridges, channels, garages, aerodromes, water storage tanks and as well as platforms, dams and power stations. Already into the 20th century, leading contributions were made by the French engineer Eugène Freyssinet, who studied and determined its characteristics. He patented his ideas in 1928, and was a structural designer and bridge builder, lacked the teaching qualities necessary to communicate his ideas to other engineers (Dinges, 2009), (Camprubí, 2017). Just like reinforced cement, pre-stressed concrete also incorporated steel but held a higher load capacity and thereby endowing greater resistance and durability to cement features and correspondingly broadening their scope of utilisation in civil construction. In Portugal, the 1920s-1930s were years of experimentation and adaptation to the principles of Modern Architecture with the application of modern materials alongside the daring solutions that only engineers knew how to design (Tostões, 2004). The modern architecture movements would foster the awareness of the artistry and capacity of reinforced cement in following the works of Auguste Perret who encourages the use of reinforced concrete due to its potentialities to find new structural systems and aesthetic solutions (Tostões, 2004). However, materials such as reinforced cement would only enter in regular use in the 1950s. Until then only a limited group of engineers knows how to apply appropriately this material given its need for unusual calculations and application manuals (Appleton, 2004). This reality, more transversal to the entire civil construction sector, did not prevent the emergence of very particular experiences in the usage of Portland - as well as the British industrialist and cement manufacturer Joseph Aspdin (1778-1855), who obtained the patent for Portland cement in 1824 (Mascarenhas-Mateus, 2018). In 1897, another significant contribution came from the French François de Hennebique with the use of iron bars and stirrups inserted in the mass of the concrete, which developed a construction system using the iron reinforced concrete that enabled the construction of spaces with spans of considerable size, and increased loads (Tostões, 2004). A 2. The utilisation of reinforced cement in civil construction in the early decades of the 20th century At the beginning of the 20th century, there remained the construction practices, techniques and materials handed down from the 19th century. Limestone, wood (especially pine) applied to floor and roof structures and as well as forged iron with steel arriving later. The new materials were used to improve the construction mainly the connection between wood and the stonemasonry. (Appleton, 2004). According to Vale (2012) house building in the early decades of the 20th-century continued to - Louis Vicat (1786- 1861), graduated in engineering at École Polytechnique de Paris and École Nationale des Ponts et Chaussées; - Louis Vicat (1786- 1861), graduated in engineering at École Polytechnique de Paris and École Nationale des Ponts et Chaussées; - the chemical engineer François Coignet (1814- 1888), deemed the inventor of reinforced cement applied to building structure (Mascarenhas- Mateus, 2018); 516 - the German engineer Matthias Koenen (1894- 1924), the first to do structural calculation of reinforced concrete elements (Moussard et al, 2017). t cement in as early as the 19th-century and the first decades of the following century. In Portugal, the first significant cement construction was the new building of Moagem do Carmujo [Caramujo Wheat Mill], built in 1898 (Toscano, 2012) and the Luiz Bandeira de Sejães Bridge on the EN333-3 over the river Vouga, dating to 1907, opening up a new paradigm in the history of construction. (Appleton, 2004). The choice of this material stemmed from the need to design industrial facilities structured into large pavilions, capable of bearing significant loads, providing stable structures and flooring simultaneously more resistant to fire and high temperatures. - the German engineer Matthias Koenen (1894- 1924), the first to do structural calculation of reinforced concrete elements (Moussard et al, 2017). Accepted M reinforced concrete elements (Moussard et al, 2017). - as well as the British industrialist and cement manufacturer Joseph Aspdin (1778-1855), who obtained the patent for Portland cement in 1824 (Mascarenhas-Mateus, 2018). In 1897, another significant contribution came from the French François de Hennebique with the use of iron bars and stirrups inserted in the mass of the concrete, which developed a construction system using the iron reinforced concrete that enabled the construction of spaces with spans of considerable size, and increased loads (Tostões, 2004). Other variants of this product were developed in the early 20th-century like the pre-stressed concrete as well as the introduction of asbestos- cement. 3. The teaching of engineering and the introduction of reinforced concrete ript From 1922 the chair of «Reinforced concrete» was taught by Theotónio Rodrigues, but in 1932 it became the responsibility of Antão Almeida Garrett, (1897-1978), recently graduated in civil engineering. M The introduction of this new material is associated with the reorganisation of engineering education, especially in civil engineering. Since 1881-82 the military School had a scientific approach, it became part of the curricula for the engineers’ training. This new material was already disseminated in the 19th- century by the review «Le Betón Armé et ses Applications» published by Paul Christophe, engineer of Ponts et Chaussés School and in Portugal by the Revista de Obras Públicas e Minas 1870-1926, edited by Associação dos Engenheiros Civis Portugueses [Association of Portuguese Civil Engineers] (Mascarenhas-Mateus, 2018). uscrip Graduated in 1925 by the University of Porto, he became professor-assistant of the First Group: Civil Constructions in the Faculty of Engineering of the University of Porto and Manus recruited in 1932 to the chair of «Reinforced Concrete». According to the educational traditions prevailing in engineering schools, he produced an anthology that included the definitions and characteristics of this material, its usages as well as the formulas and calculations for building different structures and that remained an essential reference manual throughout many years. Students, also keeping the tradition, would annually produce new editions and we highlight the contributions of the re-edited manual by Pinto Basto and Lamas Viana, Alfredo Barata da Rocha, Alberto Fontes, Vicente de Paiva, Torquato Alvares Ribeiro and as well as the engineer Edgar Cardoso, who would also be a professor of engineering at Instituto Superior Técnico, founding in 1944 his own Laboratory for the Study of Structures and Foundations. Cardoso had extensive work with the use of concrete as well as other materials. Among his projects is the Arrábida Bridge in 1963 and the S. João Railway Bridge in Porto, opened in 1991. ed M Under the Republic government, two schools were founded: the Lisbon Instituto Superior Técnico and the University of Porto. In the latter, the Technical Faculty was created in 1915 and was transformed, in 1926, into the Faculty of Engineering of the University of Porto. Accepted y The Technical Faculty of the University of Porto was one of the first schools officially to approve this discipline in the curricular plan. 1 Augusto Pereira Nobre (1865-1946) was a biologist and professor of Porto University. 2. Diogo Eugénio Cabral was a Porto industrialist and 1st A 2. The utilisation of reinforced cement in civil construction in the early decades of the 20th century In the 20th-century, new facilities came in the 1920s, with Maceira-Liz factory in Leiria, which began operating in 1923, 517 and under the Estado Novo government was founded in 1930 the major corporate group: SECIL – Companhia Geral de Cal e Cimento S.A. In 1934, Lusalite began the elaboration of fiber-cement, being an associated company to the group Sommer that centralised the entire sector. This was the result of the protectionist and interventionist policy of Salazar’s government since 1931, but the changes in the sector only began after World War II (Costa, Fazenda et al., 2010). the use of Portland Cement also due to its moulding capacities (Vale, 2012). t The active participation in public life led Xavier Esteves to embrace other projects and, in addition to his short experience in engineering education, he joined, from December 1917 to June 1918, Sidónio Pais’ government, as Minister of Commerce (between December 11, 1917, and March 7, 1918) and Minister of Finance (between 7 March and 1 June 1918). Later, his business connections led him to be elected a second term as president of the Portuense Industrial Association, between 1919 and 1930. A 2. The utilisation of reinforced cement in civil construction in the early decades of the 20th century Manuscript With the proliferation of functional modernism backed by the ongoing calculations and research, the technical intelligence of the engineers ensured the architects recognized this new material for establishing a new aesthetic language using the plasticity of this material to project large openings with extensive glazing, creating a taste for smooth surfaces and pure volumes (Tostões, 2004). In this context, there stood out in Lisbon works such as the Portugália Brewery (1912-1914); the Capitólio cinema by Cristino da Silva (1896-1976) in 1929; the Instituto Superior Técnico, designed by Porfírio Pardal Monteiro in 1927 and completed in 1936. In Porto, these were accompanied by the São João Theatre (1910-1918), the Armazéns Nascimento Department Store (1914-1927) and the Garage for O Comércio do Porto newspaper designed by the architect Rogério Azevedo (1899-1983); the Passos Manuel Garage by the architect Mário Abreu; as well as the fish fridge building in Massarelos by Januário Godinho (Tostões, 2004). Other variants of this product were developed in the early 20th-century like the pre-stressed concrete as well as the introduction of asbestos- cement. This process stemmed from the scientific progress that enabled the provision of different construction technologies coupled with experiences associated with the building of large manufacturing facilities, bridges, channels, garages, aerodromes, water storage tanks and as well as platforms, dams and power stations. The introduction of reinforced concrete in Portugal led to the publication, in 1918, of the Regulatory Instructions for the employment of Concrete, carried out based on the French norms and its later developments. (Appelton, 2004). A new regulation was published in 1935, establishing the need for rigorous calculations to meet the needs of compression, tension and safety of reinforced concrete works, among other aspects, demonstrating a broad field of applications of this material in civil construction (Decree 25.948 of October 16, 1935). In parallel, the cement industry underwent significant expansion. According to Mascarenhas- Mateus studies “The effective production of natural cement began in 1866 under the Rasca brand manufactures in Alcântara, Lisboa, by Francisco Pereira de Gusman” (Mascarenhas-Mateus, 2018, p. 905), while the first industrial production unit had been founded in 1898, Companhia Cimento Tejo in Allandra by António Teóphilo Araújo Rato (Mascarenhas-Mateus, 2018). Count of Vizela. 4. The artificial silk factory expansion plan: Company “Fibra Comercial Lusitana Lda.” Dissemination and experimentation with these new materials were also much shaped by the founding of the Laboratory for Testing Construction Materials under the auspices of the Faculty of Engineering (established officially as a Cabinet of the school of engineering in 1915). The Faculty laboratory was used by the students in practical lessons and to do their projects, but also as outsourcing services for official and private entities, carried out a leading role in testing construction materials. This was where Professor Antão Almeida Garrett do experiments with different materials, especially national woods: maritime pine from Leiria, and reinforced concrete helicoid beams as well as testing the fire resistant properties of reinforced concrete, demonstrating that when slowly exposed to high temperatures it would inevitably get destroyed (Garrett, 1938). Many other tests and studies took place not only in conjunction with the academic programs but also as a result of studies requested from industry and official entities, with the laboratory taking on a determinant role in Man Three years after licensing the first building for the artificial silk (rayon) factory, the company advanced with an investment in its expansion through the addition of a perpendicular body, with a sizeable volumetric scale and careful design, surrounded by a garden that extended as far as the avenue. The calculations for the concrete structures were of the responsibility of Antão Almeida Garrett who established the scale, loads and tensions for each construction component. The new building would form a typified example of modern architecture from the early 20th-century, with a regular composition and flat roofing surface. The imposing southern facade stands out in this otherwise classically designed building with its innovation emerging out of the scale of the vertical openings that only become feasible due to their reinforced concrete infrastructure. The flat roof with a terrace was lined by a row of sheds supported by concrete trusses. On the inside, space was divided by a concrete beam-pillar structure that replicated the design of the metallic structures that were previously applied to these buildings while ensuring a wide and very open space with a scalable to cope with the installation of heavy and large-scale machinery and equipment. The Descriptive Memory of the project details not only the calculations as well as the description of the materials. 3. The teaching of engineering and the introduction of reinforced concrete The school board decided in 1917 to recruit Francisco Xavier Esteves to be the professor of «Reinforced concrete and Bridges» (FEUP/Actas do Conselho Escolar, 1917). This teacher obtained a degree in civil engineering from the Politécnica Academy (Tavares, 2017), and in 1912 was a managing partner of the Companhia de Cimentos Tejo, using Portland cement. Among Xavier Esteves’ works, Livraria Lello (bookshop Lello) stands out, a 1904 project where the cement is used in the interior stairs, in the gallery of the store and the frame of the facade. Xavier Esteves also signed other works like the 1898 Augusto Pereira Nobre’s house 1 in the street of Castelo do Queijo (Foz do Douro) or Diogo Eugénio Cabral’s residence2 located on Rua Miguel Bombarda and which received works of expansion in 1927, using Portland cement (AHMP/CMP, L. O. nº192/1928). It is important to emphasise that in the case of the Livraria Lello the neo-gothic facade was built with Like reinforced concrete, pre-stressed concrete was also introduced in engineering education through the contacts and missions carried out by another professor of Porto University, Francisco Sarmento Correia de Araújo, who graduated in civil engineering in 1934. He carried out a mission financed by the Instituto de Alta Cultura at the Gent University (Belgium) where he worked with Gustaaf Robert Magnel, professor of reinforced concrete and founder of the Magnel Laboratory for Concrete Research one of the great centres of expertise and knowledge dissemination of reinforced and 518 engineering research. Antão Almeida Garrett would take over as its director in 1964. prestressed concrete in Europe. Gustave Magnel gave many lectures in several countries in which he explained in a simple way the principles of pre- stressed concrete and wrote the first book of design in this subject (Dinges, 2009). 4. The artificial silk factory expansion plan: Company “Fibra Comercial Lusitana Lda.” This experience ensured Correia de Araújo to played a decisive role not only in teaching civil engineering but also in the dissemination the use of reinforced concrete, participating in the technical teams for diverse public projects that resulted in some of the emblematic landmarks of Porto city. His position as head of the Serviços de Obras Municipais e Habitações Populares (1940-41) [Town Constructions and Inhabitants Houses Department] enabled his interventions in the reinforced concrete project for the Massarelos Bolsa do Pescado [Massarelos Fishing Market]; the calculations for the Massarelos bridge to fish fridge; the inspection, the calculation of the projects of the construction of the “Abrigo dos Pequeninos” [Children Shelter]; the new City Council Hall, and the calculation and inspection of the construction of the Duque de Saldanha’s local council housing project, among others. anuscript From the 1920s, new construction projects of private entities in the city of Porto allowed for the emergence of works that marked the introduction of a modern architecture capable of designing the necessary interior functionality of the buildings. One of the industrial buildings that used reinforced concrete was the factory of the company “Fibra Commercial Lusitana Lda” — designed in 1933 by the architect Leandro de Morais (1883-?) in a parcel of land situated in the crossroad between the avenue of Boavista and the street Coutinho de Azevedo, neighbouring another textile unit: Fábrica de Fiação e Tecidos da Boavista owned by William Graham. This new unit was part of the group of industrial units located in this new avenue, an important expansion axis for the city towards the west allowing the connection of the city centre to the sea, in particular to Leixões Port, through the maritime marginal or crossing of the agricultural suburbs. Accepted M Within the Porto Faculty of Engineering, the circulation of knowledge interlinked with the engineering practices of their professors but also extended to the missions financed by the Institute of High Culture (Instituto de Alta Cultura) that brought an increase of the technical intelligence able to apply and disseminate these new construction materials sustained by their respective calculations. There thus appeared new constructions held up by beams, pillars, roofing and terraces, large-scale architectural projects in their majority with high functional performance and resistance requirements. 4. The artificial silk factory expansion plan: Company “Fibra Comercial Lusitana Lda.” In parallel, he thus defended the use of national woods, referring to how such materials hold the capacities to provide solutions to the different demands of construction systems. Garrett ends his reflections by expressing the idea that technical progress in this field does' not yet have given a substantial improvement on civil construction (Garrett, 1939). M The article continues with a set of considerations against the high costs of iron imports for reinforced concrete, declaring his opposition to the incorrect employment of reinforced concrete. In parallel, he thus defended the use of national woods, referring to how such materials hold the capacities to provide solutions to the different demands of construction systems. Garrett ends his reflections by expressing the idea that technical progress in this field does' not yet have given a substantial improvement on civil construction (Garrett, 1939). We highlight that the introduction of concrete was a gradual process and with Estado Novo regime (1926-1974) started the regulation and control of the process of civil construction and housing projects, framed within the urban growth projects of the main urban centres. pted Fig. 2. Project of Shed coverage of the new building of the company Fibra Comercial Luzitana, Lda. 1936. Source: CMP / AHMP. L.O. nº 1146/ 1936, p. 426. ccepte This new industrial building is another example of the complicity established between modern architecture and engineering, in a partnership irredeemable for the experimental load that the new constructive materials imposed. Acc Antão Almeida Garrett was involved in other projects. From 1930 and 1939 we found his signature in projects for water tanks, terraces, garages, bourgeois dwellings, alterations of buildings, using always reinforced concrete, namely for the coverings, pavements, pillars and beams. 5. Antão Almeida Garrett: reflections and experiences with reinforced concrete Antão Almeida Garrett had a long career as professor and engineer, and from the 1940s, he undertook numerous studies, focusing in particular in the urban plan of Porto, working in partnership with national and foreign architects and urban planners. Antão Almeida Garrett was engaged in the task of promoting and disseminating new construction materials and techniques and their impacts on the construction industry. In 1932, he wrote an article for the Bulletin of the Civil Engineers Association of Northern Portugal, entitled “Construction Processes”, where he details a new process of using concrete in order to build walls that would enable 4. The artificial silk factory expansion plan: Company “Fibra Comercial Lusitana Lda.” In this document, the engineer Garrett presents the use of a reinforced concrete skeleton that supports the building from the first floor to the roof, showing all the calculations for beams, pillars, sheds and concludes by highlighting 519 cript homes to become more insulated from temperature variations (Garrett, 1932). Hence, this engineering professor, driven by his preference for reinforced concrete and his capacity for experimentation, set up an area to make concrete moulds at the bottom of his garden. His tests and studies led him to the production of a unique layout of moulds, resulting in a concrete beam with two support frames (Garrett, 1932). In 1938 he published “O betão armado e o fogo“ [Reinforced Concrete and the Fire] and he related the experiences made in concrete, following the studies and fire tests of the American Professor I. H. Woolson and Professor M. M. Milankovitch from University of Belgrade, and also from the Station d’ Essais de L’ Office National des Recherches et Inventions, demonstrating to be aware of the works in this area in other universities and research centres. the use of asbestos-cement in the roof (L.O. 1146/1936). Fig. 1: Architectural project of the new building of the company Fibra Comercial Luzitana, Lda. 1936. Source: CMP / AHMP. L.O. nº 1146/ 1936, p. 416. Fig. 1: Architectural project of the new building of the company Fibra Comercial Luzitana, Lda. 1936. Source: CMP / AHMP. L.O. nº 1146/ 1936, p. 416. pted M Fig. 2. Project of Shed coverage of the new building of the company Fibra Comercial Luzitana, Lda. 1936. Source: CMP / AHMP. L.O. nº 1146/ 1936, p. 426. Manuscr The rationalisation of construction systems was also a strong subject for this engineer, and he defended the use of national raw materials for civil construction. He published an article, in 1939, in the University of Porto Engineering Journal entitled “Porque se não deverá empregar tanto betão armado” [Why we should not employ so much reinforced concrete] In the opening lines, he answered by saying that iron is imported; it is applied where there is no justification, and also because reinforced concrete is generally poorly designed and badly executed (Garrett, 1939). M The article continues with a set of considerations against the high costs of iron imports for reinforced concrete, declaring his opposition to the incorrect employment of reinforced concrete. Acknowledgement: M This paper was produced under the scholarship FCT SFRH/BPD/117829/2016, dedicated to the project: History of engineering education in Portugal: 1901- 1960. M This paper was produced under the scholarship FCT SFRH/BPD/117829/2016, dedicated to the project: History of engineering education in Portugal: 1901- 1960. anu _____. (1938a). O betão armado e o fogo. In Revista Faculdade de Engenharia, IV (3), pp. 109-114. Man Faculdade de Engenharia, IV (3), pp. 109 114. ___. (1938b). Ainda as vigas helicoidais de betão armado carregadas uniformente. In Revista da Faculdade de Engenharia, IV (2), pp. 49-51. M ___. (1939). Porque se não deverá empregar tanto betão armado. In Revista da Faculdade de Engenharia, V, (4) (dez.), pp. 156-158. 6. Conclusion Cimento Armado: Lições pelo assistente Engenheiro Antão Almeida Garrett. Porto: FEUP. _____. (1938a). O betão armado e o fogo. In Revista Faculdade de Engenharia, IV (3), pp. 109-114. _____. (1938b). Ainda as vigas helicoidais de betão armado carregadas uniformente. In Revista da Faculdade de Engenharia, IV (2), pp. 49-51. _____. (1939). Porque se não deverá empregar tanto betão armado. In Revista da Faculdade de Engenharia, V, (4) (dez ) pp 156 158 d Ma 901- _____. _____. 6. Conclusion The first uses of reinforced concrete demonstrate a progressive knowledge of the properties of new materials for civil construction, but their diffusion 520 was also due to engineering schools and its teachers. They have a privileged role in the circulation of technical knowledge, the diffusion of new practices and the use of new building materials. State University. State University. Edgar, C. (1936-1837). Cimento Armado: Lições proferidas pelo Eng. Antão Almeida Garrett. Porto: FEUP. FEUP. (1959). O laboratório de Ensaios de Materiais da Faculdade de Engenharia da Universidade do Porto. Porto: FEUP. _____. (1926). Faculdade de Engenharia da Universidade do Porto: Faculdade Técnica da Universidade do Porto (1915-1926). Available: file:///C:/Users/Utilizador/Downloads/FEUP_- _Estudo_organico_e_funcional%20(6).pdf _____. SDI/ARQUIVO - Livro de Actas do Conselho Escolar, 1915 - 1922. Cota: 7(01) ARQ00000006. Porto: FEUP. The first generations of graduated engineers from the Faculdade Técnica of the University of Porto, played an essential role in the dissemination of this knowledge, especially Antão Almeida Garrett, who throughout his career as professor improved the technical intelligence in his disciples and as engineer designed small-scale projects such as concrete structures for water tanks, terraces, but also projects of concrete structures for factory buildings, houses, making extensive use of reinforced concrete and even asbestos-cement. file:///C:/Users/Utilizador/Downloads/FEUP_- _Estudo_organico_e_funcional%20(6).pdf _____. SDI/ARQUIVO - Livro de Actas do Conselho Escolar, 1915 - 1922. Cota: 7(01) ARQ00000006. Porto: FEUP. ipt Fontes, A., Paiva, V. de, Ribeiro, T.A. (1936). Materiais e Processos gerais de Construção: lições dadas pelo Ex.mo Senhor Professor Antão Almeida Garrett. Porto: Tipografia Gonçalves & Cª. cript Garrett, Antão Almeida. (1932). Processos de Construção. In Boletim da Associação dos Engenheiros Civis do Norte de Portugal, 7, pp. 30-32. Antão Almeida Garrett fostered the study of new materials, especially the reinforced concrete with his experimentation and theoretical principles improving the modernisation of the civil construction, sustained by the development of engineering. Antão Almeida Garrett fostered the study of new materials, especially the reinforced concrete with his experimentation and theoretical principles improving the modernisation of the civil construction, sustained by the development of engineering. uscri _____. (1932-33). Cimento Armado [texto policopiado]: lições professadas no ano lectivo de 19332-33 pelo assistente Engenheiro Antão Almeida Garrett, copiadas pelos alunos Germano Venade e Manuel Arala Chaves. Porto: FEUP. nus _____. (1935). Cimento Armado: Lições pelo assistente Engenheiro Antão Almeida Garrett. Porto: FEUP. (1938a) O betão armado e o fogo In Revista Manus _____. (1935). Bibliographical references: Mascarenhas-Mateus, J., Castro, C.R. (2018). The Portland Cement Industry and Reinforced Concrete in Portugal (1860-1945). In Ine Wouters, Stephanie van de Voorde, Inge Bertels, Bernard Espion. Building Knowledge: Constructing Histories. Proceedings of the 6th International Congress on Construction History (6ICCH-2018) (Vol.2, pp. 903- 911). Brussels: CRC Press. epted Appleton, J. (2004). Materiais e tecnologias de construção: um século de mudança, ou da tradição à inovação. In Manuel Heitor, J. M. Brandão de Brito; Maria Fernanda Rollo (Coord.), Momentos de Inovação e engenharia em Portugal no século XX: Grandes Temas, (Vol. II, pp. 154-178). Lisboa: Publicações Dom Quixote. ccep Brito, J. M. Brandão de, Heitor, M., Rollo, M. F. (eds). (2002). Engenho e obra: uma abordagem à história da engenharia em Portugal no século XX. Lisboa: Dom Quixote. Moussard, M., Garibaldi, P., Curbach, M. (2017). The Invention of Reinforced Concrete (1848-1906). In D.A. Hordijk, M. Lukovic (editors) - High Tech Concrete: Where Technology and Engineering Meet: Proceedings of the 2017 fib Symposium held in Maastricht, The Netherlands, June 12-14, 2017.(pp.2785-2794). Deft University of Technology fib/Springer Acc Costa, J., Fazenda, L., Honório, C. et al (2010). Os Donos de Portugal: Cem anos de poder Económico (1910- 2010). Lisboa: Edições Afrontamento. Ac ç Camprubí, L. (2017). Los Ingenieros de Franco. Barcelona: Crítica Ac Camprubí, L. (2017). Los Ingenieros de Franco. Barcelona: Crítica Póvoas, R.F. (2018) O papel dos Arquitetos na introdução do Betão em Portugal. in J. Mascarenhas-Mateus (ed) História da Construção em Portugal: Consolidação de uma disciplina. Gráfica Diário do Minho, pp.121-137 A CMP / Arquivo Histórico Municipal do Porto - Licença de Obras nº 1146/ 1936. A CMP / Arquivo Histórico Municipal do Porto - Licença de Obras nº 1146/ 1936. _____.Licença de obras nº 192/1928- _____.Licença de obras nº 192/1928- _____.Licença de obras nº 192/1928. _____.Licença de obras 65/1930. _____.Licença de obras 65/1930. Tavares, D. (2017). Transformações na Arquitectura Portuense: o caso António da Silva. Equações de Arquitectura. Porto: Dafne editora. _____.Licença de Obras nº2/1932. _____.Licença de obras 13 06/ 1935. _____.Licença de Obras nº 1146/ 1936. Tostões, Ana. (2004). Construção moderna: as grandes mudanças do século XX. In Manuel Heitor, J. M. Brandão de Brito, J.M.; Rollo, M.F. (Coord.), Momentos de Inovação e engenharia em Portugal no século XX: Grandes Temas, (Vol. II, pp.130-164). Lisboa: Publicações Dom Quixote. _____.Licença de obras 512/1936. _____.Licença de obras nº 314/1938. _ Licença de Obras nº 314/1938. Vale, M. C. P. (2011). Um alinhamento Urbano na construção do edificado do Porto – o eixo da Boavista (1927-1999). Dissertação de Doutoramento da FAUP, set.2011-janeiro 2012. Porto: FAUP. Accepted M Piedade. Dissertação de Mestrado da Universidade Aberta, 2012. Lisboa: Universidade Aberta. Piedade. Dissertação de Mestrado da Universidade Aberta, 2012. Lisboa: Universidade Aberta. _ Licença de obras 41/1940. _ Licença de obras 41/1940. Dinges, Tyson. (2009). The History of Prestressed Concret: 1888 to 1963: Relatory of Master of Science Kansas State University, 2009. Manhattan Kansas: Kansas Toscano, M.C.A. (2012). A fábrica de Moagem de Caramujo: Património Industrial da Cova da 521 Piedade. Dissertação de Mestrado da Universidade Aberta, 2012. Lisboa: Universidade Aberta. Piedade. Dissertação de Mestrado da Universidade Aberta, 2012. Lisboa: Universidade Aberta. 522
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Think out of the box: association of left congenital diaphragmatic hernia and abnormal origin of the right pulmonary artery
BMC pediatrics
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3,818
Abstract Background  We report the occurrence of a severe pulmonary hypertension (PH) in a neonate affected by a left congenital diaphragmatic hernia (CDH). PH in this patient was associated with an abnormal origin of the right pulmonary artery from the right brachiocephalic artery. This malformation, sometimes named hemitruncus arteriosus, has to the best of our knowledge never been reported in association with a CDH. Case presentation  A male newborn was hospitalized from birth in the neonatal intensive care unit after prenatal diagnosis of a left CDH. Ultrasound examination at 34 weeks of gestational age evaluated the observed-to-expected lung-to-head ratio at 49%. Birth occurred at 38+ 5 weeks of gestational age. Soon after admission, severe hypoxemia, i.e., preductal pulse oximetry oxygen saturation (SpO2) < 80%, prompted therapeutic escalation including the use of high frequency oscillatory ventilation with fraction of inspired oxygen (FiO2) 100% and inhaled nitric oxide (iNO). Echocardiography assessment revealed signs of severe PH and normal right ventricle function. Despite administration of epoprostenolol, milrinone, norepinephrine, and fluid loadings with albumin and 0.9% saline, hypoxemia remained severe, preductal SpO2 inconsistently greater than or equal to 80-85% and post ductal SpO2 lower on average by 15 points. This clinical status remained unchanged during the first 7 days of life. The infant’s clinical instability was incompatible with surgical intervention, while chest X-ray showed a relatively preserved lung volume, especially on the right side. This prompted an additional echocardiography, aimed at searching an explanation of this unusual evolution and found an abnormal origin of the right pulmonary artery, which was confirmed on computed tomography angiography subsequently. A change in the medical strategy was decided, with the suspension of pulmonary vasodilator treatments, the administration of diuretics, and the decrease in norepinephrine dose to decrease the systemic-to-pulmonary shunt. Progressive improvement in the infant respiratory and hemodynamic status enabled to perform CDH surgical repair 2 weeks after birth. Full list of author information is available at the end of the article Full list of author information is available at the end of the article © 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. A train can hide another Arthur Gavotto1,2* , Pascal Amedro3,4 and Gilles Cambonie1,5 Arthur Gavotto1,2* , Pascal Amedro3,4 and Gilles Cambonie1,5 © 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://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. BMC Pediatrics BMC Pediatrics Gavotto et al. BMC Pediatrics (2023) 23:349 https://doi.org/10.1186/s12887-023-04164-1 Open Access Abstract 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. Think out of the box: association of left congenital diaphragmatic hernia and abnormal origin of the right pulmonary artery A train can hide another Case presentation A male newborn was hospitalized after birth in the neo­ natal intensive care unit (NICU) after prenatal diagno­ sis of a left congenital diaphragmatic hernia (CDH). The infant was the second child of consanguineous (first- degree cousins) and healthy North African parents. The couple had been referred at the last trimester of preg­ nancy to the expert center for CDH in our institution. At 34 weeks of gestational age, prenatal ultrasound showed left CDH associated with various anomalies: short cor­ pus callosum (< 1st centile), palate cleft, azygous venous return, bilateral cryptorchidism, and intrauterine growth retardation (< 3rd centile according to the French refer­ ence values[11]). Ultrasound examination at 34 weeks of gestational age evaluated the observed-to-expected lung-to-head ratio at 49%, and magnetic resonance imag­ ing (MRI) at 35 weeks of gestational age measured the observed-to-expected total fetal lung volume at 33%, corresponding to a mild-to-moderate severity in terms of prediction of CDH-related lung hypoplasia [12]. In addition, MRI showed a persistent portion of the ante­ rior diaphragm, which maintained the liver in abdomi­ nal position. Standard karyotype and array comparative genomic hybridization revealed no abnormality. In newborns with CDH, respiratory failure originates from abnormal lung development, which affects the alveoli as well as their vascularization. This results in pulmonary hypoplasia, but also structural and func­ tional vascular abnormalities that cause persistent PH [1]. Underdevelopment and abnormal vasoreactivity of the pulmonary vasculature result in sustained eleva­ tion of pulmonary vascular resistance and low pulmo­ nary blood flow, causing right-to-left shunting of blood across the ductus arteriosus and/or the foramen ovale, and, ultimately, refractory hypoxemia [2]. Management mainly consists in supporting respiratory function with mechanical ventilation, with the aim of maintaining pre­ ductal SpO2 > 80% and partial pressure of carbon diox­ ide (PCO2) between 50 and 70 mmHg [3]. Treatment of CDH-associated PH with vasodilator treatments such as inhaled nitric oxide (iNO), prostacyclin, sildenafil, or mil­ rinone should be limited to severe forms after optimiza­ tion of alveolar ventilation, control of stress and pain, and correction of hypovolemia [4, 5].h This standardized support may be unsuitable in very specific situations, in particular with congenital malfor­ mations. According to a recent review, 15% of neonates with CDH have congenital heart disease, of which 42% are critical [6]. Anomalous origin of the branches of the pulmonary artery to the aorta accounts for 0.12% of con­ genital heart defects [7]. (2023) 23:349 Page 2 of 6 Gavotto et al. BMC Pediatrics Conclusions  This case recalls the interest of systematic analysis of all potential causes of PH in a neonate with CDH, a condition frequently associated with various congenital malformations. Keywords  Congenital diaphragmatic hernia, Congenital heart disease, Pulmonary hypertension, Poiseuille’s law, Pediatrics Keywords  Congenital diaphragmatic hernia, Congenital heart disease, Pulmonary hypertension, Poi P di i Background  We report the occurrence of a severe pul­ monary hypertension (PH) in a neonate affected by a left congenital diaphragmatic hernia (CDH) associated with an abnormal origin of the right pulmonary artery from the right brachiocephalic artery, also named right hemitrun­ cus arteriosus. reverse the therapeutic strategy, to restore an adequate hemodynamic. Discussion Unstable refractory hypoxemia in an infant with CDH despite apparently appropriate treatment should ques­ tion the origin of the PH and make consider multifacto­ rial causes. Several unusual data should have drawn our attention in this observation and, first of all, uncertainty about pulmonary hypoplasia, the severity of which is often superimposed on that of PH. In this respect, there was discrepancy between lung-to-head ratio, which pre­ dicted a mild disease and total fetal lung volume, which predicted a moderate-to-severe disease [12, 13]. In addi­ tion, the satisfactory recruitment of the right lung, result­ ing in PCO2 measurements regularly below the target values, were not consistent with severe restrictive respi­ ratory insufficiency. This clinical status remained unchanged during the first 7 days of life, with. The infant’s clinical instabil­ ity was incompatible with surgical intervention, while chest X-ray showed a relatively preserved lung volume, especially on the right side (Fig. 1). This prompted an additional echocardiography, aimed at searching an explanation of this unusual evolution. The pulmonary veins were in normal position, with no stenosis, and left ventricle function was normal, with no aortic coarcta­ tion. However, the right pulmonary artery was poorly visualized, and appeared to probably originate from the right brachiocephalic artery, with significant diastolic reflux in the descending aorta and increased flow in the right pulmonary vein. This abnormal origin of the right pulmonary artery was confirmed on computed tomogra­ phy angiography performed 9 days after birth (Fig. 2). fi Extracorporeal membrane oxygenation (ECMO) is a rescue support in neonatal CDH with cardio-respiratory failure, with persistent controversies about patient selec­ tion, timing of initiation and timing of surgical repair [2]. In our patient, the severity of PH and the settings of high frequency oscillatory ventilation were arguments for recourse to extracorporeal life support [14]. On the other hand, the multiple anomalies observed on prenatal ultra­ sound as on postnatal examination suggested a genetic abnormality or syndrome. After sharing this information with parents, and also taking into account the potential complications of ECMO,[15] we decided against this option. A change in the medical strategy was decided, with the suspension of pulmonary vasodilator treatments, the administration of diuretics, and the decrease in norepi­ nephrine dose to target a minimal mean blood pressure of 35–45 mmHg to decrease the systemic-to-pulmonary shunt. Progressive improvement in the infant respiratory Fig. Case presentation In most cases, the right pulmo­ nary artery arises from the posterior wall of ascending aorta, very near the aortic valve, is isolated (e.g., with­ out intracardiac malformation), as opposed to left pul­ monary artery forms [8]. From the rare cases reported in the literature, no association with genetic syndromes has been described in right hemitruncus arteriosus [9]. Without early surgical repair, the patient is exposed to severe pulmonary hypertension, and, ultimately, cardiac dysfunction [10]. This malformation has to the best of our knowledge never been reported in association with a CDH. Birth occurred at 38+ 5 weeks of gestational age by cesarean section for fetal bradycardia and membrane rupture, with a weight of 2670 g (5th centile), a height of 47 cm (8th centile), and a head circumference of 34.5 cm (55th centile). Apgar scores at 1, 5 and 10  min were, respectively, 2, 3 and 5. Arterial cord blood pH was 7.21 and cord lactate was 2.5 mmol/L. Nasotracheal intuba­ tion was achieved 2 min after birth, and the infant was transported in the NICU. Clinical examination con­ firmed palate cleft, left cryptorchidism with a short penis (19  mm), and distal arthrogryposis of the hands and feet. Soon after admission, severe hypoxemia, i.e., pre­ ductal pulse oximetry oxygen saturation (SpO2) < 80%, prompted therapeutic escalation including the use of high frequency oscillatory ventilation with fraction of inspired oxygen (FiO2) 100% oxygen and inhaled nitric oxide (iNO, 20 ppm). Echocardiography revealed signs of severe PH, with estimated systolic pulmonary artery pressure of 80 mmHg from peak tricuspid regurgitant jet velocity, inverted septal curvature, and a predominant right-to-left shunt in a large persistent ductus arteriosus The challenge of this rare association (left CDH with an abnormal origin of the right pulmonary artery from the right brachiocephalic artery) was then to totally Gavotto et al. BMC Pediatrics (2023) 23:349 Page 3 of 6 (2023) 23:349 Gavotto et al. BMC Pediatrics (2023) 23:349 and hemodynamic status enabled to perform CDH sur­ gical repair 2 weeks after birth. Then, surgical reimplan­ tation of the right pulmonary artery in the trunk of the pulmonary artery was performed 5 weeks after birth. (PDA) of 4.5 mm of diameter. Case presentation In addition, echocardiog­ raphy showed a normal right ventricle function (absence of dilation, tricuspid annular plane systolic excursion of 8.5  mm), and confirmed the absence of intracardiac defect, the absence of inferior vena cava, and the pres­ ence of the azygous venous return. Despite administra­ tion of epoprostenolol, milrinone, norepinephrine, and fluid loadings with albumin and 0.9% saline, hypoxemia remained severe, preductal SpO2 inconsistently greater than or equal to 80-85% and post ductal SpO2 lower on average by 15 points. Discussion 1  Chest X-ray at day 1 (left panel) and day 5 (right panel) of life. Chest radiography shows the bowel loops occupying part of the left hemithorax the 1st post-natal day, and a relatively preserved lung volume, especially on the right side, the 5th post-natal day Fig. 1  Chest X-ray at day 1 (left panel) and day 5 (right panel) of life. Chest radiography shows the bowel loops occupying part of the left hemithorax the 1st post-natal day, and a relatively preserved lung volume, especially on the right side, the 5th post-natal day (2023) 23:349 Page 4 of 6 Gavotto et al. BMC Pediatrics (2023) 23:349 Gavotto et al. BMC Pediatrics Fig. 2  3D reconstruction of computed tomography angiography. Reconstruction showing the anomalous origin of the right pulmonary artery from the right brachiocephalic artery (indicated by the white arrow) Fig. 2  3D reconstruction of computed tomography angiography. Reconstruction showing the anomalous origin of the right pulmonary artery from the right brachiocephalic artery (indicated by the white arrow) The classical physiology of PH in CDH distinguishes three main phenotypes: (i) mild or non-existent PH with normally functional right ventricle; (ii) precapillary PH with predominant right-to-left PDA and atrial shunts, possibly associated with right-sided heart failure with or without secondary left-sided heart failure; and (iii) post-capillary PH with primary left-sided heart failure, and predominant right-to-left ductus arteriosus shunt and left-to-right atrial shunt [2]. According to Poiseuille equation, pulmonary artery pressure depends on pul­ monary blood flow, right ventricular afterload and left atrial pressure. Thus, assessment of all potential causes of PH in a patient needs to consider PH associated with increased pulmonary vascular resistance, as well as with increased pulmonary blood flow [16].h ultrasound Doppler index to assess precapillary pulmo­ nary vascular resistance,[17] and relative shortening of pulmonary artery acceleration time has been associated with CDH severity [18]. In our patient, however, this index was not relevant, as right lung perfusion was sup­ plied by the left ventricle, whereas left lung perfusion was supplied by the right ventricle. Persistence of a right-to- left flow through a tubular ductus arteriosus, which gen­ erally indicates increased right-sided cardiac pressures, also gave the opportunity, in this hemodynamic situa­ tion, to distribute part of the systemic volume flow and to reduce PH severity of the left lung, as exceptionally observed in adults [19]. Repeated echocardiography examinations performed in this patient found no evidence for post-capillary PH. No financial support was received. No financial support was received. References In conclusion, this case reports the importance of going back to the basics of physiology in complex hemo­ dynamic situations, especially when the expected evolu­ tion is not observed. Indeed, we usually only find what we are looking for. 1. Abman SH, Baker C, Gien J, Mourani P, Galambos C. The Robyn Barst Memo­ rial Lecture: Differences between the fetal, newborn, and adult pulmonary circulations: relevance for age-specific therapies (2013 Grover Conference series). Pulm Circ. 2014;4:424–40. 2. Bhombal S, Patel N. Diagnosis & management of pulmonary hypertension in congenital diaphragmatic hernia. Semin Fetal Neonatal Med. 2022;27:101383. 2. Bhombal S, Patel N. Diagnosis & management of pulmonary hypertension in congenital diaphragmatic hernia. Semin Fetal Neonatal Med. 2022;27:101383 3. Storme L, Boubnova J, Mur S, Pognon L, Sharma D, Aubry E et al. Review shows that implementing a nationwide protocol for congenital diaphrag­ matic hernia was a key factor in reducing mortality and morbidity. Acta Paediatr Oslo Nor 1992. 2018;107:1131–9. Abbreviations CDH congenital diaphragmatic hernia ECMO extracorporeal membrane oxygenation FiO2 fraction of inspired oxygen MRI magnetic resonance imaging NICU neonatal intensive care unit iNO inhaled nitric oxide PCO2 partial pressure of carbon dioxide PH pulmonary hypertension SpO2 pulse oximetry oxygen saturation 4. Gupta VS, Harting MT. Congenital diaphragmatic hernia-associated pulmo­ nary hypertension. Semin Perinatol. 2020;44:151167. 5. Gavotto A, Thomas F, Werner O, Moreau J, Amedro P. Use of Treprostinil in Pediatric Pulmonary Hypertension: Case Reports and Review of the literature J Cardiovasc Pharmacol. 2020;76:23–31. 6. Montalva L, Lauriti G, Zani A. Congenital heart disease associated with congenital diaphragmatic hernia: a systematic review on incidence, prenatal diagnosis, management, and outcome. J Pediatr Surg. 2019;54:909–19. 7. Gnanappa GK, Laohachai K, Orr Y, Ayer J. Isolated anomalous origin of Left Pulmonary Artery from the descending aorta: an embryologic ambiguity. Ann Thorac Surg. 2016;102:e439–41. 7. Gnanappa GK, Laohachai K, Orr Y, Ayer J. Isolated anomalous origin of Left Pulmonary Artery from the descending aorta: an embryologic ambiguity. Ann Thorac Surg. 2016;102:e439–41. Discussion Careful examination confirmed the absence of pulmonary l The ratio of acceleration time over right ventricular ejection time in the main pulmonary artery is a relevant Gavotto et al. BMC Pediatrics (2023) 23:349 Page 5 of 6 Page 5 of 6 Gavotto et al. BMC Pediatrics Data Availability 12. Mehollin-Ray AR. Prenatal lung volumes in congenital diaphragmatic hernia and their effect on postnatal outcomes. Pediatr Radiol. 2022;52:637–42. The dataset supporting the conclusions of this article is contained within the manuscript. 13. Deprest JA, Benachi A, Gratacos E, Nicolaides KH, Berg C, Persico N, et al. Randomized trial of fetal surgery for moderate left diaphragmatic hernia. N Engl J Med. 2021;385:119–29. Consent for publication f d vein stenosis, mitral stenosis, left ventricle dysfunction, left outflow tract obstacle, or aortic coarctation. Written informed consent was obtained from the parents of the patient for publication of this case report and the accompanying images. A copy of the signed consent form is available for review by the Editor of this journal. l The unexpected occurrence of an increased pulmonary blood flow in the present CDH infant, led to the search for left-to-right shunt, and, ultimately, to the identifica­ tion of an anomalous origin of the right pulmonary artery from the ascending aorta. The challenge was then to totally reverse the therapeutic strategy. Our objective was first to reduce pulmonary blood flow by increasing pul­ monary vascular resistance, which involved suspension of pulmonary vasodilators, elevation of ventilation pres­ sures, and permissive hypercapnia. In addition, we aimed to reduce systemic-to-pulmonary difference in vascular resistance. Therefore, we reduced norepinephrine dose, as this drug increases systemic vascular resistance but reduces pulmonary vascular resistance in experimental CDH [16]. Authors’ contributions 8. Prifti E, Bonacchi M, Murzi B, Crucean A, Leacche M, Bernabei M, et al. Anoma­ lous origin of the right pulmonary artery from the ascending aorta. J Card Surg. 2004;19:103–12. 8. Prifti E, Bonacchi M, Murzi B, Crucean A, Leacche M, Bernabei M, et al. Anoma­ lous origin of the right pulmonary artery from the ascending aorta. J Card Surg. 2004;19:103–12. Dr. Gavotto, Prof. Amedro and Prof. Cambonie drafted the initial manuscript, and reviewed and revised the manuscript. Dr. Gavotto and Prof. Cambonie collected data, carried out the initial analyses, and reviewed and revised the manuscript. Dr. Gavotto and Prof. Cambonie coordinated and supervised data collection, and critically reviewed the manuscript. All authors approved the final manuscript as submitted and agree to be accountable for all aspects of the work. 9. Diab K, Richardson R, Pophal S, Alboliras E. Left hemitruncus associated with tetralogy of fallot: fetal diagnosis and postnatal echocardiographic and cardiac computed tomographic confirmation. Pediatr Cardiol. 2010;31:534–7. 9. Diab K, Richardson R, Pophal S, Alboliras E. Left hemitruncus associated with tetralogy of fallot: fetal diagnosis and postnatal echocardiographic and cardiac computed tomographic confirmation. Pediatr Cardiol. 2010;31:534–7. 10. Nathan M, Rimmer D, Piercey G, del Nido PJ, Mayer JE, Bacha EA, et al. Early repair of hemitruncus: excellent early and late outcomes. J Thorac Cardiovasc Surg. 2007;133:1329–35. Declarations 14. Guner Y, Jancelewicz T, Di Nardo M, Yu P, Brindle M, Vogel AM et al. Manage­ ment of Congenital Diaphragmatic Hernia Treated With Extracorporeal Life Support: Interim Guidelines Consensus Statement From the Extracorpo­ real Life Support Organization. ASAIO J Am Soc Artif Intern Organs 1992. 2021;67:113–20. Author details 1Department of Neonatal Medicine and Pediatric Intensive Care, Arnaud de Villeneuve Hospital, Montpellier University Hospital, 371 Avenue du Doyen Giraud, 34295 Montpellier, France 2PhyMedExp, CNRS, INSERM, University of Montpellier, Montpellier, France 3Paediatric and Congenital Cardiology Department, M3C National Reference Centre, Bordeaux University Hospital, Bordeaux, France 4IHU Liryc, INSERM 1045, Bordeaux University, Bordeaux, France 5Pathogenesis and Control of Chronic Infection, INSERM UMR 1058, University of Montpellier, Montpellier, France Received: 29 March 2023 / Accepted: 28 June 2023 Fundingi 11. Salomon LJ, Duyme M, Crequat J, Brodaty G, Talmant C, Fries N, et al. French fetal biometry: reference equations and comparison with other charts. Ultrasound Obstet Gynecol Off J Int Soc Ultrasound Obstet Gynecol. 2006;28:193–8. Competing interests Competing interests The authors declare that they have no competing interests. Ethics approval and consent to participate Ethics approval and consent to participate Not applicable. 15. Kays DW. ECMO in CDH: is there a role? Semin Pediatr Surg. 2017;26:166–70. 16. Hansmann G, Koestenberger M, Alastalo T-P, Apitz C, Austin ED, Bonnet D, et al. 2019 updated consensus statement on the diagnosis and treatment of pediatric pulmonary hypertension: the european Pediatric Pulmonary Page 6 of 6 Page 6 of 6 Gavotto et al. BMC Pediatrics (2023) 23:349 Gavotto et al. BMC Pediatrics (2023) 23:349 Gavotto et al. BMC Pediatrics (2023) 19. Jaillard S, Elbaz F, Bresson-Just S, Riou Y, Houfflin-Debarge V, Rakza T, et al. Pulmonary vasodilator effects of norepinephrine during the develop­ ment of chronic pulmonary hypertension in neonatal lambs. Br J Anaesth. 2004;93:818–24. 18. Kipfmueller F, Akkas S, Pugnaloni F, Bo B, Lemloh L, Schroeder L, et al. Echocardiographic Assessment of Pulmonary Hypertension in Neonates with congenital diaphragmatic hernia using Pulmonary Artery Flow characteris­ tics. J Clin Med. 2022;11:3038. g pf p 17. Levy PT, Patel MD, Groh G, Choudhry S, Murphy J, Holland MR, et al. Pulmonary artery acceleration time provides a Reliable Estimate of Invasive Pulmonary Hemodynamics in Children. J Am Soc Echocardiogr Off Publ Am Soc Echocardiogr. 2016;29:1056–65. Vascular Disease Network (EPPVDN), endorsed by AEPC, ESPR and ISHLT. J Heart Lung Transplant Off Publ Int Soc Heart Transplant. 2019;38:879–901. 17. Levy PT, Patel MD, Groh G, Choudhry S, Murphy J, Holland MR, et al. Pulmonary artery acceleration time provides a Reliable Estimate of Invasive Pulmonary Hemodynamics in Children. J Am Soc Echocardiogr Off Publ Am Soc Echocardiogr. 2016;29:1056–65. 18. Kipfmueller F, Akkas S, Pugnaloni F, Bo B, Lemloh L, Schroeder L, et al. Echocardiographic Assessment of Pulmonary Hypertension in Neonates with congenital diaphragmatic hernia using Pulmonary Artery Flow characteris­ tics. J Clin Med. 2022;11:3038. Vascular Disease Network (EPPVDN), endorsed by AEPC, ESPR and ISHLT. J Heart Lung Transplant Off Publ Int Soc Heart Transplant. 2019;38:879–901. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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Are weight status and weight perception associated with academic performance among youth?
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RESEARCH ARTICLE Open Access Are weight status and weight perception associated with academic performance among youth? Maram Livermore1, Markus J. Duncan1, Scott T. Leatherdale2 and Karen A. Patte1* Maram Livermore1, Markus J. Duncan1, Scott T. Leatherdale2 and Karen A. Patte1* (2020) 8:52 (2020) 8:52 Livermore et al. Journal of Eating Disorders https://doi.org/10.1186/s40337-020-00329-w * Correspondence: kpatte@brocku.ca * Correspondence: kpatte@brocku.ca 1Department of Health Sciences, Brock University, Faculty of Applied Health Sciences, Niagara Region, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada Full list of author information is available at the end of the article , l list of author information is available at the end of the article © The Author(s). 2020 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. Abstract Background: Emerging evidence suggests perceptions of being overweight account for many of the psychosocial consequences commonly associated with obesity. Previous research suggests an obesity achievement gap, yet limited research has explored weight perception in association with academic performance. Moreover, underweight perceptions have typically been excluded from research. The current study examined how BMI classification and weight perception relate to academic performance in a large cohort of youth. Methods: We used cross-sectional survey data from 61,866 grade 9–12 students attending the 122 Canadian schools that participated in Year 6 (2017/2018) of the COMPASS study. Mixed effect regression models were used to examine associations between students’ BMI classification and weight perceptions and their math and English/ French course grades. All models were stratified by sex and adjusted for sociodemographic covariates and school clustering. Results: For English/French grades, males and females with overweight or underweight perceptions were less likely to achieve higher grades than their peers with perceptions of being at “about the right weight”, controlling for BMI and covariates. For math grades, females with overweight perceptions, and all students with underweight perceptions, were less likely to achieve higher grades than their peers with “about the right weight” perceptions. All students with BMIs in the obesity range were less likely to report grades of 60% or higher than their peers with “normal-weight” BMIs, controlling for weight perception and covariates. Overweight BMIs were predictive of lower achievement in females for English/French grades, and in males for math grades, relative to “normal-weight” BMIs. Results for students that did not respond to the weight and weight perception items resembled those for obesity BMI and overweight/underweight perceptions, respectively. Conclusions: Overall, this study demonstrates that an obesity achievement gap remains when controlling for students’ perceptions of their weight, and that both underweight and overweight perceptions predict lower academic performance, regardless of BMI classification. Results suggest barriers to academic success exist among youth with larger body sizes, and those with perceptions of deviating from “about the right weight”. Keywords: Obesity, Overweight, Academic achievement, Weight perception, Education, Youth * Correspondence: kpatte@brocku.ca 1Department of Health Sciences, Brock University, Faculty of Applied Health Sciences, Niagara Region, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada Full list of author information is available at the end of the article Plain language summary with high BMI in North America than other cultures, possibly due to differing weight norms and given the stigma associated with overweight and obesity. Emerging evidence suggests weight perception—individuals’ sub- jective appraisal of their body weight—accounts for many of the psychosocial consequences commonly asso- ciated with obesity [12–14]. That is, the perception of being overweight, rather than body weight itself, may ac- count for risks of lower self-concept and poor mental health. One of the potential factors linking obesity and the perception of overweight to adverse outcomes is the experience of stigma and bias. An individual may need to perceive themselves as overweight, in order to internalize the bias associated with overweight/obesity. To date, the relationship between self-perceptions of weight and academic achievement has been largely over- looked. To our knowledge, only one study has examined weight perception as a predictor of academic achieve- ment [15]. Among US adolescents (ages 14 to 17) par- ticipating in the 2003 Youth Risk Behavior Study, Florin, Shultz, and Stettler found that perceived overweight sta- tus was associated with lower grades, regardless of BMI classification, and that obesity was no longer associated with grades when controlling for weight perception [15]. Replication is necessary, particularly in more recent samples, given potential shifts in social weight norms (e.g., related to obesity prevalence, body positive move- ments, and anti-obesity stigma and weight bias efforts). Furthermore, consideration of underweight perceptions in addition to overweight, and exploration of sex or gen- der differences, are warranted. Related to thinness and muscularly sociocultural body ideals, girls/women are more likely to report perceptions of underweight than boys/men, while boys/men tend to be split between per- ceptions of underweight and overweight [16]. Regardless of body size, both overweight and underweight percep- tions appear detrimental to mental and physical health relative to perceptions of being “about the right weight” [12–14, 16–25]; however, the latter has received rela- tively limited attention. g g y An obesity achievement gap has been suggested as an early contributor to later socioeconomic disparities found by weight status. To date, limited research has ex- amined how sociocultural weight norms contribute to academic performance. Emerging evidence suggests weight perception—individuals’ subjective appraisal of their body weight—accounts for many of the psycho- social consequences commonly associated with obesity. We sought to determine if body weight and weight per- ceptions predicted grades in a large sample of Canadian secondary school students. © The Author(s). 2020 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. Page 2 of 10 Page 2 of 10 Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders Plain language summary It was hypothesized that per- ceptions of being at “about the right weight” would pro- vide a protective effect. Overall, this study demonstrates that an obesity achievement gap remains when control- ling for students’ perceptions of their weight, and that weight perceptions—both underweight and overweight— predict academic performance, regardless of BMI classi- fication. Results contribute to a body of research that en- courages the consideration of both overweight and underweight perceptions and their potential impact on adolescent emotional and physical health. Further re- search is needed to determine the mechanisms under- lying these relationships, in order to remove barriers to academic success among youth with larger body sizes, and those with perceptions of deviating from “about the right weight”. Weight perception Subjective perception of weight status was determined using the question, “How do you describe your weight?” Response options included: “very underweight”, “slightly underweight”, “about the right weight”, “slightly over- weight” and “very overweight”. Responses were collapsed into three categories: underweight, about right, and overweight. In addition, missing weight perception re- sponses were included as a fourth category. Introduction About 35% of Canadian children and adolescents are at risk of having overweight or obesity [1]. Numerous stud- ies have shown that childhood obesity is associated with various physical health concerns [2]. Additionally, larger-bodied adolescents are at increased risk of adverse psychosocial outcomes [3]. Strauss and Pollack reported that children and adolescents face many challenges but “few problems in childhood have as significant an impact on emotional development as being overweight” (p.747) [4]. In fact, children with overweight or obesity report lower quality of life scores than children diagnosed with cancer [5]. Previous research also indicates the presence of an obesity achievement gap for children and adoles- cents [6, 7]. More specifically, some evidence suggests students with obesity have poorer academic achieve- ment, more absenteeism, higher dropout rates [6, 8], and are less likely to pursue and attain post-secondary edu- cation [9, 10]. Further examination of a potential weight-related achievement gap is critical to inform a learning environ- ment that will enable all youth to thrive. Deterrents to academic achievement in adolescence have critical impli- cations for future career opportunities and successful transitions to adulthood, with school failure and dropout increasing the risk of later unemployment, poverty, lower quality life, criminality, violence, and various health risk behaviors [6, 7, 26]. We sought to determine if larger-bodied students report lower grades in second- ary school than their peers with “normal-weight” BMIs. In addition, we explored whether weight perceptions predicted grades, while controlling for weight status. It was hypothesized that perceptions of being at “about the A recent meta-analysis by He et al. included 60 studies of weight status and academic performance and found a pooled correlation (r = −.111) between higher Body Mass Index (BMI) and lower grades [11]. The researchers con- cluded that the relationship between weight status and academic achievement was moderated by geographical region, with lower grades more likely to be associated Page 3 of 10 Livermore et al. Journal of Eating Disorders (2020) 8:52 Page 3 of 10 Page 3 of 10 Livermore et al. Journal of Eating Disorders (2020) 8:52 right weight” would provide a protective effect, and any relationship between BMI classification and academic achievement would be reduced when controlling for weight perception. Design and participants The COMPASS study is a prospective cohort study de- signed to collect longitudinal and hierarchical health data from a large sample of grade 9 through 12 students (ages 14–19) enrolled in Canadian secondary schools. Schools and school boards were purposely selected based on whether they permitted active-information passive-consent parental permission protocols, which are critical for collecting robust data among youth [27]. The COMPASS student questionnaire (Cq), a self-report paper-and-pencil survey, is completed once annually by full school samples during one classroom period. All grade 9 through 12 students attending participating schools were eligible to participate and could decline at any time. A full description of recruitment methods [28] and the COMPASS study are available in print [29] and online (www.compass.uwaterloo.ca). The COMPASS study received ethics approval from the University of Waterloo and Brock University Human Research Ethics Committee and all participating school boards. Academic performance Academic performance was assessed using student- reported grades. Participants reported their approximate overall mark in their current or most recent math and English (in Ontario, Alberta and BC schools) or French (in Quebec) courses. Grades were dichotomized as ≥60% or < 60% for both math and English/French grade models. p p g We used cross-sectional data from Year 6 (2017–2018 school year) of the COMPASS study, which included 66, 434 students at 122 secondary schools in Ontario (n = 61), British Columbia (n = 16), Alberta (n = 8) and Que- bec (n = 37). The overall student response rate in Year 6 was 81.85% of eligible students. Student non- participation primarily resulted from absences or sched- uled study-periods during data collection. Participants with missing outcome, sex, or covariate data were re- moved, leaving a final sample of 61,866 adolescents. Weight status Student weight status was defined by Body Mass Index (BMI; kg/m2) classification determined based on student-reported height and weight [30], and the World Health Organization [31] age-and sex-adjusted cut points (underweight, normal weight, overweight, obes- ity). A previous study found the weight status measure to be reliable, valid, and valuable for use when objective methods are not feasible [30]. Given the prevalence of missing BMI data, and as missing self-reported weight data may not be missing at random [32], two separate categories were created for missing weight status based on which variables were missing to determine BMI clas- sification: missing BMI classification due to weight not being reported, and missing BMI due to missing age, sex, or height. Covariates Participant-reported race/ethnicity (categorized into white and, non-white minority, multiethnic, or other) and school grade (9, 10, 11, 12, other [Secondary I- II in Quebec]) were entered into the model as covariates. Also, student weekly spending/saving money (catego- rized into $1–$20, $21–$100, >$100, don’t know) was included as an indicator of part-time employment and/ or allowance, as proxy for student-level SES in the ab- sence of data on parental income or education data. Statistical analysis R software [33] was used to conduct frequency descrip- tive statistics and mixed effect logistic regression models. Separate models explored the association between BMI status and weight perception with math grades and Eng- lish/French course grades, stratified by sex and control- ling for weekly spending money, school grade, and race/ ethnicity. Mixed models were used to account for school clustering by adding a random intercept at the school level. No interaction effect between weight status and weight perception was indicated when tested (results not reported). Descriptive statistics Descriptive statistics for all variables are described in Table 1. In this sample, 49.4% of participants identified as male and 50.6% as female. About two-thirds (66.6%) of the sample identified as white and one-third as non- white, mixed, or other race/ethnicity. In terms of weight status, 5.7, 12.0, 54.7 and 3.6% of the total sample had BMIs in the obesity, overweight, “normal-weight”, and underweight categories, respectively, while 19.6% of stu- dents did not report their weight, and the remaining Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders Page 4 of 10 Page 4 of 10 ti i i h i ht d t t Table 1 Descriptive statistics for secondary school students in Year 6 (2017/2018) of the COMPASS study (N = 61,886) Female (n = 31,334) Male (n = 30,552) % (n) % (n) Grade 9 24.3 (7614) 24 (7332) 10 24.5 (7677) 24.3 (7424) 11 23.3 (7301) 23.1 (7058) 12 14.9 (4669) 15.7 (4797) Othera 13.0 (4073) 12.9 (3941) Race/ethnicity White 66.7 (20889) 66.6 (20355) Non-white, multietnic, or others 33.3 (10445) 33.4 (10197) BMI Classifications Underweight 1.5 (470) 2.1 (642) “Normal Weight” 56.8 (17798) 50.6 (15459) Overweight 10.3 (3227) 13.3 (4063) Obesity 4.1 (1285) 7.4 (2261) Missing weight 21.7 (6799) 19.4 (5927) Missing age, sex, or height 5.6 (1755) 7.2 (2200) Weight Perception Underweight 11.1 (3478) 21.2 (6477) “About the right weight” 60.7 (19019) 56.2 (17170) Overweight 26.5 (8304) 20.6 (6294) Missing 1.7 (533) 2.0 (611) Weekly Spending Money None 14.2 (4449) 17.9 (5469) $1–$20 25.9 (8116) 24.7 (7546) $21–$100 25.5 (7990) 22.0 (6721) >$100 16.9 (5295) 20.4 (6233) Don’t know 17.5 (5484) 15.0 (4583) Math Grades 60–100% 51.0 (15980) 51.2 (15643) 0–59% 49.0 (15354) 48.8 (14909) English/French Grades 60–100% 51.3 (16074) 51.1 (15612) 0–59% 48.7 (15260) 48.9 (14940) aSecondary I-II in Quebec schools BMI body mass index Table 1 Descriptive statistics for secondary school students in Year 6 (2017/2018) of the COMPASS study (N = 61,886) weight” (60.7% versus 56.2%) than males. Just over half of students (51.0–51.3%) reported math and English/ French grades above 60%. g The concordance between weight perception and BMI category is presented in Fig. 1. The weighted Kappa was 0.392 among females and 0.370 among males. The ma- jority of males (74.9%) and females (81.3%) with BMIs in the obesity category reported perceptions of overweight. Descriptive statistics Among those with overweight BMIs, most females re- ported perceptions of overweight (62.2%); whereas more males reported “about right” weight perceptions (54.5%) than overweight perceptions (42.4%). Most males (64.2%) and females (61.5%) in the underweight BMI category reported underweight perceptions. In the “nor- mal weight” BMI category, more males reported under- weight perceptions (27.5%) than females (12.2%), while females were more likely to perceive their weight as “about right” (71.6%) or overweight (15.4%) than males (65.4%; 5.9%). Students with missing BMI data resembled those with “normal weight” BMIs, except a higher proportion re- ported overweight perceptions. About half of students with missing BMI data reported “about right” weight perceptions (51.1% males; 55.1% females), over a quarter reported overweight perceptions (25.1% males; 30.8% fe- males), and 9.7% of females and 19.0% of males reported underweight perceptions. Discussion The current study examined whether weight status and student perceptions of their weight were associated with academic grades in selected secondary school courses (math and English/French) in a large population study of Canadian youth. Results support the links between obes- ity, as determined by BMI, and lower academic perform- ance in both males and females. Overweight BMI classifications were also associated with lower odds of high grades in English/French courses among females, and in math classes among male students, relative to BMIs considered “normal-weight”. Similar to previous research [15], females with overweight perceptions were less likely to achieve higher course grades in math, and both males and females with overweight perceptions had lower odds of grades above 60% in their English/French courses, relative to their peers with perceptions of being at “about the right weight”, controlling for BMI classifi- cation and covariates. While no effect was found for underweight relative to “normal-weight” BMI, females and males with perceptions of being underweight had lower odds of high grades in math and English/French courses relative to students with “about the right weight” perceptions. Results for youth with missing BMI or weight perception data resembled those for obesity BMI classifications and perceptions of overweight or under- weight, respectively. Overall, this study demonstrates Math course grades g See Table 2 for model results testing BMI classification and weight perception as predictors of math grades, after stratifying by sex and controlling for covariates. In males only, having over $100 a week available for spending or saving and identifying as nonwhite, mixed, or other race/ethnicity were associated with lower odds of report- ing math grades over 60%, relative to males without any weekly spending money and of white race/ethnicity, re- spectively. Students with BMIs in the obesity range were less likely to report a math grade above 60% compared to those with BMIs considered “normal weight”. In males only, overweight BMIs were associated with a lower likelihood of report a math grade above 60% com- pared to those with “normal-weight” BMIs. No effect re- sulted for underweight BMI relative to “normal-weight” BMI. In females only, weight perceptions of overweight predicted a lower likelihood of reporting math grades above 60% when compared to perceptions of being “about the right weight”, controlling for BMI classifica- tion and covariates. In both males and females, percep- tions of underweight were associated with lower likelihood of higher math grades than perceptions of be- ing “about the right weight”. Student with missing BMI data either due to not reporting weight or missing height, age or sex data were more likely to have lower proportion were missing sex, age, or height data to categorize BMI. Additionally, a total of 23.8 and 58.7% students reported overweight and “about the right weight” perceptions respectively, while 1.4% did not re- spond to the weight perception item. More males re- ported perceptions of “underweight” than females (21.2% versus 11.1%), while more females reported perceptions of overweight (26.5% versus 20.6%) and “about the right Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders Page 5 of 10 Fig. 1 Weight perception and BMI category concordance among female and male secondary school students participating in Year 6 (2017/2018) of the COMPASS study when compared to those with “about the right weight” perceptions. math grades when compared to those in the “normal- weight” BMI category. Similarly, students with missing weight perception data were more likely to report lower math grades when compared to those with “about the right weight” perceptions. English/French course grades bl h Table 3 summarizes the resultant model testing BMI classification, weight perception, and covariates as pre- dictors of English/French grades by sex. Both males and females identifying as nonwhite, mixed, or other race/ ethnicity had lower odds of English/French grades above 60% than their counterparts identifying as white. No dif- ferences in English/French grades resulted by spending money or grade. Both male and female adolescents with BMIs in the obesity range, and females with overweight BMIs, were less likely to report higher grades than their peers with BMIs considered “normal weight”. Both males and females with weight perceptions of overweight and underweight were less likely to report higher grades (above 60%) in their English/French clas- ses when compared to those with perceptions of being at “about the right weight”. Students with missing BMI data due to either not reporting weight, or because of missing height, age, or sex data, had significantly lower odds of reporting English/French grades above 60%, when compared to those with “normal-weight” BMIs. Similarly, students with missing weight perception data were less likely to have English/French grades above 60% Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders Page 6 of 10 Table 2 Mixed-effect model testing BMI category and weight perception as predictors of Math grades ≥60% among youth Females (N = 31,334) Males (N = 30,552) AOR 95% CI AOR 95% CI BMI Category (Reference: “Normal weight”) Obesity 0.70** 0.59–0.82 0.62** 0.55–0.71 Overweight 0.90 0.80–1.02 0.87* 0.79–0.97 Underweight 0.93 0.70–1.25 0.85 0.68–1.07 Missing weight data 0.56** 0.51–0.61 0.62** 0.57–0.68 Missing sex, age, or height data 0.64** 0.55–0.74 0.65** 0.57–0.74 Weight Perception (Reference: “About the right weight”) Overweight 0.82** 0.75–0.89 0.91 0.83–1.00 Underweight 0.77** 0.69–0.86 0.90* 0.82–0.97 Missing weight perception 0.64** 0.50–0.83 0.59** 0.47–0.73 Race/ethnicity (Reference: White) Nonwhite, multiethnic, or other 0.92 0.85–1.00 0.87** 0.81–0.94 Grade (Reference: 9) 10 0.82** 0.74–0.90 0.80** 0.73–0.88 11 0.96 0.87–1.07 0.83** 0.75–0.91 12 0.91 0.81–1.02 0.88 0.79–0.99 Othera 1.10 0.95–1.26 1.14 0.99–1.31 Weekly Spending Money (Reference: None) $1–$20 0.94 0.84–1.05 0.93 0.84–1.02 $21–$100 0.94 0.84–1.05 0.89 0.80–0.99 > $100 0.94 0.83–1.07 0.86* 0.77–0.95 Don’t know 1.05 0.93–1.19 1.02 0.91–1.14 Note: Cross-sectional data from Year 6 (2017/2018) of the COMPASS study (N = 61,886). The outcome reference category is math grades < 60%. English/French course grades bl h Mixed models were used to account for school clustering by adding a random intercept at the school level *p < .01 **p < .001 aSecondary I-II in Quebec schools Table 2 Mixed-effect model testing BMI category and weight perception as predictors of Math grades ≥60% among youth accounting for overweight perceptions [15]. Over- weight perceptions have been linked to poor mental health, psychosocial distress, and low self-esteem in adolescents [26, 34–36], factors that have also been associated with lower academic achievement [37]. In fact, researchers have reported perceiving oneself as overweight to be a stronger predictor of behavioural issues and mental distress than actual weight status [12, 36, 38]. Similarly, the current results indicate that perceptions of overweight significantly predicted poorer academic outcomes independent of BMI classi- fication, with the exception of math grades in males. However, unlike Florin et al. [15], obesity BMI classi- fications remained predictive of lower grades when controlling for weight perception. that an obesity achievement gap remains when control- ling for students’ perceptions of their weight, and that weight perceptions—both underweight and overweight— predict lower academic performance, regardless of BMI classification. Further research is needed to determine the mechanisms underlying these relationships, in order to remove barriers to academic success among youth with larger body sizes, and those with perceptions of de- viating from “about the right weight”. that an obesity achievement gap remains when control- ling for students’ perceptions of their weight, and that weight perceptions—both underweight and overweight— predict lower academic performance, regardless of BMI classification. Further research is needed to determine the mechanisms underlying these relationships, in order to remove barriers to academic success among youth with larger body sizes, and those with perceptions of de- viating from “about the right weight”. To the best of our knowledge, only one previous study has examined weight perception as a predictor of academic grades. The current study provides neces- sary replication and builds on existing literature, by examining these relationships in a more recent and larger sample of youth. English/French course grades bl h In a sample of approximately 11,000 US adolescents participating in the 2003 Youth Risk Behavior Study, perceptions of overweight were found to be a stronger predictor of academic out- comes than BMI, and obesity was no longer a signifi- cant predictor of academic performance when The current study suggests other factors appear to contribute to the obesity achievement gap, such as par- ental education, mental health, or external weight bias. Students with obesity are more likely to experience weight-based bullying within the school context [15, 35]. Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders Page 7 of 10 Table 3 Mixed-effect model testing BMI category and weight perception as predictors of English/French grades ≥60% among youth Females (N = 31,334) Males (N = 30,552) AOR 95% CI AOR 95% CI BMI Category (Reference: “Normal weight”) Obesity 0.51** 0.41–0.64 0.63** 0.55–0.73 Overweight 0.71** 0.60–0.85 0.87 0.77–0.99 Underweight 1.04 0.68–1.59 0.93 0.71–1.21 Missing weight data 0.45** 0.40–0.50 0.54** 0.49–0.60 Missing sex, age, or height data 0.49** 0.40–0.59 0.58** 0.51–0.66 Weight Perception (Reference: “About the right weight”) Overweight 0.76** 0.68–0.85 0.83** 0.75–0.92 Underweight 0.59** 0.51–0.69 0.87* 0.79–0.95 Missing weight perception 0.50** 0.36–0.68 0.66** 0.51–0.84 Race/ethnicity (Reference: White) Nonwhite, multiethnic, or other 0.67** 0.60–0.75 0.74** 0.68–0.80 Grade (Reference: 9) 10 0.96 0.83–1.10 0.94 0.85–1.05 11 0.87 0.75–1.00 0.94 0.84–1.05 12 1.07 0.90–1.27 1.06 0.93–1.21 Othera 1.19 0.98–1.44 1.12 0.97–1.29 Weekly Spending Money (Reference: None) $1–$20 0.88 0.75–1.03 1.08 0.97–1.21 $21–$100 0.95 0.80–1.11 1.05 0.93–1.18 > $100 0.88 0.74–1.06 0.93 0.83–1.05 Don’t know 0.99 0.84–1.18 1.09 0.96–1.23 Note: Cross-sectional data from Year 6 (2017/2018) of the COMPASS study (N = 61,886). The outcome reference category is English/French grades < 60%. Mixed models were used to account for school clustering by adding a random intercept at the school level *p < .01 **p < .001 aSecondary I II in Quebec schools Table 3 Mixed-effect model testing BMI category and weight perception as predictors of English/French grades ≥60% among th aSecondary I-II in Quebec schools Also, weight bias has been documented in physical education teachers [9, 39–41] and given its perva- siveness across the population [9, 39], may contrib- ute to educators’ perceptions of students’ academic abilities. Several studies have indicated that the asso- ciation between BMI and academic performance was no longer significant when models adjusted for par- ental/familial characteristics [42, 43]. For instance, Datar et al. English/French course grades bl h concluded that overweight status is not a causal factor of lower academic performance, as weight-related differences in test scores became in- significant when social and behavioural variables, such as SES and parental time spent with the child were considered [43]. The authors cautioned that higher weight students may be labeled as lower achievers, as weight is a more obvious marker than sociodemographic characteristics. the high prevalence of obesity, weight stigma continues to be problematic. Stereotypes that individuals living with obesity are lazy, unintelligent, or lack willpower contribute to stigma and discrimination [39]. Internal- ized stigma, or self-stigma, occurs when individuals apply negative stereotypes to themselves and believe that the stigma is deserved [40], leading to low self-esteem and psychological distress [39]. Research indicates that bias toward individuals with overweight and obesity per- sists in health care, employment, and home settings [9]. Education, however, has received less research attention, particularly at the secondary school level. It is plausible that adolescents who perceive themselves as overweight have lower self-concepts related to internalized weight stigma, which in turn, contributes to poorer academic engagement and performance. That is, students who feel their weight is “about right” may be more likely to suc- ceed because they have not internalized negative stereotypes. Adolescents who perceive themselves as overweight may be at risk of internalizing weight stigma. Despite Page 8 of 10 Page 8 of 10 Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders (2020) 8:52 Students with underweight perceptions also reported lower grades than those with “about right” perceptions. Interestingly, the effect of underweight perceptions was more consistent than overweight perceptions in predict- ing lower grades in both females and males, and across Math and English/French grades. To our knowledge, no previous study has examined underweight perceptions in relation to academic performance. While less studied, underweight perceptions have been associated with de- pressive and anxiety symptoms in males [21, 44, 45] and suicidality and lower health-related quality of life in all youth [25, 38]. Based on this result, it is plausible that links between weight perception and academic perform- ance relate more to deviations from the social norm or sociocultural body ideals than to weight stigma. Results are consistent with sociocultural body ideals of thinness for women and muscularity for men, with more males reporting underweight perceptions than females. Limitations Several limitations require consideration. First, while the large sample supports generalizability, the COMPASS study was not designed to be representative. Second, cross-sectional data was used to explore relationships. Future longitudinal analysis of COMPASS data will as- sist in establishing temporality and testing potential mechanistic contributors (e.g., mental health, self- concept, bullying victimization, school connectedness). Third, the use of self-reported data carries risks of recall and social desirability bias. For instance, lower achieving students may over report their achievement. However, a review of 37 independent samples found strong response validity of self-reported grades in high school students [49]. Similarly, weight status was based on student- reported height and weight, and as such, results likely reflect greater concordance between weight perception and weight status than exists. However, time and cost constraints preclude the feasibility of obtaining objective height and weight measures, not to mention the poten- tial harm of weight measurements in a school-based study. Also, a strong correlation between measured and self-reported BMI has been shown in youth [30, 50]. Fourth, the reference point that youth used to answer the weight perception question is not entirely clear. That is, it is not known whether respondents were comparing their weight to their ideal body, their peers, a medical standard, or some other alternative. For instance, re- sponses of ‘about the right weight’ may indicate weight satisfaction rather than youths’ perception of how their weight compared to an external reference point. Lastly, as discussed, this study did not assess the contribution of self-esteem or mental health. Mental health may con- found the relationship between weight status or percep- tion and academic achievement. Several studies have linked poor mental health with lower grades [37], and a recent intervention promoting positive mental health and wellbeing significantly improved academic grades in participating schools [51]. Future studies, using longitu- dinal designs, standardized test grades, and including mental health, self-concept, and stigma measures should be considered. Interestingly, students that did not report their body weight or weight perception tended to have the lowest likelihood of achieving higher grades, comparable to the odds for obesity BMI classification. Far more males and females with missing BMI data reported perceptions of overweight than their peers with “normal-weight” BMIs. Adolescents are less likely to report their weight as BMI increases and if they have poor body image [32, 46]. English/French course grades bl h About one-fifth of males and one-tenth of females reported underweight perceptions; yet only 1.5 and 2.1% of female and males had BMIs classified as underweight, respect- ively. Another plausible explanation is that youth with underweight perceptions were experiencing weight re- strictions (e.g., due to food insecurity) and/or had lost weight, while “normal-weight” by BMI, which in turn contributed to reduced ability to perform in school. Re- sults highlight the importance of including weight per- ceptions across the spectrum in future research. weight-based bullying and promote weight acceptance are also advised. Previous research suggests bullying victimization predicts changes from perceptions of be- ing at “about the right weight” to underweight and overweight perceptions among youth [48]. Limitations Missing self-reported weight status and perceptions may be influenced by an awareness of societal norms of thin- ness/muscularity ideals and weight bias attitudes [46, 47]. Hence, if adolescents with larger body sizes did not report their weight due to concerns of judgment by others, results lend support to the theory that negative perceptions regarding body weights outside of “about right” contribute to lower academic performance. Future research should explore both internalized and externalized weight bias, and associated lower self-concept and mental distress, as possible mecha- nisms explaining links between higher weight status, and perceptions of overweight and underweight, with academic achievement. Upstream strategies targeting the negative connotations of varying body sizes may prove valuable, to prevent the adverse psychosocial outcomes associated with perceptions of being over- weight or underweight. 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Perception of overweight is associated with poor academic performance in US adolescents. J Sch Health. 2011;81(11): 663–70. https://doi.org/10.1111/j.1746-1561.2011.00642.x. 16. Patte KA, Laxer RE, Qian W, Leatherdale ST. An analysis of weight perception and physical activity and dietary behaviours among youth in the COMPASS study. SSM Popul Health. 2016;2:841–9. https://doi.org/10.1016/j.ssmph.2016. 10.016. Funding Th COM The COMPASS study has been supported by a bridge grant from the CIHR Institute of Nutrition, Metabolism and Diabetes (INMD) through the “Obesity – Interventions to Prevent or Treat” priority funding awards (OOP-110788; awarded to SL), an operating grant from the CIHR Institute of Population and Public Health (IPPH) (MOP-114875; awarded to SL), a CIHR project grant (PJT-148562; awarded to SL), a CIHR bridge grant (PJT-149092; awarded to KP/SL), a CIHR project grant (PJT-159693; awarded to KP), and by a research funding arrangement with Health Canada (#1617-HQ-000012; contract awarded to SL). 11. He J, Chen X, Fan X, Cai Z, Huang F. Is there a relationship between body mass index and academic achievement? A meta-analysis. Public Health. 2019;167:111–24. https://doi.org/10.1016/j.puhe.2018.11.002. 12. Ter Bogt Tom FM, Van Dorsselaer SA, Monshouwer K, Verdurmen J, Engels R, Vollebergh W. Body mass index and body weight perception as risk factors for internalizing and externalizing problem behavior among adolescents. J Adolesc Health. 2006;39(1):27–34. 13. Roberts RE, Duong HT. Perceived weight, not obesity, increases risk for major depression among adolescents. J Psychiatr Res. 2013;47(8):1110–7. https://doi.org/10.1016/j.jpsychires.2013.03.019. Acknowledgements 6. Shore SM, Sachs ML, Lidicker JR, Brett SN, Wright AR, Libonati JR. Decreased scholastic achievement in overweight middle school students. Obesity. 2008;16(7):1535–8. https://doi.org/10.1038/oby.2008.254. g The authors would like to thank the schools, school boards, and students that have participated in the COMPASS study, and all COMPASS staff and team members. 7. Benson R, Von Hippel PT, Lynch JL. Does more education cause lower BMI, or do lower-BMI individuals become more educated? Evidence from the National Longitudinal Survey of youth 1979. Soc Sci Med. 2018;211:370–7. https://doi.org/10.1016/j.socscimed.2017.03.042. Received: 25 July 2020 Accepted: 28 September 2020 Received: 25 July 2020 Accepted: 28 September 2020 Received: 25 July 2020 Accepted: 28 September 2020 Conclusion Results support the existence of an achievement gap by both weight status and weight perception. This study has widespread implications with over 2 million adoles- cents at risk of having overweight or obesity in Canada Page 9 of 10 Page 9 of 10 Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders (2020) 8:52 Livermore et al. Journal of Eating Disorders (2020) 8:52 [1], and over 40% of youth reporting weight perceptions other than “about right”. Research is needed to further examine the mechanisms underlying these associations. Academic achievement sets a lifelong trajectory of health and wellbeing. Lower academic achievement is linked to increased rates of unemployment, poverty, criminality, and negative future health outcomes [6, 7, 26, 52]. The obesity achievement gap has been suggested as an early contributor to later SES disparities found by weight sta- tus [53]. The present study contributes to a body of re- search that encourages the consideration of both overweight and underweight perceptions and their po- tential impact on adolescent emotional and physical health. Upstream strategies to prevent negative connota- tions associated with body sizes divergent from “about right” and to promote weight acceptance merit consider- ation. Further exploration is necessary to inform policies and interventions that foster a learning environment that will enable all youth to thrive. Authors’ contributions ML lead the writing of the manuscript. MJD conducted all analysis. STL is the PI of the COMPASS Study. ML and KAP conceptualized the manuscript study. All authors (ML, MJD, STL, KAP) contributed to manuscript revisions, results interpretation, and approved the final version. p 9. Puhl RM, Heuer CA. The stigma of obesity: a review and update. Obesity. 2009;17(5):941–64. https://doi.org/10.1038/oby.2008.636. y 2009;17(5):941–64. https://doi.org/10.1038/oby.2008.636. 10. Larsen JK, Kleinjan M, Engels R, Fisher JO, Hermans R. Higher weight, lower education: a longitudinal association between adolescents’ body mass index and their subsequent educational achievement level? J Sch Health. 2014;84(12):769–76. https://doi.org/10.1111/josh.12212. Author details 1 1Department of Health Sciences, Brock University, Faculty of Applied Health Sciences, Niagara Region, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada. 2School of Public Health and Health Systems, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada. Ethics approval and consent to participate The University of Waterloo Office of Research Ethics (ORE#17264) and participating school boards approved all procedures. All students attending participating schools were invited to participate using active-information passive-consent parental permission protocols. Students could withdraw from the study at any time. 17. Neumark-Sztainer DR, Wall MM, Haines JI, Story MT, Sherwood NE, van den Berg PA. Shared risk and protective factors for overweight and disordered eating in adolescents. Am J Prev Med. 2007;33(5):359–69. https://doi.org/10. 1016/j.amepre.2007.07.031. 18. Khambalia A, Hardy LL, Bauman A. Accuracy of weight perception, life-style behaviours and psychological distress among overweight and obese adolescents. J Paediatr Child Health. 2012;48(3):220–7. https://doi.org/10. 1111/j.1440-1754.2011.02258.x. Competing interests 19. Osborn J, Naquin M, Gillan W, Bowers A. The impact of weight perception on the health behaviors of college students. Am J Health Educ. 2016;47(5): 287–98. https://doi.org/10.1080/19325037.2016.1204966. The authors declare that they have no competing interests/conflicts of interests. Page 10 of 10 Page 10 of 10 Page 10 of 10 Livermore et al. Journal of Eating Disorders (2020) 8:52 20. Gaylis JB, Levy SS, Hong MY. Relationships between body weight perception, body mass index, physical activity, and food choices in Southern California male and female adolescents. Int J Adolesc Youth. 2016; 25:264–75. https://doi.org/10.1080/02673843.2019.1614465. 41. Peterson JL, Puhl RM, Luedicke J. An experimental assessment of physical educators’ expectations and attitudes: the importance of student weight and gender. J Sch Health. 2012;82(9):432–40. https://doi.org/10.1111/j.1746- 1561.2012.00719.x. 25:264–75. https://doi.org/10.1080/02673843.2019.1614465. 21. Schiefelbein EL, Mirchandani GG, George GC, Becker EA, Castrucci BC, Hoelscher DM. Association between depressed mood and perceived weight in middle and high school age students: Texas 2004-2005. Matern Child Health J. 2012;16(1):169–76. https://doi.org/10.1007/s10995-010-0733-1. 42. Li Y, Dai Q, Jackson JC, Zhang J. Overweight is associated with decreased cognitive functioning among school-age children and adolescents. Obesity. 2008;16(8):1809–15. 43. Datar A, Sturm R, Magnabosco JL. Childhood overweight and academic performance: national study of kindergartners and first graders. Obesity. 2004;12(1):58. 22. Kim Y, Austin SB, Subramanian SV, Kawachi I. Body weight perception, disordered weight control behaviors, and depressive symptoms among Korean adults: the Korea National Health and nutrition examination survey 2014. PLoS One. 2014;3(6):e0198841. https://doi.org/10.1371/journal.pone. 0198841. 44. Blashill AJ, Wilhelm S. Body image distortions, weight, and depression in adolescent boys: longitudinal trajectories into adulthood. Psychol Men Masculinity. 2014;15(4):445–51. https://doi.org/10.1037/a0034618. 23. Al Mamun A, Cramb S, McDermott BM, O'Callaghan M, Najman JM, Williams GM. (2007). Adolescents' perceived weight associated with depression in young adulthood: a longitudinal study. Obesity. 2007;15(12):3097–105. https://doi.org/10.1038/oby.2007.369. 45. Isomaa R, Isomaa AL, Marttunen M, Kaltiala-Heino R, Björkqvist K. Longitudinal concomitants of incorrect weight perception in female and male adolescents. Body Image. 2011;8(1):58–63. https://doi.org/10.1016/j. bodyim.2010.11.005. 46. Brener ND, Mcmanus T, Galuska DA, Lowry R, Wechsler H. Reliability and validity of self-reported height and weight among high school students. J Adolesc Health. 2003;2(4):281–7. https://doi.org/10.1016/S1054- 139X(02)00708-5. 24. Thurston IB, Sonneville KR, Milliren CE, Kamody RC, Gooding HC, Richmond TK. Cross-sectional and prospective examination of weight misperception and depressive symptoms among youth with overweight and obesity. Prev Sci. 2007;18(2):152–63. https://doi.org/10.1007/s11121-016-0714-8. 47. Morrison TG, Kalin R, Morrison MA. Competing interests Body-image evaluation and body-image investment among adolescents: a test of sociocultural and social comparison theories. Adolescence. 2004;39(155):571–92. 25. Eaton DK, Lowry R, Brener ND, Galuska DA, Crosby AE. Associations of body mass index and perceived weight with suicide ideation and suicide attempts among US high school students. Arch Pediatr Adolesc Med. 2005; 159(6):513–9. https://doi.org/10.1001/archpedi.159.6.513. 48. Patte KA, Qian W, Leatherdale ST. Predictors of one-year change in how youth perceive their weight. J Obes. 2020;7396948. https://doi.org/10.1155/ 2020/7396948. 26. McLaren L. Socioeconomic status and obesity. Epidemiol Rev. 2007;29(1):29– 48. 49. Kuncel NR, Credé M, Thomas LL. The validity of self-reported grade point averages, class ranks, and test scores: a meta-analysis and review of the literature. Rev Educ Res. 2005;75(1):63. 27. Courser MW, Shamblen SR, Lavrakas PJ, Collins D, Ditterline P. The impact of active consent procedures on nonresponse and nonresponse error in youth survey data: evidence from a new experiment. Eval Rev. 2009;33(4):370–95. 50. Goodman E, Hinden BR, Khandelwal S. Accuracy of teen and parental reports of obesity and body mass index. Pediatrics. 2000;106(1):52–8. 28. Reel B, Bredin C, Leatherdale ST. COMPASS year 5 and 6 school recruitment and retention: technical report series: Ontario: University of Waterloo. 2018; 5(1). 51. Dix KL, Slee PT, Lawson MJ, Keeves JP. Implementation quality of whole- school mental health promotion and students’ academic performance. Child Adolesc Mental Health. 2012;17(1):45–51. 29. Leatherdale ST, Brown KS, Carson V, et al. The COMPASS study: a longitudinal hierarchical research platform for evaluating natural experiments related to changes in school-level programs, policies and built environment resources. BMC Public Health. 2014;14:331. https://doi.org/10. 1186/1471-2458-14-331. 52. Troiano RP, Flegal KM. Overweight children and adolescents: description, epidemiology, and demographics. Pediatrics. 1998;101(3):497–504. 53. OECD. The heavy burden of obesity: the economics of prevention; 2019. https://doi.org/10.1787/67450d67-en. Accessed 18 Oct 2019. 30. Leatherdale ST, Laxer RE. Reliability and validity of the weight status and dietary intake measures in the COMPASS questionnaire: are the self- reported measures of body mass index (BMI) and Canada’s food guide servings robust? Int J Behav Nutr Phys Act. 2013;10(1):42. https://doi.org/10. 1186/1479-5868-10-42. 30. Leatherdale ST, Laxer RE. Reliability and validity of the weight status and dietary intake measures in the COMPASS questionnaire: are the self- reported measures of body mass index (BMI) and Canada’s food guide servings robust? Int J Behav Nutr Phys Act. 2013;10(1):42. https://doi.org/10. 1186/1479-5868-10-42. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 31. WHO. Growth reference data for 5–19 years. https://www.who.int/ growthref/en/. Accessed 20 Aug 2019. 31. WHO. Growth reference data for 5–19 years. https://www.who.int/ growthref/en/. Accessed 20 Aug 2019. 32. Aceves-Martins M, Whitehead R, Inchley J, Giralt M, Currie C, Solà R. Self- reported weight and predictors of missing responses in youth. Nutrition. 2018;53:54–8. https://doi.org/10.1016/j.nut.2018.01.003. 32. Aceves-Martins M, Whitehead R, Inchley J, Giralt M, Currie C, Solà R. Self- reported weight and predictors of missing responses in youth. Nutrition. 2018;53:54–8. https://doi.org/10.1016/j.nut.2018.01.003. 33. R Core Team, 2019. R: A Language and Environment for Statistical Computing. http://www.R-project.org/. 33. R Core Team, 2019. R: A Language and Environment for Statistical Computing. http://www.R-project.org/. 34. Jansen W, van de Looij-Jansen PM, de Wilde EJ, Brug J. Feeling fat rather than being fat may be associated with psychological well-being in young Dutch adolescents. J Adolesc Health. 2018;42(2):128–36. 34. Jansen W, van de Looij-Jansen PM, de Wilde EJ, Brug J. Feeling fat rather than being fat may be associated with psychological well-being in young Dutch adolescents. J Adolesc Health. 2018;42(2):128–36. 35. Crosnoe R. Gender, obesity, and education. Sociol Educ. 2007;80(3):241–60. 35. Crosnoe R. Gender, obesity, and education. Sociol Educ. 2007;80(3):241–60. 36. Paxton SJ, Neumark-Sztainer D, Hannan PJ, Eisenberg ME. Body dissatisfaction prospectively predicts depressive mood and low self-esteem in adolescent girls and boys. J Clin Child Adolesc Psychol. 2006;35(4):539– 49. 36. Paxton SJ, Neumark-Sztainer D, Hannan PJ, Eisenberg ME. Body dissatisfaction prospectively predicts depressive mood and low self-esteem in adolescent girls and boys. J Clin Child Adolesc Psychol. 2006;35(4):539– 49. 37. Deighton J, Humphrey N, Belsky J, Boehnke J, Vostanis P, Patalay P. Longitudinal pathways between mental health difficulties and academic performance during middle childhood and early adolescence. Br J Dev Psychol. 2018;36(1):110–26. 38. Hayward J, Millar L, Petersen S, Swinburn B, Lewis AJ. When ignorance is bliss: weight perception, body mass index and quality of life in adolescents. Int J Obes. 2014;38(10):1328–34. https://doi.org/10.1038/ijo.2014.78. 39. Pont SJ, Puhl R, Cook SR, Slusser W. Stigma experienced by children and adolescents with obesity. Pediatrics. 2017;140(6):1–11. https://doi.org/10. 1542/peds.2017-3034. 40. Pearl RL, Puhl RM. Weight bias internalization and health: a systematic review. Obes Rev. 2018;19(8):1141. https://doi.org/10.1111/obr.12701. 40. Pearl RL, Puhl RM. Weight bias internalization and health: a systematic review. Obes Rev. 2018;19(8):1141. Publisher’s Note https://doi.org/10.1111/obr.12701.
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zeitschrift für kritische stadtforschung s u b \ u r b a n zeitschrift für kritische stadtforschung s u b \ u r b a n themenschwerpunkt zeitschrift für kritische stadtforschung s u b \ u r b a n zeitschrift für kritische stadtforschung zeitschrift für kritische stadtforschung s u b \ u r b a n zeitschrift für kritische stadtforschung s u b \ u r b a n themenschwerpunkt zeitschrift für kritische stadtforschung s u b \ u r b a n zeitschrift für kritische stadtforschung aufsätze ‚Neue soziale Stadtpolitik‘ in Hamburg als Strategie der Verbürgerlichung Moritz Rinn ‚Demenzfreundliche Kommunen‘ zwischen sozialstaatlichem Sparmodell und Emanzipationsgewinn Mike Laufenberg debatte Die Kritik zerbricht an der documenta Tim König Machtverhältnisse überall analysieren! Jenny Künkel Elitenkritik, populare Bündnisse und inklusive Solidarität Violetta Bock, Thomas Goes, Lisa Vollmer Elitenkritik, populare Bündnisse und inklusive Solidarität Violetta Bock, Thomas Goes, Lisa Vollmer Elitenkritik, populare Bündnisse und inklusive Solidarität Violetta Bock, Thomas Goes, Lisa Vollmer magazin Feministische Klassenpolitiken in Kämpfen um soziale Reproduktion Julia Dück Das BID Reeperbahn+ und die Kampagne „St. Pauli pinkelt zurück“ Friederike Häuser rezensionen Erfolgreiches Scheitern eines politischen Projekts Sofrony Riedmann „Morningside Park: A Civil Rights Battleground“ Maxi Schreiber Die logistische Stadt Fabian Namberger
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Efficacy of Single-Dose Azithromycin for Ocular Chlamydial Infection: A Longitudinal Study
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*Address correspondence to Jeremy D. Keenan, Proctor Foundation, University of California San Francisco, 490 Illinois St., P.O. Box 0944, San Francisco, CA 94158. E-mail: jeremy.keenan@ucsf.edu †These authors contributed equally to this work. Efficacy of Single-Dose Azithromycin for Ocular Chlamydial Infection: A Lo Efficacy of Single-Dose Azithromycin for Ocular Chlamydial Infection: A Longitudinal Study Neha Pondicherry,1† Amza Abdou,2† Boubacar Kadri,2 Beido Nassirou,2 Sun Y. Cotter,1 Nicole E. Varnado,1 Travis C. Porco,1,3 Sheila K. West,4 Thomas M. Lietman,1,3,5,6 and Jeremy D. Keenan1,3* 1Francis I. Proctor Foundation, University of California, San Francisco, California; 2Programme National de Sante Oculaire, Niamey, Niger; 3Department of Ophthalmology, University of California, San Francisco, California; 4Dana Center for Preventive Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland; 5Department of Epidemiology & Biostatistics, University of California, San Francisco, California; 6Institute for Global Health, University of California, San Francisco, California 1Francis I. Proctor Foundation, University of California, San Francisco, California; 2Programme National de Sante Oculaire, Niamey, Niger; 3Department of Ophthalmology, University of California, San Francisco, California; 4Dana Center for Preventive Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland; 5Department of Epidemiology & Biostatistics, University of California, San Francisco, California; 6Institute for Global Health, University of California, San Francisco, California Abstract. Millions of doses of azithromycin are distributed each year for trachoma, yet the treatment efficacy of a single dose of azithromycin for ocular Chlamydia infection has not been well characterized. In this study, four villages in Niger received a mass azithromycin distribution for trachoma. All 426 children aged 0–5 years residing in the study villages were offered conjunctival swabbing every 6 months to test for ocular Chlamydia trachomatis. Among the children infected with ocular Chlamydia before treatment, 6% (95% CI: 2–15%) tested positive for ocular Chlamydia infection 6 months later, and 15% (95% CI: 7–28%) tested positive 12 months later. The most important predictor of post-treatment ocular Chlamydia infection was pretreatment ocular Chlamydia infection (relative risk: 3.5, 95% CI: 1.3–9.4). Although the 6-monthly monitoring schedule was suboptimal for testing the treatment efficacy of an antibiotic, these findings are nonetheless consistent with high treatment efficacy of a single dose of azithromycin and suggest that additional interven- tions might be most effective if targeted to those children infected prior to treatment. INTRODUCTION each study visit. In addition, one village from each of the four treatment groups was randomly selected for longitudinal monitoring, in which the same children were followed up at each visit (Figure 1). Here, we report results from these four longitudinally monitored villages for the period after their first mass azithromycin distribution (i.e., months 0–12 for the two annually treated villages and months 0–6 for the two biannu- ally treated villages). Trachoma, the leading infectious cause of blindness world- wide, is caused by ocular infection with Chlamydia trachomatis. As of July 2023, around 116 million people worldwide remained at risk.1 The WHO recommends 3–5years of annual mass azithromycin distributions in districts where $10% of children aged 1–9years have trachomatous inflammation–follicular (TF), according to the WHO’s simplified grading system.2 Despite the millions of doses of azithromycin distributed each year for trachoma, few studies have assessed the treatment efficacy of a single dose of azithromycin for an individual child with ocular Chlamydia infection.3–5 The objectives of the present study were to estimate the treatment efficacy of a single dose of azithromycin and to determine factors associated with an increased incidence of ocular Chlamydia infection. y g ) At all monitoring visits, the upper right eyelid was everted and graded for the presence of TF and trachomatous inflammation–intense (TI) according to the WHO’s simplified grading system. Conjunctival swabs of the everted right superior tarsal conjunctiva were collected without media and transported to the University of California, San Francisco, where they were stored at 280C. Swabs were pooled in groups of five and processed for C. trachomatis with the AMPLICOR polymerase chain reaction assay (Roche Diag- nostics, Indianapolis, IN); swabs from positive pools were subsequently tested individually. Details of swab storage, transport, and processing are reported elsewhere.6 Log- binomial regression models incorporating a random inter- cept for a village were used to estimate incidences and to assess for risk factors of post-treatment infection at month 6 and month 12. Analyses were performed using R, version 4.1.3 (R Foundation for Statistical Computing) with a signifi- cance level of 0.05. MATERIALS AND METHODS This study describes a non-prespecified analysis of chil- dren treated with azithromycin in 2010–2011 at the Niger site of the cluster-randomized Partnership for the Rapid Elimina- tion of Trachoma (PRET) trial.6 As part of the PRET trial, all residents from 48 villages in Matameye District, Zinder Region, Niger were enumerated on a door-to-door census. In 2010 the prevalence of TF among 0–5-year-olds in the study area was approximately 25%.6 Villages were subse- quently randomized in a factorial design to annual versus biannual mass azithromycin distributions and to standard (i.e., $80%) versus enhanced (i.e., $90%) antibiotic cover- age, with coverage targets based on the most recent study census. During the antibiotic distributions, a single dose of azithromycin was offered to each community member (1 g for adults, 20 mg/kg for children). Trachoma monitoring was performed at biannual study visits, with a new random sam- ple of 0–5-year-old children selected from each village at Ethical approval was obtained from the Committee on Human Research at the University of California, San Francisco and the Comite d’Ethique du Niger. Owing to the high preva- lence of illiteracy in the study area, the ethical boards approved verbal consent, which was obtained from community leaders before randomization and from participants or a caregiver at the time of antibiotic distribution and examinations. Am. J. Trop. Med. Hyg., 110(5), 2024, pp. 1010–1013 doi:10.4269/ajtmh.23-0540 Copyright © 2024 The author(s) Am. J. Trop. Med. Hyg., 110(5), 2024, pp. 1010–1013 doi:10.4269/ajtmh.23-0540 Copyright © 2024 The author(s) RESULTS The two biannually treated villages quently received a mass azithromycin distribution at 6 and thus did not contribute data from the month 12 visit for this analysis. In the two annually treated com ties that did not receive additional azithromycin over t year 215 of the 257 (84%) children swabbed at b PRET Trial 48 villages in Niger Randomized Annual azithromycin Enhanced coverage: 12 villages Standard coverage: 12 villages Biannual azithromycin Enhanced coverage: 12 villages Standard coverage: 12 villages Randomly selected for longitudinal sampling 2 villages (1 enhanced, 1 standard) 264 children 0-59 months Randomly selected for longitudinal sampling 2 villages (1 enhanced, 1 standard) 190 children 0-59 months Swabbed at 6 months 231 children Swabbed at 6 months 147 children Swabbed at 12 months 215 children Swabbed at baseline 264 children Swabbed at baseline 190 children Analyzed 231 children at 6 months 215 children at 12 months Analyzed 147 children at 6 months 0 children at 12 months Lost to follow-up 6 mos only: 13 12 mos only: 29 6 and 12 mos: 13 Lost to follow-up 6 mos only: 22 Treated at baseline 257 children Treated at baseline 169 children Next round of mass azithromycin Next round of mass azithromycin FIGURE 1. Study flow. PRET 5 Partnership for the Rapid Elimination of Trachoma trial. PRET Trial 48 villages in Niger Randomized Annual azithromycin Enhanced coverage: 12 villages Standard coverage: 12 villages Swabbed at 12 months 215 children Lost to follow-up 6 mos only: 22 Analyzed 147 children at 6 months 0 children at 12 months Analyzed 231 children at 6 months 215 children at 12 months FIGURE 1. Study flow. PRET 5 Partnership for the Rapid Elimination of Trachoma trial. follow-up and those remaining in follow-up (Table 1). Of the 378 children with a month 6 swab, 68 had evidence of Chlamydia infection at baseline, of whom four were infected 6 months after receiving azithromycin (6%, 95% CI: 2–15%). Conversely, of 310 uninfected children who received the baseline azithromycin treatment and participated in the month 6 monitoring, 11 were infected at month 6 (3%, 95% CI: 1–8%). The two biannually treated villages subse- quently received a mass azithromycin distribution at month 6 and thus did not contribute data from the month 12 study visit for this analysis. RESULTS At the baseline visit, 426 children aged 0–59 months from the four longitudinally monitored villages contributed a con- junctival swab and then received azithromycin treatment, of whom 378 (89%) were again swabbed 6 months later. Base- line characteristics were similar between children lost to 1010 1011 AZITHROMYCIN EFFICACY FOR TRACHOMA up and those remaining in follow-up (Table 1). Of the hildren with a month 6 swab, 68 had evidence of ydia infection at baseline, of whom four were infected ths after receiving azithromycin (6%, 95% CI: 2–15%). rsely, of 310 uninfected children who received aseline azithromycin treatment and participated in onth 6 monitoring 11 were infected at month 6 (3% 95% CI: 1–8%). The two biannually treated villages quently received a mass azithromycin distribution at 6 and thus did not contribute data from the month 1 visit for this analysis. In the two annually treated com ties that did not receive additional azithromycin over t year, 215 of the 257 (84%) children swabbed at b were again swabbed at month 12 Among these 215 c PRET Trial 48 villages in Niger Randomized Annual azithromycin Enhanced coverage: 12 villages Standard coverage: 12 villages Biannual azithromycin Enhanced coverage: 12 villages Standard coverage: 12 villages Randomly selected for longitudinal sampling 2 villages (1 enhanced, 1 standard) 264 children 0-59 months Randomly selected for longitudinal sampling 2 villages (1 enhanced, 1 standard) 190 children 0-59 months Swabbed at 6 months 231 children Swabbed at 6 months 147 children Swabbed at 12 months 215 children Swabbed at baseline 264 children Swabbed at baseline 190 children Analyzed 231 children at 6 months 215 children at 12 months Analyzed 147 children at 6 months 0 children at 12 months Lost to follow-up 6 mos only: 13 12 mos only: 29 6 and 12 mos: 13 Lost to follow-up 6 mos only: 22 Treated at baseline 257 children Treated at baseline 169 children Next round of mass azithromycin Next round of mass azithromycin FIGURE 1. Study flow. PRET 5 Partnership for the Rapid Elimination of Trachoma trial. up and those remaining in follow-up (Table 1). Of the hildren with a month 6 swab, 68 had evidence of ydia infection at baseline, of whom four were infected hs after receiving azithromycin (6%, 95% CI: 2–15%). sely, of 310 uninfected children who received seline azithromycin treatment and participated in 95% CI: 1–8%). DISCUSSION The treatment efficacy of azithromycin for C. trachomatis has mostly been studied in the context of sexually transmit- ted infections. For sexually transmitted Chlamydia, a single dose of azithromycin is thought to be 90–95% effective for urogenital infections but only 75% effective for rectal Chlamydia.7–9 The limited studies that have assessed the treatment efficacy of azithromycin for ocular Chlamydia have had variable results, with testing done 2–6 months after drug administration, suggesting a treatment efficacy between 70% and 94% for single-dose therapy.3,4 The present study, conducted in a trachoma-mesoendemic setting during an initial round of mass antibiotic treatments, found that 94% of infected children tested negative for Chlamydia 6 months after a single dose of azithromycin and that the most impor- tant risk factor for being infected with ocular Chlamydia after a mass antibiotic distribution was ocular Chlamydia infection prior to treatment. The values in the table are numbers (proportion). CT 5 ocular Chlamydia trachomatis; LTFU 5 lost to follow-up; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous inflammation–intense. with 12-month follow-up, 48 were infected at baseline, of whom 7 also tested positive for Chlamydia at month 12 (15%, 95% CI: 7–28%), and 167 were not infected at baseline, of whom 7 were infected at month 12 (4%, 95% CI: 2–10%). Post-treatment Chlamydia infection was more common among younger children and those with TF or TI at baseline, although the association with these baseline characteristics did not achieve statistical significance in the present study. The most important risk factor for post-treatment chlamydial infection in this population was the presence of ocular Chlamydia infection prior to treatment, a finding consistent with several previous studies.10,11 Thus, this study provides ) Associations between pretreatment exposures and ocular Chlamydia outcomes 6 and 12 months after treatment are shown in Table 2. RESULTS In the two annually treated communi- ties that did not receive additional azithromycin over the first year, 215 of the 257 (84%) children swabbed at baseline were again swabbed at month 12. Among these 215 children 1012 PONDICHERRY, ABDOU, AND OTHERS TABLE 1 Baseline characteristics of children who participated in follow-up visits and of those lost to follow-up at the 6-month and 12-month study visits Pretreatment Exposure 6 Months after Treatment in Four Villages 12 Months after Treatment in Two Villages Participated (n 5 378) LTFU (n 5 48) Participated (n 5 215) LTFU (n 5 42) Age ,1 year 49 (13%) 9 (19%) 25 (12%) 5 (12%) 1 year 69 (18%) 11 (23%) 46 (21%) 3 (7%) 2 years 79 (21%) 12 (25%) 50 (23%) 15 (36%) 3 years 97 (26%) 8 (17%) 52 (24%) 10 (24%) 4 years 84 (22%) 8 (17%) 42 (20%) 9 (21%) Sex Female 186 (49%) 21 (44%) 109 (51%) 16 (38%) Male 192 (51%) 27 (56%) 106 (49%) 26 (62%) TF Absent 274 (72%) 43 (90%) 149 (69%) 29 (69%) Present 104 (28%) 5 (10%) 66 (31%) 13 (31%) TI Absent 340 (90%) 45 (94%) 192 (89%) 39 (93%) Present 38 (10%) 3 (6%) 23 (11%) 3 (7%) CT Negative 310 (82%) 41 (85%) 167 (78%) 30 (71%) Positive 68 (18%) 7 (15%) 48 (22%) 12 (29%) Sibling with CT Yes 237 (63%) 31 (65%) 117 (54%) 26 (62%) No 141 (37%) 17 (35%) 98 (46%) 16 (38%) The values in the table are numbers (proportion). CT 5 ocular Chlamydia trachomatis; LTFU 5 lost to follow-up; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous inflammation–intense. post-treatment ocular Chlamydia infection was pretreatment ocular Chlamydia infection, which conveyed a relative risk of 1.6 (95% CI: 0.5–4.7; P 5 0.43) at 6 months and 3.5 (95% CI: 1.3–9.4; P 5 0.01) at 12 months. None of the other potential exposure variables (e.g., sex, age, presence of TF at baseline, presence of TI at baseline, or presence of an infected sibling at baseline) had significant associations with post-treatment ocular Chlamydia. TABLE 1 Baseline characteristics of children who participated in follow-up visits and of those lost to follow-up at the 6-month and 12-month study visits statistics associations with P 0.05. * Odds ratio estimated with Firth’s penalized logistic regression because of complete separation. CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous inflammation–intense. Boldface statistics associations with P ,0 05 CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation– statistics 5 associations with P ,0.05. CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model; statistics 5 associations with P ,0.05. R 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous inflammation–intense. Boldface CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation–follicular; TI 5 tracho tatistics 5 associations with P ,0 05 CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous inflammation–intense. Boldface statistics 5 associations with P ,0.05. zed logistic regression because of complete separation. DISCUSSION The most important predictor of TABLE 2 Associations between pretreatment exposures and ocular Chlamydia infection at 6 and 12 months after a single dose of azithromycin Pretreatment Exposure 6 Months after Treatment, n 5 4 Communities (N 5 378 children) 12 Months after Treatment, n 5 2 Communities (N 5 215 children) CT1/Total PR (95% CI) CT1/Total PR (95% CI) Age ,1 year 3/49 (6%) Reference 3/25 (12%) Reference 1 year 0/69 (0%) 0.1 (0–0.1.0)* 1/46 (2%) 0.2 (0–1.7) 2 years 6/79 (8%) 1.2 (0.3–5.1)* 3/50 (6%) 0.5 (0.1–2.3) 3 years 4/97 (4%) 0.6 (0.15–3.0)* 4/52 (8%) 0.6 (0.2–2.7) 4 years 2/84 (2%) 0.4 (0.1–2.2)* 3/42 (7%) 0.6 (0.1–2.7) Sex Female 11/186 (6%) Reference 10/109 (9%) Reference Male 4/192 (2%) 0.3 (0.1–1.0) 4/106 (4%) 0.4 (0.1–1.3) TF Absent 10/274 (4%) Reference 9/149 (6%) Reference Present 5/104 (5%) 1.4 (0.5–3.8) 5/66 (8%) 1.3 (0.4–3.6) TI Absent 13/340 (5%) Reference 11/192 (6%) Reference Present 2/38 (4%) 1.7 (0.4–7.3) 3/23 (13%) 2.3 (0.7–7.6) CT Negative 11/310 (4%) Reference 7/167 (4%) Reference Positive 4/68 (6%) 1.6 (0.5–4.7) 7/48 (15%) 3.5 (1.3–9.4) Sibling with CT Yes 6/237 (3%) Reference 7/117 (6%) Reference No 9/141 (6%) 2.2 (0.8–6.3) 7/98 (7%) 1.2 (0.4–3.3) CT 5 ocular Chlamydia trachomatis; PR 5 prevalence ratio from log-binomial regression model; TF 5 trachomatous inflammation–follicular; TI 5 trachomatous inflammation–intense. Boldface AZITHROMYCIN EFFICACY FOR TRACHOMA 1013 Financial support: This study was supported by the Bill & Melinda Gates Foundation (grant OPP48027). Financial support: This study was supported by the Bill & Melinda Gates Foundation (grant OPP48027). some evidence that additional interventions may be most effective if targeted to children with chlamydial infection prior to mass drug administration. Randomized trials are starting to test this hypothesis. In one trial set in a hyper-endemic area of Ethiopia, triannual azithromycin distributions were targeted only to those 0–5 years old with Chlamydia infection prior to a round of mass azithromycin treatment. Although this strategy was not found to be effective, the prevalence of ocular Chlamydia among older children not eligible for tar- geted treatments was high and likely led to increased trans- mission.12 Targeted treatments may be more effective if given as a supplement to routine annual mass azithromycin distributions. An ongoing trial is testing such a strategy (clinicaltrials.gov NCT03335072). Authors’ addresses: Neha Pondicherry, Sun Y. Cotter, Nicole E. Varnado, Travis C. Porco, Thomas M. Lietman, and Jeremy D. DISCUSSION Keenan, University of California, San Francisco, CA, E-mails: neha.pondicherry@ ucsf.edu, sun.cotter@ucop.edu, nvarnado@stanford.edu, travis.porco@ ucsf.edu, tom.lietman@ucsf.edu, and jeremy.keenan@ucsf.edu. Abdou Amza, Boubacar Kadri, and Beido Nassirou, Programme Nationale de Sante Oculaire, Niamey, Niger, E-mails: dr.amzaabdou@gmail.com, boubacarkadri@gmail.com, and nasbeido@yahoo.fr. Sheila K. West, Dana Center for Preventive Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD, E-mail: shwest@jhmi.edu. This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution, and reproduction in any medium, pro- vided the original author and source are credited. ( g ) This study has limitations. Treatment efficacy was esti- mated based on ocular Chlamydia monitoring performed 6 and 12 months after treatment. The infrequency of visits may have increased the chances of misclassification as some children may have cleared their infection after receiving antibiotics but then been reinfected in the intervening 6 months, and others may have failed to clear their infection after treatment but nonetheless had spontaneous resolution of infection. However, prior longitudinal studies have sug- gested that the median duration of an ocular chlamydial infection is approximately 17weeks, increasing the chances that a negative post-treatment test represents treatment suc- cess as well as the plausibility that an infection observed 6 months after treatment represents treatment failure.13 Geno- typic results might have been useful to differentiate treatment failures from reinfections, and antimicrobial susceptibility results could have been useful to determine the likelihood of treatment failure, but neither was performed as part of this study. Although baseline characteristics were similar, it is possible that rates of reinfection could have been different for the approximately 10–15% of children lost to follow-up. Poly- merase chain reaction tests, although highly sensitive and specific, are not perfect. The results are representative of the larger sample of villages enrolled in PRET and likely generaliz- able to other trachoma-endemic areas of Niger but may not be generalizable to areas with a different endemicity of tra- choma or different patterns of trachoma transmission.6 REFERENCES 1. World Health Organization, 2023. WHO Alliance for the Global Elimination of Trachoma: Progress report on elimination of tra- choma, 2022. Wkly Epidemiol Rec 28: 297–313. 2. Solomon AW, World Health Organization, London School of Hygiene and Tropical Medicine, International Trachoma Initiative, 2006. Trachoma Control: A Guide for Programme Managers. Geneva, Switzerland: WHO. 3. Schachter J et al., 1999. Azithromycin in control of trachoma. Lancet 354: 630–635. 4. Andreasen AA, Burton MJ, Holland MJ, Polley S, Faal N, Mabey DC, Bailey RL, 2008. Chlamydia trachomatis ompA variants in trachoma: what do they tell us? PLoS Negl Trop Dis 2: e306. 5. Toor J et al., 2021. Strengthening data collection for neglected tropical diseases: what data are needed for models to better inform tailored intervention programmes? PLoS Negl Trop Dis 15: e0009351. 6. Amza A et al., 2017. A cluster-randomized trial to assess the efficacy of targeting trachoma treatment to children. Clin Infect Dis 64: 743–750. 7. Kong FY, Tabrizi SN, Law M, Vodstrcil LA, Chen M, Fairley CK, Guy R, Bradshaw C, Hocking JS, 2014. Azithromycin versus doxycycline for the treatment of genital Chlamydia infection: a meta-analysis of randomized controlled trials. Clin Infect Dis 59: 193–205. 8. Dombrowski JC, Wierzbicki MR, Newman LM, Powell JA, Miller A, Dithmer D, Soge OO, Mayer KH, 2021. Doxycycline versus azithromycin for the treatment of rectal Chlamydia in men who have sex with men: a randomized controlled trial. Clin Infect Dis 7: 824–831. Received August 14, 2023. Accepted for publication November 11, 2023. Received August 14, 2023. Accepted for publication November 11, 2023. Published online March 19, 2024. Published online March 19, 2024. CONCLUSION 9. Lau A et al., 2021. Azithromycin or doxycycline for asymptom- atic rectal Chlamydia trachomatis. N Engl J Med 384: 2418– 2427. This study found that 94% of children infected at baseline no longer were infected with ocular Chlamydia 6 months after a single dose of azithromycin. The most important risk factor for ocular Chlamydia infection after a mass azithromycin treatment was ocular Chlamydia infection prior to treatment. If additional measures beyond annual mass antibiotic treat- ments are instituted to further interrupt Chlamydia transmis- sion (e.g., supplemental antibiotic treatments), one approach might be to focus on those most likely to have pretreatment ocular Chlamydia infection, such as preschool children. 10. Harding-Esch EM et al., 2013. Mass treatment with azithro- mycin for trachoma: when is one round enough? Results from the PRET trial in the Gambia. PLoS Negl Trop Dis 7: e2115. 11. West SK, Munoz B, Mkocha H, Holland MJ, Aguirre A, Solomon AW, Foster A, Bailey RL, Mabey DC, 2005. Infection with Chlamydia trachomatis after mass treatment of a trachoma hyperendemic community in Tanzania: a longitudinal study. Lancet 366: 1296–1300. 12. Melo JS et al., 2021. Targeted antibiotics for trachoma: a cluster-randomized trial. Clin Infect Dis 73: 979–986. 13. Grassly NC, Ward ME, Ferris S, Mabey DC, Bailey RL, 2008. The natural history of trachoma infection and disease in a Gambian cohort with frequent follow-up. PLoS Negl Trop Dis 2: e341. Published online March 19, 2024.
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Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature
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W&M ScholarWorks W&M ScholarWorks VIMS Articles Virginia Institute of Marine Science 2010 Evolutionary Characters, Phenotypes and Ontologies: Curating Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature Data from the Systematic Biology Literature Wasila M. Dahdul et al W&M ScholarWorks W&M ScholarWorks Virginia Institute of Marine Science Virginia Institute of Marine Science Follow this and additional works at: https://scholarworks.wm.edu/vimsarticles Part of the Marine Biology Commons Part of the Marine Biology Commons Recommended Citation Recommended Citation Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, et al. (2010) Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature. PLoS ONE 5(5): e10708. doi:10.1371/journal.pone.0010708 This Article is brought to you for free and open access by the Virginia Institute of Marine Science at W&M ScholarWorks. It has been accepted for inclusion in VIMS Articles by an authorized administrator of W&M ScholarWorks. For more information, please contact scholarworks@wm.edu. Abstract doi:10.1371/journal.pone.0010708 Received November 12, 2009; Accepted April 6, 2010; Published May 20, 20 ovember 12, 2009; Accepted April 6, 2010; Published May 20, 20 Copyright:  2010 Dahdul 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: The authors thank National Science Foundation (DBI 0641025), National Institutes of Health (HG002659), and the National Evolutionary Synthesis Center (NSF EF-0423641) for the support of this work. 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. * E-mail: wasila.dahdul@usd.edu (WMD); pmabee@usd.edu (PMM) Wasila M. Dahdul1,2*, James P. Balhoff2,3, Jeffrey Engeman1, Terry Grande4, Eric J. Hilton5, Cartik Kothari2,3, Hilmar Lapp2, John G. Lundberg6, Peter E. Midford2, Todd J. Vision2,3, Monte Westerfield7, Paula M. Mabee1* Wasila M. Dahdul1,2*, James P. Balhoff2,3, Jeffrey Engeman1, Terry Grande4, Eric J. Hilton5, Cartik Kothari2,3, Hilmar Lapp2, John G. Lundberg6, Peter E. Midford2, Todd J. Vision2,3, Monte Westerfield7, Paula M. Mabee1* 1 Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America, 2 National Evolutionary Synthesis Center, Durham, North Carolina, United States of America, 3 Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America, 4 Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America, 5 Department of Fisheries Science, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, Virginia, United States of America, 6 Academy of Natural Sciences, Philadelphia, Pennsylvania, United States of America, 7 Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America Recommended Citation Recommended Citation Recommended Citation Recommended Citation Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, et al. (2010) Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature. PLoS ONE 5(5): e10708. doi:10.1371/journal.pone.0010708 s Article is brought to you for free and open access by the Virginia Institute of Marine Science at W&M This Article is brought to you for free and open access by the Virginia Institute of Marine Science at W&M ScholarWorks. It has been accepted for inclusion in VIMS Articles by an authorized administrator of W&M ScholarWorks. For more information, please contact scholarworks@wm.edu. PLoS ONE | www.plosone.org Abstract Background: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. Methodology/Principal Findings: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. Conclusions/Significance: The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics. Citation: Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, et al. (2010) Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature. PLoS ONE 5(5): e10708. Introduction For example, a query with the term dorsal fin will also return dorsal fin ray because of its part_of relationship to dorsal fin. The Entity- Quality (EQ) formalism, which combines ‘entity’ terms from an anatomical or other ontology (e.g., ontologies that describe observable organism features such as behavior), with non-taxon- specific ‘quality’ terms from the Phenotype and Trait Ontology (PATO) [9,10,11] has been employed in phenotype descriptions of model organism mutants, where it has been shown to facilitate the identification of biologically similar phenotypes in different species [12]. Ontologies and the EQ formalism have also recently been applied to the standardization of taxonomic descriptions [13]. While the curation of data from the literature, and the annotation or tagging of those data using ontology terms, may be practices that are less familiar to evolutionary biologists than those in molecular genetics communities, they are nonetheless closely analogous to the curation of museum specimens and their associated metadata, such as locality. Figure 1. A systematic character and state, compared to a phenotype represented by Entity-Quality syntax. In EQ syntax, the entity being described is represented by a term from an anatomical ontology, and the variable (‘‘characteristic’’) aspect of the entity is represented using a term chosen from a quality ontology. Note that the ‘‘shape’’ attribute is an explicit part of the systematic character but is expressed only implicitly within the quality term. doi:10.1371/journal.pone.0010708.g001 As part of the Phenoscape Project (http://www.phenoscape. org), which aims to integrate model organism with evolutionary phenotype data using ontologies, we mounted a large-scale initiative to curate a significant data set of evolutionarily-varying phenotypes from the phylogenetic systematic literature. Specifi- cally, we curated 4,617 characters pertaining to a monophyletic group of teleostean fishes, the Ostariophysi (catfishes, characins, knifefishes, carps, and minnows; [21]), which also includes the model organism, zebrafish (Danio rerio). There are many decisions and details involved in the implementation that are not necessarily intuitive or straightforward; these decisions affect how the annotated data can be used. As a result of this experience, we recommend standards and procedures that will enable more consistent and efficient translation of complex phenotype descrip- tions into computable data. These in turn will enable accurate character and phenotype comparisons and integration on a much broader scale. Introduction tions exist almost exclusively in a free-text or natural language format that is not amenable to computational processing. For example, the diverse ways of describing the shape of the first infraorbital bone in fishes (‘‘lacrymal bone … flat’’ [4]; ‘‘lacrimal … triangular’’ [5]; ‘‘first infraorbital (lachrimal) shape…flattened’’ [6]) _msocom_3might seem obviously similar to a human but would not be recognized as similar by a computer. Natural language, although allowing the expressive and precise description of biological form, has serious limitations for comparing or Variation in observable features, or phenotypes, is intensely studied and richly documented within and between species in the literature of systematic biology (e.g., [1]_msocom_2), between wild-type and mutant lines in model organism databases (e.g., [2]), and among genetic phenotypes of humans (e.g., [3]). Although fundamentally important to our understanding of genetics, development, and evolutionary relationships, phenotypic descrip- PLoS ONE | www.plosone.org May 2010 | Volume 5 | Issue 5 | e10708 May 2010 | Volume 5 | Issue 5 | e10708 1 Curation of Evolutionary Data Figure 1. A systematic character and state, compared to a phenotype represented by Entity-Quality syntax. In EQ syntax, the entity being described is represented by a term from an anatomical ontology, and the variable (‘‘characteristic’’) aspect of the entity is represented using a term chosen from a quality ontology. Note that the ‘‘shape’’ attribute is an explicit part of the systematic character but is expressed only implicitly within the quality term. doi:10.1371/journal.pone.0010708.g001 integrating data across studies, linking to genetic databases, and data mining. To facilitate comparison and integration of phenotypes across organisms, model organism communities have spearheaded the representation of mutant phenotypes using ontologies and formal semantics [7]. An ontology extends the notion of a controlled vocabulary by associating names with formally defined entities, which include classes and relationships among those classes (c.f., [8]). Here we use ‘term’ to refer to those names associated with classes, in contrast to names of relationships. The application of ontologies to the curation of phenotype data from the model organism literature and sharing of these annotations in community databases has promoted clarity in communication among researchers and allowed for integration of large quantities of data. In addition to facilitating interoperability among databases, ontologies allow users to query using very specific or broad anatomical terms and obtain organized groups of annotations. Introduction The EQ formalism has been suggested as a means to integrate data across systematic studies and with phenotypes and genetics of model organisms [15,16,17]. For example, a character may describe how a structure (e.g., supraorbital bone) and its attribute (e.g., shape) vary among taxa (Figure 1); the character states specifying the value of the attribute (e.g., sigmoid). In comparing EQ syntax to systematic characters, the quality term represents the character state and, by implication through the subtype relationships of the quality ontology, the attribute of the character (e.g., sigmoid is a subtype of shape, Figure 1). S f l ifi h f d b i d h Introduction The principles and best practices for the curation of complex phenotypes that we have developed from this exercise are generally applicable, as are the challenges inherent in aligning rich textual descriptions with ontologies and syntactic relations. Phenotypic variability across species has been documented in rich natural language in the comparative literature of evolutionary biology and most formally in phylogenetic systematics. This variability is described in systematic characters, which consist of two or more character states contrasting some aspect (e.g., morphology, behavior) of the taxa under study [14]. Character states are assigned to taxa in a character-by-taxon matrix that is analyzed with phylogenetic methods to infer hypotheses of evolutionary relationships. The EQ formalism has been suggested as a means to integrate data across systematic studies and with phenotypes and genetics of model organisms [15,16,17]. For example, a character may describe how a structure (e.g., supraorbital bone) and its attribute (e.g., shape) vary among taxa (Figure 1); the character states specifying the value of the attribute (e.g., sigmoid). In comparing EQ syntax to systematic characters, the quality term represents the character state and, by implication through the subtype relationships of the quality ontology, the attribute of the character (e.g., sigmoid is a subtype of shape, Figure 1). Software tools specific to the type of data being curated have proven to be a critical ingredient of an efficient annotation workflow (e.g., for journal articles using Textpresso [18]; or gene structures using Apollo [19]). To link ontology terms with phenotypic systematic characters and taxa, we developed the Phenex curation tool [20]. Upon launch, Phenex automatically downloads the most recent versions of the required anatomy, quality, taxonomy, and other ontologies. Phenex allows curators to use EQ syntax to represent evolutionary characters [16,17]. Using Phenex, this simple combinatorial EQ syntax can be elaborated, for example, to accommodate multiple related entities and to describe complex entities. Phenotypic variability across species has been documented in rich natural language in the comparative literature of evolutionary biology and most formally in phylogenetic systematics. This variability is described in systematic characters, which consist of two or more character states contrasting some aspect (e.g., morphology, behavior) of the taxa under study [14]. Character states are assigned to taxa in a character-by-taxon matrix that is analyzed with phylogenetic methods to infer hypotheses of evolutionary relationships. Curator training, curation experiments, and quality control Curator training, curation experiments, and quality control Curation of the complex phenotypic descriptions contained in systematics publications required the input of domain experts who were knowledgeable on the anatomy of the target taxa. Curation was done by five ichthyologists under the direction of a lead curator (W. Dahdul). Curators were trained one-on-one by the lead curator at annotation workshops or remotely by conference calls. A Guide to Character Annotation was maintained on the Phenoscape wiki [69] that kept curators up-to-date on the developing best practices for curation. The phenoscape-curators mailing list [70] was used for discussion and communication of data curation issues, solutions, and progress. Participation in and discussion of issues on several OBO Foundry [22] community mailing lists, particularly obo-discuss [71] and obo-phenotype [72], also contributed to the development of standards for the curation process. Selection of ontology terms for taxa. The Materials list and character matrix of each systematics publication contain names of the taxa and individual specimens (voucher specimens) that were examined by the authors. These form the basis of observations for phylogenetic characters. Taxon names from the Materials list and matrix were linked to currently accepted (according to the Catalog of Fishes, CoF, [25]) taxon names from the TTO by undergraduate student workers using Phenex. A taxonomic expert then reviewed the taxon list and, after verifying taxonomic status in the CoF, requested addition of names or synonyms missing from the TTO using the SourceForge term request tracker [74]. Unknown or unidentified species were added to the TTO with reference to the publication in parenthesis (e.g., Akysis sp. 1 (de Pinna 1996) TTO:10000093, Akysis sp. 2 (de Pinna 1996) TTO:10000094). Most synonyms were added to the TTO with a scope of RELATED (rather than BROAD, NARROW or EXACT), indicating that the relationship between the synonym and its primary term was not known. Species names incorrectly spelled by an author were added to the TTO as synonyms with a scope of EXACT and an associated synonym category of ‘misspelling.’ The eleven misspellings and missing taxon names discovered in the CoF through this process were communicated to the CoF administrators for correction or addition. As part of our curation quality control, we conducted two annotation experiments at Phenoscape project workshops to identify areas of improvement in curator training, ontology development, and software tools. Curator training, curation experiments, and quality control We wanted to determine how often, and for what reasons, curators choose divergent EQ statements for the same character and character states. Curator training consisted of a hands-on group annotation exercise, and at least one full day of individual work on each curator’s own publications with assistance from the lead curator and other project personnel. The Guide to Character Annotation [69], with examples of character types commonly encountered in the fish systematic literature, was also provided to the curators. In both curation experiments, the same 10 characters sampled from the ichthyological literature were annotat- ed by 4 or 5 curators in parallel. Some publications partially or wholly replicated the species names from the Materials list in the phylogenetic matrix. However, many publications used higher-level taxa (e.g., genus, family) for the taxonomic units represented in the matrix. Because we recorded phenotypes as properties of species unless specifically asserted to a higher-level taxon by an author, any higher-level taxon used in a matrix was replaced by all the species within that taxon as listed in the Materials list. This procedure sometimes required contacting a taxon expert for assistance in assigning species to the correct higher-level taxon in the matrix. Curation of Evolutionary Data Curation of Evolutionary Data standard that permits systematic data to be tagged with ontology terms [25]. experts, the use of specialized curation software (Phenex), online tools, and community input. Free text entry. Free-text data were manually entered into Phenex by undergraduate student workers. The data entered included character and character state descriptions, taxon names, phylogenetic matrices, and specimen collection numbers. Although a few matrices were obtained from authors, most were transcribed by undergraduate students from the original publications using Mesquite [73], and subsequently imported as NEXUS files into Phenex. Matrices for our publications of interest had not been deposited into public data repositories such as TreeBASE (http://treebase.org), an online source of user- contributed phylogenetic matrices. Literature selection and collection An initial list of 420 studies, including published species descriptions, taxonomic revisions, phylogenetic studies, and unpublished theses and dissertations, was compiled from sugges- tions by 10 experts on the morphology of ostariophysan fishes and close relatives. These experts helped prioritize the list to emphasize studies on higher-level groups for broad taxonomic coverage, and studies that included data matrices for the efficient annotation of phenotypic characters. We describe here the results of curation of all characters reported in a total of 47 studies on ostariophysans, their clupeomorph relatives, and some euteleosts (percomorphs and salmoniforms). These studies were published between the years 1981–2008. They included 26 peer-reviewed publications [4,6,21,26–48], 12 book chapters [49–60], eight Ph.D. disserta- tions [5,61–67], and one M.S. thesis [68]. Because this collection of studies spans the decades prior to the widespread availability of publications in electronic format, we obtained electronic versions from numerous sources: approximately half (23) were scanned from hard copies with text translated by Optical Character Recognition (OCR), 19 were obtained online from institutional libraries, two hard-copies were acquired through Interlibrary Loan, one was purchased from ProQuest UMI Dissertation Publishing, one was downloaded from the Biodiversity Heritage Library, and one was obtained from the corresponding author. Curation software and ontologies g For annotation of the 47 studies from the fish phylogenetic literature with EQ syntax, we used Phenex [20], the annotation software that we developed for evolutionary biologists to link phenotype descriptions (characters and character states) with ontology terms. Phenex can be configured to load any ontology in OBO (Open Biological and Biomedical Ontologies; [7]) format. We configured it to load the Teleost Anatomy Ontology (TAO) [15] and Teleost Taxonomy Ontology (TTO) (Midford et al., in prep), in addition to several other shared community ontologies including the Phenotype and Trait Ontology (PATO), Gene Ontology (GO), Spatial Ontology (BSPO), Relations Ontology (RO), Evidence Code Ontology (ECO), and Unit Ontology (UO). These ontologies are available for download from the OBO Foundry [22]. A list of museum codes [23] derived from the Catalog of Fishes [24] was also loaded into Phenex. Phenex files were saved in NeXML format, a phylogenetic data exchange Software tools specific to the type of data being curated have proven to be a critical ingredient of an efficient annotation workflow (e.g., for journal articles using Textpresso [18]; or gene structures using Apollo [19]). To link ontology terms with phenotypic systematic characters and taxa, we developed the Phenex curation tool [20]. Upon launch, Phenex automatically downloads the most recent versions of the required anatomy, quality, taxonomy, and other ontologies. Phenex allows curators to use EQ syntax to represent evolutionary characters [16,17]. Using Phenex, this simple combinatorial EQ syntax can be elaborated, for example, to accommodate multiple related entities and to describe complex entities. PLoS ONE | www.plosone.org May 2010 | Volume 5 | Issue 5 | e10708 May 2010 | Volume 5 | Issue 5 | e10708 2 PLoS ONE | www.plosone.org Curation workflow We recorded phenotype descriptions as properties of species, and these were assigned one of three evidence codes based on the type of evidence given by an author. These codes are part of the Evidence Codes Ontology [78], which is used by the broader biological community. A phenotype description that is explicitly tied to a specimen was assigned IVS (Inferred from Voucher Specimen); these referenced an institutional catalog number. A phenotype description in which the author does not reference a specimen was given one of two weaker evidence codes (NAS, Non-traceable Author Statement, or TAS, Traceable Author Statement); no catalog number could be associated. NAS is used for statements that an author makes with no results or citation presented. TAS is used for author statements that are attributable to another source. This same methodology was extended to statements about higher- level taxa. Here, species-level phenotype annotations were generated for every species included in the higher-level taxon (as listed in the Materials list). In this case, these particular species were given a strong evidence code (such as IVS) with catalog numbers attached. When the author did not reference the species that were observed to make character assertions about higher-level taxa, the higher-level taxa were assigned a weaker evidence code. The phenotypes described in most of the publications that we curated were based on observations of voucher specimens and so merited the strong IVS evidence code. Granularity of curation. To maximize curation consistency among curators and to meet the needs of the larger purpose of our work, which is to integrate the phenotypic data of evolutionary morphology with phenotype descriptions of zebrafish mutants, we did a ‘first pass’ curation of the characters to a coarse level of granularity. By coarse, we mean that we selected higher-level terms, or those with less specificity, for quality and sometimes entity. Coarse-level qualities from the Phenotype and Trait Ontology (PATO) are those at the attribute level such as size, shape, and composition (i.e., those terms in blue font in Figure 3). The supraorbital bone, for example, is described as having a sigmoid shape in some characiform fishes [48]. The coarse-level EQ annotation for this phenotype is E:supraorbital bone, Q:shape, whereas the fine-level annotation is E:supraorbital bone, Q:sigmoid (Figure 4). Curation workflow The workflow for curation of publications (Figure 2) required the coordinated activities of students, taxonomic and anatomical PLoS ONE | www.plosone.org May 2010 | Volume 5 | Issue 5 | e10708 May 2010 | Volume 5 | Issue 5 | e10708 3 Curation of Evolutionary Data Figure 2. Workflow for the curation of phenotypic characters from systematic studies. doi:10.1371/journal.pone.0010708.g002 Curation of Evolutiona Figure 2. Workflow for the curation of phenotypic characters from systematic studies. doi:10.1371/journal.pone.0010708.g002 Selection of anatomy ontology terms for representation of character states. When curators encountered a term in the literature that was not in an ontology, they first assessed its use and context in the publication to determine whether it was a new term or a synonym of an existing term (synonyms include misspellings). This involved reading all uses of the term in the paper and checking figures to see whether the author provided further information. Sometimes this also required searching the referenced literature pertaining to the term. If it was deemed to be a new term, the curator wrote a corresponding genus- differentia definition [7] and proposed the relationships of that term to other terms in the ontology. For example, a term was requested for the hypomaxilla, a bone of the upper jaw in clupeomorph fishes. The request included a proposed definition, ‘‘Dermal bone found in the anterior margin of the upper jaw, posterior to the premaxilla,’’ and proposed relationships to other terms (is_a dermal bone, part_of palatoquadrate arch, part_of dermatocranium). The curator submitted this request through the TAO SourceForge Term Tracker [75], which triggered an automated email to the community mailing list [76]. The ontology administrator closed the request after the conclusion of mailing list discussion, and then updated the ontology to include PLoS ONE | www.plosone.org May 2010 | Volume 5 | Issue 5 | e10708 4 Curation of Evolutionary Data author’s assertion that a change in some aspect of shape is evident between species. Annotations at this coarse level, i.e., shape, allow aggregation of all entities and species that have experienced an evolutionary change in shape. After curation of the 47 papers at a coarse level was complete, we did a ‘second pass’ of finer-scale curation of qualities by selecting a more specific child term and finer-scale curation of some entities by using post-composition. the requested change and associated community comments. Curation workflow A similar term request procedure was followed for quality terms needed for PATO. An alternative to adding terms to an ontology is to create a new term at the time of annotation by post-composition, which is the process of combining terms from one or more ontologies to create a new term ([77]; also see Guide to Character Annotation in Text S1). Frequently, curators needed terms for the processes, margins, and regions of specific structures. Rather than adding these directly to an ontology, relevant terms from the spatial ontology (e.g., anterior margin) and anatomy ontology (frontal bone) can be joined by a relation (part_of) to create a post-composed term (the anterior margin that is part_of the frontal bone). Generally, terms were post-composed when they were not expected to be used repeatedly in annotation. Those known to exist in multiple species and referenced repeatedly in the literature were added to the anatomy ontology (e.g., supraoccipital process). Evidence codes for phenotype observations. We recorded phenotype descriptions as properties of species, and these were assigned one of three evidence codes based on the type of evidence given by an author. These codes are part of the Evidence Codes Ontology [78], which is used by the broader biological community. A phenotype description that is explicitly tied to a specimen was assigned IVS (Inferred from Voucher Specimen); these referenced an institutional catalog number. A phenotype description in which the author does not reference a specimen was given one of two weaker evidence codes (NAS, Non-traceable Author Statement, or TAS, Traceable Author Statement); no catalog number could be associated. NAS is used for statements that an author makes with no results or citation presented. TAS is used for author statements that are attributable to another source. This same methodology was extended to statements about higher- level taxa. Here, species-level phenotype annotations were generated for every species included in the higher-level taxon (as listed in the Materials list). In this case, these particular species were given a strong evidence code (such as IVS) with catalog numbers attached. When the author did not reference the species that were observed to make character assertions about higher-level taxa, the higher-level taxa were assigned a weaker evidence code. The phenotypes described in most of the publications that we curated were based on observations of voucher specimens and so merited the strong IVS evidence code. Evidence codes for phenotype observations. Curation workflow Coarse annotation meets the immediate use of linking to zebrafish genetic phenotypes in the Phenoscape Knowledgebase (http://kb.phenoscape.org), because most of the zebrafish phenotypes are currently annotated to a coarse level by ZFIN. In addition, the coarse-level annotations, though lacking the detail that free-text provides, do express the Review of annotations for consistency among curators. Annotation summary reports in the form of a spreadsheet containing annotations for all 47 publications were generated regularly from the Phenoscape Knowledgebase to review annotation consistency. Additionally, Phenex can export files in Figure 3. Attribute-level quality terms from the Phenotype and Trait Ontology used to curate systematic characters. Terms in blue font represent the higher-level concepts used to describe phenotypic variation at a coarse level (see Figure 4). Qualities are divided into those that inhere in a single entity (quality of single physical entities; green fill) and those that inhere in multiple entities (quality of related physical entities; red fill). Examples of children of some terms are also shown. doi:10.1371/journal.pone.0010708.g003 Figure 3. Attribute-level quality terms from the Phenotype and Trait Ontology used to curate systematic characters. Terms in blue font represent the higher-level concepts used to describe phenotypic variation at a coarse level (see Figure 4). Qualities are divided into those that inhere in a single entity (quality of single physical entities; green fill) and those that inhere in multiple entities (quality of related physical entities; red fill). Examples of children of some terms are also shown. doi:10.1371/journal.pone.0010708.g003 May 2010 | Volume 5 | Issue 5 | e10708 PLoS ONE | www.plosone.org 5 Curation of Evolutionary Data Figure 4. Comparison of coarse-level and fine-level phenotype annotations for the observation of a sigmoid-shaped supraorbital bone. doi:10.1371/journal.pone.0010708.g004 Figure 4. Comparison of coarse-level and fine-level phenotype annotations for the observation of a sigmoid-shaped supraorbital bone. doi:10.1371/journal.pone.0010708.g004 Excel format, so that consistency can be checked for individual files. We developed a series of review tasks that checked for proper EQ syntax and consistent annotation of different character types. Curation workflow These include checking that a related entity was recorded when a relational quality was used; checking that a related entity was not recorded with a quality of a single entity; checking for incomplete annotations (e.g., only one state annotated); and checking that post-composed terms were nested correctly (e.g., process (part_of (anterior region (part_of (maxilla)))) versus process (part_of (anterior region))((part_of (maxilla))) and created with logically correct relations (e.g., part_of, connected_to, overlaps_with, adjacent_to and spatial relations such as anterior_to). Undergraduate student workers also proofread the curated files to check for the correct transcription of data matrices and numerical values of counts. characters, taxa, specimens, and matrices were presented in the different studies. These led to the creation of annotation guidelines (summarized in Text S1; [69]). The standards and the variation encountered in the literature also drove the development of our annotation software (Phenex). ( ) Character and character states and EQ annotation. The curation of 4,617 characters, or 10,512 character states, resulted in 12,861 ontology-based phenotypes or Entity-Quality statements. Characters and character states were divided among several categories in the process of EQ annotation. First we distinguished among characters and states that involved a single entity vs. those that involved two or more entities, terminology that follows the division of quality terms in PATO [11]. For example, a character might involve a single anatomical structure, such as the shape of the dorsal fin (‘‘dorsal fin … acuminate’’ [49]) versus a character that involves the relationship between two structures (‘‘dorsal fin origin anterior to that of pelvic fin’’ [49]). Selection of specific entities from the appropriate ontology was generally the next step in the curation process (described further in Discussion). The third step was to determine the particular quality, initially at the attribute level, that is required to represent the phenotype described in the character state. If a single entity is involved, a monadic quality (quality of a single physical entity; Figure 3), i.e., one that inheres in a single entity is required. If two (or more) entities are involved in the phenotype, frequently a relational quality (quality of related physical entities; Figure 3), i.e., one that inheres between multiple entities, is required. Size comparisons among entities require special consideration, and involve monadic qualities (see Text S1). Last, we considered whether a character state contained single or multiple logical qualities and thus required single (non-composite characters) or multiple (composite characters) EQ statements. Curation workflow Frequently we found that several different attribute qualities (e.g., color and shape; Figure 3) were required for the annotation of composite characters (see Systematic Character Types and Application of EQ Formalism). Author contact and verification. fter the curation of each publication was completed and verified for consistency, the primary author was notified by email that their published data had been curated for inclusion in the Phenoscape Knowledgebase. Authors were sent a spreadsheet with the original character and taxonomic data and its ontological representation (e.g., free-text character descriptions vs. EQ phenotypes; published vs. currently accepted taxonomic names). Authors were invited to send suggestions or corrections prior to upload of the data to the public version of the Phenoscape Knowledgebase. Two authors returned corrections to their published data. Author contact and verification. fter the curation of each publication was completed and verified for consistency, the primary author was notified by email that their published data had been curated for inclusion in the Phenoscape Knowledgebase. Authors were sent a spreadsheet with the original character and taxonomic data and its ontological representation (e.g., free-text character descriptions vs. EQ phenotypes; published vs. currently accepted taxonomic names). Authors were invited to send suggestions or corrections prior to upload of the data to the public version of the Phenoscape Knowledgebase. Two authors returned corrections to their published data. Data upload to Phenoscape Knowledgebase. Phenotypes and corresponding matrix information were loaded into the Phenoscape Knowledgebase, a relational database built on the Ontology-Based Database (OBD) schema, in which all data are represented as semantic links between ontology terms (Kothari et al., in preparation). The deductive reasoning and the query interface of OBD support analyses of the anatomical and taxonomic disposition of phenotypic annotations at any level of granularity that is present within the logical structure of the ontologies. In addition to the Knowledgebase itself, we created a web interface (http://kb.phenoscape.org/) that allows users to browse and query the phenotype data in ways that exploit the ontological context. Taxonomic names. From the 47 publications, we curated phenotype data to 3,449 taxa (mostly species), of which 2,682 were nonredundant names, of which there were a corresponding 2,410 valid names (according to the Catalog of Fishes, CoF [24]). Of the 2,682 names, 729 are now invalid or were misspelled. Curation workflow The invalid names were annotated to the currently valid name as listed in CoF using the TTO, or the invalid or misspelled name was added as a synonym, if not already present in CoF. Three hundred and ten taxon names were added to the TTO as unknown, uncertainly identified, or unnamed taxa (out of 36,895 taxonomic terms total). PLoS ONE | www.plosone.org Discussion Higher-level taxa appeared in 35 of the 45 published data matrices. These taxa were expanded to the species level to represent the particular species examined in a publication. As mentioned previously, this was not always straightforward because some authors did not indicate which species belong to these higher-level taxa used in the matrix. For example, one author [63] categorized species by family in the Materials list, but additionally used subfamilies in the matrix. In this case, curation of species to the correct matrix subfamily (and thus to the correct phenotype descriptions) required personal communication with an expert taxonomist. Additionally, some authors (e.g., [65]) organized species in the Materials list by higher-level taxa proposed in their own study (and reflected in their matrices) instead of by currently recognized higher-level taxa. Again, curation of species to the correct matrix taxon, and thus to the correct character data, required personal communication with an expert taxonomist. Our experience in successfully transforming a large collection (10,512 character states) of legacy systematic character data into the ontology-based EQ syntax resulted in a recognition of several distinct systematic character types with respect to the logical categorization enforced by ontologies. It also contributed to the growth and improvement of several domain and community ontologies, and it resulted in the development of standards and best practices for phenotype curation. Moreover it offers a new view of morphological characters that is valuable for practicing systematists. Curation effort The time required for curation of the chosen papers [4– 6,21,26–68] to the level described herein was approximately 5 person-years. This included significant time investment by personnel in software development, testing and improvement, initiation of new ontologies, and development of curation standards and workflow. Character-by-taxon matrices. Forty-five of the 47 curated publications included data matrices. From the two publications that lacked them, one was supplied by the author [4] and the other was reconstructed from the text [21]. Some matrices contained numerical character states that were not textually described. We annotated EQ statements for only those character states that were documented. Curation of Evolutionary Data Curation of Evolutionary Data We included reference to the author(s) and year in the term name for these 310 publication-specific taxa (e.g., Akysis sp. 1 (de Pinna 1996), TTO:10000093). proportion of characters were annotated correctly to the higher- level quality term (Figure 3) although only two of the 10 characters were annotated identically among curators for the more specific child term. The overall variability in annotation consistency resulted from different interpretations of shape and size descrip- tors, inexperience and unfamiliarity with the ontologies and software, difficulties in creating post-compositional terms, and lack of adequate terms in the ontologies, particularly for shape descriptors. Specimens and materials examined. In most of the publications (42 of the 47) a list of materials was presented, giving the provenance and other information about the particular specimens that were examined. Synthesis papers [55] or book chapters [51,52] frequently did not include a Materials list, but specimen collection numbers were sometimes provided in figure captions (e.g., [36]). We obtained a list of materials examined from the authors of these papers where possible. Some authors referred to previous publications for a full list of materials (e.g., [28,59]), and where feasible, we curated specimens from these. Specimens and materials examined. In most of the publications (42 of the 47) a list of materials was presented, giving the provenance and other information about the particular specimens that were examined. Synthesis papers [55] or book chapters [51,52] frequently did not include a Materials list, but specimen collection numbers were sometimes provided in figure captions (e.g., [36]). We obtained a list of materials examined from the authors of these papers where possible. Some authors referred to previous publications for a full list of materials (e.g., [28,59]), and where feasible, we curated specimens from these. Systematic character types and application of EQ formalism Systematists use the expressiveness and richness of natural language to describe precisely the morphological variation that they observe among species. These phenotype descriptions are represented in a somewhat formalized way as characters and character states in the systematic literature [14]. EQ formalism provides a rigorous yet flexible syntax for these data; it is to some extent, a ‘natural fit’. As previously described (Figure 1), systematic characters typically consist of a short character header (e.g., maxilla shape) denoting the relevant structure(s) (entity: maxilla) and attribute (high-level quality: shape) that varies among taxa, followed by several character states that specify the value of the quality (round, rectangular, triangular, etc…). Many systematic characters, however, do not follow this format (see [14] for review), and a standardized logical framework, consistent with EQ formalism, has been recently proposed [14]. In systematic characters, entities and qualities can be found in the character description, in the character state description, or in both. Irrespective of this, the morphological descriptions of variants among species in the literature conform to the general formalism of EQ syntax and semantics. From the breadth of our curation work emerged standards and recommendations for deploying this formalism, and we relate these below and in our Guide to Character Annotation ([69]; Text S1). Ontology growth As a result of literature curation, the ontologies that we used grew in number of new terms, synonyms, definitions, and relationships among terms. The TAO more than doubled its skeletal terms, from 253 in version 1 [15] to 644 skeletal terms of 2,662 total in the most recent version (March 2010). The TTO grew to 36,895 taxon terms, including 154 fossil taxa (from an initial 36,080 terms with no fossil taxa), 43,215 synonyms (from an initial 38,269), 30,865 species, 5,107 genera, and 551 families. Our curators contributed 16 terms, four synonyms, three name changes, and one relationship change to PATO. We added four terms (parental care, oral incubation, adult foraging behavior, foraging by probing substrate) to the Biological Process hierarchy of the Gene Ontology (GO-BP), and 41 terms and six synonyms to the Spatial Ontology. Museum codes were based on the CoF list [79] (479 entries) that was enhanced with 37 additional codes identified during the process of paper curation. PLoS ONE | www.plosone.org Characteristics of the data reported in the source publications From our comprehensive undertaking to represent complex phenotype data using ontologies, patterns emerged in how May 2010 | Volume 5 | Issue 5 | e10708 6 Curation of taxa Our finding that more than one quarter (729 of 2,682) of the species names used in the 47 curated publications were outdated was unexpected, given the recency of these publications (1981– 2008). These fishes may present an unusual case, however, because two of the groups that we curated (catfishes and cypriniforms) have undergone extensive recent taxonomic revi- sion. Given that some taxa will be revised more frequently than others, the rapid turnover in taxonomic names draws attention to the need for adaptable resources such as taxonomy ontologies like the TTO, that record the relationships among not only current, but also synonymous, taxonomic names thus supporting compar- isons across studies in the literature. Ontologies provide the capability to accommodate the needs of the specific literature or type of data under curation. Systematic characters are sometimes framed such that different character states involve different logical qualities (e.g., absent and shape). For example, variation in the spermatophoral gland in brachiopods (a phylum of invertebrates) is described with three states [81]: ‘‘Absent, Simple, Composite’’. Although some systematists have previously raised concerns about the logical structure of these characters, it does not pose a problem for phenotype annotation from a practical standpoint, e.g., the EQ statements for these character states are: E:spermatophoral gland, Q:absent; E: spermatophoral gland, Q:simple; E: spermatophoral gland, Q:composite (see Text S1 for discussion of the semantics for absent and present). From the standpoint of reasoning with ontologies within a database, presence can be implied by an annotation to any quality term (e.g., tubular or lamellar) other than absent. Phenotypes are recorded from observations on individual organisms in both model organism genetics and evolutionary biology. Curation of the evolutionary literature, however, presented a special challenge because it required distinguishing between author statements that were based on direct observation of specimens and generalizations to higher-level taxa. We discovered that authors represented species observations using one or more higher-level taxa in more than 75% of the published data matrices that we curated. Generalizing to a higher-level taxon from observations on a single or only a few exemplar species is in fact common practice in systematic studies of many taxonomic groups. Curation experiments and curator consistency ‘‘fused medial and proximal anal-fin radials’’, which is a complex entity not named in the literature, we annotated this as a relational character using the qualities fused with and separated from to describe the relationship between two separate entities (state 0: E:medial anal-fin radial, Q:fused with, RE:proximal anal-fin radial; state 1: E:medial anal-fin radial, Q:separated from, RE:proximal anal- fin radial). The advantage of representing this using two separate recognized and defined entities is that they can thereby be linked to other annotations of these entities. Character states were generally translated into a single EQ statement, but not uncommonly we noted that multiple aspects of a structure or multiple structures are described within a single character state, requiring the annotation of multiple EQ statements. This may reflect an investigator’s observation that the structures co- vary, and perhaps an assumption that they are non-independent and thus represent a single character state. We termed these ‘composite’ character states. For example, variation in the pectoral fin is described as follows [26]: ‘‘Pectoral fin size. 0: pectoral fin large and pigmented; more than 43% head length; membrane infused with numerous small chromatophores; 1: pectoral fin small and unpigmented; less than 43% head length; membrane without chromatophores.’’ Here each character state corresponds to two phenotypes (e.g., state 0, EQ1: E:pectoral fin, Q:size‘in- creased_in_magnitude_relative_to (E:pectoral fin in_ taxon X) and EQ2: E:pectoral fin, Q:pigmented). Dividing the distinct logical components (size and color in this case) into multiple EQ statements is necessary for reasoning with them independently using ontologies – and possibly, but not necessarily, for phylogenetic character construction. By recording separate EQ statements, one may query on independent logical qualities of a character state (e.g., size) and expect to find similar annotations. However, if a systematist separates them into separate characters, it results in increasing the weight of potentially non-independent characters in the phylogenetic analysis. On the other hand, representing them as a single character may underrepresent them in the analysis. The process of dissociating the states of some characters (composite) into multiple, distinct EQ statements, and the states of other characters into EQ statements with different logical values has implications for their potential use in phylogenetic analysis. Characters are the units of homology in phylogenetic analysis, and the alternative character states have been judged by the researcher to be homologues of one another. Curation experiments and curator consistency In the first curation experiment, only one of 10 characters was annotated identically among four curators. The reasons for this variability among curators included curation software bugs, difficult aspects of the ontologies (e.g., lack of appropriate quality terms from PATO), lack of standardized guidelines for unusual cases, and differing interpretations of the text descriptions. For the second experiment, curators were told to curate characters to a coarse level of granularity for quality. In this experiment, a greater Systematists typically represent only one aspect of a structure in a character state. An example from bird systematics involves variation in the shape of the external naris in stem rollers: ‘‘ovoid (0); triangular with a flat ventral margin (1)’’ [80]. Here each character state corresponds to a single phenotype: state 0, for example, corresponds to the EQ: E:external naris, Q:ovoid. Occasionally, however, authors represent observations in ways that may be interpreted as either monadic or relational. An May 2010 | Volume 5 | Issue 5 | e10708 May 2010 | Volume 5 | Issue 5 | e10708 7 Curation of Evolutionary Data ischiac process: small or posteriorly elongate (0); falciform (1); falciform and strongly developed (2).’’ To represent ‘‘small or posteriorly elongate’’ using PATO qualities, the qualities size‘de- creased_in_magnitude_relative_to(E in_taxon X) and elongated are applied. However, the parent of these two terms is size, not shape. A consequence of this mismatch between natural language and the ontology is that querying the resulting annotations for ‘‘pelvic bone’’ and ‘‘shape’’ will not return annotations corresponding to the author’s state 0. Thus applying mutually exclusive terminology to annotate these aspects from a morphological description can be difficult and possibly result in misrepresentation of an author’s intention. Many investigators, however, would recognize that many aspects of size variation also relate to shape and vice versa. Size and shape terms were a frequent source of inconsistency among curators. In cases such as the example above, we recommended that curators annotate coarsely to shape. example from fishes [48] is a character involving two elements of the anal fin described as: ‘‘Presence or absence of fusion of medial and proximal anal-fin radials: (0) absent; (1) present.’’ Rather than annotate this as a monadic character by adding a new term to the anatomy ontology, i.e. Curation experiments and curator consistency To the extent that they are atomized using EQ, they may lose their genealogical connection. On the other hand, the task of homologizing complex phenotypic characters across different studies and taxa has proved difficult to impossible for phylogeneticists thus far, and it may be the case that EQ statements provide the broad initial grouping of characters and character states that facilitate subsequent broader-scope phylogenetic evaluation. PLoS ONE | www.plosone.org Curation of phenotypes in the legacy literature: challenges and feasibility The solutions that we suggest and have at least partially implemented are generally useful for other phenotype efforts, and they are described below. New attempts to curate phenotypes from the legacy literature of other taxonomic groups (phylogenetic treatments or not) will require overcoming the initial hurdle of creating new ontologies or expanding existing ones for the inclusion of terms required to represent the diversity of organism features and taxonomy under consideration. In our experience, we found it efficient to build from existing ontologies where available. We used, for example, the existing PATO ontology for annotation of qualities, and we built the Teleost Anatomy Ontology (TAO) from the Zebrafish Anatomical Ontology [15]. As we annotated the literature, we concurrently added required terms and relationships to these and other ontologies. In this way, ontology growth and development was driven by active curation of the literature. For example, in the course of curating evolutionary phenotypes for the fishes in this study, we more than doubled the number of primary terms (not including synonyms) for the skeletal system axis of the TAO. In contrast, no new terms were proposed for cell types, embryonic structures, or the immune system, because no evolutionary variants of these anatomical structures were documented in the literature we curated. As a consequence, ontologies might appear to be incomplete or missing basic terms, and may not provide the encyclopedic knowledge that some may expect of an anatomy ontology. Although terms, definitions, and relationships can be supplied at any time, the effort required for curators to break away from direct annotation and turn to ontology development is significant; 15–50% of an individual curator’s time might be spent on ontology development. In particular, curation of publications covering taxa that have not been previously annotated require the addition of new taxonomy and anatomy terms and is thus more time consuming. We anticipate that future curation of the fish literature will be more time efficient because of our significant refinement and enlargement of the core ontologies (TAO, TTO, PATO). For new efforts in different taxonomic domains, once the respective ontologies have been populated, the curation of additional publications will require less time. In summary, term addition to shared ontologies broadened their scope and provided greater utility to others in the community. Curation of phenotypes in the legacy literature: challenges and feasibility familiarity with the tools, ontologies, and syntax for creation of phenotypes. Consistency improved as curators gained familiarity with the ontologies, acquired experience using curation software and tools, became more aware of the developing annotation standards, and were restricted in their term choices. The almost daily updated documentation of annotation problems, examples, and standards in the Guide to Character Annotation [69] was important in promoting these annotation standards. High-level oversight of the process and manual and automated consistency checks by the lead curator before making the data public were critical to maintaining consistency and data quality, and contributed to improvements in consistency. The rich literature that documents the similarities and differences among taxa goes back several centuries, spans many languages, and at first appearance, seems almost insurmountably large to render computable using ontology-based curation methods. By initially focusing on large-scale treatments where phenotypic descriptions are most formalized, i.e., the phylogenetic studies, we reduced the number of papers for more than 8,000 species of ostariophysan fishes to approximately 50. This struck us as surprisingly few such papers; however, given that the phylogenetic approach has been mainstream only over the past 30+ years, and that morphological treatments of this sort may take an author 6–10 years to produce, the number may well be representative for other taxonomic groups. If this is the case, with annotation software and ontologies in place at the outset, we estimate that similar phenotype annotation projects can be done in possibly half the time (approximately 2.5 person years). Addition- ally, by incorporating semi-automated methods to extract character states from the literature and associate ontology terms, the time involved could be further reduced. A significant level of phenotypic data, however, remains in non-phylogenetic studies, e.g., species descriptions, and methods for efficient EQ curation of this literature remain a critical challenge. The results of our curation experiments and subsequent work with individual curators pinpointed several general problems that required improvement in curation procedures and software tools to increase curator consistency and efficiency. Importantly, we discovered that curators had a difficult time navigating large ontologies to determine whether an appropriate term was present. This is almost certainly a general problem in annotation of phenotype descriptions and not specific to systematic biology literature. The absence of the correct ontology term led to inconsistent use of existing terms by curators or a time-consuming change of focus to the process of term addition and definition. Curation of phenotypes in the legacy literature: challenges and feasibility A i ifi l h ll f l bli h d i To help remediate the navigation of large ontologies problem, we implemented software restrictions to reduce the number of terms available for use in annotations. For example, if only the skeleton is being annotated, then a ‘slim’ version of the TAO containing only terms from the skeletal system might be made available. Restricting which terms are available is particularly important in large community ontologies (e.g., the Gene Ontology) that contain many terms not applicable to the particular data under curation. We, for example, implemented a ‘slim’ version of the Relations Ontology, with only a small subset of relations (such as part_of, towards, etc.) available for use by our curators. We found that it is critical for relations to be restricted for use in post- composition. Curators, for example, improperly used left_of rather than in_left_side_of and contained_in rather than located_in. In the future we feel it will be useful to further restrict availability of particular terms and relations, depending on the literature under curation, so that for example, the relation connected_to is the only one available for use when annotating the relation of scales to the body of fishes. Thus a curator would be forced to annotate scale connected_to head versus (incorrectly) scale part_of head. Such restrictions are expected to decrease the effort required by a curator to find an appropriate term or relation, and increase significantly the consistency of curation and thus the logical value of the annotations. The second part of the curation problem is that after a curator determined that a term was truly missing from an ontology (versus in some part of the ontology that they may not have browsed), they then needed to request that a new term be added to the ontology. This was a significant interruption in the curation process, as curators turned their attention from the phenotype description to composing a new term definition. To help expedite the term addition process for curators, we provided easy links to term trackers on the Phenoscape wiki [69] for different ontologies. We also encouraged curators to provide basic definitions that could later be improved upon by community feedback on the term request mailing list [15]. A significant general challenge for newly established curation projects is the consistent annotation of phenotypes among curators. Curation of taxa Sometimes an author explicitly asserts in the correspond- ing text that a particular phenotype pertains to all species included in a higher level taxon, but other times using a higher-level taxon in a matrix is simply shorthand for reference to the species that were actually examined. To compare data across multiple studies, however, it is critical to interpret appropriately the meaning of the author’s use of these higher-level taxa. The natural language used in the original description of systematic characters sometimes corresponds to a term in an ontology that is different from the author’s intent; in other words, there is a mismatch between an author’s free-text description and the literal match to an ontology term. For example, authors sometimes describe variability in the shape of a structure using terms that are not types of shape in the quality ontology. Variation in the pelvic bone, for example, is described as [29]: ‘‘Shape of May 2010 | Volume 5 | Issue 5 | e10708 8 Curation of Evolutionary Data PLoS ONE | www.plosone.org Curation of Evolutionary Data appropriate fine-scale quality term in PATO, mainly due to the incomplete development of this ontology (i.e., the term was missing). This led to individual curators choosing different, fine- scale terms that approximated the author’s intent, but did not fully or adequately represent it. Rather than expedite the term addition process here, we used the Phenex software to restrict term choices primarily to higher-level attribute qualities (Figure 3). Consistency and efficiency improved as a result. Additionally, term restriction had an educational and training value in that our curators learned to abstract quickly the essence of the varying quality from complex descriptions. The negatives of this approach are that the PATO ontology did not grow at the leaf-node level, at least initially, as a result of our work, and that queries across qualities cannot be made at a fine scale. That is, querying for all ‘elongate’ jaws, for example, would return jaws of all shapes because all descriptions of jaw shape variation are annotated to the high level term shape. The cost of further annotation refinement must be judged against the intended use of the annotations. ways that investigators describe their observations makes it difficult to combine or compare data across studies, and renders the observations vulnerable to misinterpretation. Many of the issues we encountered in curation (different terminologies, noncompa- rable attributes among character states) could be avoided prospectively if systematists are provided access to data collection tools that link to community anatomy, quality, and taxonomic ontologies. Use of ontologies for complex phenotype descriptions has the potential to clarify the identity of structures under consideration, allow comparison of similar phenotypes, and facilitate the application of characters across studies and taxonomic groups. Moreover, use of a mapping to EQ syntax during the course of a study can generally promote higher levels of standardization. Curated data that a computer can understand and reason with facilitates the aggregation and comparison of data on a scale that is unmanageable for individual researchers. The expressiveness, creativity, and precise descriptions possible with natural language, however, are not easily replaced, despite the promise and advantages of computational methods. The inherent human ability to describe and interpret complex phenotypes will always be an essential element in biological fields that involve compar- isons of the visible phenotype. These, however, are complemented by computational tools such as ontologies that promote clarity and communication among researchers and interoperability of data. Conclusions The benefits of using an ontology in communication in any discipline include standardization of terminology, explicit defini- tions of concepts, logical relations among concepts, and the creation of structured and precise representations of information that facilitate computability. From a practical standpoint, communities benefit because communication is clearer and less ambiguous. Using multiple ontologies to describe more complex concepts such as phenotypes can promote similar benefits at a broader level and to a broader community, promote comparisons of phenotypes across studies and taxonomic groups, and allow interoperability with different data types. Currently the multiple Supporting Information Text S1 Phenoscape Guide to Character Annotation. We describe our standard practices for annotation of entities and qualities in the Guide to Character Annotation. Our online version describes more specialized cases and issues (https://www. phenoscape.org/wiki/Guide_to_Character_Annotation). Found at: doi:10.1371/journal.pone.0010708.s001 (0.09 MB DOC) Text S1 Phenoscape Guide to Character Annotation. We describe our standard practices for annotation of entities and qualities in the Guide to Character Annotation. Our online version describes more specialized cases and issues (https://www. phenoscape.org/wiki/Guide_to_Character_Annotation). Curation of Evolutionary Data It is a significant remaining challenge to curate complex phenotype descriptions using EQ syntax fully. This challenge extends beyond systematic biology to all curation efforts (e.g., Human Phenotype Ontology; http://www.human-phenotype- ontology.org) that seek fine-scale representation of phenotypes, including those that compare human genetic phenotypes to those of model organisms. This is because full or fine-scale curation of complex phenotype descriptions (e.g., the antero-dorsally project- ing process of the posterior maxilla is located posterior to the laterally projecting and bent knob of the ethmoid in species X) requires elaborate post-compositional combinations of ordered sets of terms from multiple ontologies. All efforts to represent complex phenotypes will require multiple ontologies and post-composition, and they will thus experience the same general problems. Although the Phenex software supports such compositions [20], and although sophisticated and biologically relevant reasoning across these compositions is feasible [77], the curatorial burden of accurate and consistent annotation at this scale is high. Our work to reduce the burden of curation of these phenotypes by developing standards, restricting ontology terms available for annotation, and making it easier to add new terms, represents a significant step forward. 1. Grande L, Bemis W (1998) A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy. An empirical search for interconnected patterns of natural history. Society of Vertebrate Paleontology Memoir 4: supplement to Journal of Vertebrate Paleontology. pp 1–690. Acknowledgments We thank the many taxonomic experts and other contributors to the development of the ontologies, their curation work, and participation at Phenoscape workshops (http://kb.phenoscape.org/contributors/). J. 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Available online http://arthritis-research.com/content/10/1/R20 Research article Open Access Vol 10 No 1 What do we know about communicating risk? A brief review and suggestion for contextualising serious, but rare, risk, and the example of cox-2 selective and non-selective NSAIDs R Andrew Moore1, Sheena Derry1, Henry J McQuay1 and John Paling2 1Pain Research and Nuffield Department of Anaesthetics, University of Oxford, Oxford Radcliffe NHS Trust, The Churchill, Headington, Oxford OX3 7LJ, UK 2Risk Communication Institute, 5822 NW 91st Boulevard, Gainesville, Florida 32653, USA Corresponding author: R Andrew Moore, andrew.moore@pru.ox.ac.uk Received: 4 Apr 2007 Revisions requested: 22 May 2007 Revisions received: 6 Dec 2007 Accepted: 7 Feb 2008 Published: 7 Feb 2008 Arthritis Research & Therapy 2008, 10:R20 (doi:10.1186/ar2373) This article is online at: http://arthritis-research.com/content/10/1/R20 © 2008 Moore 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 Communicating risk is difficult. Although different methods have been proposed – using numbers, words, pictures or combinations – none has been extensively tested. We used electronic and bibliographic searches to review evidence concerning risk perception and presentation. People tend to underestimate common risk and overestimate rare risk; they respond to risks primarily on the basis of emotion rather than facts, seem to be risk averse when faced with medical interventions, and want information on even the rarest of adverse events. Methods We identified observational studies (primarily in the form of meta-analyses) with information on individual nonsteroidal anti-inflammatory drug (NSAID) or selective cyclooxygenase-2 inhibitor (coxib) use and relative risk of gastrointestinal bleed or cardiovascular event, the background rate of events in the absence of NSAID or coxib, and the likelihood of death from an event. Using this information we present the outcome of additional risk of death from gastrointestinal bleed and cardiovascular event for individual NSAIDs and coxibs alongside information about death from other causes in a series of perspective scales. Introduction Many factors contribute to an incomplete understanding and evidence base for risk and risk presentation. We should not be surprised when both patients and professionals are confused about risk, about competing risks, and about comparing risks with benefits. Decisions are based on facts and emotions, both of which may be manipulated, and it may well be that emotions dominate the facts. This is important in the frame- Results The literature on communicating risk to patients is limited. There are problems with literacy, numeracy and the human tendency to overestimate rare risk and underestimate common risk. There is inconsistency in how people translate between numbers and words. We present a method of communicating information about serious risks using the common outcome of death, using pictures, numbers and words, and contextualising the information. The use of this method for gastrointestinal and cardiovascular harm with NSAIDs and coxibs shows differences between individual NSAIDs and coxibs. Conclusion Although contextualised risk information can be provided on two possible adverse events, many other possible adverse events with potential serious consequences were omitted. Patients and professionals want much information about risks of medical interventions but we do not know how best to meet expectations. The impact of contextualised information remains to be tested. work of medical decision-making and specifically in the choice of pharmacological and interventional therapies for individuals. Risk has two main components. One is that of chance, the pure statistical likelihood that an event will happen (probability). The other is that of a bad outcome – danger, injury, harm or loss – together with an indication of severity. To some extent the term is used commonly to process or communicate the Coxibs = selective cyclooxygenase-2 inhibitors; NSAIDs = non-steroidal anti-inflammatory drugs. Page 1 of 16 (page number not for citation purposes) Arthritis Research & Therapy Vol 10 No 1 Moore et al. product of probability and severity, and the complexities have been reviewed elsewhere [1]. from gastrointestinal bleeding or cardiovascular events with NSAIDs and coxibs might be presented by using this method. We can recognise three main areas that have to be considered to help professionals understand their patients' risk, and patients to understand their own risk. Broadly these can be aggregated under the headings of perception (influences on how individuals and populations relate to risk information), presentation (how information – data – can be conveyed, and possibly manipulated, for clarity or impact), and pertinent facts (accurate data with clear, decisive relevance to the matter in hand, and which may be used as the basis of future outcomes). These broad areas are not independent of each other, but it helps understanding to try to organise the many different facets of risk. The only certainty is that there is uncertainty. We wish to emphasise that these explorations are not intended to be definitive; indeed, they cannot be without extensive testing. However, given the growing emphasis of patient involvement in decision-making, methods have to be developed that can deliver risk information effectively. 'Everything is poison, there is poison in everything. Only the dose makes a thing not a poison.' Paracelsus might have been intrigued by the controversy that has arisen over the cardiovascular adverse effects that have lately been associated with traditional NSAIDs and selective cyclooxygenase-2 inhibitors (coxibs) [2]. Traditional NSAIDs have long been associated with upper gastrointestinal bleeding, renal impairment, and congestive heart failure, and, more recently, with injury to the lower bowel. The only expected benefit of coxibs over NSAIDs was reduced levels of upper gastrointestinal bleeding. NSAIDs and coxibs have become some of the most studied drugs ever, with at least 145,000 patients enrolled in randomised trials [3], and with up to 3.5 million patients in observational studies [4]. There is unprecedented information on different adverse events associated with particular drugs, especially for the outcomes of upper gastrointestinal bleeding and cardiovascular risk. Different drugs, even within a class, can have different rates of particular adverse events. For NSAIDs there are large differences between drugs and between different doses of the same drug in terms of upper gastrointestinal bleeding. Individual patient meta-analysis showed that low-dose ibuprofen was not different from non-use, whereas high-dose naproxen had an odds ratio of 16 [5]. In observational and other studies of NSAIDs there were large differences between drugs [6]. Similarly, differences between individual coxibs are apparent for gastrointestinal bleeding [7], and between individual coxibs and NSAIDs for myocardial infarction [4,3,8]. This review set out to do three things: to examine the background to our understanding and perception of risk; to examine how risk can be presented, and explore the possibility of using a common outcome, death, and contextualising information on non-medical life risks with a presentation involving numbers, words, and pictures, based on visual aids introduced by Paling [9]; and to explore how competing risks of death Page 2 of 16 (page number not for citation purposes) Materials and methods We initially searched PubMed using a number of free-text terms for the particular area of interest. Thus for literacy, for instance, we sought articles with literacy in the title. Other searches were aimed at numeracy, risk, and risk presentation or perception. An iterative search process was then applied to identify additional studies; this involved checking the 'Web of Knowledge Cited References', and the 'Related Articles' link in PubMed using details of retrieved studies from the initial search. When the iterative process indicated alternative search terms, we repeated searches using these new terms. Terms were generally restricted to title only, at least initially, to avoid impossibly large numbers of references using words with many other common meanings (such as relative risk). We also checked the bibliographies of any relevant studies, risk websites (see [10], for instance) and books, reviews and articles on risk presentation. We looked for full journal-published articles without language restrictions. Results Background to risk perception Literacy and numeracy An inability to handle words or numbers at an appropriate level (literacy and numeracy skills) are fundamental to communicating risk probability or severity. Illiteracy in patients is known to be a barrier to communication. In a survey of 127 rheumatology patients in Glasgow [11], 3 were unable to read and 18 were functionally illiterate, so that 17% (1 in 6) would at best struggle with patient education material and 1 in 20 could not read prescription labels. An identical value of 17% with limited reading ability was found in 999 diabetic patients in primary care in Vermont [12]. Health numeracy has been provided with a set of definitions [13]. Using three simple questions to test for numeracy, Sheridan [14,15] showed that 5% (1 in 20) of US medical students and 71% (7 in 10) of patients at an internal medicine clinic could answer only one or none correctly. Half (1 in 2) of patients attending an anticoagulation clinic in North Carolina had numeracy and literacy skills that would limit their understanding [16]. Risk information that people want A large study of 3,500 adults in Kansas indicated that 90% of them wanted information on all adverse events (not just Available online http://arthritis-research.com/content/10/1/R20 serious adverse events) occurring in at least one person in every 100,000 [17]. This standard, if real, poses challenges in obtaining and communicating information on risk. How the general public responds to risk information People consistently overestimate rare risk and underestimate common risk. This was first shown for estimates of mortality three decades ago [18], and has been confirmed more recently [19] to demonstrate that the trend is common throughout society, although more educated and perhaps older people with more life experience have more accurate risk beliefs. Where causes of death involved fewer than 10 deaths a year in the USA (fireworks, measles, botulism), overestimation was by almost two orders of magnitude [19]. Where causes of death involved many deaths a year (100,000 to 700,000 deaths: stroke, cancers, heart disease), underestimation was almost one order of magnitude. At the extremes, then, people overestimate rare risks by 100-fold or more, whereas they underestimate common risks by a factor of 10. The degree of overestimation or underestimation is startling. Interestingly, both studies [18,19] showed that people were likely to judge the level of risk correctly when the risk was associated with about 1,000 deaths per year in the USA. It is also worth noting that different societies can have very different perceptions of the same risk. An important determinant may well be the state of technological development [20]. How this societal attitude relates to or affects individual attitude is not understood. In some circumstances, patients can be very risk averse, as a study of patients attending an emergency department in Boston demonstrated [26]. They were presented with a scenario in which they had come to hospital with chest pain that could not be diagnosed by standard procedures, and doctors asked them to participate in a trial using a safe and approved test involving a small amount of radioactivity that might help make a diagnosis. The study was about whether using the test in the emergency room rather than elsewhere in the hospital was acceptable, given that it had a very small level of risk. The trivial level of risk was presented in various ways, like being equivalent to 20 chest X-rays, smoking a small number of cigarettes, driving 150 miles, or breathing radon in a house for 2.5 years while living in Boston. Between 40% and 60% of patients would have refused to have the test in the emergency room, with more refusing than accepting it, however the risk was presented. Yet the additional risks were not only small, but equivalent to those they accepted as part of their life in any event, because they smoked, drove, or lived in Boston. Dimensions of risk Risk has a number of dimensions (Figure 1), with extremes that make a risk more or less tolerable. There is no good evidence about which dimensions are most important, how they affect patient or professional judgement, and in what circumstance they might do so. Attitudes to risk, at least to drug therapy, can be affected by direct-to-consumer advertising. Examining consumer responses to a US survey indicated that such advertising was associated with a greater willingness to talk with doctors about advertised drugs in those with a chronic condition, and that advertising made prescription drugs appear harmless [21]. US Food and Drug Administration research is quoted as showing that patients and physicians believe that consumerdirected advertising frequently overstates the benefits of drugs and understates the risks [22]. It is generally assumed that risks over which individuals have no control are less acceptable than those over which they do have control, or that novel risks have greater impact than those with which we are familiar. Man-made risks appear to be worse than natural risks. For instance, the risks of radiation are often posed as a major concern, yet in the USA in 2002 there were no deaths from radiation, compared with 66 from lightning, 63 from cataclysmic storm, 31 from earthquake or other earth movements, and 9 from flood. There were 767 deaths of pedal cyclists in the USA in 2002 [27]. Some risks are not highly related to demographic variables such as sex or age (road traffic accidents, for example). Others, such as the risk of death by choking, are so related; here annual risk is lowest at 1 in 1,000,000 in children aged 5 to 18 years, but approaches 1 in 1,000 in the over-90s. How patients respond to risk information A number of small studies have assessed what patients think about risk and the effectiveness of interventions. There is a tendency for patients to overestimate the risk of something bad happening [23]. For instance, 65% (2 in 3) of women either overestimated or grossly overestimated their own chance of breast cancer [24]. Women also tended to overestimate the chance of harm with hormonal contraceptives and underestimate their effectiveness [25]. For other methods of contraception, women could overestimate effectiveness (female sterilisation or female condom) or underestimate it (hormonal implants and intrauterine devices). These are trivial compared with the top two causes of death in the USA in the same year: heart disease and cancer [28]. Considerable research has shown that modifiable lifestyle factors such as diet, exercise, and refraining from smoking and being overweight can exert a massive reduction, but most people ignore this advice. The US Nurses' Study exemplified how big the beneficial effect of healthy living can be [29]. The greater the number of low-risk lifestyle factors women had, the lower their risk of heart attack or stroke was. The implications are that, in women, 82% (95% confidence interval 58 to 93%) of heart attacks and 74% (95% confidence interval 55 to 86%) of heart attacks or strokes are preventable by having a good Page 3 of 16 (page number not for citation purposes) Arthritis Research & Therapy Vol 10 No 1 Moore et al. Figure 1 Antecedents and consequences How individuals assess and process risk information is dependent on their circumstances or medical condition at that time. Attitudes and choices about an intervention depend on the state of illness as well as on the perceived benefits that accompany the risk. For instance, adherence to statins or lowdose aspirin for cardioprotection is low. In the USA it is estimated that only about 50% (1 in 2) of patients continue at 6 months, and 30 to 40% (1 in 3) at 1 year [31], and in the UK 50% (1 in 2) of patients prescribed low-dose aspirin have discontinued within a year [32]. This low adherence may be a combination of low expectation of personal benefit for therapies that are measures of prevention, combined with an adverse event that crosses a consequential boundary for the individual. Where benefit is greater and more tangible, adherence is likely to be higher, even if adverse events are common. Thus in renal transplant patients, only 15% (1 in 7) were non-adherent to immunosuppressants under stringent criteria [33]. The consequence of non-adherence, rejection of a transplanted kidney, was particularly significant, with an absolute risk increase averaging 26% (1 in 4) over a number of studies. Some dimensions and qualities of risk and risk decisions. decisions lifestyle. Despite widespread advice about healthy living, four out of five US citizens have lifestyles that put them at increased risk of heart attack and stroke [30]. When the number of deaths from heart disease (684,000 in the USA in 2003) and stroke (158,000) is so large, the implication is that people in general are content with large numbers of avoidable deaths from some causes, which are well known, largely within their control, and perhaps 'natural'. Yet the same people can cavil over extremely remote risks from nuclear power plants, electricity power lines or mobile phones, over which they have, or believe they have, no control, and which are man-made. New risks need to be put into perspective, and this might be considered an important aspect of evidencebased decision-making that has, as yet, received little attention. The lesson is that, in practice, patients' response to risk is influenced by more than just hard facts. It may be that if risks were presented in an appropriate context, people's attitudes to risk or behaviour might change. Page 4 of 16 (page number not for citation purposes) At face value, the idea of placing a catheter in the epidural space alongside the spinal cord does not seem to be a good one, because of the possibility of direct physical damage, indirect physical damage from a haematoma, or infection, any of which could result in transient or permanent neurological damage. Yet 2.4 million of the 4 million births in the USA every year involve epidural analgesia, a procedure accepted because the benefits of pain relief are immediate and great, the risk is small (persistent neurological injury 1 in 240,000; transient 1 in 6,700 [34]), and not all risks are directly connected with the epidural. Childbirth is common, women may have experienced an epidural themselves or be familiar with the experience of others, and all these antecedents influence the acceptance of a low risk. Perhaps one of the most striking examples of antecedent effects on risk behaviour is smoking cessation. In primary care, nurse interventions for smoking cessation had no effect, with about 4% (1 in 25) quitting with or without intervention by a nurse. In hospital settings and patients after cardiac surgery, heart attack, or with cancer there were high quit rates (25%; 1 in 4) without intervention by a nurse, and even higher rates (32%; 1 in 3) with an intervention [35]. The difference between the presence and the absence of serious illness changed attitudes of smokers towards quitting and therefore changed the effects of intervention to help stop smoking. Attitudes to risk and measures of prevention seem to change when an event becomes a more immediate problem. Available online http://arthritis-research.com/content/10/1/R20 Presenting risk To find studies of any description regarding risk perception and presentation, a number of broad, free-text searches were undertaken with PubMed (up to September 2006). Combinations of words, for instance 'risk AND presentation', or 'risk AND communication' were used, and any original studies or reviews likely to be pertinent were obtained, in as much as they related to communicating medical risks. Bibliographies were examined to uncover other relevant studies, because electronic searching alone is inadequate [34,36]. Studies found were used to inform thinking about risk and risk communication, rather than to constitute a formal systematic review. The wide range of issues relating to risk perception and presentation, and the fragmented and often sparse research literature, rules out a conventional systematic review. Frequency, probability, and words Probability, in terms of simple frequencies or odds, is often used to describe or communicate risk, sometimes in numbers, often with associated verbal descriptors (common, rare, negligible), and sometimes also with graphical presentations. Some of the more commonly used risk scales have been reviewed by Adams and Smith [37]. There is an assumption, perhaps unstated, that we can couple the numbers and words externally so that their relationship remains fixed. Patients are known to respond differently to how adverse events are presented. For instance, the patients estimated the likelihood of an adverse event as three to nine times greater with verbal rather than numerical information [38]. Similar differences can be seen in professionals. Graduate students and healthcare professionals in Singapore were asked to match frequency with one of six phrases, from very common to very rare, when a hypothetical situation about adverse events of an influenza vaccine was presented to them in either a probability format (5%) or a frequency format (1 in 20) [39]. With either format of numerical presentation, a risk of 1 in 20 was described verbally from rare to very common, with somewhat more consistency for frequency format than probability. The European Union has guideline descriptors for the frequency of an adverse event, with verbal descriptors linked to frequency. Thus very common is more than 10% (or greater than 1 in 10) and very rare is less than 0.01% (less than 1 in 10,000). Four studies involving more than 750 people demonstrate that people invariably grossly overestimate frequency from these verbal descriptors [40]. Overestimation occurred at all frequencies, but for the very rare adverse events they were overestimated by at least 400-fold. The way in which we perceive and process numbers seems to be very different from how we perceive and process words, and different in different people. Moreover, different numbers are linked to similar words in different scales; for instance, the European Union descriptors are not the same as those proposed by Calman [41] or others (Table 1). Framing risk for patients When patients are provided with information about drug therapy or surgery, the way in which information is provided can affect patient decisions in a major way, and the extensive literature has been reviewed, especially in terms of benefits or losses, situation, and context [42]. Our knowledge of the extent of framing effects on patients and outcomes is limited by small numbers of relatively small studies [43]. Patients respond very differently depending on how data about benefits of therapy are framed. Hypertensive patients only rarely would have refused hypertensive therapy when information about efficacy was presented as relative risk reduction, but refusal rose to 23% (1 in 4) for absolute risk reduction, 32% (1 in 3) for number needed to treat, and 56% (6 in 10) with information presented as patient-specific probability of benefit [44]. The choice between having surgery or a cast for a fracture [45], or different types of surgery [46], is Table 1 Risk frequency and various verbal descriptors Frequency range (1 in) EU descriptors Calman verbal scale 1–9 Very common 10–99 Common High 100–999 Uncommon Moderate 1,000–9,999 Rare Low 10,000–99,999 Very rare Very low Calman descriptive scale Paling perspective scale Very high Frequent, significant High Moderate Tolerable, reasonable Low Very low 100,000–999,999 Minimal Acceptable Minimal 1,000,000–9,999,999 Negligible Insignificant, safe Negligible Data are taken from [41] and other sources. EU, European Union. Page 5 of 16 (page number not for citation purposes) Arthritis Research & Therapy Vol 10 No 1 Moore et al. influenced by framing effects of different types of data presentation, verbal renderings of outputs such as relative risk reduction, or number needed to treat. It is not only patients who respond differently to data depending on presentation or framing. A number of studies have documented the fact that relative presentation (like relative risk reduction) has a much greater influence on professionals' decision-making than absolute risk difference or number needed to treat. This is true for purchasers [47], hospital doctors [48], general practitioners [49,50] and pharmacists [51]. Although a systematic review of randomised trials supports this general finding, it also indicates that framing is susceptible to modification by other factors [52]. Pictorial representation of risk Calman and Royston [53] reviewed a number of different ways of explaining risk, including pictorial representations involving logarithmic scales, expressing results in terms of distance, or population, and the use of visual presentation. Paling [54] had already suggested a visual presentation of risk with logarithmic scales, and later expanded risk presentation with a number of different presentations into the clinical, rather than the predominantly environmental, field [55,56]. Other types of representation have been suggested, based, for instance, on number needed to treat [57], although women favoured simple bar charts for the presentation of absolute lifetime risks [58]. Figure 2 Early attempt to contextualise risk [63]. [63] Cigs, cigarettes. Page 6 of 16 (page number not for citation purposes) Other suggestions have expanded use of the scales, with some contextualising information [59], into mainly anaesthetic [37] or obstetric and gynaecological risks [60]. The utility of logarithmic scales such as the Paling scale in delivering better information about risk has been tested at least once [61]: both visual and comprehensive written information on transfusion risks improved patient knowledge to the same extent. This agrees with a systematic review, which also showed that decision aids improved patient involvement, knowledge, and realistic expectation of benefits and harms[62]. Visual risk scales have not been used extensively. Scales might be made more relevant by adding contextualising information to medical risk (Figure 2) [63]; contextualising anchors were chosen only because they seemed useful at the time, and they can be criticised for not necessarily being relevant to the specific risks arising from the intervention. Although the risks may be contextualised, the wrong context was used. It is difficult to obtain good information for all grades of risk or adverse event, with their various dimensions. Population data are available, though, on death from various causes. Serious but rare adverse events are often associated with death. Myocardial infarction, gastrointestinal bleeding, and rhabdomyolysis, for example, can be fatal or non-fatal, and the fatality rate is known. It is therefore possible to link the risk of death associated with an intervention to other, common risks that we face as individuals. Available online http://arthritis-research.com/content/10/1/R20 A series of examples follow, using a vertical form of the Paling Perspective Scale, populated with numerical and verbal descriptors of risk, together with information on the risk of death from various causes taken from US data in 2002 [27,28]. The contextualising examples include high mortality risk from heart disease (about 1 in 400 per year for US adults, although obviously skewed to older people), and death from any accident (about 1 in 2,000). Low risks include death from an automobile accident (about 1 in 20,000) or from any fall (about 1 in 70,000). Very low risks include death from firearm (about 1 in 300,000) or in a cataclysmic storm or lightning (about 1 in 3,000,000). Figure 3 Data on risk of mortality from medical interventions were taken from systematic reviews or large observational studies, and, if needed, mortality was calculated from the rate of the adverse events and the known or estimated mortality rate from that event. The examples are as follows: 1. Risk of serious skin reactions with coxibs [64]. Because these data come from adverse event reporting they almost certainly underestimate the true risk, but from these data the risks varied between 1 in 300,000 for valdecoxib, to 1 in 1,000,000 for celecoxib, and 1 in 1,700,000 for rofecoxib (Figure 3). 2. Risk of muscle adverse events of statins, including rhabdomyolysis and death from rhabdomyolysis [65]. The risk of death from rhabdomyolysis is about 1 in 300,000 a year (Figure 4). 3. Risk of cardiac adverse events, including death, associated with use of propofol anaesthesia [66]. Here the risk of death from asystole was estimated at about 1 in 70,000 (Figure 5). 4. Risk of hip fracture associated with use of proton pump inhibitor for 1 year or more in people aged over 65 years. Data from the UK General Practice Database suggesting a doubling of risk [67] are supported by evidence of an increased risk seen in Denmark [68]. The risk of death from hip fracture while using a proton pump inhibitor is 1 in 4,500 (Figure 6). 5. Risk of death from gastrointestinal bleeding with NSAID or full-dose aspirin for 2 months or longer [69]. This gave a risk of death of 1 in 1,200 (Figure 7). The presentation of risk with these methods – a common outcome of death, and the Paling Perspective Scale – requires that a body of evidence is available to allow the appropriate calculations. As the rather disparate examples in Figures 3 to 7 show, it is unusual to have a coherent set of data available for a single topic because the amount or extent of evidence is not available. A notable exception is the case of NSAIDs and coxibs, and the outcomes of gastrointestinal and cardiovascular events, which have been the subject of extensive investiga- Risk of serious skin reactions with coxibs [64]. [64] tion in both randomised trials and a retrospective metaanalysis of them, and meta-analyses of substantial numbers of observation studies examining the use of NSAIDs and coxibs in the community. Death from gastrointestinal and cardiovascular events with NSAIDs and coxibs Systematic reviews and meta-analyses of observational studies published since 2000 reporting either upper gastrointestinal bleeding or cardiovascular events with particular NSAIDs and/or coxibs were used for relative risk estimates. For upper gastrointestinal bleeding, we also used individual observational studies published since 2000, because searching uncovered only a single systematic review [6], which was devoid of information on coxibs. The search strategy avoided meta-analyses of randomised trials, because many of the data in those came from trials with higher than licensed doses of coxibs, and maximum daily doses of NSAIDs. This does not reflect clinical practice, in which guidance is to use the lowest dose possible for the Page 7 of 16 (page number not for citation purposes) Arthritis Research & Therapy Vol 10 No 1 Moore et al. Figure 4 Figure 5 Risk of [65] statins myopathy, rhabdomyolysis and death from rhabdomyolysis with statins [65]. Risk of cardiac propofol anaesthesia adverse [66] events, including death, associated with use of propofol anaesthesia [66]. shortest possible time. By contrast, observational studies reflect actual clinical practice, including dose, more accurately, and also have the benefit of being larger, with many more events. Data on event rates for individual NSAIDs and coxibs Table 2 summarises the main findings. One systematic review and meta-analysis of upper gastrointestinal bleeding [6] collected information from observational studies of NSAIDs in the 1990s but was devoid of coxib data. Data on coxibs and additional NSAIDs were available in four individual studies published subsequently [5,7,70,71]. Estimates of relative risk were generally in good agreement. The influence of duration of use was uncertain; one individual study found higher risk with short-term versus long-term use [5], although no relationship between increased event rate and duration was evident in a systematic review [6]. We also sought studies that would provide information on background rates of upper gastrointestinal bleeding or cardiovascular events in the absence of use of NSAIDs or coxibs, initially from studies in the original search, but supplemented with additional searches and the use of bibliographies. In addition, we required information on the likely mortality rate for upper gastrointestinal bleeding and cardiovascular events to provide a suitable and consistent context. The background rate of events, the relative risk with NSAID or coxib, and the probability of dying could then be used to calculate the additional risk of death from gastrointestinal and cardiovascular events associated with the use of particular NSAIDs and coxibs. Two systematic reviews provided essentially identical estimates of relative risk for cardiovascular events [4,8] (Table 2). One further systematic review [72] was without pooled estimates for individual drugs. We used figures for relative risk of upper gastrointestinal bleeding from the meta-analysis for NSAIDs, and an average figure from observational studies for coxibs. We used relative Page 8 of 16 (page number not for citation purposes) Available online http://arthritis-research.com/content/10/1/R20 Figure 6 Figure 7 Risk of hip fracture associated with proton pump inhibitor [67]. [67] Use for 1 year or more in people aged over 65 years. Risk of [68] aspirin death from gastrointestinal bleeding with NSAID or full-dose aspirin [68]. Use for 2 months or longer. risks for cardiovascular events from the meta-analysis with the largest body of data [4]. Results of both systematic reviews were broadly in line with a pooled analysis of cardiovascular events in randomised trials [3], namely a significant difference between coxibs and placebo in trials of colorectal polyps (but not dementia or arthritis trials, in which background event rates are higher), and an increase with doses of rofecoxib above 25 mg a day. As regards non-users of NSAIDs, Mamdani and colleagues [74] reported a rate of myocardial infarction of 8.2 per 1,000 person years. This is in line with reports of the incidence of acute myocardial infarction without including pre-admission deaths from Holland [75] and England [76]. Background rates of events without NSAID or coxib The main patient-specific influences on the background incidence of both gastrointestinal bleeding and myocardial infarction are age and sex. For serious upper gastrointestinal bleeding or perforation in non-users of NSAIDs, a systematic review of epidemiological studies [73] suggests a rate of 1 in 1,000 persons a year, although at age 60 years a higher rate of about 2 or 3 per 1,000 would apply, similar to that of a large survey in Spain [71]. A cohort study in Canada [7] showed matched nonusers (mean age 75 years) to have a rate of 2.2 per 1,000. We used background rates of 2.2 per 1,000 for gastrointestinal bleed and 8.2 per 1,000 for myocardial infarction as being typical of non-users of NSAIDs or coxibs selected as controls in large observational studies. Mortality from upper gastrointestinal bleeding and cardiovascular events Gastrointestinal bleeding carries a risk of death of about 6% according to a large, recent, Spanish observational study with most patients aged over 60 years [77], up to 14% in a recent Dutch study [78], and in the range of 6 to 12% in a meta-analysis combining randomised trials and observational studies [69]. Page 9 of 16 (page number not for citation purposes) Arthritis Research & Therapy Vol 10 No 1 Moore et al. Table 2 Relative risk (95% confidence interval) for serious upper gastrointestinal bleed or myocardial infarction Information source Relative risk compared with non-use of coxib or NSAID Ibuprofen Naproxen Diclofenac All NSAIDs Upper GI bleed [6] 1.9 (1.6–2.2) 4.0 (3.5–4.6) 3.3 (2.8–3.9) 4.2 (3.9–4.6) Upper GI bleed [5] 1.7 (1.1–2.5) 9.1 (6.0–14) 4.9 (3.3–7.1) Celecoxib Rofecoxib Hospital admission [7] 4.0 (2.3–6.9) 1.0 (0.7–1.6) 1.9 (1.3–2.8) Upper GI bleed [70] 3.3 (2.4–4.4) 1.3 (0.7–2.8) 2.1 (1.2–3.5) Upper GI bleed [71] 4.1 (3.1–5.3) 7.3 (4.7–11.4) 3.1 (2.3–4.2) 5.3 (4.5–6.2) 1.0 (0.4–2.1) 2.1 (1.1–4.0) CV events [4] 1.07 (1.02–1.12) 0.98 (0.92–1.05) 1.44 (1.32–1.56) 1.09 (1.06–1.13) 0.96 (0.90–1.02) 1.26 (1.17–1.36) CV events [8] 1.07 (0.97–1.18) 0.97 (0.87–1.07) 1.40 (1.16–1.70) 1.10 (1.00–1.21) 1.06 (0.91–1.23) 1.35 (1.15–1.59) Results for NSAIDs and coxibs were compared with non-use, from observational studies. These did not, or were unable to, produce dose-specific results. Bold lines represent relative risks or equivalent from systematic reviews and meta-analyses. Coxib, cyclooxygenase-2 inhibitor; NSAID, non-steroidal anti-inflammatory drug; GI = gastrointestinal; CV = cardiovascular. About 1 in 3 people who have a heart attack die before they reach hospital [79,80]. Mortality within 30 days of a hospital admission with myocardial infarction was 11% in a recent Danish study of people aged 30 to 74 years [81]. However, sudden cardiac death rate before hospital admission is higher than this, with overall 28-day mortality, including sudden cardiac death outside hospital, of about 40% [76]. In Finland the 28-day case mortality rate for men was 34% and for women it was 20% [82]. To estimate mortality for risk calculations we chose to use rounded estimates of 10% mortality for gastrointestinal bleeding and 30% for myocardial infarction. Calculating competing risks Table 3 shows calculations of risk for individual NSAIDs and coxibs compared with non-use, using the background rates of 2.2 per 1,000 for gastrointestinal bleed and 8.2 per 1,000 for myocardial infarction [4,15]. It provides an indication of the Table 3 Additional gastrointestinal bleeding events and myocardial infarction associated with using NSAIDs and coxibs Event and drug Relative risk Additional events per 1,000 Additional deaths per 1,000 Frequency (1 in) Gastrointestinal bleeding (background rate 2.2 per 1,000) Ibuprofen 1.9 1.98 0.20 5,051 Naproxen 4.0 6.60 0.66 1,515 Diclofenac 3.3 5.06 0.51 1,976 All NSAIDs 4.2 7.04 0.70 1,420 Celecoxib 1.1 0.22 0.02 45,455 Rofecoxib 2.0 2.20 0.22 4,545 Myocardial infarction (background rate 8.2 per 1,000) Ibuprofen 1.07 0.57 0.17 5,807 Naproxen 0.98 -0.16 -0.05 -20,325 Diclofenac 1.44 3.61 1.08 924 All NSAIDs 1.09 0.74 0.22 4,517 Celecoxib 0.96 -0.33 -0.10 -10,163 Rofecoxib 1.26 2.13 0.64 1,563 Any dose of drug was allowed in the data, and the table additionally shows the rate and frequency of additional events. The calculations used a mortality rate of 10% for gastrointestinal bleeding and 30% for cardiovascular events. NSAID, non-steroidal anti-inflammatory drug; coxib, cyclooxygenase-2 inhibitor. Page 10 of 16 (page number not for citation purposes) Available online http://arthritis-research.com/content/10/1/R20 Figure 8 Figure 9 Additionalevent vascular risk of with dying ibuprofen from an upper gastrointestinal bleed or cardiovascular event with ibuprofen. GI, gastrointestinal. Additional vascular event risk of with dying naproxen from an upper gastrointestinal bleed or cardiovascular event with naproxen. For representational purposes an additional risk of 1 in about 100,000 was assumed where there was no numerically increased cardiovascular risk. GI, gastrointestinal. likely risks for an average patient. The calculations were for additional number of events, the likely number of additional deaths, and the frequency of those deaths. For example, for gastrointestinal bleeding with a background rate of 2.2 bleeds per 1,000 patients per year, use of ibuprofen would result in 1.98 extra bleeds (calculated as (2.2 × 1.9) -2.2, or 4.18 -2.2, or 1.98). With a death rate of 10%, this would mean 0.2 additional deaths per 1,000 per year, at a frequency of 1 in 5,051 (calculated as 1,000 ÷ (1.98 ÷ 10)). Results for other drugs or outcomes were derived similarly. Where there was no significant difference between use of NSAID or coxib and non-use, a risk frequency of 1 in 100,000 was assumed. Presenting contextualised risks Figures 8 to 10 show the additional risk over background of dying with an upper gastrointestinal bleed or cardiovascular event for users of ibuprofen, naproxen and diclofenac, respectively. Figures 11 and 12 show the same information calculated for celecoxib and rofecoxib. In these representations, the events have been described as gastrointestinal bleeding or heart attack, for simplicity, and to be less technical to facilitate possible use with patients rather than professionals. The figures show that additional risks can vary from moderate (gastrointestinal bleeding with naproxen and cardiovascular risk with diclofenac) through to very low or negligible (gastrointestinal bleeding with celecoxib and cardiovascular risk with naproxen and celecoxib). There are considerable differences between the five drugs. An alternative version of the scale (Figure 13) presents the five drugs, together with all NSAIDs combined, on a single, horizontal, version. This might allow easier comparison, both between drugs and with some acceptable level of risk provided by contextualising information. Page 11 of 16 (page number not for citation purposes) Arthritis Research & Therapy Vol 10 No 1 Moore et al. Figure 10 Figure 11 Additionalevent vascular risk of with dying diclofenac from an upper gastrointestinal bleed or cardiovascular event with diclofenac. GI, gastrointestinal. Additionalevent vascular risk of with dying celecoxib from an upper gastrointestinal bleed or cardiovascular event with celecoxib. For representational purposes an additional risk of 1 in about 100,000 was assumed where there was no numerically increased risk, here for either risk. GI, gastrointestinal. GI, gastrointestinal. Discussion It is important to recognise that the method of presenting risk outlined in this paper is only one way in which the relative consequences of treatment might be shown. Whether the method is useful to patients or professionals in some of the contexts shown is not known, and we stress that it still has to be evaluated. The value of the method is also dependent on the quality and quantity of evidence about risk in any given situation. That said, patient-led healthcare means that patients need to be supported in making choices about, and taking control of, their health and healthcare. Not only must services evolve to provide personalised care by listening and responding to patients, but information also needs to be provided to them to help in decision-making. Patients react adversely to hypothetical risk [83], and providing information about a rare but serious risk of treatment may lead them to make different judgements. When asked, patients want to know about even rare risks of adverse events [17]. Page 12 of 16 (page number not for citation purposes) Most adverse events are mild, reversible and predictable, although common. They pose some prospect of discomfort and may lead to drug discontinuation if they cannot be tolerated, but they are not dangerous. More problematic are those adverse events that are serious, irreversible and unpredictable. They will be rare because no drug could be marketed if these adverse events were also common. It is these rare but serious events that attract attention. Paradoxically, more effective and widely used medicines are more likely to attract pressure for bans based on adverse events [84]. This is because with only a few hundred or a few thousand people using a drug, a rare but serious adverse event at the 1 in 100,000 level would never attract attention. By contrast, use in 2 million people would result in 20 events that could well attract attention. Where a medical intervention is performed for major life-saving or life-enhancing purposes (such as cardiac revascularisation or joint replacement), possible adverse events are offset by Available online http://arthritis-research.com/content/10/1/R20 Figure 12 Figure 13 An alternative version of the Paling Perspective Scale Scale. It puts the five drugs from Figures 8 to 12 together with all NSAIDs combined, on a single, horizontal, version. GI, gastrointestinal; NSAID, non-steroidal anti-inflammatory drug; coxib, cyclooxygenase-2 inhibitor. Additionalevent vascular risk of with dying rofecoxib from an upper gastrointestinal bleed or cardiovascular event with rofecoxib. GI, gastrointestinal. significant, important and largely immediate benefit; only major adverse events, such as mortality, are likely to form a part – and perhaps only a small part – of decision-making. By contrast, where an intervention delivers less immediate benefits or where there are alternative therapies available, the risk of avoidable adverse events becomes a more significant part of decision-making. Herein lies the problem. Rare risks of major, irreversible, consequences are by their nature difficult to measure precisely. To this uncertainty must be added the uncertainty of how information on the risk can be presented in a way that is understood. This is especially true when there is a background rate in the population, which we must know or guess, and we then have to apply an imprecise relative risk, to make judgements about the severity of different outcomes. It all makes for complex mental arithmetic, and a representation of the additional risk faced compared with other risks we assume in life has obvious benefits, especially when the event is common to all. Figures 3 to 7 present a series of risks of death associated with treatments in the range (roughly) of 1 in 1,000,000 to 1 in 1,000, all of which would be regarded are rare. The information about life events regarded as rare allows that to be interpreted and judged, and to provide a context in which individual decisions can be made. Any judgement will depend not just on the level of risk but also on the benefits. The fact that a rare death from a cutaneous adverse event from valdecoxib (Figure 3) is judged differently from a similar risk of death from rhabdomyolysis from a statin (Figure 4) is not necessarily inconsistent. There are few easy cases when it is possible to say that a proposed therapy is universally effective or safe, and especially both effective and safe. Most situations are complex, and none apparently more so than that of choice of NSAID or coxib for chronic pain. The examples here have considered only additional risk of death from gastrointestinal bleeding or cardiovascular events, compared with different background rates without drug therapy. Other levels of risk could have been chosen, including non-fatal outcomes. Moreover, we have deliberately ignored renovascular events, congestive heart failure, lower bowel problems, anaemia, hypertension and other adverse events, more and less severe, that might have been included, especially from individual patient meta-analysis of randomised trials [85]. In any therapeutic area there are competing risks and benefits of alternative therapeutic interventions. This paper explores ways in which risk of just two possible adverse events can be displayed for several NSAIDs and coxibs that display numerically quite different risks from each other. We have no evidence about how best to convey these to patients in a way Page 13 of 16 (page number not for citation purposes) Arthritis Research & Therapy Vol 10 No 1 Moore et al. that will be fully comprehended, nor have we the evidence to personalise risk presentation for the individual, so we have to rely on average results. This is an important omission, because consequences of treatment are likely to differ for individual patients, and this now has theoretical underpinning with regard to coxibs [86]. There are other ways in which risk may be presented. A large observational study of more than 500,000 over-65s in Canada [87] examined both myocardial infarction and gastrointestinal bleeding to produce a combined estimate of risk. It used a different method, but for individual drugs and for patients taking or not taking low-dose aspirin. Alternatively, data from metaanalyses of randomised trials have been used to present annualised risk estimates for placebo, pooled NSAIDs, and coxibs [88]. Attitudes of individuals presented with information about possible risks and benefits of treatments will differ as they see the possible consequences for themselves differently. The product of information presented, their own experience, and emotional factors results in widely differing choices between individuals [89,90]. All communicated facts will finally be filtered by emotions before a decision is made. We have to acknowledge that there is a danger of focusing more on how to calculate and present numerical conclusions about risk, while ignoring our ignorance of other aspects of decision-making. There are a number of possible next steps. Contextualised risk presentations such as these need to be refined. It may well be that other forms of presentation, or different contextualising risks, would make them clearer and more relevant for professionals and patients. Risk presentation methods are likely to have different degrees of success with people of different backgrounds, languages and cultures. We might consider whether it is possible to develop risk presentations with greater utility for physicians. An example is the Joint British Societies coronary risk prediction charts found in every copy of the British National Formulary. Conclusion We suggest one way of communicating information about the risk of rare adverse events that can result in death, by combining words, numbers, pictures and context. The area of risk communication requires significantly more research because the communication of risk has a limited knowledge base, irrespective of whether it is common or rare, serious or inconsequential. ties and government sources at various times. RAM is the guarantor. JP earns his living from teaching about and consulting on risk communication with doctors, healthcare organisations and pharmaceutical companies. As part of his services, JP offers special visual aid formats for licensing by commercial organisations. However, free web-based programs enable unrestricted access to all parties to build and print customised versions of JP's main decision aids for non-commercial purposes such as all individual doctor-patient communications and for trial and evaluation (see http://www.riskcomm.com/ introvisualaids.html). No author has any direct stock holding in any pharmaceutical company. Authors' contributions RAM was involved with the original concept, planning the study, searching, analysis and preparing a manuscript. SD and HJM were involved with planning, data extraction, and writing. JP was involved with planning, writing and visual aids formats to explain risks. All authors read and approved the final manuscript. Acknowledgements Pain Research is supported in part by the Oxford Pain Research Trust, and this work was also supported by an unrestricted educational grant from Pfizer Ltd. Neither organisation had any role in the design, planning or execution of the study, or in writing the manuscript. The terms of the financial support from Pfizer included freedom for authors to reach their own conclusions, and an absolute right to publish the results of their research, irrespective of any conclusions reached. Pfizer did have the right to view the final manuscript before publication, and did so. The use of Paling Perspective Scale for purposes beyond use or dissemination of this article are subject to copyright; see http://www.riskcomm.com. These decision aids are made freely available for authors in all academic publications provided that the Risk Communication Institute's copyright is always legibly shown on each graphic. With permission of the Risk Communication Institute http://www.riskcomm.com. References 1. 2. 3. 4. 5. 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Prevalence of Arcobacter and Other Pathogenic Bacteria in River Water in Nepal
Water
2,019
cc-by
5,557
Received: 11 June 2019; Accepted: 8 July 2019; Published: 10 July 2019 Abstract: This study aims to determine the diversity of pathogenic bacteria in the Bagmati River, Nepal, during a one-year period. A total of 18 river water samples were collected from three sites (n = 6 per site) along the river. Bacterial DNA, which were extracted from the water samples, were analyzed for bacterial 16S rRNA genes by next-generation sequencing for 13 of 18 samples, and by quantitative PCR targeting Arcobacter for all 18 samples. The 16S rRNA sequencing identified an average of 97,412 ± 35,909 sequences/sample, which were then categorized into 28 phyla, 61 classes, and 709 bacterial genera. Eighteen (16%) genera of 111 potential pathogenic bacteria were detected with abundance ratios of >1%; Arcobacter, Acinetobacter, and Prevotella were the dominant genera. The Arcobacter abundance ratios were 28.6% (n = 1), 31.3 ± 15.8% (n = 6), and 31.8 ± 17.2% (n = 6) at the upstream, midstream, and downstream sites, respectively. Arcobacter was detected in 14 (78%) of 18 samples tested, with concentrations ranging from 6.7 to 10.7 log10 copies/100 mL, based on quantitative PCR. Our results demonstrate the poor bacterial quality of the Bagmati River water, suggesting a need for implementing more measures to reduce fecal contamination in the river water. Keywords: Arcobacter; next-generation sequencing; pathogenic bacteria; quantitative PCR; river water Prevalence of Arcobacter and Other Pathogenic Bacteria in River Water in Nepal Rajani Ghaju Shrestha 1 , Sarmila Tandukar 2 , Dinesh Bhandari 3,4 , Samendra P. Sherchan 5, Yasuhiro Tanaka 6, Jeevan B. Sherchand 3 and Eiji Haramoto 1,* Rajani Ghaju Shrestha 1 , Sarmila Tandukar 2 , Dinesh Bhandari 3,4 , Samendra P. Shercha Yasuhiro Tanaka 6, Jeevan B. Sherchand 3 and Eiji Haramoto 1,* 1 Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan 2 Department of Natural, Natural, Biotic and Social Environment Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan 2 Department of Natural, Natural, Biotic and Social Environment Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan 3 Institute of Medicine, Tribhuvan University, Maharajgunj, Kathmandu 1524, Nepal 4 School of Public Health, The University of Adelaide, Adelaide, South Australia 5005, Australia 5 Department of Global Environmental Health Sciences, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, USA 3 Institute of Medicine, Tribhuvan University, Maharajgunj, Kathmandu 1524, Nepal 4 School of Public Health, The University of Adelaide, Adelaide, South Australia 5005, Australia 5 Department of Global Environmental Health Sciences, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, USA 6 Department of Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan * Correspondence: eharamoto@yamanashi.ac.jp; Tel.: +81-55-220-8725 Water 2019, 11, 1416; doi:10.3390/w11071416 water water water water www.mdpi.com/journal/water 1. Introduction Industrial pollution load, poor sewage and wastewater treatment facilities, inadequate water pollution control laws, and rapid urbanization have all contributed to the increased degradation of the river water environment in developing countries [1,2]. The Bagmati River, which flows from the northern boundary southwards across the urban areas of the Kathmandu Valley in Nepal, is suffering from chemical, biological, and solid waste pollution [1,3–9]. Arcobacter, which is widely recognized as an emerging waterborne and foodborne pathogen [10–12], has been detected in river water samples in Japan, Nepal, and Spain [4,13–16]. Arcobacter in river water samples has been linked to fecal contamination from animal or human sources [11,13]. In Nepal, only a few studies using next-generation sequencing (NGS) and quantitative PCR (qPCR) have detected Arcobacter in the river and groundwater samples [4,14]. The abundance ratios and concentrations of Arcobacter were highest in river water samples in these studies [4,14]. NGS has been a useful tool in Water 2019, 11, 1416; doi:10.3390/w11071416 www.mdpi.com/journal/water Water 2019, 11, 1416 Water 2019, 11, x FOR 2 of 9 2 of 8 d obtaining large numbers of sequences to determine microbial diversity and community structure, as explained in a previous study that was conducted by Caporaso et al. (2012) [17]. community structure, as explained in a previous study that was conducted by Caporaso et al. (2012) [17]. A study that was conducted in three sites of the Bagmati River (Sundarijal (upstream) A study that was conducted in three sites of the Bagmati River (Sundarijal (upstream), Thapathali (midstream), and Chovar (downstream)) reported that the microbiological quality of the river water upstream was less degraded when compared to those at the other two sites [9]. Indicator bacteria, potential index viruses, and human-fecal markers were more frequently detected than protozoa and human enteric viruses at all three Bagmati River sites. However, it is essential to also understand the bacterial community of river water at these sites. Therefore, this study aimed to determine the bacterial diversity and quantify Arcobacter at three Bagmati River sites. A study that was conducted in three sites of the Bagmati River (Sundarijal (upstream), Thapathali (midstream), and Chovar (downstream)) reported that the microbiological quality of the river water upstream was less degraded when compared to those at the other two sites [9]. Indicator bacteria, potential index viruses, and human-fecal markers were more frequently detected than protozoa and human enteric viruses at all three Bagmati River sites. 2.1. Collection of River Water Samples and Extraction of Bacterial DNA 2.1. Collection of River Water Samples and Extraction of Bacterial DNA As previously described [9], the Bagmati River water samples were collected every two months from the upstream, midstream, and downstream regions during a one-year period between November 2015 and September 2016, as shown in Figure 1. The sampling sites were selected based on population density in three regions of the Bagmati River basin, where the population density is lower in the upstream region when compared to the midstream and downstream regions, and also to observe the difference in bacterial community in start and end point of the Bagmati River flowing through the urban area of the Kathmandu Valley. The water samples were collected in 100-mL sterile plastic bottles and transported to the laboratory in dry ice, kept at 4 ◦C, and then processed within 4 h. As previously described [9], the Bagmati River water samples were collected every two months from the upstream, midstream, and downstream regions during a one-year period between November 2015 and September 2016, as shown in Figure 1. The sampling sites were selected based on population density in three regions of the Bagmati River basin, where the population density is lower in the upstream region when compared to the midstream and downstream regions, and also to observe the difference in bacterial community in start and end point of the Bagmati River flowing through the urban area of the Kathmandu Valley. The water samples were collected in 100-mL sterile plastic bottles and transported to the laboratory in dry ice, kept at 4 °C, and then processed within 4 h Figure 1. Map of the Kathmandu Valley showing three sampling sites. Figure 1. Map of the Kathmandu Valley showing three sampling sites. Figure 1. Map of the Kathmandu Valley showing three sampling sites. Figure 1. Map of the Kathmandu Valley showing three sampling sites. Ten milliliters of the river water samples were filtered through a 0.22-µm filter paper, which was used to extract the bacterial DNA using CicaGeneus DNA Extraction Reagent (Kanto Chemical, Tokyo, Japan). Briefly, the membrane filter containing the microorganisms was resuspended in 5 mL of Tris-EDTA buffer (pH 7.4) into a 50 mL plastic tube. Bacterial DNA was extracted from the mixture Ten milliliters of the river water samples were filtered through a 0.22-µm filter paper, which was used to extract the bacterial DNA using CicaGeneus DNA Extraction Reagent (Kanto Chemical, Tokyo, Japan). 1. Introduction However, it is essential to also understand the bacterial community of river water at these sites. Therefore, this study aimed to determine the bacterial diversity and quantify Arcobacter at three Bagmati River sites. 2.3. Quantification of Total Bacteria and Arcobacter Total bacterial 16S rRNA genes were quantified by qPCR while using the 515F and U806R primers [19,20]. The qPCR mixture components were as follows: 2.0 µL of template DNA, 0.1 µL of 50 pmol/µL each of the forward and reverse primers, and 12.5 µL of SYBR Premix Ex TaqII (Tli RNaseH Plus) (Takara Bio, Otsu, Japan), with a final volume of 25.0 µL. The thermal cycling conditions were at 95 ◦C for 30 s, followed by 35 cycles at 94 ◦C for 15 s, 55 ◦C for 30 s, and 72 ◦C for 20 s, as previously described [4]. Arcobacter spp. were quantified by SYBR Green-based qPCR using a reaction volume of 25 µL containing 2.0 µL of template DNA, 12.5 µL of a MightyAmp for Real Time (SYBR Plus) (Takara Bio), 0.1 µL of 50 pmol/µL each of Arco-F and Arco-R-rev primers [14]. The thermal conditions were as follows: at 98 ◦C for 2 min, followed by 35 cycles at 98 ◦C for 10 s, at 55 ◦C for 30 s, and at 68 ◦C for 40 s, and finally at 95 ◦C for 15 s, at 60 ◦C for 30 s, and at 95 ◦C for 15 s to identify a specific single peak melting temperature (Tm) [14]. 2.4. Statistical Analysis The Pearson’s correlation coefficient test was performed with Microsoft Excel 2016 (Microsoft Corporation, Redmond, WA, USA) to determine the relationship of Arcobacter with fecal indicator bacteria, human-fecal markers, and index viruses [9]. Differences were considered to be statistically significant if the resulting p value was <0.05. 2.1. Collection of River Water Samples and Extraction of Bacterial DNA 2.1. Collection of River Water Samples and Extraction of Bacterial DNA Briefly, the membrane filter containing the microorganisms was resuspended in 5 mL of Tris-EDTA buffer (pH 7.4) into a 50 mL plastic tube. Bacterial DNA was extracted from the mixture Water 2019, 11, 1416 3 of 9 using the CicaGeneus DNA extraction kit after shaking and vortex mixing at 50 ◦C with a speed of 300 rpm (Kanto Chemical). Bacterial DNA that were extracted from the river water samples were used both in a study that was conducted by Tandukar, et al., in 2018 as well as in this study [9]. 2.2. NGS for the Characterization of Bacterial Communities Of the 18 samples collected, 13 samples, excluding five of six samples from Sundarijal in which bacterial DNA concentrations were not enough high, were subjected to metagenomics sequencing using a MiSeq gene sequencer (Illumina, San Diego, CA, USA) as previously described [18]. Briefly, the 16S rRNA library was prepared, and the sequence data were analyzed after purification, amplification, library quantification, normalization, and pooling. Operational taxonomic units were analyzed at the bacterial domain, phylum, family, and genus levels. A genus was considered to be a potentially pathogenic bacterium if any one species of the genus was categorized as biosafety level 2 or 3 by the American Biological Safety Association (https://my.absa.org/tiki-index.php?page=Riskgroups), as previously described [4]. The raw sequences were registered in the National Center for Biotechnology Information (NCBI) Sequence Read Archive under the accession number PRJNA547952. 3.1. Characterization of Bacterial Community by NGS At Sundarijal, Thapathali, and Chovar, the abundance ratios of Acinetobacter were 10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected at abundance ratios of 5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Thapathali, and Chovar, respectively. At Sundarijal, Thapathali, and Chovar, the abundance ratios of Acinetobacter were 10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected at abundance ratios of 5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Figure 2. Distribution of bacterial phyla. i b f b l l 0 20 40 60 80 100 May 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Sundarijal Thapathali Chovar Abundance (%) Actinobacteria Bacteroidetes Firmicutes Proteobacteria Fusobacteria Others 0 20 40 60 80 100 May 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Sundarijal Thapathali Chovar Abundance (%) Bacteroidia Betaproteobacteria Clostridia Epsilonproteobacteria Gammaproteobacteria Flavobacteriia Others Figure 2. Distribution of bacterial phyla. Figure 2. Distribution of bacterial phyla. Figure 3. Distribution of bacterial classes. 0 20 40 60 80 100 May 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Sundarijal Thapathali Chovar Abundance (%) Actinobacteria Bacteroidetes Firmicutes Proteobacteria Fusobacteria Others 0 20 40 60 80 100 May 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Sundarijal Thapathali Chovar Abundance (%) Bacteroidia Betaproteobacteria Clostridia Epsilonproteobacteria Gammaproteobacteria Flavobacteriia Others Figure 3. Distribution of bacterial classes. Figure 2. Distribution of bacterial phyla. 0 20 40 60 80 100 May 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Sundarijal Thapathali Chovar Abundance (%) Bacteroidia Betaproteobacteria Clostridia Epsilonproteobacteria Gammaproteobacteria Flavobacteriia Others Figure 2. Distribution of bacterial phyla. Figure 3. Distribution of bacterial classes. 0 20 40 60 80 100 May 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Sundarijal Thapathali Chovar Abundance (%) Bacteroidia Betaproteobacteria Clostridia Epsilonproteobacteria Gammaproteobacteria Flavobacteriia Others Figure 3. Distribution of bacterial classes. 3.1. Characterization of Bacterial Community by NGS Thirteen water samples that were collected from three Bagmati River sites were subjected to the Illumina MiSeq sequencing, where the average number of 16S rRNA gene sequences obtained was 97,412 ± 35,909 per sample. As shown in Figure 2, among the 28 phyla identified, Proteobacteria (59–80%) was the most dominant in all of the samples, followed by Bacteroidetes (10–25%) and Firmicutes (6–15%). Epsilonproteobacteria (29–57%) was dominant in nine river water samples among the 61 classes that were detected, whereas Betaproteobacteria (27–32%) was dominant in four river water samples, as shown in Figure 3. The abundance ratios of classes Gammaproteobacteria and Bacteroidia in all of the samples tested ranged from 6–24% and 5–15%, respectively. Of the 111 potential pathogenic bacteria identified, 18 genera were detected at abundance ratios of >1% in at least one of the 13 samples tested, as summarized in Table 1. Arcobacter was the most dominant genus at all three sites, with abundance ratios of 28.6% (n = 1), 31.3 ± 15.8% (n = 6), and 31.8 ± 17.2% (n = 6) at Sundarijal, Thapathali, and 4 of 9 4 of 8 4 of 8 Water 2019, 11, 1416 Water 2019 11 x FOR Water 2019, 11, x FOR Chovar, respectively. At Sundarijal, Thapathali, and Chovar, the abundance ratios of Acinetobacter were 10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected at abundance ratios of 5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Thapathali, and Chovar, respectively. At Sundarijal, Thapathali, and Chovar, the abundance ratios of Acinetobacter were 10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected at abundance ratios of 5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Thapathali, and Chovar, respectively. At Sundarijal, Thapathali, and Chovar, the abundance ratios of Acinetobacter were 10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected at abundance ratios of 5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Chovar, respectively. At Sundarijal, Thapathali, and Chovar, the abundance ratios of Acinetobacter were 10.3%, 5.3 ± 5.3%, and 5.0 ± 3.9%, respectively, whereas Prevotella was detected at abundance ratios of 5.9%, 6.8 ± 2.4%, and 4.6 ± 1.5%, respectively. Thapathali, and Chovar, respectively. 3.1. Characterization of Bacterial Community by NGS Thapathali Figure 3 Distribution of bacterial classes Figure 3. Distribution of bacterial classes. 5 of 9 Water 2019, 11, 1416 Table 1. Abundance ratios of potential pathogenic bacteria. Table 1. Abundance ratios of potential pathogenic bacteria. Table 1. Abundance ratios of potential pathogenic bacteria. Genus Abundance Ratio (%) Sundarijal (n = 1) Thapathali (n = 6) Chovar (n = 6) Acidovorax 2.2 1.0 ± 0.8 1.1 ± 0.6 Acinetobacter 10.3 5.3 ± 5.3 5.0 ± 3.9 Arcobacter 28.6 31.3 ± 15.8 31.8 ± 17.2 Bacteroides 1.7 2.6 ± 0.9 2.3 ± 1.1 Blautia 0.4 0.8 ± 0.4 0.7 ± 0.6 Burkholderia 0.3 0.5 ± 0.6 0.5 ± 0.2 Chromobacterium 0.4 0.4 ± 0.3 0.6 ± 0.5 Chryseobacterium 1.4 0.9 ± 0.6 1.5 ± 1.0 Clostridium 0.3 0.7 ± 0.2 0.7 ± 0.3 Comamonas 2.1 1.1 ± 1.4 1.0 ± 0.7 Escherichia 1.1 0.4 ± 0.2 0.3 ± 0.1 Flavobacterium 4.7 3.0 ± 4.3 3.4 ± 3.9 Mycobacterium 0.1 0.2 ± 0.1 0.4 ± 0.8 Parabacteroides 0.4 0.8 ± 0.7 1.1 ± 0.9 Plesiomonas 2.2 1.2 ± 0.6 1.5 ± 0.7 Prevotella 5.9 6.8 ± 2.4 4.6 ± 1.5 Pseudomonas 1.6 1.6 ± 0.9 1.8 ± 1.0 Sphingobacterium 1.9 0.1 ± 0.0 0.2 ± 0.1 3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples Water 2019, 11, x FOR PEER REVIEW Chryseobacterium 1.4 0.9 ± 0.6 1.5 Clostridium 0.3 0.7 ± 0.2 0.7 Comamonas 2.1 1.1 ± 1.4 1.0 Escherichia 1.1 0.4 ± 0.2 0.3 Flavobacterium 4.7 3.0 ± 4.3 3.4 Mycobacterium 0.1 0.2 ± 0.1 0.4 Parabacteroides 0.4 0.8 ± 0.7 1.1 Plesiomonas 2.2 1.2 ± 0.6 1.5 Prevotella 5.9 6.8 ± 2.4 4.6 Pseudomonas 1.6 1.6 ± 0.9 1.8 Sphingobacterium 1.9 0.1 ± 0.0 0.2 3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples 3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples 3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples 3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples 3.2. Occurrence of Total Bacteria and Arcobacter in River Water Samples As shown in Figure 4, the total bacteria and Arcobacter levels in six river water samples each from Sundarijal, Thapathali, and Chovar were quantified using qPCR. The minimum and maximum concentrations of total bacteria at the three sites were 7.1 and 10.5 log10 copies/100 mL, respectively. 3.1. Characterization of Bacterial Community by NGS In Sundarijal, Thapathali, and Chovar, Arcobacter was detected in two (33%), six (100%), and six (100%) river water samples, with concentrations of 6.7–10.4, 9.0–10.4, and 8.4–10.7 log10 copies/100 mL, respectively. As shown in Figure 4, the total bacteria and Arcobacter levels in six river water samples each from Sundarijal, Thapathali, and Chovar were quantified using qPCR. The minimum and maximum concentrations of total bacteria at the three sites were 7.1 and 10.5 log10 copies/100 mL, respectively. In Sundarijal, Thapathali, and Chovar, Arcobacter was detected in two (33%), six (100%), and six (100%) river water samples, with concentrations of 6.7–10.4, 9.0–10.4, and 8.4–10.7 log10 copies/100 mL, respectively. Figure 4. Concentrations of 16S rRNA genes of total bacteria and Arcobacter. 6 8 10 12 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Nov. 2015 Jan. 2016 Mar. 2016 May 2016 July 2016 Sep. 2016 Sundarijal Thapathali Chovar log copies/100 mL Total bacteria Arcobacter Arcobacter (-) log10 copies/100 mL Figure 4. Concentrations of 16S rRNA genes of total bacteria and Arcobacter. Total bacteria Arcobacter Arcobacter Figure 4. Concentrations of 16S rRNA genes of total bacteria and Arcobacter. Figure 4. Concentrations of 16S rRNA genes of total bacteria and Arcobacter. 4 Discussion 4. Discussion 4. Discussion Diverse groups of potential pathogenic bacteria, such as Arcobacter, Acinetobacter, and Prevotella, were detected by NGS in all three regions of the Bagmati River during a one-year sampling period. In this study, the abundance ratio of the class Epsilonproteobacteria was higher than that of class Diverse groups of potential pathogenic bacteria, such as Arcobacter, Acinetobacter, and Prevotella, were detected by NGS in all three regions of the Bagmati River during a one-year sampling period. In this study, the abundance ratio of the class Epsilonproteobacteria was higher than that of class Betaproteobacteria, Water 2019, 11, 1416 6 of 9 whereas Gammaproteobacteria had the highest abundance ratio in previous studies [4,14]. This may be attributed to differences in the time and place of sample collection. Although the bacterial community in the upstream Sundarijal sample was identified, the results of sequencing of only one sample will not be enough to represent a one-year sampling period, unlike Thapathali and Chovar. Among the potential pathogenic bacterial 16S rRNA genes detected by NGS, those of Arcobacter were found in the highest abundance ratio. Comparable results have been reported in previous studies, although a limited number of river water samples were tested [4,14]. During a year of water sampling, Arcobacter was detected in all sampling months at Thapathali and Chovar. In a previous study, the highest Arcobacter concentration was found in a river water sample (9.1 log10 copies/100 mL) among the 13 Arcobacter-positive samples that were collected from shallow dug wells, deep tube wells, and a river [14]. The detection of Arcobacter in wastewater samples, irrigation water, sludge, drinking water, surface water, groundwater, and seawater [10,12] shows the bacterium’s capability to survive and multiply in water with a broad range of qualities. p y g q People living in the Kathmandu Valley are highly dependent on groundwater use [21]. However, the poor availability of the required volume of water in the valley for domestic purposes leads to the use of polluted river water for irrigation and for washing vegetables [7,22]. The indirect consumption of such polluted river water contaminated with different enteric viruses, protozoa, and bacteria may have adverse effects on human health. The polluted river water not only pollutes its surroundings, but it also contaminates any nearby groundwater. 4 Discussion 4. Discussion Chemical analysis has provided evidence for the interconnectivity between groundwater and surface water, a link that allows for the exchange of chemicals between each water source [23]. The same interconnectivity of waterborne pathogens may thus occur, which increases the risk of waterborne diseases in the Kathmandu Valley. There is evidence that the physical, chemical, and biological deterioration of water of the Bagmati River shows an alarming situation of river environment, which affects the surrounding environment. The lowest abundance ratio of Arcobacter at Sundarijal indicates that the upstream region has been less affected by anthropogenic pollution when compared to the midstream and downstream regions. This result is supported by a previous study that found lower concentrations of protozoa and human enteric viruses at Sundarijal than at Thapathali and Chovar [9]. In addition to the microbiological water quality, solid waste levels and the chemical quality of river water in the downstream region become worse as the river travels through urban areas [24,25]. The relationships of Arcobacter with fecal indicator bacteria (Escherichia coli), human-fecal markers (BK and JC polyomaviruses, and human Bacteroidales), and plant viruses (tobacco mosaic virus and pepper mild mottle virus) were determined using data from Tandukar et al. (2018) [9]. Index viruses were also included in this analysis because they have been proposed as an indicator of the prevalence of human enteric viruses in irrigation water sources in the Kathmandu Valley [7]. The Pearson’s correlation coefficient (r) values in Table 2 show the significant correlation between Arcobacter and E. coli, BK polyomaviruses, pepper mild mottle virus, and human Bacteroidales, but there was no significant correlation between Arcobacter and JC polyomaviruses and tobacco mosaic virus. The lack of correlation with the second group of viruses may be due to the difference in the properties between viruses and bacteria. The presence of Arcobacter, along with other fecal indicator bacteria, human-fecal markers, index viruses, and human enteric viruses in the river water samples, should not be neglected. Thus, the river water’s microbial quality needs to be studied more, and strict rules and regulations should be imposed in order to improve waste disposal and management in facilities impacting the river. 7 of 9 Water 2019, 11, 1416 Table 2. Relationships of fecal indicator bacteria, human-fecal markers, and index viruses with Arcobacter. Bacteria and Viruses Tested # Indicators r Value with Arcobacter Fecal indicator bacteria E. 4 Discussion 4. Discussion coli 0.86 * Human-fecal markers BK polyomaviruses 0.72 * JC polyomaviruses 0.54 Human Bacteroidales 0.93 * Index viruses Tobacco mosaic virus 0.36 Pepper mild mottle virus 0.60 * # Data from Tandukar et al. (2018) [9]; * Statistically significant (p < 0.05). 5. Conclusions In summary, of the 111 potential pathogenic bacteria that were identified by NGS, 18 (16%) had abundance ratios of >1%. Arcobacter, Acinetobacter, and Prevotella were frequently detected at the three sites of the Bagmati River. The bacterial communities in upstream, midstream, and downstream of the Bagmati River were identified with a wide range of bacteria. Using qPCR, Arcobacter was successfully detected in 14 (78%) of 18 river water samples, at concentrations of 6.7–10.7 log10 copies/100 mL. Arcobacter was detected in all of the samples that were collected from the midstream and downstream sites of the Bagmati River. The prevalence of Arcobacter, along with other presumptive bacterial pathogens in river water samples, shows poor water quality, which suggests a need to prevent further fecal contamination of the river water. Author Contributions: R.G.S. processed the samples, analyzed the results, and prepared a draft of the manuscript. S.T. and D.B. conceived the design of the study and processed the samples, S.P.S. processed the samples, Y.T. checked the analyzed results and corrected the draft of the manuscript, J.B.S. conceived the design of the study. E.H. conceived the design of the study, checked the analyzed results, and corrected the draft of the manuscript. Funding: This study was supported by Kurita Water and Environment Foundation, the Science and Technology Research Partnership for Sustainable Development (SATREPS) program of Japan International Cooperation Agency (JICA) and Japan Science and Technology Agency (JST), entitled “Hydro-microbiological Approach for Water Security in Kathmandu Valley, Nepal”, and the Japan Society for the Promotion of Science (JSPS) through Fund for the Promotion of Joint International Research (Fostering Joint International Research (B) (grant number JP18KK0297)). Acknowledgments: The authors thank Bijay Man Shakya (University of Yamanashi, Japan) for his help in map preparation. Conflicts of Interest: The authors declare no conflict of interest. 5. Haramoto, E.; Yamada, K.; Nishida, K. 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ISME J. 2012, 6, 1621–1624. [CrossRef] [PubMed] 18. References 1. Kannel, P.R.; Lee, S.; Lee, Y.-S.; Kanel, S.R.; Pelletier, G.J. Application of automated QUAL2Kw for water quality modeling and management in the Bagmati River, Nepal. Ecol. Model. 2007, 202, 503–517. [CrossRef] 2. Karn, S.K.; Harada, H. Surface water pollution in three urban territories of Nepal, India, and Bangladesh. Environ Manag 2001 28 483–496 1. Kannel, P.R.; Lee, S.; Lee, Y.-S.; Kanel, S.R.; Pelletier, G.J. Application of automated QUAL2Kw for water quality modeling and management in the Bagmati River, Nepal. Ecol. Model. 2007, 202, 503–517. [CrossRef] 2. Karn, S.K.; Harada, H. Surface water pollution in three urban territories of Nepal, India, and Bangladesh. Environ. Manag. 2001, 28, 483–496. 1. Kannel, P.R.; Lee, S.; Lee, Y.-S.; Kanel, S.R.; Pelletier, G.J. Application of automated QUAL2Kw for water quality modeling and management in the Bagmati River, Nepal. Ecol. Model. 2007, 202, 503–517. [CrossRef] 2. Karn, S.K.; Harada, H. Surface water pollution in three urban territories of Nepal, India, and Bang Environ. Manag. 2001, 28, 483–496. 3. Bhatt, M.P.; McDowell, W.H.; Gardner, K.H.; Hartmann, J. Chemistry of the heavily urbanized Bagmati River system in Kathmandu Valley, Nepal: Export of organic matter, nutrients, major ions, silica, and metals. Environ. Earth Sci. 2014, 71, 911–922. [CrossRef] 3. Bhatt, M.P.; McDowell, W.H.; Gardner, K.H.; Hartmann, J. Chemistry of the heavily urbanized Bagmati River system in Kathmandu Valley, Nepal: Export of organic matter, nutrients, major ions, silica, and metals. Environ. Earth Sci. 2014, 71, 911–922. [CrossRef] 4. Ghaju Shrestha, R.; Tanaka, Y.; Malla, B.; Bhandari, D.; Tandukar, S.; Inoue, D.; Sei, K.; Sherchand, J.B.; Haramoto, E. Next-generation sequencing identification of pathogenic bacterial genes and their relationship with fecal indicator bacteria in different water sources in the Kathmandu Valley, Nepal. Sci. 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Geol. 2007, 10, 21–32. [CrossRef] Water 2019, 11, 1416 9 of 9 24. Bajracharya, R.; Nakamura, T.; Shakya, B.M.; Kei, N.; Shrestha, S.D.; Tamrakar, N.K. Identification of river water and groundwater interaction at central part of the Kathmandu valley, Nepal using stable isotope tracers. Int. J. Adv. Sci. Tech. Res. 2018, 8, 29–41. [CrossRef] © 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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Factors Influencing Adjustment to Remote Work: Employees’ Initial Responses to the COVID-19 Pandemic
International journal of environmental research and public health/International journal of environmental research and public health
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UvA-DARE (Digital Academic Repository) Factors influencing adjustment to remote work: Employees’ initial responses to the covid-19 pandemic van Zoonen, W.; Sivunen, A.; Blomqvist, K.; Olsson, T.; Ropponen, A.; Henttonen, K.; Vartiainen, M. DOI 10.3390/ijerph18136966 Publication date 2021 Document Version Final published version Published in International Journal of Environmental Research and Public Health License CC BY Link to publication Citation for published version (APA): van Zoonen, W., Sivunen, A., Blomqvist, K., Olsson, T., Ropponen, A., Henttonen, K., & Vartiainen, M. (2021). Factors influencing adjustment to remote work: Employees’ initial responses to the covid-19 pandemic. International Journal of Environmental Research and Public Health, 18(13), Article 6966. https://doi.org/10.3390/ijerph18136966 UvA-DARE (Digital Academic Repository) Factors influencing adjustment to remote work: Employees’ initial responses to the covid-19 pandemic Citation for published version (APA): van Zoonen, W., Sivunen, A., Blomqvist, K., Olsson, T., Ropponen, A., Henttonen, K., & Vartiainen, M. (2021). Factors influencing adjustment to remote work: Employees’ initial responses to the covid-19 pandemic. International Journal of Environmental Research and Public Health, 18(13), Article 6966. https://doi.org/10.3390/ijerph18136966 General rights General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare uva nl) Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible.   7 Department of Industrial Engineering and Management, Aalto University, Maarintie 8, 00076 Aalto, Finland; matti.vartiainen@aalto.fi * Correspondence: w.vanzoonen@uva.nl Citation: van Zoonen, W.; Sivunen, A.; Blomqvist, K.; Olsson, T.; Ropponen, A.; Henttonen, K.; Vartiainen, M. Factors Influencing Adjustment to Remote Work: Employees’ Initial Responses to the COVID-19 Pandemic. Int. J. Environ. Res. Public Health 2021, 18, 6966. https://doi.org/10.3390/ijerph 18136966 Citation: van Zoonen, W.; Sivunen, A.; Blomqvist, K.; Olsson, T.; Ropponen, A.; Henttonen, K.; Vartiainen, M. Factors Influencing Adjustment to Remote Work: Employees’ Initial Responses to the COVID-19 Pandemic. Int. J. Environ. Res. Public Health 2021, 18, 6966. https://doi.org/10.3390/ijerph 18136966 Abstract: The COVID-19 crisis has disrupted when, where, and how employees work. Drawing on a sample of 5452 Finnish employees, this study explores the factors associated with employees’ abrupt adjustment to remote work. Specifically, this study examines structural factors (i.e., work independence and the clarity of job criteria), relational factors (i.e., interpersonal trust and social isolation), contextual factors of work (i.e., change in work location and perceived disruption), and communication dynamics (i.e., organizational communication quality and communication technology use (CTU)) as mechanisms underlying adjustment to remote work. The findings demonstrate that structural and contextual factors are important predictors of adjustment and that these relationships are moderated by communication quality and CTU. Contrary to previous research, trust in peers and supervisors does not support adjustment to remote work. We discuss the implications of these findings for practice during and beyond times of crisis. Keywords: work adjustment; remote work; structural factors; relational factors; contextual factors; COVID-19 pandemic Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Disclaimer/Complaints regulations f UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) will be contacted as soon as possible. Download date:24 Oct 2024 International Journal of Environmental Research and Public Health International Journal of Environmental Research and Public Health Article Factors Influencing Adjustment to Remote Work: Employees’ Initial Responses to the COVID-19 Pandemic Ward van Zoonen 1,* , Anu Sivunen 2 , Kirsimarja Blomqvist 3, Thomas Olsson 4 , Annina Ropponen 5 , Kaisa Henttonen 6 and Matti Vartiainen 7 1 Amsterdam School of Communication Research, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands 2 Department of Language and Communication Studies, University of Jyväskylä, Seminaarinkatu 15, 40014 Jyväskylä, Finland; anu.e.sivunen@jyu.fi 2 Department of Language and Communication Studies, University of Jyväskylä, Seminaarinkatu 15, 40014 Jyväskylä, Finland; anu.e.sivunen@jyu.fi y y jy 3 School of Business and Management, LUT University, Yliopistonkatu 34, 53850 Lappeenranta, Finland; kirsimarja.blomqvist@lut.fi 4 Faculty of Information Technology and Communication Sciences, Tampere University, Kalevantie 4, 33100 Tampere, Finland; Thomas.olsson@tuni.fi p 5 Finnish Institute of Occupational Health, 40, 00032 Helsinki, Finland; annina.ropponen@ttl.fi 6 6 UEF Business School, Kuopio Campus, University of Eastern Finland, 1627, 70211 Joensuu, Finland; kaisa.henttonen@uef.fi   Citation: van Zoonen, W.; Sivunen, A.; Blomqvist, K.; Olsson, T.; Ropponen, A.; Henttonen, K.; Vartiainen, M. Factors Influencing Adjustment to Remote Work: Employees’ Initial Responses to the COVID-19 Pandemic. Int. J. Environ. Res. Public Health 2021, 18, 6966. https://doi.org/10.3390/ijerph 18136966 Academic Editors: Jose M. León-Pérez, Mindy K. Shoss, Aristides I. Ferreira and Gabriele Giorgi Received: 29 May 2021 Accepted: 25 June 2021 Published: 29 June 2021 1. Introduction Even the most conservative estimates anticipate that at least 45 million jobs in the EU-27 labor market (approximately 23% of the total EU-27 employment) are directly at risk from the coronavirus disease 2019 (COVID-19) disruptions [1]. The outbreak of COVID-19 has had a drastic impact on work at a global scale [2]. Changes in when, where, and how work is completed are profound, evidenced, for instance, by widespread remote work directives [3–5]. The extent to which employees can adjust to remote work is crucial for individual outcomes (e.g., mental health, well-being, job satisfaction) and organizational outcomes (e.g., organizational performance). Hence, this study explores factors related to employees’ adjustment to remote work practices during the first phases of the COVID-19 pandemic. In achieving the aim of this study, we contribute to emerging research on the impact of the COVID-19 pandemic on work [3,5–8]. 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/). In line with Raghuram et al. [9], we view adjustment to remote work as an overall state of adaptation to environmental demands and conditions. Several critical indicators of Int. J. Environ. Res. Public Health 2021, 18, 6966. https://doi.org/10.3390/ijerph18136966 https://www.mdpi.com/journal/ijerph Int. J. Environ. Res. Public Health 2021, 18, 6966 2 of 19 adjustment to remote work have been identified, including employees’ satisfaction with remote work conditions, perceived job performance as a consequence of remote work, and the ability to balance work and non-work demands [9,10]. In contrast to previous investiga- tions of adjustment [9], the COVID-19 crisis required organizations and their employees to abruptly change their work environments and ways of working. As such, there is a need to understand what factors are related to employees’ adjustment to remote work during this crisis [6]. Based on the theory of work adjustment [11,12] and previous work on individual adjustment in a work context [10,13] and adaptation to virtual work [9], we identify and examine a framework of environmental factors that may affect individual adjustment to remote work during the COVID-19 pandemic. 1. Introduction Specifically, based on cross-sectional survey data, we provide empirical insights into the extent to which employees’ adjustment to remote work is associated with structural factors (i.e., work independence and clarity of job criteria), relational factors (i.e., social isolation and interpersonal trust), and contextual factors (i.e., perceived disruption and change in work location). Furthermore, we investi- gate moderating factors (i.e., organizational communication quality and communication technology use (CTU)) that potentially influence the relationships underlying employees’ adjustment to remote work. Organizational communication quality has been found to be pivotal when dealing with uncertainty and crises, including organizational responses to the COVID-19 pandemic [14]. At the same time, technological advances have been heralded for their ability to facilitate work across spatial distances and both synchronous and asynchronous collaboration [15–18]. Hence, we investigate the role of organizational communication quality and CTU in qualifying the impact of structural, relational, and contextual factors on adjustment to remote work. j Remote work settings involve temporal and spatial dispersion and depend on CTU to allow employees to interact across these boundaries [19–23]. Remote work is defined as “work done by an individual while at a different location than the person(s) directly supervising and/or paying for it” [24] (p. 2). In the context of the COVID-19 pandemic, this location was typically employees’ homes. Although previous studies have indicated that working from home might help employees collaborate across time zones, concentrate better than in the primary work location, and accomplish work tasks [25], it is unclear what factors impact employees’ ability to adjust to new demands of their work environment when they are mandated to work from home. We use remote work to refer to the current situation in which employees are mandated to work from home during the pandemic (i.e., the Finnish government introduced the Emergency Powers Act on 16 March, 2020, and advised all workplaces in Finland to utilize remote work if possible). 2. Literature Review and Hypotheses This study takes a work adjustment perspective to examine how employees have ad- justed to an abrupt transition to remote work. Adjustment to new work contexts typically involves adaptation to new environmental stimuli or demands. It has been suggested [9] that adjustment to virtual work refers to employees’ ability to adapt to virtual work modes as they transition from traditional office environments to remote work. Specifically, adjust- ment refers to an overall state of adaptation because a transition to remote work highlights the inherent tradeoffs involved in adjustment [9]. Several aspects are considered critical indicators of employees’ successful adaptation to a virtual work including satisfaction, commitment, productivity, and the ability to balance work and nonwork demands. Success- ful adaptation often requires a trade-off between these aspects. To examine the underlying factors that impact employees’ adjustment to remote work, we identified several structural, relational, and contextual factors that may impact employees’ adaptation (see Figure 1). These factors align with those proposed by Raghuram and colleagues [9], but we extend this framework by including crisis-specific concepts such as perceived disruptions and social isolation. Our conceptual model (see Figure 1) has its theoretical roots in the theory of work adjustment [11,12,26] and in the interactional model of individual adjustment [13]. It identifies several categories of factors relevant to individual adjustment, including in- Int. J. Environ. Res. Public Health 2021, 18, 6966 3 of 19 dividual, job, and organizational factors. Recently, Carillo and colleagues [6] adopted a similar approach to identify the individual, job, and organizational factors underlying telework adjustment in a crisis context. We further extend this work by exploring the role of several moderating factors, including organizational communication quality and CTU. Figure 1. Hypothesized model. 2 1 S l Figure 1. Hypothesized model. 2.1. Structural Factors Structural factors are the fundamental preconditions and organizational expectations related to a job description that may facilitate or forestall the possibilities to work remotely. Key aspects include work independence and clarity of job criteria [9]. When work can be conducted independently and the criteria for a specific job are clear, employees may be more confident in their ability to complete work remotely, facilitating better adjustment. 2.1.1. Work Independence Work independence refers to the ability of remote employees to complete tasks without having to engage in continual interaction with their coworkers [27]. Work independence can be facilitated by supporting asynchronous work, for example, allowing access to common databases through technology and ensuring that colleagues can connect with others if needed [9]. Remote employees, who must rely continually on their coworkers, thereby mak- ing them reciprocally or sequentially interdependent with others, are likely to experience time pressures, loss of control, and a decline in personal productivity [28,29]. However, independence may facilitate adjustment to remote work [9] because it allows workers to exercise more control over their behavior, for instance, when drawing boundaries between work and nonwork [30] or when enacting discipline to organize their work and apply their skills in an isolated work environment [9]. Hence, employees with greater degrees of independence are found to experience greater adjustment to a remote work context [9]. This is in line with research suggesting that individuals have an innate need for autonomy and self-determination [31,32]. Thus, we propose the following: Hypothesis 1 (H1). Work independence is positively associated with employees’ adjustment to remote work. 2.1.2. Clarity of Job Criteria The clarity of job criteria means that performance assessment at work is perceived as objective, quantifiable, and transparent [9]. Clear and explicit criteria are especially beneficial to guide the performance of remote employees and develop accurate expecta- Int. J. Environ. Res. Public Health 2021, 18, 6966 4 of 19 tions among them [9,30]. This is because remote employees, compared with non-remote employees, have fewer opportunities to seek or receive informal performance feedback or clarifications from their supervisors and coworkers. Unclear evaluation criteria may lead to insecurity and uncertainty concerning work-related expectations. However, when clear and explicit evaluation criteria are in place, remote employees may be even more capable of managing themselves, which may lead to enhanced performance and satisfaction [9,30]. Additionally, clear evaluation criteria can help build mutual expectations and perceptions of procedural fairness and establish perceptions of equity among remote employees who cannot use physical behaviors to compare work outcomes [29,33]. When evaluation criteria are clearly understood, remote employees are also more likely to work on initiatives that are valued by their organization [34]. Hence, we propose the following: Hypothesis 2 (H2). Clarity of job criteria is positively associated with employees’ adjustment to remote work. 2.2.1. Interpersonal Trust Because remote work inherently involves physical and psychological distances, fac- tors that create a stronger sense of relationships between coworkers may prevent physical distance from becoming psychological distance [9] and are expected to have a positive influence on employees’ ability to adjust to remote work [36]. Feelings of trust, for instance, may give remote employees greater confidence in their role within the work group or organization and facilitate further adjustment [37]. Interpersonal trust can be defined as the willingness to accept vulnerability and a positive expectation of others’ trustwor- thiness [38]. It has been shown to have a positive effect on workplace cooperation [39], knowledge sharing [40], and organizational commitment [41]. Trusting relations between employees [42] and employees’ trust in supervisors [43] enhance organizational change and can therefore affect how employees adjust to remote work. Trust also lowers the need for both employees and their supervisors to monitor and verify each other’s work in the virtual context [44] and is crucial to the effectiveness of virtual workers [45]. Thus, we hypothesize the following: Hypothesis 3 (H3). Interpersonal trust is positively associated with employees’ adjustment to remote work. 2.2. Relational Factors Relational factors refer to the social relationships and forms of collaboration within an organization. In the context of remote work, they relate to, for example, support and interpersonal trust [9] among employees working remotely and their supervisors and coworkers. Hence, we examine how trust can help to overcome barriers to adjusting to remote work [9]. In addition, issues of social isolation at work are especially profound dur- ing the COVID-19 pandemic; hence, we investigate how these issues may deter adjustment to remote work [35]. 2.2.2. Social Isolation Social isolation is related to physical and psychological distance between coworkers. Isolation can be defined as the perception of a lack of availability of support and recognition, missed opportunities for informal interactions with coworkers, and not being part of the group [35]. In other words, isolation is a state of mind or a belief that one is out of touch with others in the workplace; as such, the desire to feel socially connected is thwarted [46]. In a remote work setting, perceptions of social isolation may be exacerbated, even though it is proposed that isolation is created mainly due to the lack of availability and not just spatial distance [35]. Perceived isolation has been identified as a potential obstacle for effectiveness among remote employees [47] and may reduce job satisfaction [46]. Hence, we hypothesize the following: 5 of 19 Int. J. Environ. Res. Public Health 2021, 18, 6966 Hypothesis 4 (H4). Social isolation is negatively associated with employees’ adjustment to remote work. Hypothesis 4 (H4). Social isolation is negatively associated with employees’ adjustment to remote work. 2.3.2. Disruption of Work Routines Unlearning refers to the “breakdown of routines, habits, and cognitive frameworks” [49] (p. 509). We use the term disruption to refer to an unlearning process in which routines, habits, norms, and procedures are changing [50] as a result of the COVID-19 pandemic. The adjustment required by employees depends on the level of disruption experienced by employees: greater disruption requires greater adjustment. Prior research demonstrates that environmental turbulence causes organizations and their subunits to face performance gaps, work stress, toxic work environments, and blame shifting as well as anxiety and fears [50]. Hence, we hypothesize the following: Hypothesis 6 (H6). Disruption of work routines is negatively associated with employees’ adjust- ment to remote work. 2.3. Contextual Factors We extend previous models [9] of adjustment by explicitly considering the COVID-19 context within which adjustments are required. Specifically, we suggest that the severity of the change in work location—here, the discrepancy between earlier remote work experi- ence and current remote work frequency—and the extent of broader disruptions of work routines triggered by the COVID-19 crisis impact on employees’ adjustment to the “new normal” [5,48]. 2.3.1. Change in Work Location The sudden requirement to work from home has led most employees to increase the frequency with which they work from home. For some, these changes are more substantial because they either did not engage in remote work practices or did so to a very limited extent prior to the COVID-19 outbreak. In contrast, for employees who are more familiar with these work practices either because they frequently work remotely or are used to working with dispersed colleagues, these new work realities may require less adjustment. Limited connections and access in remote locations seem to be the main challenges of virtual working spaces despite recent technological advances. We examine the role of changes in work location as the discrepancy between current remote work practices and remote work practices before the COVID-19 crisis. Transitioning to a remote work location may require adjustment to the working environment, including physical, technological, and social conditions of work [16]. The intuitive hypothesis here is that larger differences indicate more substantial changes in where work is conducted, which in turn could complicate adjustment. Hypothesis 5 (H5). Changes in work location are negatively associated with employees’ adjustment to remote work. 2.4. Moderating Factors In addition to structural, relational, and contextual factors, remote work is structured and shaped by communication technologies that enable employees to interact across temporal and spatial boundaries. The quality of organizational communication and the frequency of CTU in times of changing work environments and dispersed work may prove to be of particular importance for employees to adjust to new work conditions. Organizational communication quality is defined here as the informativeness, accuracy, and timeliness of communication about organizational changes during the pandemic [51]. 6 of 19 Int. J. Environ. Res. Public Health 2021, 18, 6966 2.4.1. Organizational Communication Quality and Relational and Contextual Factors g y Communication has been found to mitigate the relationship between geographical distribution and conflict [52]. Although not directly related to adjustment, these findings imply that communication might have a positive impact on conflict identification and conflict handling, and as such may optimize remote work effectiveness and satisfaction, which are key indicators of adjustment. In addition, high-quality organizational com- munication can be viewed as a sign of organizational support that may help employees refocus on collective goals [53] to meet their performance expectations. In the absence of a traditional office environment, the role of organizational communication may be even more profound because it may substitute in part for a lack of face-to-face interaction while facilitating the information purposes of social support networks that are normally present in organizations [54]. Finally, communication tends to clarify role expectations and enhance performance by reducing uncertainty [51]. Therefore, we ask the following question: RQ1: Does organizational communication quality moderate the impact of structural, relational, and contextual factors underlying adjustment? 2.4.2. Communication Technology Use and Relational and Contextual Factors Communication technologies are the enabling force behind most remote work set- tings, allowing workers to maintain necessary levels of connectivity to share information and coordinate work across various boundaries [55,56]. In addition, the effective use of communication technology is an important facilitator of trust in virtual teams [17,57,58]. Indeed, many organizations can be argued to have adopted some degree of virtual prac- tices under the studied conditions, and collaboration strongly depends on the effective use of communication technology. ter Hoeven and van Zoonen [59] demonstrated that control over CTU reduces the negative consequences of spatial distance in remote work arrangements for helping behavior. 2.4. Moderating Factors Because CTU may amplify the positive association of relational factors (e.g., interpersonal trust) with adjustment while mitigating the negative impact of other relational factors (e.g., social isolation), we pose the following research question: RQ2: Does CTU moderate the impact of relational and contextual factors underlying adjustment? 3. Materials and Methods This cross-sectional study targeted employees who had been asked to work remotely in Finland since the lockdown began in mid-March 2020. The survey started on the 26th of March 2020 and was open for responses until the 13th of April 2020. Open survey invitations were published online, and we solicited the help of several large labor unions and ministries to distribute the survey link to their members. The survey included about 100 items in total, including background questions and attention checks. The survey was administered through the XM platform Qualtrics and programmed such that all statements needed to be answered for the survey to be completed and responses to be considered for analysis. Explicit informed consent was obtained from all participants prior to the survey. Data were exported to IBM statistical software packages SPSS and AMOS for further analysis. There were no missing values as we used forced response options, respondents who failed the attention checks or dropped out were automatically excluded. Embedded data (e.g., IP addresses) and identifying information (i.e., email addresses) were assessed to guard against duplicate responses, but were not used in the analysis stage. This convenience sampling procedure resulted in a total response of 5452 Finnish employees. Employees in our sample indicated low probabilities of job loss in the near future, with 84.4% indicating that this was (highly) improbable (M = 2.07 SD = 1.43; on a 7-point scale). The average age of the respondents was 45.3 years old (SD = 10.7). Most respondents were female (N = 3747; 69%), and 1593 were male (29%). Most respondents were employed by the state or public utility (N = 3267; 60%), while 1318 respondents worked for private enterprises (24%), and others worked in nongovernmental (2%) or semigovernmental (8%) Int. J. Environ. Res. Public Health 2021, 18, 6966 7 of 19 organizations. The respondents mostly worked in organizations with 50 to 249 employees (22%), 250 to 999 employees (29%), or more than 2000 employees (25%). The majority of respondents worked remotely 4 or more days per week (90.8%), 6.5% worked remotely 2 or 3 days, and 2.6% worked remotely 1 day per week or less. Furthermore, respondents indicated they worked 38.6 h per week on average (SD = 6.6), and the average reported overtime was 2.3 h per week (SD = 5.9). 3.1.3. Relational Factors Interpersonal trust was measured using four items based on [61] adopted from [9]. In line with earlier research [9], our measurement strategy focused on an overall measure of trust rather than assessing the many specific determinants of trust. Two items relate how much the individual trusts his/her supervisor and colleagues, and two items measure the extent to which the respondent perceives that his/her supervisor and colleagues trust the individual. Social isolation was measured using three items derived from [35]. Social isolation measures the extent to which employees feel isolated and separated from others in the workplace. 3.1. Measures All statements were measured using seven-point response scales ranging from strongly disagree to strongly agree unless indicated otherwise. All survey items were derived from earlier studies and reviewed by the research team, but we did not conduct a pilot study. Table 1 lists all measurement items, including descriptive statistics and factor loadings. 3.1.2. Structural Factors Independence was measured using four items adopted from [60]. Similar to Raghuram et al. [9], respondents were asked to indicate the degree to which their performance was dependent on working with others. Clarity of job criteria was measured using four items adopted from [61]. The items deal with handling problems on the job, figuring out what should be done to accomplish one’s work, and being sure of how the job needs to be done. Items are based on role conflict and role ambiguity scales proposed by House and colleagues [62]. 3. Materials and Methods Approximately 14% of the respondents worked in a managerial position, their average organizational tenure was 10.9 years (SD = 10.1), most respondents were part of single (N = 1029; 19%) or two-person (N = 2152; 40%) households, and 40% had at least 1 child under the age of 18 in their household. 3.1.1. Dependent Variable Adjustment to remote work was measured with a five-item scale assessing satisfaction with remote work, perceived performance as the consequence of remote work, and ability to balance work and non-work demands. The measure was adopted from Raghuram et al. [9], who used it in the context of virtual work. Adjustment refers to an overall state of adaptation because a transition to remote work highlights the inherent tradeoffs involved in adjustment [9]. For instance, research by [9] indicated that expending greater efforts to increase (or maintain) productivity may come at the expense of greater work/nonwork balance. Hence, an overall measure of adjustment may most accurately assess employees’ relative level of adaptation to environmental demands. 3.1.5. Moderators Organizational communication quality was measured using six items from Bordia et al. [64]. These items have previously been applied in the context of uncertainty during organi- zational change. Quality of communication was measured using items such as “the communication my organization provided adequately answered my questions about the changes.” g Communication technology use was measured by asking respondents to indicate the frequency with which they used various technologies to communicate with their colleagues. The communication technologies we inquired about were email, telephone, instant messag- ing (e.g., WhatsApp), online meetings (e.g., through Zoom or MS Teams), collaborative tools (e.g., Google Drive or Office365), enterprise social media (e.g., Yammer), and public social media (e.g., Facebook). Responses ranged from 1 (never) to 7 (hourly). The items were computed to indicate an overall score for the frequency of CTU, with higher scores indicating more frequent communication with colleagues through these technologies. Table 1. Measurement items and descriptive statistics. Table 1. Measurement items and descriptive statistics. Measurement Items Mean (SD) R2 St. Factor Loading Unst. 3.1.5. Moderators Factor Loading Se Adjustment to remote work [9] All in all, I am satisfied with remote work 5.66 (1.43) 0.61 0.781 1.000 Remote work allows me to perform my job better than I ever could when I worked in the office 4.39 (1.62) 0.76 0.871 1.261 0.02 If I were given the choice to return to a traditional office environment (i.e., no longer work remotely), I would be very unlikely to do so 3.98 (2.02) 0.43 0.657 1.184 0.02 Since I started working remotely, I have been able to balance my job and personal life 4.87 (1.75) 0.44 0.663 1.036 0.02 Since I started working remotely, my productivity (e.g., sales orders, output, support) has increased 4.39 (1.66) 0.70 0.835 1.076 0.02 Structural Factors Independence [59] I have to obtain information and advice from colleagues to complete my work (R) c 4.15 (1.66) 0.69 0.832 1.000 I depend on colleagues for the completion of my work (R) 3.85 (1.75) 0.73 0.855 1.082 0.02 I rarely have to check in with other people to do my work 4.72 (1.61) 0.35 0.587 0.685 0.02 I have to work closely with other people to do my job properly (R) 4.06 (1.82) 0.43 0.659 0.869 0.02 Clarity of job criteria [60] I frequently don’t know how to handle problems that occur in my job (R) 2.28 (1.30) 0.51 0.713 1.000 I often find that I cannot figure out what should be done to accomplish my work (R) 1.96 (1.15) 0.76 0.869 1.073 0.02 I am frequently confused about what I have to do on my job (R) 1.86 (1.15) 0.80 0.894 1.100 0.02 I am frequently unsure about how to do my work (R) 1.94 (1.19) 0.77 0.875 1.115 0.02 Relational Factors Interpersonal trust [9] I trust my supervisors 5.64 (1.35) 0.60 0.773 1.000 My supervisors trust me 5.84 (1.03) 0.48 0.694 0.690 0.02 I trust my peers 6.00 (0.86) 0.34 0.587 0.485 0.02 My peers trust me 5.96 (0.82) 0.29 0.541 0.422 0.02 Social isolation [35] I am separated from my coworkers 5.29 (1.67) 0.61 0.712 1.000 I often feel I am no longer close to anyone 3.33 (1.71) 0.35 0.592 0.849 0.03 I am isolated from others at work 4.35 (1.82) 0.71 0.841 1.281 0.03 Contextual Factors Remote work location a How often did you normally (before the COVID-19 pandemic) work remotely (e.g., from home)? 3.1.4. Contextual Factors Change of work location was measured by calculating the difference between remote work before the pandemic and current remote work frequency. Respondents were asked about the frequency with which they normally (before the pandemic) worked remotely, ranging from 1 (never) to 7 (6 or 7 days per week). Subsequently, we asked respondents to indicate the frequency with which they worked remotely since the moment their organiza- tion took measures related to the COVID-19 crisis. By subtracting the scores, we calculated Int. J. Environ. Res. Public Health 2021, 18, 6966 8 of 19 a difference score such that a higher value indicates a larger discrepancy in remote work practices compared with normal circumstances. Perceived disruption was measured by adopting eight items from [50,63]. The items address changes in work routines. Since routines are reflected in operating procedures during the performance of work, changes in plans, deadlines, and information-sharing mechanisms are indicative of an overall disruption of work. We asked employees to indicate the extent to which several activities, including project plans and deadlines, have changed since the organization took measures related to the COVID-19 crisis. Independence [59] Interpersonal trust [9] I trust my supervisors My supervisors trust me I trust my peers My peers trust me Social isolation [35] I am separated from my coworkers I often feel I am no longer close to anyone I am isolated from others at work 3.1.5. Moderators 2.77 (1.40) - - - - How often have you worked at home during the COVID-19 pandemic? 5.70 (1.05) - - - - Table 1. Measurement items and descriptive statistics. Organizational communication quality [63] Notes: a Change was calculated as a difference score between two observed variables and therefore not included in the CFA; b a sum score indicating the average frequency of communication technology use was calculated and therefore not included in the CFA. c (R) indicates that items were reverse coded. Notes: a Change was calculated as a difference score between two observed variables and therefore not included in the CFA; b a sum score indicating the average frequency of communication technology use was calculated and therefore not included in the CFA. c (R) indicates that items were reverse coded. Remote work location a Disruptions [50] During the COVID-19 crisis, the following aspects of my work changed: Work procedures 4.37 (1.74) 0.39 0.624 1.000 Project plans 3.67 (1.51) 0.41 0.643 0.895 0.02 Technologies used to complete work tasks 3.80 (1.85) 0.42 0.649 1.108 0.03 Decision-making processes 3.35 (1.56) 0.44 0.666 0.957 0.02 My work tasks 2.97 (1.66) 0.51 0.715 1.092 0.03 The coordination of my work 3.56 (1.66) 0.54 0.737 1.130 0.03 The deadlines of work projects 3.41 (1.74) 0.38 0.619 0.994 0.03 Remote work location a 9 of 19 Int. J. Environ. Res. Public Health 2021, 18, 6966 Table 1. Cont. Measurement Items Mean (SD) R2 St. Factor Loading Unst. Factor Loading Se Disruptions [50] During the COVID-19 crisis, the following aspects of my work changed: Work procedures 4.37 (1.74) 0.39 0.624 1.000 Project plans 3.67 (1.51) 0.41 0.643 0.895 0.02 Technologies used to complete work tasks 3.80 (1.85) 0.42 0.649 1.108 0.03 Decision-making processes 3.35 (1.56) 0.44 0.666 0.957 0.02 My work tasks 2.97 (1.66) 0.51 0.715 1.092 0.03 The coordination of my work 3.56 (1.66) 0.54 0.737 1.130 0.03 The deadlines of work projects 3.41 (1.74) 0.38 0.619 0.994 0.03 Moderators Organizational communication quality [63] The communication my organization provided has been useful 5.65 (1.11) 0.71 0.840 1.000 The communication my organization provided has adequately answered my questions about the changes 5.50 (1.28) 0.73 0.854 1.167 0.02 The communication my organization provided has been positive 5.25 (1.22) 0.55 0.743 0.975 0.02 The communication by my organization has been appropriate 5.63 (1.11) 0.79 0.890 1.056 0.01 The communication my organization provided has been timely 5.25 (1.36) 0.69 0.829 1.206 0.02 The communication my organization provided has been accurate 5.87 (1.02) 0.58 0.760 0.826 0.01 Communication technology use b Over the past two weeks, how often did you communicate about your work with colleagues using Phone calls 3.08 (1.37) - - - - E-mails 4.79 (0.94) - - - - Online meetings (e.g., Skype, MS Teams, Zoom) 4.27 (1.05) - - - - Text or instant messaging (e.g., WhatsApp, Messenger) 3.06 (1.64) - - - - Collaboration tools (e.g., Office 365, Google Drive) 2.81 (1.75) - - - - Enterprise social media (e.g., Yammer, Happeo) 1.91 (1.45) - - - - Public social media (e.g., Facebook, Twitter) 1.58 (1.15) - - - - Notes: a Change was calculated as a difference score between two observed variables and therefore not included in the CFA; b a sum score indicating the average frequency of communication technology use was calculated and therefore not included in the CFA. c (R) indicates that items were reverse coded. Table 1. Cont. 4.1. Measurement Model A confirmatory factor analysis (in AMOS) was used to examine the hypothesized factor structure and investigate the validity of our measurement model. Subsequently, we examined common method variance using a common latent factor approach. The model demonstrated good model fit: χ2 (469) = 4432.49; CFI = 0.96; TLI = 0.95; SRMR = 0.04; PClose 1.000; and RMSEA = 0.039 (CI: 0.038, 0.040). Following recom- mendations and threshold values reported by Hair et al. [65], the model demonstrated convergent and discriminant validity of the measures in our model (see Table 1). The average variance extracted (AVE) ranged between 0.43 and 0.71. Discriminant validity was examined through the maximum shared variance (MSV), which ranged between 0.07 and 0.37 for the constructs in our model and is smaller than the AVE values. Additionally, the square root of the AVE was greater than the inter-construct correlations. Inspection of the model parameters indicated the absence of cross-loadings, overall suggesting good discriminant validity. Reliability was examined through the composite reliabilities (CR) and the maximum reliability (H), which ranged between 0.75 and 0.93 and between 0.77 and 0.93, respectively. Second, we examined common method variance using a common latent factor ap- proach. Squared regression estimates indicated that common method variance was 3.6%, indicating that common method variance is not a substantial concern in our data. Curve estimations for all relationships in our model indicated that these relationships were suf- ficiently linear. Finally, the correlation between interpersonal trust and communication quality was relatively high (0.61; see Table 2). Hence, we inspected collinearity statistics (i.e., the variance inflation factor, VIF) for all independent variables and discovered no Int. J. Environ. Res. Public Health 2021, 18, 6966 10 of 19 10 of 19 problems with multicollinearity. In sum, these results justify further inspection of the structural model. Table 2. Correlation Matrix of variables with validity statistics. Variable M (SD) CR AVE MSV MaxR(H) 1 2 3 4 5 6 7 8 9 1. Independence 4.20 (1.40) 0.83 0.55 0.07 0.86 0.74 2. Clarity of job criteria 5.99 (1.05) 0.91 0.71 0.10 0.92 −0.27 0.84 3. Interpersonal trust 5.86 (0.82) 0.75 0.43 0.37 0.77 0.06 0.32 0.66 4. Social isolation 4.32 (1.41) 0.76 0.52 0.09 0.80 0.03 −0.25 −0.10 0.72 5. Disruption 3.59 (1.21) 0.85 0.44 0.08 0.85 0.13 −0.28 −0.12 0.15 0.67 6. Change a 3.92 (1.53) − − − − 0.14 −0.11 0.01 0.15 0.18 – 7. 4.1. Measurement Model Communication quality 5.53 (1.01) 0.93 0.67 0.37 0.93 0.05 0.22 0.61 −0.13 −0.11 −0.01 0.82 8. Technology use b 3.07 (0.75) − − − − 0.27 0.10 0.09 0.13 0.12 0.07 0.11 − 9. Adjustment 4.66 (1.34) 0.88 0.59 0.10 0.90 −0.25 0.32 0.06 −0.30 −0.26 −0.32 0.15 0.06 0.77 Notes: CR = composite reliability; AVE = average variance extracted; MSV = maximum shared variance; MaxR(H) = maximum reliability. Square root of the AVE is reported on the diagonal. a Change was calculated as a difference score between two observed variables and therefore not included in the CFA; b a sum score indicating the average frequency of communication technology use was calculated and therefore not included in the CFA. Technology use is treated as the index score, where higher scores mean higher general technology use. All correlations equal to or above 0.03 are significant at p < 0.05. Table 2. Correlation Matrix of variables with validity statistics. Notes: CR = composite reliability; AVE = average variance extracted; MSV = maximum shared variance; MaxR(H) = maximum reliability. Square root of the AVE is reported on the diagonal. a Change was calculated as a difference score between two observed variables and therefore not included in the CFA; b a sum score indicating the average frequency of communication technology use was calculated and therefore not included in the CFA. Technology use is treated as the index score, where higher scores mean higher general technology use. All correlations equal to or above 0.03 are significant at p < 0.05. 4.2. Controls We considered several potentially confounding factors in our analysis. Specifically, we controlled for gender, age, working hours per week, managerial position, organizational tenure, and job security. Gender significantly predicted adjustment (B = 0.091, p = 0.009), suggesting that female respondents were better able to adjust to remote work. Gender did not affect any of the hypothesized relationships in the model. Age did not affect adjustment to remote work (B = 0.000, p = 0.766). Similarly, the number of work hours per week did not significantly affect adjustment to remote work (B = −0.001, p = 0.691). However, the results indicated that managerial positions had a significant and negative relationship with adjustment (B = −0.176, p < 0.001), suggesting that individuals in managerial positions seem to have more difficulties adjusting to remote work. Finally, organizational tenure (B = −0.001, p = 0.202) and job security (B = 0.012, p = 0.274) did not affect adjustment to remote work or any of the relationships in our model. In sum, all hypothesized relationships remained unaffected when these variables were included. Hence, these variables were excluded from the final model for reasons of parsimony. 4.3. Hypotheses Testing The hypothesized model was examined using path modeling in AMOS by estimating regression coefficients between the structural, relational, and contextual factors on adjust- ment to work. Table 3 provides the standardized and unstandardized regression results for the full model. Structural factors. Hypothesis 1 assumes that work independence is positively related to adjustment to remote work. The results demonstrate a significant positive relationship (B = 0.168 (0.143; 0.192), p = 0.001). Hence, hypothesis 1 is supported. In addition, hypoth- esis 2 reflects the assumption that clarity of job criteria makes it easier for employees to adapt to remote work. The findings demonstrate a significant positive relationship between the clarity of job criteria and adjustment to remote work (B = 0.174 (0.136; 0.211), p = 0.001). Hence, hypothesis 2 is also supported. Overall, these results provide strong support that the structural factors of an employee’s job have an important influence on the employee’s adjustment to remote work. Relational factors. Hypothesis 3 posits that interpersonal trust is positively related to employees’ adjustment to remote work. The results demonstrate a significant negative relationship between trust and adjustment (B = −0.069 (−0.117; −0.021), p = 0.006). Hence, contrary to our expectations, trust between coworkers and supervisors does not increase adjustment to remote work but rather decreases it. A possible explanation could be that employees who exhibit lower levels of trust in their peers and supervisors rather work (alone) remotely, as this gives them more autonomy from people they do not trust and, Int. J. Environ. Res. Public Health 2021, 18, 6966 11 of 19 11 of 19 therefore, they are less frequently confronted with such relationships. However, as the relationship is in the opposite direction than the one we hypothesized, we do not find support for hypothesis 3. Hypothesis 4 suggests that social isolation is negatively related to adjustment to remote work. The results demonstrate a significant negative relationship between perceived social isolation and adjustment to remote work (B = −0.178 (−0.202; −0.152), p = 0.001), providing support for Hypothesis 4. Contextual factors. Hypothesis 5 reflects the rationale that the relative change in work locations influences employees’ adjustment to remote work. The results show that a change in work location is negatively related to adjustment to remote work (B = −0.209 (−0.234; −0.186), p = 0.001). 4.3. Hypotheses Testing This result suggests that a larger change in work location (e.g., a change in remote work from half a day per week to five days per week versus a change in remote work from two days per week normally to five days per week currently) reduces employees’ adjustment to remote work. Hence, hypothesis 5 is supported. This implies that employees who were already used to working remotely before the pandemic adjusted better to the new situation. Hypothesis 6 suggests that perceived disruption is negatively related to adjustment to remote work. The findings demonstrate a significant negative relationship (B = −0.122 (−0.153; −0.093), p = 0.001), providing support for hypothesis 6. The more work practices changed during the pandemic, the less employees were able to adjust. Table 3. Parameter estimates of path model. Table 3. Parameter estimates of path model. Table 3. Parameter estimates of path model. Bootstrapping BC 95% CI B SE Beta Lower Upper p Hypotheses H1 Independence →Adjustment 0.168 0.012 0.175 0.143 0.192 0.001 H2 Clarity of job criteria →Adjustment 0.174 0.017 0.136 0.136 0.211 0.001 H3 Interpersonal trust →Adjustment −0.069 0.023 −0.042 −0.117 −0.021 0.006 H4 Social isolation →Adjustment −0.178 0.012 −0.188 −0.202 −0.152 0.001 H5 Remote work transition →Adjustment −0.209 0.011 −0.239 −0.234 −0.186 0.001 H6 Perceived disruption →Adjustment −0.122 0.014 −0.110 −0.153 −0.093 0.001 RQ1: Communication quality × Relational and contextual factors RQ1 Communication quality × Trust →Adjustment 0.002 0.015 0.002 −0.039 0.041 0.995 Communication quality × Isolation →Adjustment 0.019 0.010 0.023 −0.007 0.043 0.149 Communication quality × Change in location →Adjustment −0.045 0.010 −0.057 −0.070 −0.021 0.001 Communication quality × Disruption →Adjustment 0.007 0.130 0.007 −0.025 0.036 0.722 Communication quality × Independence →Adjustment 0.016 0.011 0.014 −0.012 0.039 0.263 Communication quality × Clarity of job criteria →adjustment −0.009 0.015 −0.010 −0.044 0.024 0.620 RQ2: Communication technology use × Relational and contextual factors RQ2 Technology use × Trust →Adjustment −0.107 0.024 −0.053 −0.168 −0.046 0.002 Technology use × Isolation →Adjustment 0.009 0.015 0.007 −0.007 0.043 0.149 Technology use × Change in location →Adjustment −0.031 0.014 −0.028 −0.065 −0.001 0.045 Technology use × Disruption →Adjustment 0.050 0.017 0.035 0.013 0.085 0.006 Notes: Bootstrapping is a technique from which the sampling distribution of statistic is estimated by taking repeated samples from the dataset. Bootstrapping was used to obtain model estimates. BC95% CI indicate the bias-corrected 95% confidence interval of the beta coefficient. 4.4. Moderations Before discussing the interactions, it should be noted that both moderators, organiza- tional communication quality (B = 0.114 [0.075; 0.152], p = 0.001) and the frequency of CTU (B = 0.103 [0.059; 0.152], p = 0.001), are significantly and positively related to adjustment. Note that all variables that comprise product terms were mean centered prior to testing the interactions. For all interactions, we inspected the values of the interactions effect at different values of the moderator using the Johnson–Neyman technique. When the interac- tion reported was not significant at all values of the moderator, we reported the value of Int. J. Environ. Res. Public Health 2021, 18, 6966 12 of 19 12 of 19 the moderator at which the interaction becomes significant. To facilitate interpretation, the mean-centered values are also reported as actual (raw) values. the moderator at which the interaction becomes significant. To facilitate interpretation, the mean-centered values are also reported as actual (raw) values. p Organizational communication quality. There was no significant interaction effect be- tween organizational communication quality and trust (B = 0.002 (−0.039; 0.041), p = 0.995), social isolation (B = 0.019 (−0.007; 0.043), p = 0.149), and disruption (B = 0.007 (−0.025; 0.036), p = 0.722) on employees’ adjustment to remote work. There was a significant in- teraction between organizational communication quality and change in work location (B = −0.045 (−0.070; −0.021), p = 0.001) on adjustment to remote work. This result sug- gests that at low levels of organizational communication quality starting at −4.11 (i.e., 1.42 in raw values), perceived change in work location negatively impacts adjustment to remote work. Organizational communication quality has a limited impact in mitigating this negative relationship. Finally, we did not find significant interactions between orga- nizational communication quality and clarity of job criteria on adjustment (B = −0.010 (−0.044; 0.024), p = 0.620), nor did we find an interaction between communication quality and job independence on adjustment (B = 0.014 (−0.012; 0.039), p = 0.263). j p j p Communication technology use. There were no significant interactions between social isolation and CTU (B = 0.009 (−0.007; 0.043), p = 0.149). CTU was found to moderate the negative relationship between trust and adjustment to remote work (B = −0.107 (−0.168; −0.046), p = 0.002). The result indicates that trust negatively affects adjustment to work when the mean-centered value of CTU is below 0.562 (i.e., 3.63 in raw values). 4.4. Moderations This suggests that when CTU is low, trust stifles adjustment to remote work, but when CTU is high (above 0.562, approximately 22% of the responses), there is no significant negative effect of trust on adjustment to remote work. Arguably, frequent CTU is important when trust is low, to mitigate a decline in employees’ commitment, satisfaction, and productivity. However, CTU is also important for adjustment when trust is high as a lack of communication may be more detrimental to adjustment in high-trusting environments. For instance, trust may be an indicator of high-quality relationships, missing out on such relationships in remote work settings may be detrimental to several aspects of adjustment, increasing the frequency of CTU to communicate and collaborate with trusted peers and supervisors might reduce the negative impact on employees’ adjustment. g p p y j In addition, CTU was found to moderate the negative relationship between change in work location and adjustment (B = −0.031 (−0.065; −0.001), p = 0.045). The findings suggest that change is negatively related to adjustment at all levels of CTU. However, smaller levels of change and a higher frequency of CTU yield the highest levels of adjust- ment. At one standard deviation below the mean (−1.92) of change, adjustment is higher (5.33) when CTU is one standard deviation above the mean (0.786) rather than below the mean (−0.786), in which case adjustment is 5.07. Finally, CTU moderates the relationship between disruption and adjustment to remote work (B = 0.050 (0.013; 0.085), p = 0.006). The confidence interval of the slope indicates that disruption has a negative impact on adjustment to remote work at all levels of CTU. However, it should be noted that higher frequencies of CTU allow employees to adjust better to remote work when disruption is high than when the frequency of CTU in these situations is low. 5.1. Theoretical Implications The findings have several theoretical implications. First, based on the theory of work adjustment [12] and the interactional model of individual adjustment [13], this study identified several crisis-specific environmental factors [6] in addition to “traditional” environmental factors proposed by [9] that may underlie employees’ adjustment to remote work. For instance, we demonstrated that isolation is a relevant predictor that could be conceptualized as a relational factor underlying adjustment. In addition, we conceptualized contextual factors that include crisis-specific indicators such as changes in work location and perceived disruptions that impact adjustment. Finally, this study further considered how communication quality and CTU may mitigate some of the challenges in adapting to remote work. Ultimately, the study contributes to the literature on adjustment by identifying how employees’ ability to adjust to abrupt transitions to remote work has been affected by various relevant factors of the work environment. Specifically, this study contributes to person–environment theories and the theory of work adjustment by identifying how the work environment may enable or constrain employees’ ability to adapt. In other words, the work environment has reinforcement capabilities that can satisfy a person’s needs (in this case, adjustment) [12]. p j Second, work independence and clarity of job criteria were positively and significantly related to work adjustment. This suggests that employees who know what is expected from them and can complete their tasks without others adjust better to working remotely. Hence, with regard to the structural factors underlying remote work, we were able to replicate the findings presented by [9] in the context of virtual work and add that these factors operate in similar ways across organizational settings during a global health pandemic characterized by abrupt lockdowns and en masse remote work directives. Furthermore, the findings align with [66], who find that telecommuters with higher autonomy report greater job satisfaction relative to those with less autonomy. Our findings are in line with previous literature linking performance management and goal-setting theory in co-located work settings. It has been established that specific goals can enhance motivation and performance by leading people to focus their attention on specific objectives [67], facilitate their attempts to achieve these objectives [68], persist in the face of setbacks [69], and invent new strategies to better deal with complex challenges related to goal attainment [70]. 5. Discussion The findings of this cross-sectional study during the early phase of the COVID-19 outbreak in 2020 in Finland indicate that structural factors (i.e., high work independence and clarity of job criteria) make it easier for employees to adjust to remote work settings. In turn, relational factors (i.e., interpersonal trust and isolation) are negatively related to adjustment. Contrary to our expectations and to the earlier findings by [9], interpersonal trust was negatively associated with adjustment to remote work. Arguably, trust serves as a proxy for important interpersonal functions, such as socialization and support; when such cues are missing, employees may feel less satisfied and effective and may therefore experience lower levels of adjustment to remote work. Our findings also show that feelings of social isolation decrease adjustment to remote work, providing further evidence that Int. J. Environ. Res. Public Health 2021, 18, 6966 13 of 19 13 of 19 the social dynamics of work present a key barrier in adjustment during the COVID-19 pandemic. Furthermore, the results indicate that greater discrepancy between the amount of current and “normal” remote work and greater disruption in work practices (i.e., contex- tual factors) both decrease adjustment. These results imply that beyond smaller changes in work location, greater experience with remote work seems to enhance adjustment to remote work. Finally, the findings demonstrate a relatively small positive impact of organizational communication quality and CTU in adapting to increased remote work. Organizational communication quality does not mitigate the negative impacts of relational factors on adjustment (i.e., interpersonal trust and feelings of isolation) or facilitate the relationship between disruption of work practices and adjustment. However, more frequent use of various communication technologies with colleagues seems to mitigate the negative re- lationship between trust and adjustment, probably by reviving social relations. More research is needed to study the potential buffering effects of communication technology use and remote work adjustment. 5.1. Theoretical Implications More broadly, the finding that work independence and clarity of job criteria are positively related to adjustment also signals a potentially important tension in remote work designs. While some level of independence and clarity at the individual level is desirable for job satisfaction, effectiveness, and performance in remote settings, modern work tasks require some level of interdependency, and employees may desire feedback, socialization and relatedness with peers. For example, in self-determination theory, relatedness is considered a basic human need that consists of interacting with, being connected to, and experiencing caring for others [31]. Recent studies on remote work [69] and global Int. J. Environ. Res. Public Health 2021, 18, 6966 14 of 19 14 of 19 work [54] demonstrate the importance of considering both the job characteristics (e.g., complexity and problem solving) and the social characteristics (e.g., social support and interdependence) of work. Research [54,55] indicates that as workers are afforded more autonomy and work becomes more unpredictable and volatile, employees need to adapt to contend with the demands of their work environment, including relational demands. This means that employees are active agents crafting their own jobs rather than passive recipients of work characteristics. This perspective aligns well with the findings of this study, which refer to agentic processes—here, independence and clarity, which empower employees to meet the demands of remote work and to adjust. p y j Third, with regard to the relational factors, our findings do not support the hypothesis of a positive relationship between interpersonal trust and adjustment to remote work. The negative relationship between trust and remote work adjustment is a counterintuitive finding that contradicts most of the past research on the relationship between trust and remote work [9,71]. The findings indicate that higher levels of interpersonal trust decrease individual’s adjustment to remote work. Alternatively, the reverse is also true as employees who report low levels of trust seem to adjust better to remote work. This result can be understood from an “out of sight out of mind” perspective, suggesting that some employees may benefit from being separated from colleagues or supervisors they do not trust, or even distrust. Indeed, in the context of this pandemic, scholars have chronicled that the transition to remote work may have benefits for employees as they might be less exposed to toxic workplace relationships, or relieved from bullying colleagues [5]. Our findings align with such insights. 5.1. Theoretical Implications In addition, trust among colleagues and in supervisors could be an indication of a valued interpersonal relationship. Having to miss such a relationship may reduce one’s satisfaction with their job and make it more difficult to maintain productivity levels or overall job performance—all indicators of adjustment. Hence, employees who report high levels of trust in coworkers and supervisors and who feel trusted by them may be less satisfied with remote work, feel less effective, and feel less adjusted. Employees may even want to return to the office as soon as possible to reconnect with their colleagues because the gratification of social needs is arguably satisfied through recurring physical interactions with colleagues. Furthermore, trust built in the physical context may not have transferred to the technology-mediated interactions of remote work environments yet, and if the respondents see limited opportunities to do so, this could lead to a less gratifying remote work experience. Finally, the notion that greater disruption requires greater adaptation certainly rings true for most individuals. The findings suggest that employees who experience greater disruption appear to face more difficulties adjusting to the work setting. Hence, it seems that disruption may indeed require adaptation, but the negative relationship suggests that employees have difficulty making the required adjustments, arguably because adaptation in these cases requires employees to learn new skills and competencies to deal with environmental demands. Hence, the findings demonstrate that employees’ adjustment to abrupt remote work transitions is complicated by the perceived “strength” of the disruption. Overall, the findings suggest that factors underlying agentic processes (i.e., independence and clarity of job criteria) facilitate adaptation and the reappraisal of event outcomes, while relational factors—trust and isolation—operate as barriers to adjustment. This phenomenon calls for further research into the managerial and sociopsychological processes that help to understand the relationship between disruptive events and organizational outcomes. 5.2. Practical and Managerial Implication This study investigated the antecedents of adjustment to remote work. Some factors are directly within the scope of organizational control (e.g., structural factors), while others may be more difficult to influence directly (e.g., contextual factors). However, the results provide important and actionable implications for organizations. First, our results indicate that employees who report higher levels of independence and clarity of job instructions are better able to adjust to remote work. In these circumstances, organizations could Int. J. Environ. Res. Public Health 2021, 18, 6966 15 of 19 15 of 19 provide clearer objectives and goals (decreasing ambiguity) and minimize interdependen- cies between organizational members by designing and allocating autonomous jobs and tasks where possible. In doing so, organizations facilitate agentic processes of individual employees, improving their adjustment to these settings. In addition, organizations need to ensure that there are adequate resources for employees to conduct work independently while maintaining interdependencies at the collective level. For instance, our findings show that CTU in particular, as well as organizational communication quality, may bolster adjustment to remote work. j Managing relational factors deserves slightly more thought because higher levels of trust reduce adjustment, but isolation also reduces adjustment. Social isolation can be reduced in various ways, such as through synchronous video meetings and informal communication. For example, virtual coffee breaks may help employees feel connected to their coworkers and may lead to less isolation in the workplace. In addition, these initiatives might be important in the context of trust. We found a negative relationship with adjustment; however, we argue that trust in this case signals the absence of important interpersonal cues in the physical workplace. Hence, facilitating interpersonal mechanisms of socialization and support might mitigate the negative impact of trust on adjustment. Furthermore, to facilitate greater adjustment in times where resources could be particularly scarce and feelings of isolation particularly high, scholars have suggested that teleconsulta- tions and informal online support groups could help people stay connected [72–74]. In addition, the findings demonstrate that greater change in work location and greater perceived disruption hamper adjustment to remote work. This is important because it sig- nals that organizations and managers should be attentive, especially to employees whose work processes require the greatest adaptation. Our findings show that employees with more experience in remote work adapt to new situations better because they have already learned some practices and competencies needed in remote work. 5.2. Practical and Managerial Implication This implies the impor- tance of training. Organizational support for work–home issues significantly improves well-being [75] and may aid adjustment. For instance, organizations may support their employees through lower workloads or other job demands, giving them greater opportuni- ties to adjust. Additionally, for employees working on vital processes, organizations could have different approaches based on the extent to which the work routines of individuals or groups are disrupted. For instance, these workers could be given priority to use workplace facilities. 5.3. Limitations and Future Research Several limitations need to be acknowledged. First, this study relies on cross-sectional survey data obtained through a convenience sampling method. This method presents two limitations. First, the data do not permit any causal inferences and do not permit us to track how changes in, for instance, perceived disruptions and continued adjustment to the work environment develop over time. Second, the sampling method resulted in a relatively homogeneous group of employees, limiting the generalizability of the findings. The nonrandom sampling technique as well as the sample and population information do not provide sufficient auxiliary information to correct survey responses using weight adjustments. The sample consisted predominantly of Finnish civil servants (60%), many of whom engaged in what could best be described as knowledge work. In addition, we surveyed respondents who had the available means to participate in the study (e.g., stable Internet connection and time). Furthermore, the relatively stable work context of these employees and the Finnish socioeconomic system may be fertile ground for the adjustment of employees, which may not be the case in other types of occupations [5], other socioeconomic systems, or countries that were (at least at the time of the study) more strongly affected by the pandemic (e.g., France, Italy, and Spain) [6]. Future research is needed to demonstrate the generalizability of our findings across a broader range of occupations, countries, and socioeconomic systems. Int. J. Environ. Res. Public Health 2021, 18, 6966 16 of 19 Second, some of the effect sizes are relatively small, which raises questions about the predictive validity of the model. To substantiate these findings, future research is needed to confirm these results over time with various occupational groups in different socioeconomic systems. In addition, although the measures were adopted from previous studies, not all measures have been validated and we do not have pre-pandemic benchmark indices for our population, limiting our ability to draw a conclusion about the relative changes. In addition, responses were collected within the first month of the outbreak. Although this timeframe is considered appropriate to investigate adjustment processes, these processes are also likely to continue as the pandemic evolved. In addition, people now have had more time to adjust and find ways to meet challenges and demands associated with teleworking. Hence, it would be worthwhile to follow up on this study as the relative newness of the pandemic and associated teleworking has decreased. 5.3. Limitations and Future Research Finally, our findings suggest that employees seem to adjust well to remote work. This aligns with studies that conclude that the general attitude toward working from home seems positive [76]. However, this study was conducted in the early stages of the pandemic; therefore, limited assumptions can be made about the long-term implications. In addition, future research may probe more deeply into different aspects that are central to adjustment to remote work, such as those related to work–life dynamics. For instance, now is the opportune time to study whether childless and single employees face increased expectations and work responsibilities, and how these demands may interfere with non-work demands [3]. 6. Conclusions The findings presented in this study provide important insights into the factors that are consequential to employees’ adjustment to remote work. These findings contribute to our understanding of how the COVID-19 pandemic has impacted work. This is impor- tant because the current crisis is far from over [74,77], future pandemics are increasingly likely [74], and other disruptive events, such as economic downturn, natural disasters, activism, and war, may require continuous adjustment from employees and organizations. Our findings contribute to an understanding of how employees adjust to (abrupt) changes in their work environment by identifying and demonstrating the interplay between various environmental and contextual factors. Author Contributions: Conceptualization, W.v.Z., A.S., K.B., T.O., A.R., K.H., and M.V.; methodology, W.v.Z.; software, W.v.Z.; validation W.v.Z.; formal analysis, W.v.Z.; investigation, W.v.Z.; resources, A.S. and K.B.; data curation, W.v.Z.; writing—original draft preparation, W.v.Z.; writing—review and editing, W.v.Z., A.S., K.B., T.O., A.R., K.H., and M.V.; supervision, K.B.; project administration, A.S. and K.B. All authors have read and agreed to the published version of the manuscript. Author Contributions: Conceptualization, W.v.Z., A.S., K.B., T.O., A.R., K.H., and M.V.; methodology, W.v.Z.; software, W.v.Z.; validation W.v.Z.; formal analysis, W.v.Z.; investigation, W.v.Z.; resources, A.S. and K.B.; data curation, W.v.Z.; writing—original draft preparation, W.v.Z.; writing—review and editing, W.v.Z., A.S., K.B., T.O., A.R., K.H., and M.V.; supervision, K.B.; project administration, A.S. and K.B. All authors have read and agreed to the published version of the manuscript. Funding: This research received no external funding. Funding: This research received no external funding. Institutional Review Board Statement: Ethical review and approval were waived for this study, as the study did not involve any of the following: underage subjects, exposure to strong stimuli, potential for long-term mental distress, or intervention with the physical integrity of the participants. Informed Consent Statement: Informed consent was obtained from all participants involved prior to the study. Data Availability Statement: The data presented in this study are not publicly available. Survey respondents were assured raw data would remain confidential and would not be shared. Data Availability Statement: The data presented in this study are not publicly available. Survey respondents were assured raw data would remain confidential and would not be shared. Conflicts of Interest: The authors declare no conflict of interest. Conflicts of Interest: The authors declare no conflict of interest. ) 2. Hodder, A. New Technology, Work and Employment in the era of COVID-19: Reflecting on legacies of research. New Technol. Work Employ. 2020, 35, 262–275. [CrossRef] [PubMed] 1. Pouliakas, K.; Branka, J. EU Jobs at Highest Risk of Covid-19 Social Distancing: Will the Pandemic Exacerbate Labour Market Divide? IZA Discussion Paper No. 13281. 2020. 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Building Trust in Virtual Teams. Professional Communication. IEEE Trans. Prof. Commun. 2004, 47, 95–104. [CrossRef] 57. Coppola, N.W.; Hiltz, S.R.; Rotter, N.G. Building Trust in Virtual Teams. Professional Communication. IEEE Trans. Prof. Commun. 2004, 47, 95–104. [CrossRef] 58. Zakaria, N.; Yusof, S.A.M. Crossing Cultural Boundaries Using the Internet: Toward Building a Model in Global Virtual Teams. J. Int. Manag. 2020, 26, 1–19. [CrossRef] g 59. ter Hoeven, C.L.; van Zoonen, W. Helping Others and Feeling Engaged in the Context of Workplace Flexibility: The Importance of Communication Control. Int. J. Bus. Commun. 2020, 1–22. [CrossRef] J [ ] 60. Staples, D.S.; Hulland, J.S.; Higgins, C.A. References A self-efficacy theory explanation for the management of remote employees in virtual organizations. Organ. Sci. 1999, 10, 758–776. [CrossRef] 60. Staples, D.S.; Hulland, J.S.; Higgins, C.A. A self-efficacy theory explanation for the management of remote employees in virtual organizations. Organ. Sci. 1999, 10, 758–776. [CrossRef] 61. Brockner, J.; Siegel, P.A.; Daly, J.P.; Tyler, T.; Martin, C. When trust matters: The moderating effect of outcome favorability. Adm. Sci. Q. 1997, 42, 558–583. [CrossRef] 61. Brockner, J.; Siegel, P.A.; Daly, J.P.; Tyler, T.; Martin, C. When trust matters: The moderating effect of outcome favorability. Adm. Sci. Q. 1997, 42, 558–583. [CrossRef] 62. House, R.J.; Schuler, R.S.; Levanoni, E. Role Conflict and Ambiguity Scales: Realities or Artifcats? J. Appl. Psychol. 1983, 68, 334–337. [CrossRef] 62. House, R.J.; Schuler, R.S.; Levanoni, E. Role Conflict and Ambiguity Scales: Realities or Artifcats? J. Appl. Psychol. 1983, 68, 334–337. [CrossRef] 19 of 19 19 of 19 Int. J. Environ. Res. Public Health 2021, 18, 6966 63. Moorman, C.; Miner, A.S. The impact of organizational memory on new product performance and creativity. J. Mark. Res. 1997, 34, 91–106. [CrossRef] , [ ] 64. Bordia, P.; Hobman, E.; Jones, E.; Gallois, C.; Callan, V.J. Uncertainty during Organizational Change: Types, Consequences, and Management Strategies. J. Bus. Psychol. 2004, 18, 507–532. [CrossRef] g g y 65. Hair, J.; Black, W.; Babin, B.; Anderson, R. Multivariate Data Analysis, 7th ed.; Prentice-Hall, Inc.: Upper Saddle River, NJ, USA, 2010. 66. Allen, T.D.; Golden, T.D.; Shockley, K.M. How Effective Is Telecommuting? Assessing the Status of Our Scientific Findings. Psychol. Sci. Public Interest 2015, 16, 40–68. [CrossRef] [PubMed] 67. Locke, E.; Bryan, J. Performance goals as determinants of level of performance and boredom. J. Appl. Psychol. 1967, 51, 120–130. [CrossRef] [PubMed] ne, D. Self-Evaluative and Self-Efficacy Mechanisms Governing the Motivational Effects of Goal Systems. J 83, 45, 1017–1028. [CrossRef] 68. Bandura, A.; Cervone, D. Self-Evaluative and Self-Efficacy Mechanisms Governing the Motivational E Pers. Soc. Psychol. 1983, 45, 1017–1028. [CrossRef] 69. Latham, G.P.; Locke, E.A. Increasing productivity with decreasing time limits: A field replication of Parkinson’s law. J. Appl. Psychol. 1975, 60, 524–526. [CrossRef] 70. Wood, R.E.; Locke, E.A. Goal setting and strategy effects on complex tasks. In Research in Organizational Behavior; Staw, B., Cummings, L.L., Eds.; JAI Press: Greenwich, CT, USA, 1990; pp. 73–109. 71. Wilson, J.M.; Straus, S.G.; McEvily, B. All in due time: The development of trust in computer-mediated and face-to-face teams. Organ. References Behav. Hum. Decis. Process. 2006, 99, 16–33. [CrossRef] 72. Ng, Q.X.; Chee, K.T.; De Deyn, M.L.Z.Q.; Chua, Z. Staying connected during the COVID-19 pandemic. Int. J. Soc. Psychiatry 2020, 66, 519–520. [CrossRef] 73. Hixon, T. Get Ready to Live with COVID-19. Available online: https://www.forbes.com/sites/todd ready-to-live-with-covid-19/#26f55d347824 (accessed on 23 April 2020). 74. Desmond-Hellmann, S. Preparing for the Next Pandemic. Available online: https://www.wsj.com/articles/preparing-for-the- next-pandemic-11585936915 (accessed on 27 April 2020). p p 75. Golden, T.D.; Raghuram, S. Teleworker knowledge sharing and the role of altered relational and technological interactions. J. Organ. Behav. 2010, 31, 1061–1085. [CrossRef] g 76. Beauregard, T.A. Direct and Indirect Links between Organizational Work-Home Culture and Employee Well-being. Br. J. Manag. 2011, 22, 218–237. [CrossRef] 77. Beck, M.J.; Hensher, D.A.; Wei, E. Slowly coming out of COVID-19 restrictions in Australia: Implications for working from home and commuting trips by car and public transport. J. Transp. Geogr. 2020, 88, 102846. [CrossRef] [PubMed]
https://openalex.org/W2783520694
https://www.cambridge.org/core/services/aop-cambridge-core/content/view/949402C56ECEC4CBCBC2A519BEE8BD76/S0955603600085822a.pdf/div-class-title-black-marks-for-black-daisies-div.pdf
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Black marks for Black Daisies
Psychiatric bulletin of the Royal College of Psychiatrists/Psychiatric bulletin
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Psychiatry and the media Black marks for Black Daisies Brice Pitt reviews 'Black Daisies for the Bride' by Tony Harrison; directed by Peter Symes; Screenplay, BBC2 Brice Pitt reviews 'Black Daisies for the Bride' by Tony Harrison; directed by Peter Symes; Screenplay, BBC2 ::•' Scene from 'Black Daisies for the Bride' (Copyright BBC) I've had difficulty in writing this review. I initially caught the last half of Tony Harrison's 'docudrama' about Alzheimer's disease shown at the outset of Alzheimer Awareness Week in July and hated it. My heart sank at the Brechtian device of putting the dialogue to the tune of a hymn (in this case the carol 'In the Bleak Midwinter'), and I found the approach to the three 'star' patients chosen for the film from those in Whernside ward. High Royds Hospital, sentimental and patronising. Scene from 'Black Daisies for the Bride' (Copyright BBC) p g Yet Harrison isa highly respected poet and drama tist. His translation of Le Misanthrope delighted National Theatre audiences in 1973, his Phaedra Britannica in 1975 was a notable achievement, and his translation of The Oresteia, directed by Peter Hall, in 1981was one of the NT's greatest triumphs. A more recent poem is The Mother of the Muses (who is, of course, Memory) in 1987, the product of his involvement in his father-in-law's Alzheimer's disease. This, then, is a return to a subject which clearly concerns him deeply. Neurological disorders are increasingly fascinating to other than doctors- hence the adaptation to the cinema of'Awakenings', to opera of 'The Man who Mistook his wife for his Hat' and the impressive film about finding a treatment for adrenoleucodystrophy, 'Lorenzo's Oil'. N th t I' f d lf t t h th h l agreed to do so and were paid. What about the patients? Do they now hold Equity cards? Was Leeds Community and Mental Health Services Teaching NHS Trust happy to give its consent to their exposure? I f d th 'd ' t f th pI found the 'docu' part of the programme more successful than the drama. Whernside isan authentic dementia ward and one wouldn't doubt that the patients need to be there. The screams, yells and squawks, the tussle between two old ladies, Kathleen's relentless perambulations, the slurped yoghurt now on the floor are utterly real; only the shit is missing. "Thinking what they all have been Makes Alzheimer's horrible and obscene". Well, yes. But is that all? Is it enough to be made aware of just how dreadful an affliction it is? https://doi.org/10.1192/pb.17.11.672 Published online by Cambridge University Press Psychiatrie Bulletin (1993), 17,672-673 Psychiatrie Bulletin (1993), 17,672-673 (or My Girlfriend is a Rover Metro) RICHARDC. BARNES,Registrar in Psychiatry, Rathbone Hospital, Mill Lane, Liverpool L13 4AW; and STEPHENEARNSHAW,Registrar in Psychiatry, Winwick Hospital, WarringtonWA28RR The main source of topical information in most parts of the world is through the mass media - principally newspapers and television. Television news and current affairs have a duty to remain impartial, as they provide a service for the whole population. Newspapers, on the other hand, have a greater journalistic and editorial freedom as they target subgroups. British newspapers are currently being scrutinised as to how they report both factual and speculative information of a general kind. At the same time there seems to be an increase in their interest in psychological matters. However, work on newspaper reporting of psychiatric disorders (Day & Page, 1986; Matas et al, 1986) has shown that the mentally ill are usually portrayed in a rather negative light with few positive images. about mental illness, and these totalled 7 (13%) in The Mirror and 15 (33%) in The Independent. Of the broadsheet articles, 13 were written by journalists and two by medically trained writers. They covered a wide range of illnesses, and six of the articles reported directly on published work in psychiatric journals as part of a regular review of medical literature. In contrast to this, the tabloid newspaper, with only seven articles, had no reports on scientific research, and over half of the articles were written by the newspaper's resident medical journalist, a practising general practitioner. g p Reports of individual cases of mental illness formed the second group, and yielded 39 (71%) tabloid and 20 (43%) broadsheet items. Despite the large numbers of cases reported on, only seven were reported in both newspapers. This meant a total of 52 cases, 31 of which related to criminal acts or suicide. The study The tabloid newspaper contained a much greater proportion of reports of suicides, 12 (31%) com pared with two (10%), and these typically in unusual or otherwise noteworthy circumstances ('Love-rift tycoon's suicide horror', 'Santa's suicide plunge', 'Suicide of pilot who nearly hit a hotel'). In total, nine cases of people with identifiable psychotic illness were reported, and in all these cases the circum stances involved violent crime or murder. Of those cases concerning non-psychotic illness, all the re ports (11 in total) linked the illness to unusual and generally humorous presentations ('Bizarre bagpipe phobia baffles doctors', 'Student stuns shrinks, "My girlfriend is a Rover Metro" ', 'Little boy eats nothing but Spam'). Nine further articles mentioned doctors working in the psychiatric field, all but two We have recently examined two different formats of newspaper; 'broadsheet' (The Independent) and 'tabloid' (The Mirror), collecting all reports related to mental illness over the three months from October to December 1992. The Mirror has average daily sales of around 3.5 million, while The Independent's, circulation averages around 368.000. Black marks for Black Daisies doll". Cringe-making? Possibly-until Maria gives him her wonderful 'A' and Kathleen first sways and then claps to the rhythm! Music, for the moment, makes a link between these lost souls and the world they have almost left. In a thoughtful epilogue on The Late Show', Michael Ignatieff, who has a grim family history of the disease, accuses the poet of offering too much hope! He is referring to the one sequence which I shall treasure. Enter guitarist Richard Muttonchops(i/f), who serenades the ladies with "Oh, you beautiful Psychiatry and the media Black marks for Black Daisies On the other hand the arty direction- shots in a convex mirror, confetti, petals, leaves and snowflakes in the blizzard which symbolises Alzheimer's, veils and bridal gloves discarded in woodland - sometimes borders on kitsch. The link ing of the ward's coded entrance to the patients' loss of an access code to their memories, and the remark that Death has the only exit code from Whernside, is somewhat pretentious. But I liked the echoing howl which turns out to be the electric trolley making its way through the corridors of the old mental hospital. Now that I ve forced myself to watch the whole film I see that it is better than my first impression, but qualms remain. The 'black daisies' are the motif of a mosaic floor at High Royds. and Harrison links this to the song 'Daisy, Daisy' and shows the younger selves of his protagonists as brides. The still beautiful Maria, an opera singer, who can now sing only one note, a thrilling 'A', is seen as Lucia di Lammermoor. Kathleen, 'angler, climber, gardener, cook, accordionist and pianist', who now just cleans and cleans, is shown as a bride singing of motorbike mountaineering with her fiance Harold. One or other of two Muriels - one was a 'therapist', the other says little more than 'I love you' - is also a bride. Another person of few words is Matthew, who just says 'Go away'. Actresses play the younger trio (and a rather challenging therapist) and presumably What is Harrison trying to say? In one of his (fairly excruciating) couplets his angry therapist remarks: "Thinking what they all have been Makes Alzheimer's horrible and obscene". Well, yes. But is that all? Is it enough to be made aware of just how dreadful an affliction it is? 672 https://doi.org/10.1192/pb.17.11.672 Published online by Cambridge University Press 2 Published online by Cambridge University Press 673 Black marks for Black Daisies Findings Th The survey yielded a total of 55 reports in "The Mirror' and 46 in 'The Independent', and these reports were divided up into four groups. The first group included those reports giving information 2 Published online by Cambridge University Press
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https://essd.copernicus.org/preprints/essd-2023-331/essd-2023-331.pdf
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ERROR: type should be string, got "https://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nThe Total Carbon Column Observing Network’s GGG2020 Data\nVersion\nJoshua L. Laughner1 , Geoffrey C. Toon1 , Joseph Mendonca2 , Christof Petri3 , Sébastien Roche4,5 ,\nDebra Wunch6 , Jean-Francois Blavier1 , David W.T. Griffith7 , Pauli Heikkinen8 , Ralph F. Keeling9 ,\nMatthäus Kiel1 , Rigel Kivi8 , Coleen M. Roehl10 , Britton B. Stephens11 , Bianca C. Baier13 ,\nHuilin Chen14 , Yonghoon Choi15,16 , Nicholas M. Deutscher7 , Joshua P. DiGangi15 , Jochen Gross17 ,\nBenedikt Herkommer17 , Pascal Jeseck18 , Thomas Laemmel19,* , Xin Lan12,13 , Erin McGee6 ,\nKathryn McKain13 , John Miller13 , Isamu Morino20 , Justus Notholt3 , Hirofumi Ohyama20 , David\nF. Pollard21 , Markus Rettinger22 , Haris Riris23 , Constantina Rousogenous24 , Mahesh Kumar Sha25 ,\nKei Shiomi26 , Kimberly Strong6 , Ralf Sussmann22 , Yao Té18 , Voltaire A. Velazco7,27 , Steven C. Wofsy4 ,\nMinqiang Zhou25,** , and Paul O. Wennberg10,28\n1\n\nJet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA\nClimate Research Division, Environment and Climate Change Canada, Toronto, ON, Canada\n3\nInstitute of Environmental Physics, University of Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany\n4\nJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA\n5\nCenter for Astrophysics, Harvard & Smithsonian, Cambridge, MA, USA\n6\nDepartment of Physics, University of Toronto, Toronto, Canada\n7\nCentre for Atmospheric Chemistry, School of Earth, Atmospheric and Life Sciences, University of Wollongong,\nWollongong, New South Wales, Australia\n8\nSpace and Earth Observation Centre, Finnish Meteorological Institute, Sodankylä, Finland\n9\nScripps Institute of Oceanography, La Jolla, California, USA\n10\nDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA\n11\nEarth Observing Laboratory, National Center for Atmospheric Research (NCAR), Boulder, CO, USA\n12\nCooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, USA\n13\nNOAA Global Monitoring Laboratory, Boulder, USA\n14\nCenter for Isotope Research, University of Groningen, Groningen, the Netherlands\n15\nNASA Langley Research Center, Hampton, VA 23681\n16\nAnalytical Mechanics Associated, Hampton, VA 23666\n17\nKarlsruhe Institute of Technology (KIT), Institute of Meteorology and Climate Research (IMK-ASF), Karlsruhe, Germany\n18\nLaboratoire d’Études du Rayonnement et de la Matière en Astrophysique et Atmosphères (LERMA-IPSL), Sorbonne\nUniversité, CNRS, Observatoire de Paris, PSL Université, 75005 Paris, France\n19\nUniversité Paris-Saclay, CEA, CNRS, UVSQ, Laboratoire des Sciences du Climat et de l’Environnement (LSCE/IPSL),\nGif-sur-Yvette, France\n20\nNational Institute for Environmental Studies (NIES), Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan\n21\nNational Institute of Water and Atmospheric Research Ltd (NIWA), Lauder, New Zealand\n22\nKarlsruhe Institute of Technology (KIT), IMK-IFU, Garmisch-Partenkirchen, Germany\n23\nNASA Earth Science Technology Office (ESTO), B22, 242, 8800 Greenbelt Rd., Greenbelt, MD. 20771\n24\nClimate and Atmosphere Research Centre (CARE-C), The Cyprus Institute, Nicosia, Cyprus\n25\nRoyal Belgian Institute for Space Aeronomy, Brussels, Belgium\n26\nEarth Observation Research Center (EORC), Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan\n27\nDeutscher Wetterdienst, Meteorological Observatory Hohenpeissenberg, 82383 Hohenpeissenberg, Germany\n28\nDivision of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA\n2\n\n1\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n*\n\nNow at: University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences and Oeschger Center for\nClimate Change Research, Bern, Switzerland\n**\nNow at: Institute of Atmospheric Physics, Chinese Academy of Sciences, China\nCorrespondence: Joshua Laughner (josh.laughner@jpl.nasa.gov)\nAbstract. The Total Carbon Column Observing Network (TCCON) measures column-average mole fractions of several greenhouse gases (GHGs) beginning in 2004 from over 30 current or past measurement sites around the world, using solar absorption\nspectroscopy in the near infrared region. TCCON GHG data have been used extensively for multiple purposes, including in\nstudies of the carbon cycle and anthropogenic emissions as well as to validate and improve observations made from space5\n\nbased sensors. Here, we describe an update to the retrieval algorithm used to process the TCCON near IR solar spectra and\nthe associated data product. This version, called GGG2020, was initially released in April 2022. It includes updates and improvements to all steps of the retrieval, including but not limited to: converting the original interferograms into spectra, the\nspectroscopic information used in the column retrieval, post hoc airmass dependence correction, and scaling to align with the\ncalibration scales of in situ GHG measurements.\nAll TCCON data are available through tccondata.org and hosted on CaltechDATA (data.caltech.edu). Each TCCON site has\n\n10\n\na unique DOI for its data record. An archive of all sites’ data is also available with the DOI 10.14291/TCCON.GGG2020\n(Total Carbon Column Observing Network (TCCON) Team, 2022). The hosted files are updated approximately monthly, and\nTCCON sites are required to deliver data to the archive no later than one year after acquisition. Full details of data locations\nare provided in the data availability section.\n\n15\n\n1\n\nIntroduction\n\nThe Total Carbon Column Observing Network (TCCON) is a network of nearly 30 ground-based, solar-viewing, Fourier\ntransform infrared (FTIR) spectrometers that report observations of column average mole fractions of CO2 , CH4 , N2 O, CO,\nHF, H2 O, and HDO in the atmosphere. The first two TCCON stations were established in 2004, with additional stations\njoining over the following years. As of July 2023, 30 sites exist. In that time, TCCON data have been used to estimate or\n20\n\nevaluate carbon fluxes (e.g. Keppel-Aleks et al., 2012; Peiro et al., 2022), for satellite validation (e.g. Wunch et al., 2017; Chen\net al., 2022; Lorente et al., 2022), for model verification (e.g. Byrne et al., 2023), and for other purposes.\nTCCON instruments measure solar spectra in the near-infrared (NIR) wavelengths; these spectra are converted into the final\ncolumn average mole fractions (henceforth denoted as “Xgas ”, e.g. “XCO2 ”) using the retrieval software GGG.1 Major versions\nof GGG are identified by the year of development. The previous version used to generate public TCCON data was GGG2014\n\n25\n\nand is described in Wunch et al. (2015). GGG2020 is the first major update applied to TCCON public data since GGG2014.\nGGG retrieves trace gas column amounts by iteratively scaling an a priori vertical trace gas profile until the best fit between\na spectrum simulated from those trace gas profiles by the built-in forward model and the observed spectrum is found. A single\ngas may be fit in more than one spectral window; for example, GGG2020 retrieves the standard TCCON CO2 product from\n1 GGG\n\nis the proper name of the software, and is not an acronym.\n\n2\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\ntwo separate windows (6220 to 6260 cm−1 and 6297 to 6382 cm−1 ). Each window is run separately and produces its own\n30\n\nposterior scaled trace gas profile, which can be integrated to generate a column density. Retrieving each window separately,\nrather than concatenating the spectral information, makes it simpler to handle non-contiguous windows that need different state\nvector elements. It also allows biases that differ between these windows to be expressed separately in the resulting output data\nand, if necessary, corrected separately. The output values (column densities and profile scaling factors) from different windows\nwith similar averaging kernels for the same target gas are combined in a weighted average during post processing.\n\n35\n\nThe post processing step includes the above window-to-window averaging alongside an empirical airmass-dependent correction, a scaling correction to tie TCCON data to the relevant calibration scales, and the conversion from column densities\nto column-average mole fractions. Airmass-dependent errors can arise from, for example, errors in the relative intensities of\nstrong and weak absorption lines for a target gas. At large solar zenith angles (SZAs), the longer light paths through the atmosphere will cause strong absorption lines to completely absorb incoming light within their core wavelengths; such lines may be\n\n40\n\nreferred to as “blacked out”. Blacked out lines cannot contribute information to the retrieval, so the retrieval must get a greater\nfraction of its information from weaker lines in the spectral window or the wings of saturated lines. If there is a different bias\nin the forward model between the strong and weak lines, it will manifest as an error in the retrieved column amounts that varies\nwith SZA and is symmetric about solar noon. Once the magnitude of this error is derived (§7.1), a post-processing correction\ncan be applied to remove it.\n\n45\n\nThe scaling factor used to tie to calibration scales is necessary because the spectroscopic parameters needed by the forward\nmodel are not in general known to the ∼ 0.25% or better accuracy needed for greenhouse gas data. However, since all TCCON\n\nsites use the same retrieval (and thus the same forward model), we use a single mean scaling factor to remove the mean bias\ncaused by errors in the spectroscopic parameters. This does implicitly assume that imperfect instrument line shape (ILS) or\n\nimperfect representation of the instrument in the forward model are either (a) consistent across sites and thus accounted for by\n50\n\nthe scaling factor or (b) random and average to zero. The scaling factors for the various gases are derived from comparisons\nbetween TCCON data and in situ vertical profiles measured by aircraft- or balloon- borne instruments (§7.3).\nFinally, the conversion from column densities to column-average dry mole fractions is done by dividing the target gas column\n(Vgas ) by the O2 column (VO2 ), then multiplying by the mean O2 mole fraction (fO2 ) in the atmosphere:\nXgas =\n\n55\n\nVgas\n· fO2\nVO2\n\n(1)\n\nGGG2020 assumes that fO2 = 0.2095 for all retrievals except those listed in §7.3.2. The advantages of normalizing to the O2\ncolumn are:\n1. It normalizes for path length. Observations at surface elevations will have smaller column densities compared to those\nfrom lower altitudes, due to the shorter vertical extent. Normalizing to the O2 column removes this effect.\n2. Because O2 and the primary TCCON gases are measured on the same detector, many biases related to the detector and\n\n60\n\npointing will be cancelled out (Wunch et al., 2011, Appendices A and B).\n\n3\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nGGG is comprised of several sub-programs, which handle these various elements of the retrieval. Each of these has been\nupgraded for GGG2020:\n– i2s: converts interferograms to spectra. Updates include identifying detector nonlinearity and better phase correction\n(§5).\n– gsetup: prepares the input files needed to run gfit (a priori meteorology and trace gas profiles, atmospheric path infor-\n\n65\n\nmation, etc.) in the required formats. Updates include the source of a priori meteorology and trace gas profiles and the\nretrieval grid (§4).\n– gfit: retrieves column densities from the spectra output by i2s. Updates include the forward model spectroscopy (§3) and\ncontinuum fitting (§6).\n– Post processing: a suite of programs that collates the output from gfit and applies any required post hoc corrections.\n\n70\n\nUpdates include the airmass correction (§7.1), window to window averaging (§7.2), and scaling to tie to in situ calibration\nscales (§7.3).\nGGG2020 data is available through tccondata.org. A repository containing the full set of publicly available data is available\nthrough CaltechDATA (Total Carbon Column Observing Network (TCCON) Team, 2022). Each TCCON site’s data record\n75\n\nhas its own unique DOI. On occasions that a site needs to reprocess and redeliver data already released to the public, the\nrevised dataset will receive a new DOI with the revision number incremented. TCCON sites are permitted to withhold data\nfrom the public archive for up to one year from acquisition. This public archive is updated approximately once per month\nwith newly delivered or released data. The TCCON data product is documented extensively through the TCCON Wiki (https:\n//tccon-wiki.caltech.edu/). Users are asked to familiarize themselves with the data use policy and license, which are available\n\n80\n\nat https://tccon-wiki.caltech.edu/Main/DataUsePolicy.\n2\n\nNew Xgas products\n\nGGG2020 introduced XCO2 mole fractions retrieved in two new windows: a strong band between 4809.74 and 4896.0 cm−1\nand a weak band between 6041.8 and 6105.2 cm−1 . We refer to these as “lCO2 ” and “wCO2 ”, respectively. These are reported\nas separate CO2 products (XlCO2 and XwCO2 ) and are not averaged together with the standard TCCON XCO2 product. Figure\n85\n\n1 shows the column averaging kernels (AKs) and CO2 absorption lines in these two windows. The lCO2 AKs increase towards\nthe surface, while, at small slant Xgas amounts (i.e. small solar zenith angle) the wCO2 AKs are greater in the stratosphere\nthan in the lower troposphere. This is because, as seen in Fig. 1b and d the CO2 absorption lines in the lCO2 band are mostly\nsaturated at the line center, while the wCO2 lines are not. In theory, when used together with the standard TCCON XCO2\nproduct (which has an AK profile that is more constant with altitude than the wCO2 or lCO2 products, see Fig. 25), this\n\n90\n\nprovides the potential to separate changes in CO2 at the surface, from those in the free troposphere or stratosphere (Parker\net al., 2023).\n4\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nTable 1. List of TCCON sites and their associated data citations as of 20 Dec 2022. Some sites (Lauder, JPL) have had different FTIR\ninstruments operating over different periods, and so are listed multiple times.\nSite ID\n\nSite Name\n\nLocation\n\nData Citation\n\nae\n\nascension01\n\nAscension Island, Saint Helena\n\nFeist et al. (2017)\n\nan\n\nanmeyondo01\n\nAnmyeondo, South Korea\n\nGoo et al. (2017)\n\nbi\n\nbialystok01\n\nBialystok, Poland\n\nPetri et al. (2017)\n\nbr\n\nbremen01\n\nBremen, Germany\n\nNotholt et al. (2022)\n\nbu\n\nburgos01\n\nBurgos, Philippines\n\nMorino et al. (2022c)\n\nci\n\npasadena01\n\nPasadena, California, USA\n\nWennberg et al. (2022c)\n\ndb\n\ndarwin01\n\nDarwin, Australia\n\nDeutscher et al. (2023a)\n\ndf\n\nedwards01\n\nAFRC, Edwards, CA, USA\n\nIraci et al. (2022b)\n\net\n\neasttroutlake01\n\nEast Trout Lake, Canada\n\nWunch et al. (2022)\n\neu\n\neureka01\n\nEureka, Canada\n\nStrong et al. (2022)\n\nfc\n\nfourcorners01\n\nFour Corners, NM, USA\n\nDubey et al. (2022b)\n\ngm\n\ngarmisch01\n\nGarmisch, Germany\n\nSussmann and Rettinger (2017a)\n\nhf\n\nhefei01\n\nHefei, China\n\nLiu et al. (2022)\n\nhw\n\nharwell01\n\nHarwell, UK\n\nWeidmann et al. (2023)\n\nif\n\nindianapolis01\n\nIndianapolis, Indiana, USA\n\nIraci et al. (2022a)\n\niz\n\nizana01\n\nIzana, Tenerife, Spain\n\nBlumenstock et al. (2017)\n\njc\n\njpl01\n\nJPL, Pasadena, California, USA\n\nWennberg et al. (2022e)\n\njf\n\njpl02\n\nJPL, Pasadena, California, USA\n\nWennberg et al. (2022a)\n\njs\n\nsaga01\n\nSaga, Japan\n\nShiomi et al. (2022)\n\nka\n\nkarlsruhe01\n\nKarlsruhe, Germany\n\nHase et al. (2022)\n\nlh\n\nlauder01\n\nLauder, New Zealand\n\nSherlock et al. (2022a)\n\nll\n\nlauder02\n\nLauder, New Zealand\n\nSherlock et al. (2022b)\n\nlr\n\nlauder03\n\nLauder, New Zealand\n\nPollard et al. (2022)\n\nma\n\nmanaus01\n\nManaus, Brazil\n\nDubey et al. (2022a)\n\nni\n\nnicosia01\n\nNicosia, Cyprus\n\nPetri et al. (2023)\n\nny\n\nnyalesund01\n\nNy-Ålesund, Svalbard, Norway\n\nBuschmann et al. (2022)\n\noc\n\nlamont01\n\nLamont, Oklahoma, USA\n\nWennberg et al. (2022d)\n\nor\n\norleans01\n\nOrleans, France\n\nWarneke et al. (2022)\n\npa\n\nparkfalls01\n\nPark Falls, Wisconsin, USA\n\nWennberg et al. (2022b)\n\npr\n\nparis01\n\nSorbonne Université, Paris, FR\n\nTe et al. (2022)\n\nra\n\nreunion01\n\nReunion Island, France\n\nMaziere et al. (2022)\n\nrj\n\nrikubetsu01\n\nRikubetsu, Hokkaido, Japan\n\nMorino et al. (2022a)\n\nso\n\nsodankyla01\n\nSodankylä, Finland\n\nKivi et al. (2022)\n\ntk\n\ntsukuba02\n\nTsukuba, Ibaraki, Japan, 125HR\n\nMorino et al. (2022b)\n\nwg\n\nwollongong01\n\nWollongong, Australia\n\nDeutscher et al. (2023b)\n\nxh\n\nxianghe01\n\nXianghe, China\n\nZhou et al. (2022)\n\nzs\n\nzugspitze01\n\nZugspitze, Germany\n\nSussmann and Rettinger (2017b)\n\nBeginning with GGG2020, experimental mid-IR data products will be available from select TCCON sites equipped with an\nInSb (indium antimonide) detector that enables measurements in the 1800 to 4000 cm−1 frequency range. Gases measured in\nthis range include, but are not limited to, O3 , N2 O, CO, CH4 , NO, NO2 , carbonyl sulfide, formaldehyde, and ethane. These\n95\n\nproducts offer the potential to extend the applications of TCCON data to new areas of research. However, it is important to\n\n5\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n104\n\n0\n\n(b)\n\nSlant XlCO2\n\nPressure (hPa)\n\n200\n400\n\n103\n\n600\n800\n\n(c)\n\n0\n\n0.00 0.25 0.50 0.75 1.00 1.25 1.50 1.75\nXlCO2 column AK (unitless)\n\n104\n\nSlant XwCO2\n\nPressure (hPa)\n\n200\n400\n\n103\n\n600\n800\n1000\n0.50 0.75 1.00 1.25 1.50 1.75 2.00 2.25\nXwCO2 column AK (unitless)\n\n0.8\n0.6\n0.4\n0.2\n0.0\n\n102\n\n(d)\nIntensity (arbitrary units)\n\n1000\n\n1.0\n\nIntensity (arbitrary units)\n\n(a)\n\n102\n\n4820\n\n1.00\n\n4840\n4860\nFrequency (cm 1)\n\n4880\n\n4900\n\n0.95\n0.90\n0.85\n0.80\n6040\n\n6050\n\n6060\n\n6070 6080\nFrequency (cm 1)\n\n6090\n\n6100\n\nFigure 1. Column averaging kernels (panels a, c) and calculated CO2 absorption lines (panels b, d) in the lCO2 (panels a, b) and wCO2\n(panels c, d) windows, respectively. The absorption lines in panels (b) and (d) are for a TCCON spectrum measured at solar zenith angle =\n39.684◦ in Jul 2004 at Park Falls, WI, USA. In panels (a) and (c), the different colors indicate AKs for different slant Xgas amounts. “Slant\nXgas ” is a measure of total absorber column along the light path. See §9.1 for details.\n\nnote that these data do not have any postprocessing corrections for airmass dependence (§7.1) or scaling to in situ data (§7.3)\napplied.\n3\n\nUpdated spectroscopy\n\n3.1\n100\n\nTelluric & Solar line lists\n\nThe telluric linelist (atm.161, Toon, 2022c) is a \"greatest hits\" compilation based heavily on HITRAN predecessor lists, but\nwith ad hoc empirical corrections performed to some lines, bands, and gases. The linelist is updated when improved linelists\nbecome available, as determined by 1) improved fits to laboratory and atmospheric spectra, 2) better consistency of retrieved\ngas amounts from different windows and bands, and 3) reduced airmass-dependence of the retrieved gas amounts. Since the\nGGG2016 version of the linelist, there have been many improvements to the H2 O and HDO spectroscopy throughout the main\n\n105\n\nTCCON region (4000 to 8000 cm−1 ).\nThe solar linelist (Toon, 2022b) is completely empirical, based on high-resolution solar spectra measured by various instruments from the ground, balloon, and space. In the 4000 to 8000 cm−1 spectral region covered by TCCON, the linelist is based\nprimarily on ground-based Kitt Peak and TCCON spectra, with additional balloon-borne MKIV spectra from 40 km altitude\nup to 5600 cm−1 . To deduce which absorption features are solar, rather than telluric, we fit out the telluric spectrum as best we\n\n110\n\ncan. Remaining dips in the residuals are solar, unless they grow with airmass, in which case they are missing tellurics. Since\nGGG2016 the improvements have been modest, adding new weak lines (< 0.1% depth) in the TCCON windows.\n\n6\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n3.2\n\nNon-Voigt lineshapes for O2 , CO2 , and CH4\n\nAbsorption coefficients calculations were improved in GGG2020. In previous versions of GGG absorption coefficients were\ncalculated using a Voigt spectral line shape. Numerous spectroscopic studies have shown that the Voigt line shape is insufficient\n115\n\nfor use with CO2 and other molecules, so a more sophisticated line shape is required to achieve the necessary retrieval accuracy.\nSo quadratic speed-dependent Voigt (qSDV) with line mixing (LM) code from Tran et al. (2013) was implemented into forward\nmodel of GGG (Toon, 2022a).\nIt was shown in Mendonca et al. (2016) that using the qSDV with first order LM and adopting the spectroscopic parameters\nfrom Devi et al. (2007b) for the CO2 lines in CO2 window centered at 6220 cm−1 and Devi et al. (2007a) for the window cen-\n\n120\n\ntered at 6339 cm−1 resulted in an up to 40% improvement to both spectral fit RMS and a reduction in the airmass dependence\nof the retrieved XCO2 . For the strong CO2 band lines, in the window centered at 4850 cm−1 , the spectroscopic parameters\nfrom Benner et al. (2016) are used with the qSDV and first order LM to calculate absorption coefficients. This resulted in\nimproving the quality of XCO2 retrievals from this spectral region. New spectroscopic studies aimed at improving CO2 absorption coefficient calculations are ongoing. Recent studies like Hashemi et al. (2020) that provide spectroscopic parameters\n\n125\n\nfor CO2 can be tested with TCCON spectra to see if the retrievals can be improved.\nTCCON CH4 is retrieved from three windows that are composed of the P, Q, and R branches of the 2ν3 CH4 band. To\nimprove the forward model of GGG the spectroscopic parameters from Devi et al. (2015, 2016) are used to calculate the\nabsorption coefficients with the qSDV with full line mixing. Unlike CO2 that uses first order line mixing requiring one extra\nparameter to be added to the linelist per spectral line, CH4 requires full line mixing. This requires spectroscopic parameters\n\n130\n\nfrom all coupled lines (i.e. a relaxation matrix) be used to calculate the effective spectral line parameters for each spectral line.\nIn previous versions of GGG absorption coefficients could only be calculated by reading in spectroscopic parameters line by\nline making it awkward to take into account full line mixing. GGG2020 has been updated to read in spectroscopic parameters\nand the relaxation matrix (supplied with Devi et al. (2015, 2016)) at the same time for spectral lines that require full line mixing.\nMore details on how this is done are provided in Mendonca et al. (2017). The improved absorption coefficient calculations for\n\n135\n\nCH4 lines for the 2ν3 CH4 band has improved the quality of the spectral fits and airmass dependence of the retrieved XCH4 .\nThe addition of full line mixing can be extended to other molecules to improve retrievals.\nTo improve the retrievals of O2 columns, which are required to calculate Xgas , spectroscopic parameters for the O2 singlet\ndelta band were retrieved by fitting cavity ring down spectra as detailed in Mendonca et al. (2019). The spectroscopic parameters derived from the cavity ring down spectra were tested on TCCON spectra where they were shown to slightly improve the\n\n140\n\nquality of the spectral fit as well as greatly decrease the airmass dependence of the retrieved O2 column. The study by Mendonca et al. (2019) is the first to show the need for a spectral line shape that takes into account speed-dependence. Since then,\nnewer spectroscopic studies such as Tran et al. (2020) and Fleurbaey et al. (2021) have shown the need to take into account\nDicke narrowing and line mixing in order to fit new cavity ring down spectra in the O2 singlet delta band. The spectroscopic\nparameters of Mendonca et al. (2019), Tran et al. (2020), and Fleurbaey et al. (2021) were used to fit TCCON O2 spectra in\n\n7\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n145\n\nTran et al. (2021). The study showed that the newer spectroscopic parameters slightly improved the quality of the spectral fit\nbut they should also be assessed on how they impact the airmass dependence of retrieved O2 columns.\n3.3\n\nEmpirical optimization of O2 line widths\n\nDuring pre-release testing, we found that a diagnostic quantity we call Xluft had a noticeable temperature dependence (Fig.\n2a). Xluft is a ratio of two ways of calculating the column of dry air (one from surface pressure and the a priori H2 O profile,\n150\n\nand one from the column of O2 retrieved in the singlet delta band—or put another way, it is the column-average mole fraction\nof dry air), and thus should not have a temperature dependence. Since dry mole fractions of O2 in the atmosphere are highly\nconstant over space and time, this implied that either temperature-dependence or the water broadening of the O2 line widths in\nthe forward model was incorrect, as the concentration of water in the atmosphere is generally correlated with temperature.\nTo disentangle the effect of temperature and water, we first examined data from the Darwin, Australia TCCON station.\n\n155\n\nDarwin is located in the tropics, and so experiences greater water columns and a narrower range of temperatures than other\nTCCON sites (Fig. 3a,b). We chose approximately 14 months of data from Darwin when the instrument was performing well,\nand processed that year three times, with water broadening set to 1.0, 1.4, and 1.8 times that of the air broadening half width.\nTo identify the optimal strength for water broadening, we examined the slope of Xluft vs. water column in 10° SZA bins\nfor each of these tests. Binning the data by SZA helps to separate the water dependence from airmass dependence. Figure 3c\n\n160\n\nshows that a water broadening of 1.4 times that of air minimized the dependence of Xluft on water.\nWith the water broadening optimized, we turned to the temperature dependence of the O2 line widths. Reducing the dependence of Xluft on temperature was the primary goal; however, we had to account for the interplay between the temperature and\npressure dependence. In particular, our concern was that changing the temperature dependence of the O2 line widths would\nintroduce or increase an SZA dependence by changing the average line widths.\n\n165\n\nOur solution was to simultaneously adjust both the temperature and pressure dependence of the O2 line widths. To find the\noptimal combination of these coefficients, we minimized a cost function of three quantities. For each quantity, we tested how\nthe results changed using a different collection of TCCON sites:\n1. The average magnitude of the Xluft vs. temperature at 700 hPa (T700) slope across various combinations of 1–3 of the\nEast Trout Lake, Lamont, and Park Falls sites.\n\n170\n\n2. The variance of the Xluft vs. SZA slopes across the Darwin, East Trout Lake, Lamont, and Park Falls sites.\n3. The variance of the magnitude of Xluft across the same sites as #2.\nOur rationale was that the temperature dependence of Xluft was the most important error to eliminate, thus minimizing its\nmagnitude took priority. T700 is taken from the a priori meteorology data and was chosen as a useful metric of synoptic-scale\nchange (Keppel-Aleks et al., 2011). We then minimized the variance in slopes of Xluft vs. SZA across different TCCON sites\n\n175\n\nbecause GGG already has a well-tested program to remove spurious SZA dependencies in the output Xgas products, so long as\nthose dependencies are the same across sites. While minimizing the magnitude of the SZA dependence itself would have been\n8\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n(a) 1.005\n\ny = 1.03 + -0.00013x\n\n102\n\n0.995\n\nCounts\n\nXluft (unitless)\n\n1.000\n\n101\n0.990\n0.985\n0.980\n\n100\n\n(b) 1.015\n\ny = 1.01 + -3.31e-05x\n\n102\n\n1.005\n\nCounts\n\nXluft (unitless)\n\n1.010\n\n101\n1.000\n0.995\n0.990\n\n260\n\n270\nT700 (K)\n\n280\n\n290\n\n100\n\nFigure 2. Correlation between Xluft and temperature at 700 hPa (a) before and (b) after optimizing the O2 line broadening in terms of\nits water, pressure, and temperature dependencies. Note that (a) is not from the previous TCCON data version (GGG2014), it is from a\npreliminary beta test of GGG2020. In both panels, the colored background is a 2D histogram, the gray diamonds mark the mean Xluft in 5\nK bins, and the black line is a linear fit to the gray diamonds. The data shown here is from the Lamont TCCON site between 2 Sep 2017 to\n30 Sep 2018. Note that the y-axis limits shift between the panels; this is because the mean magnitude of Xluft changed with the increase of\nO2 line intensities (see text) between the tests plotted in the two panels. The slope is visually comparable between the panels, since the span\nof Xluft is the same (0.025) in both panels.\n\n9\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n# spectra per bin\n\n(a)\n\nDarwin, Australia\nLamont, OK, USA\n\n15000\n10000\n5000\n0\n\n255\n\n260\n\n265\n\n6000\n5000\n4000\n3000\n2000\n1000\n0\n\n280\n\n285\n\n290\n\n0.00 0.25 0.50 0.75 1.00 1.25 1.50 1.75\n1e23\nH2O column (molec. cm 2)\nH2O +0%\n1e 26\n\n(c)\n\nSlope of Xluft vs. H2O column\n( 1/[molec. cm 2] )\n\n270 275\nT700 (K)\n\nT700\n\nH2O +40%\n\nH2O +80%\n\n[281.0 K, 285.0 K]\n\n0.5\n\n8000\n\n0.0\n\n6000\n\n# spectra\n\n# spectra per bin\n\n(b)\n\n0.5\n\n4000\n\n1.0\n\n2000\n\n1.5\n0\n\n10\n\n20\n\n30\n\n40 50\nSZA\n\n60\n\n70\n\n80\n\n0\n\nFigure 3. (a) Histogram of temperatures at 700 hPa at the Darwin (located at 12.5° S) and Lamont (at 36.6° N) TCCON sites. (b) Histogram\nof water column amounts at the same sites. (c) Slopes of Xluft vs. water column in 10° SZA bins at Darwin with water broadening of O2 set\nas equal to, 40% greater, and 80% greater than air. The grey bars give the number of spectra in each bin. The Lamont data in (a) and (b) is\nfrom the period 2 Sep 2017 to 30 Sep 2018, and the Darwin data in all bins is from 21 Jul 2015 to 30 Sep 2016.\n\n10\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nNot optimal\n\nOptimal\n\nTest parameter / original value\n\n1.50\n1.25\n1.00\n0.75\n0.50\n0.25\n0.00\n0.25\n\ns.\npe v\n\n0\n\nT70\n\nSlo\n\nA)\n. SZ\ns\nv\npe\n2 (Slo\n\nuft)\n\n2 ( Xl\n\nGGG2020\n\n(c)\n\nO2 T-dependent pres. broadening half-width\n\n(b)\nO2 air broadening half-width (cm 1/atm)\n\n(a)\n\nGGG2014\n0.055\n0.050\n0.045\n0.040\n0.035\n0.030\n0.025\n\n7800 7900 8000\nFrequency (cm 1)\n\n0.825\n0.800\n0.775\n0.750\n0.725\n0.700\n0.675\n7800 7900 8000\nFrequency (cm 1)\n\nFigure 4. Result of the O2 spectroscopy optimization. (a) The values of each criterion for each test using different values of pressure and\ntemperature broadening coefficients. The values are normalized to their values in the baseline test (before optimizing the O2 spectroscopy).\nThe points within each parameter are spread horizontally for clarity. (b) The air broadening half widths used in GGG2020 (after optimization)\ncompared with GGG2014. The mean GGG2020/GGG2014 ratio is 1.0025, so the points are barely different on this scale. (c) As (b), but for\nthe temperature broadening coefficient. The mean GGG2020/GGG2014 ratio is 0.9323.\n\npreferable, we were not certain there would be enough flexibility in the Xluft -O2 spectroscopy relationship to simultaneously\nminimize the temperature and SZA dependencies. Similarly, we minimized the variance in Xluft itself because the average\nmagnitude of Xluft depends on the strengths of the O2 lines, rather than the pressure and temperature effects on line width\n180\n\nadjusted in this initial experiment.\nTo carry out this optimization, we ran approximately one year of data from four TCCON sites (Darwin, Australia; East Trout\nLake, Canada; Lamont, OK, USA; Park Falls, WI, USA) multiple times. In each test, we scaled the temperature dependence,\npressure dependence, or both of all lines in the O2 band. We could then interpolate between these test runs to estimate the three\ncost function quantities for any pressure/temperature broadening coefficients, and from that find the combination of coefficients\n\n185\n\nthat minimized the overall cost function. Note that we did not use Darwin data to calculate the Xluft versus T700 slopes for the\ncost function, as the small range of temperatures that Darwin experiences (Fig. 3a) make it difficult to get reliable fits versus\ntemperature.\nThe results of the optimization are shown in Fig. 4. Figure 4a shows how the three criterion described above (slope of Xluft\nvs. T700, variance in slope of Xluft vs. SZA, variance in Xluft ) varied across the tests performed with different pressure and\n\n190\n\ntemperature broadening coefficients. The values are normalized to their respective pre-optimization values. We found that the\nbest combination of coefficients reduced the slope of Xluft vs. T700 by 82%, the variance in Xluft vs. SZA slopes across\nTCCON sites by 89%, and the variance in Xluft itself by 49%. The optimized air broadening half widths and temperature\ndependence coefficients for GGG2020 are shown in Fig. 4, panels b and c respectively, with GGG2014 values for comparison.\n\n11\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nThe air broadening half widths were increased by 0.25% and the temperature dependence coefficients were decreased by\n195\n\n6.77%. The effect on the Xluft vs. T700 relationship is shown in Fig. 2b, where the slope is reduced by a factor of 4 compared\nto its pre-optimization value.\nFinally, the O2 line intensities were increased by ∼ 1% to bring Xluft closer to 1. This effect is apparent in Fig. 2, where the\n\npost-optimization Xluft in panel b is near 1, but the pre-optimization values are between 0.990 and 0.995.\n4\n200\n\nImproved a priori profiles\n\n4.1\n\nModified retrieval grid\n\nIn GGG the retrieval is done on a fixed altitude grid. In GGG2014 the altitude grid had a constant spacing of 1 km with 71\nlevels between 0-70 km above sea level. In GGG2020 the grid was updated to 51 levels between 0-70 km above sea level with\nspacing increasing away from the surface following the expression:\n\nzi = i · (0.4 + 0.02 · i)\n205\n\n(2)\n\nwhere zi is the altitude of the ith level in kilometers. As the altitude grids are fixed to sea level, this does mean that some\nsites have some levels below the terrain which are not included in the integration.\n4.2\n\nMeteorological updates\n\nIn GGG2014 the a priori H2 O, pressure, density, and temperature profiles were derived from NCEP 6-hourly reanalyses. In\nGGG2020, these profiles are now derived from GEOS 5 FP-IT 3-hourly product in addition to potential temperature, potential\n210\n\nvorticity, O3 , and CO profiles. The potential vorticity profiles are used to derive equivalent latitude profiles based on the\nequation in Allen and Nakamura (2003). Equivalent latitude is used in deriving the stratospheric part of the a priori trace gas\nconcentration profiles (Laughner et al., 2023). GGG2020 will transition to the GEOS IT product when it replaces GEOS FP-IT;\nan analysis to quantify the impact of that change on TCCON Xgas products is planned.\n4.3\n\n215\n\nTrace gas profile updates\n\nGGG2020 includes a substantial redesign of the algorithm that generates the CO2 , CH4 , N2 O, HF, CO, and O3 a priori\nprofiles. Generating these profiles is now handled by ginput, a separate program from gsetup. The ginput algorithm is described\nin detail in Laughner et al. (2023). Briefly, the CO2 , CH4 , and N2 O profiles are tied to the long term records from the NOAA\nobservatories in Mauna Loa, Hawaii and American Samoa (Lan et al., 2022b, a, c), in order to ensure the growth rates of these\ngases are correctly accounted for. Individual profiles are produced based on the mean transport time between the profile location\n\n220\n\nand the Mauna Loa/American Samoa observatories and (in the stratosphere) chemical loss. HF profiles are derived from CH4\nprofiles using the HF-CH4 relationships previously identified by Washenfelder et al. (2003) and Saad et al. (2014, 2016). CO\n12\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nprofiles are drawn from the GEOS FP-IT chemical product2 (Lucchesi, 2015) with adjustments in the stratosphere to better\nmatch observations. (See Laughner et al. (2023) for details on these adjustments.)\nOne additional change compared to GGG2014 is that the a priori profiles are now given in wet, rather than dry, mole fraction.\n225\n\nThis is necessary as GGG calculates absorber number densities as the prior mole fractions times the number density of air,\nwhich is assumed to include water. The a priori profiles provided in the published data files are also in wet mole fraction. Thus,\nwhenever comparing GGG2020 a priori profiles in the published netCDF files with other sources, care must be taken to ensure\nthat the comparisons convert both profiles to the same (wet or dry) mole fractions.\n5 Improved interferogram-to-spectrum conversion\n\n230\n\nThere have been substantial code changes and streamlining of common code in i2s, the interferogram-to-spectrum conversion\nsubroutine. The main substantive improvements to the code are in the handling of detector nonlinearity, the phase correction,\nand other changes.\n5.1\n\nDetector nonlinearity\n\nThe largest signals in an interferogram generated by a Fourier transform spectrometer are found near zero-path difference\n235\n\n(ZPD), where light from all wavelengths is in phase. The signal levels drop significantly away from ZPD. If the detector\nmeasuring the interferogram has a nonlinear response, the variations in the signal near ZPD will be more distorted than in\nthe rest of the interferogram. This causes a discrepancy between the low-resolution spectral envelope and the high resolution\nspectral lines. Nonlinear detector responses can be strongly pronounced or subtle, and several improvements to i2s have been\nmade to address these situations.\n\n240\n\nWe have implemented a check early in i2s processing to remove interferograms affected by detector or signal chain saturation, an extreme form of detector nonlinearity. If the signal intensity is too large, the ZPD signal will reach the maximum\nvalue permitted by the detector electronics, and no additional light can be detected. We call this “detector saturation” and this\ncauses irreversible detector nonlinearity in which spectral information is permanently lost. To resolve the problem, detectors\nused for TCCON measurements have reduced pre-amplifier gain settings. Additionally, we must limit the number of photons\n\n245\n\nincident on the detector through reducing the field stop or aperture stop diameter or by placing an optical filter in the beam.\nMeasured interferograms that are saturated cannot be recovered, and therefore should be discarded before producing their\nspectra. Because this effect depends on sunlight intensity, saturation could occur near noon but not later or earlier in the day,\nit can be seasonally dependent, or dependent on the amount of water vapor in the atmosphere. In GGG2020, we have implemented a detector saturation check to discard any saturated interferograms based on the maximum and minimum values of the\n\n250\n\ninterferogram signal.\nWe now compute and store a detector nonlinearity diagnostic variable (“DIP”) as part of the regular TCCON data processing.\nKeppel-Aleks et al. (2007) described the solar intensity variation correction applied to the TCCON interferograms that has been\n2 We\n\nexpect to transition to the GEOS IT product when it supersedes GEOS FP-IT. However, that had not yet occurred at time of writing.\n\n13\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\npart of the TCCON processing software since 2007. In this correction, a low-pass filtered interferogram is used to re-weight\nthe original interferogram, largely removing the impacts of solar intensity fluctuations during a measurement. As part of this\n255\n\nwork, Keppel-Aleks et al. realized that detector nonlinearity becomes observable in the low-pass filtered interferogram as a\n“dip” at zero path difference (see Fig. 6b in Keppel-Aleks et al., 2007). The magnitude of this dip is a diagnostic of the severity\nof detector nonlinearity, and is now computed, stored, and reported as part of the routine TCCON processing.\nA subtle detector nonlinearity in the Sodankylä TCCON data persisted from early in their record until the problem was\nfound in 2017. The problem in the early data was resolved by applying the nonlinearity correction developed by Hase (2000)\n\n260\n\ndirectly to the interferogram before transforming it into a spectrum. This correction process and its results are described in\ndetail in Appendices A and B of Sha et al. (2020). In that paper, the authors show that the nonlinearity caused a bias in XCO2\nof about 0.5 ppm in the 2017 Sodankylä data. After 2017, the problem was resolved by optically limiting the light entering\nthe interferometer. This correction process is being applied to GGG2020 data at other sites for periods when significant nonlinearity is identified. We are in the process of incorporating the correction process as a standardized part of the interferogram-\n\n265\n\nto-spectrum processing to make this process easier to complete in the future.\nA second class of nonlinearity results in supralinear detector response, rather than sublinear response as was seen at Sodankylä. The correction procedure described in the last paragraph is not effective at correcting the supralinear behavior as it\nhas a different physical cause than the sublinear behavior. Based on tests performed at the Garmisch TCCON site, our current\nhypothesis is that this behavior results from overfilling the detector element with the light beam (Corredera et al., 2003), and\n\n270\n\nthe magnitude of the effect varies from detector to detector. Another possible cause of supralinearity in detectors can come\nfrom absorptive layers on the InGaAs active region itself (Fox, 1993), but we do not yet have evidence that this is occurring in\nour instruments.\n5.2\n\nPhase correction\n\nSampled interferograms are always asymmetrical, either because the sampling grid does not include the ZPD position, or\n275\n\nbecause the under-lying continuous igram is already asymmetrical even before it is sampled. This asymmetry causes the\nresulting, post-FFT, complex spectrum to have substantial imaginary terms. A phase correction is necessary to resample the\ninterferogram such that is it sampled symmetrically about ZPD, resulting in a computed spectrum that has the signals of interest\n\n280\n\nin the real component and only the noise is divided between both the real and imaginary component.\n√\nIf we used a power spectrum ( <2 + =2 ), avoiding phase correction, it would compute a spectrum that is entirely real, but\n\nwould retain all of the noise in the real and imaginary component of the spectrum. Therefore the final noise level in a power\n√\nspectrum would be a factor of 2 greater than in a phase-corrected and Fourier transformed spectrum. Additionally, in a power\nspectrum, saturated (zero intensity) regions would no longer be centered at zero, as any noise present is rectified and so made\nall positive. For these reasons, we compute a phase correction.\nWe use the phase correction method described by Forman et al. (1966), with a spectral domain convolution as described by\n\n285\n\nMertz (1965, 1967). The phase correction is performed using a low resolution double-sided interferogram, apodized with a cos2\nfunction, to compute the angle between the real and imaginary components of the spectrum. This angle is a smoothly varying\n14\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nfunction of wavenumber, and is called the phase curve. Its counterpart in interferogram space is called the phase correction\noperator. In regions of the spectrum with sufficient signal, the phase curve well defined, but where the spectrum is blacked out\nby water vapor, another strong absorber, or an optical component, it can become undefined. Therefore, to compute the phase\n290\n\ncorrection operator, we need to set a signal threshold so that we can compute a well-behaved phase curve across the spectral\nregion of interest. We interpolate the phase curve linearly across the blacked-out regions of the spectrum where the phase curve\nis below the signal threshold. The phase curve is interpolated to 0 at 0 cm−1 and at the Nyquist frequency (15798 cm−1 ).\nIn GGG2014, several TCCON stations showed retrievals of Xgas with systematic differences between spectra generated\nfrom interferograms collected while the scanning mirror moves away from zero path difference (“forward” scans) and while\n\n295\n\nmoving toward zero path difference (“reverse” scans). These differences are typically less than 0.5 ppm in XCO2 , but with\nlarger differences observed at the Ny Ålesund, Eureka, Paris, and Zugspitze TCCON stations. This forward-reverse bias was\ntracked down to the phase correction operator, and, more specifically, the minimum signal level threshold for which the phase\noperator is calculated. We have lowered the phase curve threshold from 0.02 (2%, in GGG2014) to 0.001 (0.1%, in GGG2020)\nof the peak spectral signal which improves the consistency between forward and reverse scans. This does not completely\n\n300\n\nresolve the problem, and we hope to develop a future version with a phase correction scheme that is independent of the signal\nlevel.\n5.3\n\nOther i2s changes\n\nWe now make better use of the entire interferogram collected by the spectrometer in i2s. In typical linear single-passed Fourier\ntransform spectrometers, we collect most of our interferometric data between zero path difference (ZPD) and the maximum\n305\n\noptical path difference (MOPD) positions of the scanning mirror. However, in order to perform a phase correction, a small\namount of data must be collected on the other side of ZPD, which we call the “short arm” of the interferometer. The “long\narm” is the section from ZPD to MOPD. In previous versions of GGG, the short arm data were discarded after the phase\ncorrection was completed. We now use the short arm data along with the long arm data to compute the spectrum. This is a\nmore efficient use of the data collected.\n\n310\n\n6\n\nContinuum fitting\n\nTCCON spectra are a combination of narrow features due to solar and telluric absorptions superimposed on the much broader\nspectral responses of the instrument and the solar Planck function (the continuum). To accurately fit the telluric features\nof interest, all other components of the spectrum must be accurately modelled simultaneously. Since TCCON spectra are\nnot radiometrically calibrated, the continuum can vary from instrument to instrument or even from day to day (if optical\n315\n\ncomponents are inserted or replaced) and therefore a general approach was needed to model the continuum. Prior to GGG2014,\nthe continuum was fitted with only two terms (mean and slope) over the <100 cm−1 wide windows used to retrieve atmospheric\ngases. To make use of wider spectral windows, it became necessary to include additional complexity in the model of the\ncontinuum, to account for optical components within the instrument (e.g., detectors, optical filters, beamsplitter, etc.) that\n15\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\ninduce curvature in the spectral response (e.g., Kiel et al., 2016b). In GGG2014, we implemented the ability to fit higher order\n320\n\npolynomials to the continuum level using discrete Legendre polynomials for test purposes, although this capability was not\nuniformly used in the GGG2014 TCCON data processing (Wunch et al., 2015). Higher order polynomials are now used widely\nin the GGG2020 spectral windows to better account for continuum shape changes between instruments and over time. The\ncontinuum curvature fitting option is not intended to fit out spectroscopic deficiencies; they will be airmass-dependent and\nso should be fixed separately. The default polynominal order in GGG2020 for each window has been chosen to capture the\n\n325\n\ncontinuum shapes of all sites in GGG2020 and reduce the spectral residuals without over-fitting the spectrum.\n6.1\n\nChannel Fringe Fitting\n\nParallel optical surfaces delay a small fraction of the transmitted beam, which subsequently interferes with the main, un-delayed\nbeam, resulting in a small periodic modulation of the spectral transmittance. This modulation has an amplitude of R2 where R\n330\n\nis the reflectivity of each surface, and a period of (2 · n · d · cos θ)−1 cm−1 , where n in the refractive index of the optic, d is its\n\nthickness (in cm) and θ is the angle to the normal.\n\nFor decades, GFIT has the capability to fit a channel fringe to determine its amplitude (as a fraction of the continuum), its\nperiod, and its phase, and then remove it from the measured spectrum during the spectral fitting. This capability was not used\nby TCCON until GGG2020, when spectral fits from some sites were noticed to exhibit the tell-tale periodicities in the residuals.\nLeft untreated, channel fringes can seriously bias the retrieved gas amounts, by an amount that can vary from instrument to\n335\n\ninstrument and even over time for a single instrument, e.g., if its temperature changes.\nAn important code change for GGG2020 was to prevent channel fringes from being mistaken for higher-order continuum\nterms. This was much less of a problem for GGG2014 when we only ever fitted a straight line to represent the continuum. But\nnow, if a particular wavelike feature in the continuum could be fitted by a higher order polynomial or by a channel fringe, this\ntends to slow down convergence as the continuum fitting and channel fringe fitting vie with each other. To prevent this, a lower\n\n340\n\nlimit was imposed on the channel fringe period that was fittable in a given window, such that it always was narrower than the\nperiodicities in the continuum fitting polynomial. So if we are fitting an N -term polynomial to the spectrum (called the number\nof continuum basis functions, or NCBF ), in a window of width w cm−1 , then the period of the fitted channel fringes must be\nless than w/(NCBF − 1).\n7\n\n345\n\nPost-retrieval data processing\n\nGGG incorporates several post-retrieval steps to (1) collate and average data (§7.2) from the individual retrieval windows into\nthe final Xgas products and (2) correct post hoc for known errors in the forward model. There are two corrections. The first is\nan airmass-dependent correction (§7.1), which aims to eliminate spurious dependence of Xgas quantities on SZA. The second\nis an in situ-based, or airmass-independent correction (§7.3), which aims to eliminate the mean bias in Xgas values arising\nfrom incorrect spectroscopic line strengths.\n\n350\n\nIn the following sections, the post processing steps are presented in the order in which they are applied in GGG2020.\n16\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n7.1\n\nUpdated airmass dependence correction\n\nIn the limit of no horizontal variation in trace gas dry air mole fraction, Xgas quantities are independent of atmospheric path\nlength, as the change in column density due to path length is multiplicative and so will cancel out between the target gas in\nthe numerator and O2 in the denominator. However, a spurious dependence of Xgas on airmass can arise from errors in the\n355\n\nspectroscopic forward model.\nGGG2020, like GGG2014, applies a post hoc correction to the Xgas values to remove airmass dependences. We calculate a\ncorrection for each Xgas value as\n\nfc =\n\n\u0012\n\nθ+g\n90 + g\n\n\u0013p\n\n−\n\n\u0012\n\n45 + g\n90 + g\n\n\u0013p\n\n(3)\n\nand use this to correct the Xgas value as\n\n360\n\nXgas,corr =\n\nXgas,raw\n1 + αfc\n\n(4)\n\nIn Eq. (4), α is a coefficient for each gas (in GGG2014) or each window (in GGG2020). In Eq. (3), θ is the solar zenith angle\n(SZA) in degrees and g and p are coefficients chosen to best represent the SZA-dependent behavior. This form was chosen to\nnormalize to a 90° window centered on (45 + g)◦ . While the basic approach is the same in GGG2020 as it was in GGG2014,\nwe made two changes to the implementation:\n365\n\n1. In GGG2014, column densities from different spectral windows used to retrieve a target gas were averaged first, then\na single airmass correction applied to each gas. In GGG2020, each spectral window is airmass corrected first, then the\nresulting Xgas values are averaged.\n2. In GGG2014, g = 13 and p = 3 for all gases. In GGG2020, different values of g and p were selected for each window.\nThe rationale for the first change is clear from Fig. 5. The standard TCCON CO2 and CH4 products are derived from two\n\n370\n\nand three spectral windows, respectively. Although the overall SZA dependence has a similar shape for all windows of a given\ngas, there are clear differences in low and high SZA behavior. Thus, we decided to apply an SZA dependent correction to\nindividual windows, rather than the average Xgas value.\nThe rationale for the second change is that we do not know a priori the best form to represent the airmass dependence in\nany given window. For GGG2020, we used data from the Darwin TCCON site for all of 2015 to choose the values of g and\n\n375\n\np for each window. We used Darwin because, as a tropical site, it sees a wide range of SZAs (useful for examining SZA\ndependence) and water columns (useful to check for water effects on the derived airmass dependence). We used 2015 data\nbecause the instrument at Darwin was well aligned during that year.\n\n17\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nXCO2 - daily medians (ppm)\n\n(a)\n\n0.5\n0.0\n0.5\n1.0\nCO2 6220\nCO2 6339\n\n1.5\n\nXCH4 - daily medians (ppb)\n\n(b)\n2\n0\n2\nCH4 5938\nCH4 6002\nCH4 6076\n\n4\n6\n10\n\n20\n\n30\n\n40 50 60\nSZA (degrees)\n\n70\n\n80\n\nFigure 5. Variation of (a) the two CO2 and (b) three CH4 windows used by TCCON with SZA without the airmass correction applied.\nIn both panels, the y-axis is column average dry mole fraction of CO2 or CH4 derived from a single spectral window, with the central\nwavenumber given in the legend. The y values have the daily median values subtracted (to remove day-to-day variability), and each point\nrepresents the median of all such values in a 5° SZA bin.\n\nTo understand how g and p were determined, we must first explain how the airmass dependent correction factor (ADCF, i.e.\nα in Eq. 4) is calculated for a given g and p. The ADCF is calculated by fitting the following function to each day’s data:\n\n380\n\nf (t, θ|c1 , c2 , c3 ) = c1 + c2 · (2π(t − tnoon )) + c3 fc\n\n(5)\n\nwhere t and tnoon are the measurement time and solar noon time (in day of year), fc is the polynomial defined in Eq. (3), and\nc1 , c2 , and c3 are the fitted coefficients. The coefficients and their errors are calculated with a weighted least squares fit using\nthe individual windows’ Xgas uncertainties as the weights. The ADCF for a given window is the error-weighted mean of all\ndays’ c3 values.\n385\n\nTo find the optimal g and p values, we derived ADCFs for five subsets of the 2015 Darwin data (data with SZA > 20°, 30°,\n40°, 50°, and 60°, all with H2 O column < 1.1 × 1023 molec. cm−2 ) for values of g between −45 and +45 and p between 1\nand 6. We then find the combination of g and p that gives the smallest standard deviation across all five subsets and choose that\n18\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n0.005\n0.010\n0.015\n0.020\n\n20\n\n25\n\n30\n\n35 40 45\nSZA min (deg)\n\n50\n\n55\n\n40\n20\n10\ng\n\n0.009474\n0.008421\n0.007368\n0.006316\n0.005263\n0.004211\n0.003158\n0.002105\n0.001053\n0.000000\n\n0\n10\n20\n30\n40\n1\n\n2\n\n3\n\np\n\n4\n\n5\n\n6\n\n1\n\n0.005\n0.010\n0.015\n0.020\n\n60\n\n20\n\n25\n\n30\n\n35 40 45\nSZA min (deg)\n\n50\n\n55\n\n40\n\nxco2_6220 ADCF std. dev.\n\n30\n\nCO2 from window centered on 6339 cm\n\n0.000\nxco2_6339 ADCF\n\nxco2_6220 ADCF\n\n1\n\n30\n\n60\n0.009474\n0.008421\n0.007368\n0.006316\n0.005263\n0.004211\n0.003158\n0.002105\n0.001053\n0.000000\n\nxco2_6339 ADCF std. dev.\n\nCO2 from window centered on 6220 cm\n\n0.000\n\n20\n10\n0\n10\n20\n30\n40\n1\n\n2\n\n3\n\np\n\n4\n\n5\n\n6\n\nFigure 6. Example of how g and p in Eq. (3) were chosen for the two TCCON CO2 windows. The left two panels are for the CO2 window\ncentered at 6220 cm−1 and the right two for the window at 6339 cm−1 . The line plots at the top show how the value of the ADCF (α in\nEq. (4)) changes as we increase the lower limit in SZA for the data fit to. Each gray line represents one combination of g and p, with the\nblack line representing the combination with the smallest standard deviation in the ADCF. The contour plots show the standard deviation\nof the ADCF across different minimum SZAs for each combination of g and p. The white star represents the combination with the smallest\nstandard deviation; it corresponds to the test show with the black line in the line plots.\n\nas the optimal combination. This approach assumes that the values of g and p (and thus the form of fc ) which best capture the\nairmass dependence of a particular window will have the smallest change in ADCF as smaller subsets of data are fit.\n390\n\nThis procedure is illustrated for the two TCCON CO2 windows in Fig. 6. In the top panels, the gray lines show the variation\nin ADCF with the minimum SZA in the subset of data fit to; each line represents one combination of g and p. It is clear that the\nvariation in ADCF is much greater for some combinations of g and p than others. The contour plots in Fig. 6 show the standard\ndeviation of ADCF for each g and p combination. In both windows, there is a clear minimum valley. The white stars in the\ncontour plots and thicker black lines in the upper panels show the g and p combination with the smallest standard deviation.\n\n395\n\nThe final step in selecting ADCFs for GGG2020 was to account for spurious temperature dependence in the Xgas values. As\nwe saw with O2 in §3.3, incorrect temperature dependence in the line widths introduces a temperature dependence in retrieved\nXgas , which could alias into the airmass dependence. To check this, we derived ADCFs from data from 18 TCCON sites, using\ntwo month long subsets of data to sample different temperatures. Figure 8 shows how the CH4 ADCFs vary with potential\ntemperature averaged between 500 and 700 hPa (θmid ) as an example. (Figure 7 shows how θmid and T700 relate to assist\n\n400\n\ncomparisons with Fig. 2.) Here, we see that the 6002 cm−1 and 6076 cm−1 windows’ ADCFs have no or little temperature\ndependence (Fig. 8b,c), but the 5938 cm−1 window has a clear temperature dependence. To compute the final ADCFs for\neach window, we used the value of the fit to this data at θmid = 310 K. 310 K was chosen as it is approximately the midpoint\ntemperature for the TCCON network, as can be seen in Fig. 8.\n\n19\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n320\n\n101\n\n280\n\n#\n\nmid\n\n(K)\n\n300\n\n260\n240\n\n240\n\n260\n\n280\n300\nT700 (K)\n\n320\n\n100\n\nFigure 7. A heatmap of the relationship between θmid and T700, taken from the Park Falls TCCON data. The red dashed line denotes the\n1:1 line.\n\nADCF\n\n(a) 0.015\n\nADCF\n\n1\n\n0.010\n0.005\n0.000\n0.005\n0.010\n0.015\ny = (0.0711 +/- 0.00729) + (-0.000261 +/- 2.35e-05)x\n0.020\n290\n295\n300\n305\n310\n315\n\n(b) 0.015\n\nCH4 from window centered on 6002 cm\n\n320\n1\n\n0.010\n0.005\n0.000\n0.005\n0.010\n0.015\ny = (-0.0085 +/- 0.00788) + (7.99e-06 +/- 2.53e-05)x\n0.020\n290\n295\n300\n305\n310\n315\n\n(c) 0.015\n\nADCF\n\nCH4 from window centered on 5938 cm\n\nCH4 from window centered on 6076 cm\n\n0.010\n0.005\n0.000\n0.005\n0.010\n0.015\ny = (0.0356 +/- 0.00698) + (-0.000134 +/- 2.24e-05)x\n0.020\n290\n295\n300\n305\n310\n315\nmid (K)\n\n320\n1\n\nBialystok\nBurgos\nPasadena\nDarwin\nArmstrong\nEast Trout Lake\nGarmisch\nJPL 01\nSaga\nKarlsruhe\nLauder 03\nLamont\nOrleans\nPark Falls\nReunion Island\nRikubetsu\nTsukuba 02\nWollongong\n\n320\n\nFigure 8. ADCFs derived from two month periods from 18 sites throughout the TCCON network versus mean potential temperature between\n500 hPa and 700 hPa over the same two month period. Each panel is one of the TCCON CH4 windows. The text inset in each panel gives\nthe intercept and slope of the robust fit through the data shown by the black dashed line.\n\n20\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nADCF\n\n0.2\n\nCO from window centered on 4233 cm\n\n1\n\n(b)\n\n0.1\n\n0.1\n\n0.0\n\n0.0\n\n0.1\n0.2\n0.3\n\n0.1\n\n0.3\n\n320\n\nwCO2 from window centered on 6073 cm\n\n1\n\n0.000\n\n0.000\n0.005\n\n0.010\n0.015\n\ny = (0.133 +/- 0.0715) + (-0.000486 +/- 0.000229)x\n290\n295\n300\n305\n310\n315\n320\n\nwCO2 from window centered on 6500 cm\n\n(d) 0.005\n\n0.005\n\n0.020\n\n1\n\n0.2\ny = (-0.448 +/- 0.139) + (0.00132 +/- 0.000446)x\n290\n295\n300\n305\n310\n315\n\nADCF\n\nADCF\n\n(c) 0.005\n\nCO from window centered on 4290 cm\n\n0.2\n\nADCF\n\n(a)\n\n1\n\nBialystok\nBurgos\nPasadena\nDarwin\nArmstrong\nEast Trout Lake\nGarmisch\nJPL 01\nSaga\nLauder 03\nLamont\nOrleans\nPark Falls\nReunion Island\nRikubetsu\nTsukuba 02\nWollongong\n\n0.010\n0.015\n\ny = (0.000425 +/- 0.00238) + (-8.95e-06 +/- 7.64e-06)x\n290\n295\n300\n305\n310\n315\n320\n\n0.020\n\ny = (0.0225 +/- 0.00412) + (-0.000104 +/- 1.33e-05)x\n290\n295\n300\n305\n310\n315\n320\nmid (K)\n\nFigure 9. Similar to Fig. 8, except for two CO windows (a, b) and two weak CO2 windows (c, d).\n\nThe magnitude of this temperature dependence varies from gas to gas: the primary TCCON CO2 windows have almost\n405\n\nno slope, while the N2 O windows have slopes of ADCF vs. θmid similar to or larger than the CH4 5938 window. We plan to\ninvestigate these temperature dependence behaviors more thoroughly in the next major GGG version and identify spectroscopic\nimprovements that will reduce or eliminate this behavior using a similar approach to that described for O2 in §3.3.\n7.1.1\n\nFitting windows excluded in GGG2020\n\nBased on the ADCF analysis, several spectral windows were excluded from the TCCON GGG2020 product. Figure 9 shows\n410\n\nthe ADCF versus θmid plots for two CO windows and two weak CO2 windows. The CO window centered on 4233 cm−1\n(Fig. 9a) has slightly stronger temperature dependence and clearly larger scatter than the 4290 cm−1 CO window (Fig. 9b). We\nsuspect this is due to water interference; the 4233 cm−1 CO window has more water lines in it than the 4290 cm−1 window.\nWe examined the spectral residuals in both CO windows to try to identify and correct the water interference, but were not able\nto reduce it to satisfactory levels. Thus, in GGG2020, the XCO product relies on only the 4290 cm−1 window.\n\n415\n\nSimilarly, the new XwCO2 product was planned to use two windows, one centered on 6073 cm−1 and another on 6500 cm−1 .\nHowever, as shown in Fig. 9c and 9d, the 6500 cm−1 window’s ADCF have more scatter and stronger temperature dependence\nthan the 6073 cm−1 window. As the 6500 cm−1 also has more water interference than the 6073 cm−1 window, we elected to\nuse only the 6073 cm−1 window.\nLastly, we also removed a number of HCl windows. TCCON used 16 windows to measure HCl in GGG2014, but like the CO\n\n420\n\nand wCO2 windows, many of these have water absorption lines in them. We can diagnose unaccounted for water interference\nby computing the ADCFs for each HCl window from Darwin 2015 data, split by the amount of water in the column. The\nresult is shown in Fig. 10. Most of the GGG2014 windows have a clear difference in ADCF with small or large water column\namounts. Based on this, we chose to only retain the 5625, 5687, 5702, 5735, and 5739 cm−1 windows. Most of the windows\nremoved clearly have a water interference. The 5754 and 5763 cm−1 windows are special cases. The 5754 cm−1 window was\n\n21\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n0.06\n\nH2O < 1.1 × 1023 molec. cm\nH2O 1.1 × 1023 molec. cm\n\nADCF\n\n0.04\n\n2\n2\n\n0.02\n0.00\n0.02\n5577 5597 5625 5683 5687 5702 5706 5719 5735 5739 5749 5754 5763 5767 5779 5790\nWindow central wavenumber\n\nFigure 10. ADCF calculated for each HCl window from 2015 Darwin data, divided by the total column amount of water.\n425\n\nrejected because its airmass dependence is slightly more negative than the retained windows. The 5763 cm−1 window was\nrejected because it exhibits a clear temperature dependence in the window-to-window scale factors (§7.2).\n7.2\n\nUpdated window-to-window averaging\n\nMany gases retrieved by GGG are retrieved in more than one spectral window. GGG retrieves the column amount in each\nwindow separately, then averages together the columns with similar averaging kernels to produce a mean value. Specifically,\nP\n2\nj sj yij /\u000fij\n430 y i = P 2 2\n(6)\nj sj /\u000fij\nwhere subscript j represents the spectral window. That is, the average value for the ith measurement (y i ) is an error weighted\n\naverage of the individual windows’ column amounts (yij , with errors \u000fij ) with a mean bias in each window removed by the\nper-window scale factor, sj . The errors \u000fij are the posterior errors in the Xgas amounts as calculated from the retrieval error.\nIn GGG2014, the sj values were determined online, using an iterative process that minimizes the differences between yij\n435\n\nand the corresponding sj y i values. While this calculates sj values that best fit the data being averaged, it means that how the\nwindows are combined depends on how much data is averaged at once—processing a month could give different results than\nprocessing a year of data, for example. Thus, while GGG2020 retains the capability to compute the sj values on-the-fly, the sj\nvalues are prescribed for standard TCCON processing.\nTo determine the standard TCCON sj values, we used a very similar approach to how we derived the ADCFs in §7.1.\n\n440\n\nSpecifically, we calculated the sj values for two month subsets of data from the same 18 TCCON sites as in §7.1 and fit these\nvalues versus θmid . As with the ADCFs, we used the values of the fit at θmid = 310 K as the final choices of sj .\n7.3\n\nUpdated in situ bias correction\n\nAs in GGG2014, the GGG2020 XCO2 , XCH4 , XN2 O , and XH2 O products are tied to standard scales by in situ aircraft, balloon,\nand/or radiosonde measurements to remove any mean multiplicative bias introduced by error in absorption line intensity.\n445\n\nUnlike GGG2014, XCO in GGG2020 is not tied to in situ measurements, due to previous work that found the difference\n22\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nbetween TCCON XCO and both NDACC (Kiel et al., 2016a) and MOPITT (Hedelius et al., 2019) XCO was approximately the\nmagnitude of the in situ correction. However, we do evaluate XCO against a subset of in situ data from AirCore only below.\nComparison of TCCON data against in situ data follows the following steps:\n1. Identify in situ vertical profiles in available data and convert to a standardized file format\n450\n\n2. Extend the profiles’ tops to 70 km altitude using the standard GGG2020 priors and to the surface by extrapolation or use\nof surface data\n3. Match profiles to available TCCON spectra\n4. Run custom retrievals using the match profiles as the a priori trace gas profile\n5. Compare integrated in situ Xgas values against matched TCCON data, accounting for TCCON vertical sensitivity\n\n455\n\nPoints 1–4 are described in detail in Appendix C. Briefly, we use profiles from:\n– the GlobalviewPLUS 5.0 CO2 (Cooperative Global Atmospheric Data Integration Project, 2019) and GlobalviewPlus\n2.0 CH4 ObsPack (Cooperative Global Atmospheric Data Integration Project, 2020) products,\n– AirCore balloon measurements (Tans, 2009; Karion et al., 2010) flown by NOAA (v20201223, Baier et al., 2021) at\nmultiple TCCON sites and by FMI/LSCE/RUG at the Sodankylä, Finland (Kivi and Heikkinen, 2016) and Nicosia,\nCyprus (Rousogenous, in prep) TCCON sites,\n\n460\n\n– the Infrastructure for Measurement of the European Carbon Cycle (IMECC) campaign,\n– Profiles over the Manaus, Brazil TCCON site (Dubey et al., 2016),\n– ARM radiosondes over the Darwin, Australia (Deutscher et al., 2010) and Lamont, OK, USA TCCON sites\nCH4 profiles have an additional correction to the stratospheric levels obtained from the GGG2020 priors, see §C3 for details.\n465\n\nWe have addressed the recent change of CO2 data from the X2007 to X2019 WMO scales, which will be covered in §7.3.2.\nDue to the relative sparsity of N2 O profiles, GGG2020 TCCON N2 O products were evaluated against surface N2 O data and a\ndifferent approach, which will be covered in §7.3.3.\n7.3.1\n\nCO2 , CH4 , CO, and H2 O in situ comparisons\n\nThe first step in comparing TCCON XCO2 , XCH4 , XCO , or XH2 O to their respective in situ profiles is to match each in situ\n470\n\nprofile to temporally proximate, good quality TCCON retrievals. For this step, we define custom quality filters. A TCCON\nretrieval is considered to be good quality in this context if:\n– Fractional variation in solar intensity (FVSI) is ≤ 0.05. This filters out observations impacted by intermittent clouds.\n23\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n– Solar zenith angle (SZA) is ≤ 80◦ . This avoids observations at large airmasses, where spectroscopic errors can be more\npronounced.\n\n475\n\n– The unscaled Xgas value is > 0 mol mol−1 . A negative retrieved value is unphysical, and the distribution of retrieved\nvalues should not be large enough to make negative values a reasonable part of it.\n– The Xgas error is < 2\u000fmedian , where \u000fmedian is the median error for that Xgas across all the spectra used for the given\ngas. This limits for observations where the observed spectra was fit reasonably well.\n– The median Xluft for a comparison is between 0.996 and 1.002. Xluft and this rational are explained near the end of this\nsubsection.\n\n480\n\nFor each in situ profile, we require 30 TCCON observations passing these quality checks within a certain window of time\naround the corresponding profile’s lowest altitude measurement. Our initial window is ±1 hour. If 30 points meeting these\ncriteria are not present within ±1 hour, we increase both the time window and the allowed Xgas error, trying the combinations\n\n(±1 hr, < 2\u000fmedian ), (±2 hr, < 3\u000fmedian ), and (±3 hr, < 4\u000fmedian ). We use the smallest of these time/error window that yields\n485\n\n30 passing TCCON observations, but if a profile does not have 30 passing TCCON observations in the (±3 hr, < 4\u000fmedian )\nrange, it is removed from the comparison.\nThe remaining in situ profiles are integrated following Wunch et al. (2010), where the integrated in situ Xgas value, zinsitu\nis calculated as:\n\nzinsitu = I(γxa , p, xH2 O ) + I(δx, p, xH2 O )\n490\n\n(7)\n\nwhere\n– p is the vector of pressure at each profile level\n– xH2 O is the vector of water dry mole fractions at each profile level\n– γxa is the TCCON posterior profile (i.e. the prior times the retrieved VMR scale factor γ)\n– δx is the difference between the in situ and TCCON posterior profiles, modified by the TCCON averaging kernel:\nδxi = ai (xinsitu,i − γxa,i )\n\n495\n\nI represents the pressure-weighted integration function:\n· dpi · Di\ni dpi Di\n\u0012\n\u0013\nMH2 O\nDi = gi · Mair · 1 + xH2 O,i ·\nMair\n\nI(x, p, xH2 O ) =\n\nwhere\n\nP\n\nxi\niP\n\n(8)\n(9)\n\n24\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n500\n\n– dpi represents the pressure thickness of layer i\n– gi represents the acceleration from gravity at layer i,\n– Mair and MH2 O represent the mean molecular masses of dry air and water, respectively.\nThe integrated in situ Xgas values are compared against the median of the TCCON Xgas values from the matched observations. The TCCON Xgas values used here have the airmass correction (§7.1) and window-to-window averaging (§7.2) applied.\n\n505\n\nBecause we expect the bias in the TCCON data to arise from incorrect absorption line strengths or broadening coefficients, it\nshould be a multiplicative bias. Therefore, we calculate an uncertainty-weighted mean of the TCCON/in situ Xgas values to\nderive the bias correction. We consider five sources of uncertainty.\n1. Measurement error in the in situ data.\n2. Uncertainty from the unmeasured portion of the free troposphere. (Will be zero if the in situ vertical profile extends\n\n510\n\nthrough the tropopause.)\n3. Uncertainty from the unmeasured portion of the stratosphere.\n4. Random error in the TCCON observations.\n5. Bias in the TCCON observations from instrument misalignment or similar hardware concerns.\nThe calculation of each term and how they are combined is detailed in Appendix C6.\n\n515\n\nThe results of the TCCON-in situ comparison are shown in Fig. 11. In this plot, the y-axes are the ratio of TCCON to in\nsitu Xgas amounts and the x-axes show Xluft , a diagnostic quantity defined as the ratio of the column of dry air derived from\nsurface pressure to the column of dry air derived from the O2 retrieval. We will return to the significant of Xluft shortly. The\nuse of TCCON to in situ ratios to derive the in situ correction is equivalent to the best fit lines forced through the origin used\nin Wunch et al. (2010), as the best fit line through the origin is essentially the mean TCCON to in situ ratio. The use of ratios\n\n520\n\ndirectly in Fig. 11 allows us to more clearly identify outliers and evaluate the correlation of the TCCON vs. in situ bias with\nother variables, such as Xluft here.\nThe ratios from Fig. 11 indicate that the mean biases are within approximately 1% of unity in all cases, with water being the\nfurthest from unity at 0.9883 (−1.17%). The differences among the CO2 products are interesting; the standard CO2 product\nis biased about 1% high before correction (which is in line with expected uncertainties for the CO2 lines), while the other two\n\n525\n\nCO2 products are much closer to unity (0.08% for wCO2 and 0.14% for lCO2 ). This suggests that the absorption coefficients\nin these latter two windows are more accurate than in the standard TCCON windows (which are centered on 6220 and 6339\ncm−1 ). However, as the wCO2 and lCO2 are more sensitive to the upper and near-surface atmosphere, respectively, it may be\nthat this reflects other factors, such as the accuracy of the a priori temperatures at those levels.\nThe CO comparison (Fig. 11e) suggests that, without scaling, the GGG2020 XCO has no significant bias with respect to\n\n530\n\nAirCore CO measurements. Figure 11e shows significant variation in the TCCON/in situ CO agreement, with individual points\n25\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n(b)\n\n(c)\n1.015\n\n1.015\n\n1.010\n\n1.010\n\n1.010\n\n1.005\n1.000\n0.995\n\nr = 1.01010\n2 r = 0.00050\n\n1.005\n1.000\n0.995\n0.990\n\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\n(d)\n\n0.995\n0.990\n\nTCCON XCO / in situ XCO\n\n1.010\n1.005\n1.000\n0.995\n0.990\n\nr = 1.00310\n2 r = 0.00140\n\n0.980\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\n(f)\n\n1.8\n1.6\n\n1.2\n1.0\n0.8\n0.6\n\nr = 1.00140\n2 r = 0.00070\n\nr = 1.00850\n2 r = 0.05260\n\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\nATom\nAirCore\nCOBRA\nGSFC\nHIPPO\nHarvard\nIMECC\nLARC\nNOAA Manaus\nORCAS\nRadiosonde\n\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\n1.4\n\n1.015\nTCCON XCH4 / in situ XCH4\n\n1.000\n\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\n(e)\n\n1.020\n\n0.985\n\nr = 1.00080\n2 r = 0.00050\n\n1.005\n\nTCCON XH2O / in situ XH2O\n\n0.990\n\nTCCON XlCO2 / in situ XlCO2\n\n1.015\nTCCON XwCO2 / in situ XwCO2\n\nTCCON XCO2 / in situ XCO2\n\n(a)\n\n1.4\n1.2\n1.0\n0.8\n0.6\n0.4\n\nr = 0.98830\n2 r = 0.01570\n\n0.2\n0.996 0.997 0.998 0.999 1.000 1.001 1.002\nXluft (mol/mol)\n\nAnmyeondo\nArmstrong\nBialystok\nBremen\nDarwin\nLamont\nLauder 01\nLauder 02\nManaus\nNicosia\nPark Falls\nPasadena\nRikubetsu\nSodankyla\n\nFigure 11. Plots of the TCCON/in situ Xgas ratios for (a) CO2 , (b) wCO2 , (c) lCO2 , (d) CH4 , (e) CO, and (f) H2 O. In all plots, the y-axis\nis the ratio of TCCON/in situ Xgas and the x-axis is the median Xluft value for the TCCON observations in a comparison (see text for\nexplanation of Xluft ). The marker style of each comparison indicates the source of the in situ data and the color indicates which TCCON site\nthe comparison occurred at. The text inset in the lower-right corner of each plot gives the uncertainty-weighted mean TCCON/in situ ratio\nand its 2σ uncertainty. The dashed black lines mark the mean ratio. Panels a, b, and c are set to use the same y-limits; some of the error bars\nin (b) go outside the y-limits.\n\nalso having large uncertainty. This resulting 2σ uncertainty in the mean ratio is significantly larger than for the other gases, at\n0.0526. Thus, the mean TCCON/in situ CO ratio is well within its 2σ uncertainty of 1. We do acknowledge that limiting the\nCO comparisons to AirCore profiles alone may contribute to a larger uncertainty than if aircraft campaigns were included, due\nto the use of a CO-spiked fill gas in AirCores (see §2.1 of Martínez-Alonso et al., 2022). However, comparing TCCON XCO\n535\n\nto AirCore profiles was significantly more straightforward than including aircraft profiles, since the already-matched AirCore\nprofiles for CO2 and CH4 intrinsically include CO as well. Given the other reasons discussed above for not applying an in\nsitu-derived scaling to GGG2020 XCO and the process needed to match aircraft data with TCCON (see Appendix C1.1), we\nchose to accept the additional uncertainty from using AirCore profiles only. Future versions of the TCCON data product will\nreevaluate the inclusion of aircraft profiles alongside AirCore ones.\n\n540\n\nFigure 11 also provides insight into how instrumental errors affect different TCCON products. Under ideal circumstances,\nXluft (the quantity on the x-axis) should be 1; in practice, the nominal value for the TCCON network is 0.999, due to small\nresidual biases in the O2 spectroscopy. Deviations of Xluft from the nominal value indicate either (a) variable errors in spectroscopy, such as temperature or pressure broadening, or (b) instrument issues, such as a misalignment in the beam path. From\nFig. 11a, we can see that the TCCON/in situ ratio tends to be less when Xluft < 0.999 and greater when Xluft > 0.999. The\n\n26\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n545\n\nslope for Fig. 11a is 0.363. This translates to a bias in CO2 of about 0.15%, or approximately 0.5 ppm, when Xluft is 0.004 units\naway from the nominal value of 0.999 (0.15% = 0.0015 = 0.363 × 0.004). To keep this bias well below the expected 0.25%\naccuracy, we limit the comparison used here to those where Xluft is between 0.996 and 1.002 and have instituted additional\n\nquality checks of TCCON data that filter out observations when Xluft is outside the range of 0.995 to 1.003 for an extended\nperiod of time. Additionally, Xluft is now reported in the public data set alongside other Xgas retrievals.\n550\n\nWe note that the standard CO2 and the near surface-sensitive lCO2 products show the clearest dependence on Xluft . The\nreason for this is not clear at this time, though it implies a stronger dependence of these products on instrument line shape\n(ILS) compared to the other four products discussed in this section. Future versions of GGG are planned to account for errors\nin the ILS, which we hope will mitigate this bias and improve the accuracy of CO2 data when Xluft is outside the 0.995 to\n1.003 range.\n\n555\n\nThe correlation of XCO2 and XlCO2 with Xluft implies that we could develop an Xluft -based bias correction for those CO2\nproducts. Such a correction is planned for a minor update to the GGG data product. Our aim is to quantify the underlying\nphysical drivers of the XCO2 bias and use the correlation of those factors with Xluft to derive the bias correction. This would\nallow us to use the comparison to in situ data shown here as an independent verification of the bias corrections efficacy.\n7.3.2\n\n560\n\nAddressing the CO2 scale change from X2007 to X2019 and changing O2 mole fraction\n\nThe update from the previous WMO CO2 X2007 calibration scale to the new X2019 calibration scale (Hall et al., 2021)\noccurred late enough in the process of releasing GGG2020 that we were not able to incorporate it into the initial release. Given\nthe clear need expressed by the community to have TCCON data tied to the same scale as in situ data, we have since derived\nnew in situ correction factors to tie all three TCCON XCO2 products to the X2019 scale. Doing so required obtaining in situ\ndata that had been adjusted to the new scale, which we did in one of three ways:\n\n565\n\n1. The preferred approach was for the data originator to fully recalibrate their data to the new scale using the updated standards provided by the NOAA Global Monitoring Laboratory. NOAA AirCore and some NOAA ObsPack data followed\nthis approach.\n2. The second approach was for the data originator or an intermediate provider to adjust the CO2 data using the linear\ncorrection described in §9.1 of Hall et al. (2021). The remaining NOAA ObsPack data not covered by approach #1\n\n570\n\nfollowed this approach.\n3. The third approach was for us to perform the same linear correction as #2 ourselves. All other data used this approach.\nAlso recall that the profiles must be extended to 70 km altitude using the TCCON standard priors to ensure that the same\nvertical extent is captured in the in situ and TCCON column averages. As discussed in Laughner et al. (2023), the standard\npriors are derived from NOAA data at the Mauna Loa and American Samoa observatories, and so are also intrinsically tied to\n\n575\n\nWMO calibration scales. To ensure consistency throughout the in situ profiles, we used the latest available monthly average\n\n27\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nCO2 flask data on the X2019 scale as input to the priors when generating the profile extensions. Once this was complete, we\nredid the analysis described in §7.3 with the in situ profiles adjusted to the X2019 scale to generate updated correction factors.\nThe overall effect of the scale change for each of the three TCCON CO2 products is shown in Fig. 12 compared to the “raw,”\nun-bias corrected XCO2 value on the x-axis. The magnitude is about +0.15 ppm for typical current XCO2 values of 400 ppm.\n580\n\nIn the TCCON data products, there are three CO2 variables with the suffix _x2019 which are adjusted to the new X2019\nscale.\nAnother source of bias that is of similar magnitude to the effect of the scale change is the assumed O2 mole fraction. As\nshown in Eq. (1), the column-average mole fractions reported by TCCON are computed by dividing the column density of the\ntarget gas by the O2 column density, and scaling by the mean O2 mole fraction in the atmosphere. We have assumed that this\n\n585\n\nmole fraction is fixed for the initial GGG2020 data products; however, it is in fact changing over time due to various processes,\npredominantly fossil fuel combustion and the land biosphere (Keeling et al., 1998; Keeling and Manning, 2014).\nBecause the effect of ignoring the change in the global average O2 mole fraction is of similar magnitude to the X2007 to\nX2019 scale change, we decided to account for the change in O2 mole fraction over time in the CO2 products updated to the\nX2019 scale. We did not retroactively apply this correction to the X2007 XCO2 or the other Xgas products, as doing so would\n\n590\n\nchange the Xgas values and require a new data version. This correction will be applied to all Xgas values in the next GGG data\nversion.\nOur approach to account for changing O2 mole fraction takes advantage of the anticorrelation between atmospheric O2 and\nCO2 to derive the O2 mole fraction from CO2 measured by TCCON. (For our application, this assumption is sufficiently\naccurate; however, we note that this is not generally true for other applications of O2 /N2 ratio data.) Specifically, the value for\n\n595\n\nfO2 in Eq. (1) is calculated as (see Appendix E1 for the full derivation):\n\nfO2 = (α − α · fO2 ,ref − fO2 ,ref ) ·\n\nXCO2 − XCO2 ,ref\n+ fO2 ,ref\n1 − XCO2 − α · XCO2\n\n(10)\n\nwhere:\n– α = ∂NO2 /∂NCO2 = −1/0.4575, i.e. the change in the number of moles of O2 in the atmosphere for a given change in\n600\n\nthe number of moles of CO2 in the atmosphere. The choice of −1/0.4575 comes from the agreement with the measured\nchange in fO2 as shown in Fig. 13. This value is chosen to remove the effect of long term trends in the O2 mole fraction,\nand ignores synoptic-scale variations due to e.g. photosynthesis or fossil fuel emissions.\n\n– fO2 ,ref is the reference value for the mole fraction of O2 . We use 0.209341 based on the value measured by Aoki et al.\n(2019) at Hateruma Island, Japan in 2015 and adjusting by ∼ 2 ppm to approximate the global mean fO2 by using the\n\ndifference between the annual mean CO2 reported for Hateruma Island by Aoki et al. (2019) and that for the NOAA\n605\n\nglobal marine boundary layer reference. (A revised calculation accounting for possible influence of fossil fuel emissions\non Hateruma Island puts the global mean O2 mole fraction closer to 0.209347, however the 0.209341 value is what is\nused in GGG2020.)\n28\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nX2019 - X2007\nX2019+Var. O2 - X2019\nX2019+Var. O2 - X2007\n\nXCO2 (ppm)\n\n(a)\n0.0\n0.5\n1.0\n\n350\n\n400\n450\n500\n\"Raw\" XCO2 (ppm)\n\n550\n\n350\n\n400\n450\n500\n\"Raw\" XwCO2 (ppm)\n\n550\n\n350\n\n400\n450\n500\n\"Raw\" XlCO2 (ppm)\n\n550\n\nXwCO2 (ppm)\n\n(b)\n0.0\n0.5\n1.0\n\nXlCO2 (ppm)\n\n(c)\n0.0\n0.5\n1.0\n\nFigure 12. The change in TCCON (a) XCO2 , (b) XwCO2 , and (c) XlCO2 due to the WMO scale change, change in assumed O2 mole\nfraction, and the combination of both. The x-axis is the “raw” XCO2 value that has no in situ bias correction and assumes a fixed O2 mole\nfraction. The “X2019 – X2007” line shows the difference due to only the CO2 WMO scale change, the “X2019+Var O2 – X2019” shows\nthe difference due to only the change from fixed to variable O2 mole fraction, and the “X2019+Var. O2 – X2007” line shows the total change\nfrom both effects combined.\n\n29\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nReference\nBest estimate\n= 1/0.4575\n= 1/0.4000\n= 1/0.5000\n\nfO2 (mol/mol)\n\n0.209425\n0.209400\n0.209375\n0.209350\n0.209325\n\n1995 2000 2005 2010 2015 2020\nYear\nFigure 13. Comparison of fO2 values calculated using Eq. (10) for three different values of α versus a best estimate of fO2 using δ(O2 /N2\nfrom the Scripps Intitute of Oceanography (Scripps O2 Program, 2022) and NOAA global mean CO2 (Lan et al., 2023) data. The three\ncolored lines also use NOAA global mean CO2 data for the XCO2 and XCO2 ,ref values in Eq. (10). The black circle marks our reference\nvalue of fO2 = 0.209341.\n\n– XCO2 ,ref is a reference value for the column-average mole fraction of CO2 . We use 4 × 10−4 (400 ppm) to approximate\n\nthe value seen in TCCON data during 2015 (the same year as the fO2 ,ref value), though as discussed below, it is not\n\n610\n\ncrucial that the O2 and CO2 reference values be for exactly the same time.\n– XCO2 is the “raw” measured TCCON XCO2 with airmass correction and assuming fO2 = fO2 ,ref = 0.209341.\nTo validate this approach, we also compute the change in fO2 (including the effect of CO2 dilution) using δ(O2 /N2 ) data\nmeasured by the Scripps Institution of Oceanography at Alert, NWT, Canada (station code ALT); La Jolla Pier, California,\nUSA (LJO); and Cape Grim, Australia (CGO) and NOAA CO2 annual trend data (Lan et al., 2023). To approximate a global\n\n615\n\nmean δ(O2 /N2 ) value, we follow §5.15.4.2 of Keeling and Manning (2014) and combine the data from these stations as (ALT\n+ LJO)/4 + CGO/2.\nThe results of this comparison are shown in Fig. 13. The black line shows the change in fO2 computed using the Scripps\nδ(O2 /N2 ) data (see Appendix E2 for the methodology), while the other three lines represent fO2 calculated with Eq. (10)\n\n620\n\nand various values of α. We can see that Eq. (10) with α = −1/0.4575 gives quite good agreement with the change in fO2\ncomputed using the Scripps δ(O2 /N2 ) and NOAA global CO2 data.\n\nThe final step in adopting the variable O2 mole fraction was to recompute the in situ correction factor once more, using the\nvariable O2 mole fraction in the TCCON Xgas values for the comparison. Doing so ensures that any constant multiplicative\nbias introduced by incorrect or inconsistent values for the fO2,ref or XCO2 ,ref values is scaled out. This is why, in the discussion\nabove about the choice of those reference values, we note that it is not critical to have the O2 and CO2 reference value exactly\n625\n\nconsistent.\nThe orange lines in Fig. 12 show the effects of the change from a fixed O2 mole fraction to the variable one. For XCO2\nvalues around 400 ppm, the change is generally small in all three CO2 products. If CO2 mixing ratios continue to increase in\n30\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nthe future, the difference between using the incorrectly fixed and correctly varying O2 mole fraction would increase to 0.75 to\n1 ppm in magnitude.\n630\n\nThe green lines in Fig. 12 show the combined effect of the CO2 calibration scale change and the switch to a variable O2\nmole fraction. For low “raw” XCO2 values (i.e. values without the in situ bias correction and using a fixed O2 mole fraction)\nthe two effects reinforce each other, but as the raw XCO2 increases, the O2 mole fraction change starts to counteract part of the\nCO2 scale change.\nXCO2 , XwCO2 , and XlCO2 on the X2019 scale and accounting for the variable O2 mole fraction are now available in the pub-\n\n635\n\nlic data set as variables xco2_x2019, xwco2_experimental_x2019, and xlco2_experimental_x2019. Users\ncomparing to other data or model simulations/assimilations on the X2019 scale should use these variables. Anyone needing\nto compare against data still on the X2007 scale can use xco2, xwco2_experimental, and xlco2_experimental\ninstead.\n7.3.3\n\n640\n\nN2 O in situ comparisons\n\nTo derive an in situ correction for N2 O, we adopted a different approach than the other gases due to the small number of\nN2 O profiles over TCCON sites which our matching algorithm found in the NOAA CCGG Aircraft Program v1.0 ObsPack\n(Sweeney et al., 2018). Figure 14a shows the 10 profiles identified from the ObsPack, and Fig. 14b shows the TCCON/in situ\nratio vs. Xluft relationship for these profiles. We note that this scarcity of profiles was partly due to the criteria used to filter\nfor good quality profiles (Appendix C1.1). However, given how well-mixed N2 O is in the troposphere, the criteria intended to\n\n645\n\nensure a profile had enough vertical resolution to capture plumes of CO2 or CH4 could be relaxed for N2 O in future TCCON/in\nsitu comparisons to increase the number of available N2 O profiles for comparison.\nThe available profiles were further restricted by our criteria for coincidence with good quality TCCON observations. 2 of\nthese 10 profiles do not meet the coincidence criteria for inclusion in Fig. 14b, and 5 of the remaining 8 fall outside the allowed\nXluft range of 0.996 to 1.002. With the available data, it is difficult to distinguish whether there is significant correlation\n\n650\n\nbetween Xluft and TCCON XN2 O bias, and therefore whether those 5 comparisons below Xluft = 0.996 should be excluded.\nAs their exclusion would significantly alter the in situ correction for XN2 O , we tested a second approach to derive the N2 O\ncorrection.\nThis alternate approach uses NOAA surface N2 O data from the NOAA Halocarbons and other Atmospheric Trace Species\n(HATS) program (Dutton et al., 2023) combined with the GGG2020 priors to generate pseudo-in situ profiles. This takes\n\n655\n\nadvantage of the limited vertical variation in N2 O up to the tropopause seen in Fig. 14a and the good accuracy of the GGG2020\npriors in the stratosphere (Laughner et al., 2023). These pseudo-in situ profiles use the HATS N2 O data for the tropospheric\nVMRs, the GGG2020 priors for VMRs above 380 K potential temperature, and linearly interpolates in between. These pseudoin situ profiles are then integrated following Eq. (8) to produce a pseudo-in situ XN2 O and compared to TCCON in the same\nmanner as the other gases. As we are not limited by when an aircraft provided an N2 O profile over a TCCON site, we can\n\n660\n\ncompare to TCCON observations from any time. We use spectra from the same sites and days as the other gases, filtered for\nthe following criteria:\n31\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n(a)\n\n(b)\nTCCON XN2O / in situ XN2O\n\nPressure (hPa)\n\n200\n400\n600\n\nEast Trout Lake\nLauder 02\nLamont\nTroposphere\nAbove tropopause\n1000\n270 280 290 300 310 320 330\nN2O DMF (ppb)\n800\n\n(c)\nTCCON XN2O / in situ XN2O\n\n1.02\n1.01\n\nEast Trout Lake\n\nLauder 02\n\n0.990\n0.985\n0.980\n0.975\nr = 0.98250\n0.970 2 r = 0.00750\n0.986\n\n0.988\n\n0.990\n\n0.992 0.994\nXluft (mol/mol)\n\n0.996\n\n0.998\n\n1.000\n\ny = (0.782 +/- 0.0023) + (0.000646 +/- 7.53e-06)x\nFit = 0.98216 at x = 310.000\n\n1.00\n0.99\n0.98\n0.97\n0.96\n0.95\n\nLamont\n\n0.995\n\nr = 0.97905\n2 r = 0.00024\n285\n\n290\n\n295\n\n300\n\n700\n\n(K)\n\n305\n\n310\n\n315\n\nAscension Island\nAnmyeondo\nBremen\nPasadena\nDarwin\nArmstrong\nEast Trout Lake\nGarmisch\nLauder 01\n\nLauder 02\nManaus\nNicosia\nLamont\nOrleans\nPark Falls\nRikubetsu\nSodankyla\nWollongong\n\n320\n\nFigure 14. (a) The available N2 O profiles over TCCON sites from the NOAA CCGG Aircraft Program v1.0 ObsPack (Sweeney et al., 2018).\n(b) TCCON/in situ ratio vs. Xluft similar to Fig. 11, but for N2 O. (c) The TCCON/in situ XN2 O ratio derived using surface NOAA N2 O\ndata versus mid-tropospheric potential temperature. The dashed gray line is a robust fit to the data. The text in the lower right hand corner\ngives the mean TCCON/in situ ratio (denoted also by the horizontal dashed black line) and its 2σ standard deviation. The points are colored\nby TCCON site.\n\n– FVSI ≤ 0.05, as for the other gases\n– Xluft between 0.996 and 1.002, as for the other gases\n– The difference between prior HF column density and retrieved HF column density is < 2 × 1014 molec. cm−2 .\n665\n\nThe filtering on HF column helps to remove cases where the stratosphere prior N2 O used in the pseudo-in situ profiles is\nincorrect. HF is a gas found almost exclusively in the stratosphere, and in GGG2020, the HF and N2 O stratospheric priors\nare coupled. Thus, when the retrieved HF column is substantially different from the prior, that indicates that the HF prior was\nincorrect, which implies the same for the N2 O profile. HF columns tend to be between 1 and 2×1015 molec. cm−2 , so 2×1014\nmolec. cm−2 represents a 10% to 20% error in the HF prior. Given that the stratosphere component of N2 O is < 20% of the\n\n670\n\ncolumn, and assuming that the percent error in the N2 O prior is similar, this keeps the random error in the pseudo-in situ XN2 O\nto less that 2% to 4%. All together, these filtering criteria retain approximately 8600 TCCON observations from the initial set\nof ∼ 20, 000 observations used in the in situ correction analysis.\n\nThis larger sample set for N2 O allowed us to identify a correlation in XN2 O bias with atmospheric temperature. Figure 14c\n\nshows how the TCCON/in situ XN2 O ratio varies with potential temperature at 700 hPa. As in the ADCF analysis (§7.1), these\n675\n\npotential temperature values come from the GEOS FP-IT meteorology used as input to the GGG retrievals. The presence of\nthis bias suggests that there is an error in the temperature dependence of the N2 O cross sections (similar to that we identified\n32\n\n\fTCCON / in situ XN2O\n\nhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n1.04 (a)\n1.02\n\nGGG2020 fit: y = 0.00066x + 0.79616\nGGG2020.1 fit: y = 0.00000x + 0.99985\n\n1.00\n0.98\n290\n\n300\n700\n\n(K)\n\n310\n\n320\n\n1.02 (b)\nGGG2020\nNotional GGG2020.1\nEast Trout Lake\nLauder 02\nLamont\nRatio = 1\n\n1.01\n1.00\n\n330\n\n285 290 295 300 305 310 315\n700 (K)\n\n(c)\n\n102\n# observations\n\nNotional GGG2020.1 XN2O (ppb)\n\n0.99\n\n320\n\n101\n\n310\n300\n300\n\n310\n320\nGGG2020 XN2O (ppb)\n\n330\n\n100\n\nFigure 15. Future correction for XN2 O . (a) Similar to Fig. 14c, except showing the ratio between TCCON and the surface-derived XN2 O\nfrom GGG2020 with the in situ correction factor of 0.9821 applied in blue, and the expected temperature-corrected XN2 O in orange, with\ntheir respective fits. (b) Similar to Fig. 14b, but like panel (a) of this figure, comparing the ratios of GGG2020 and temperature-corrected\nXN2 O to in situ. (c) A 2D histogram comparing the current and notional corrected XN2 O\n\nand removed for O2 , §3.3). In the near term, we plan to develop a post-processing correction for this temperature bias in\nN2 O for inclusion in a minor update to the TCCON GGG2020 data within 2–3 years. Long term, the underlying error in the\nspectroscopic model will be corrected so that the next major TCCON data release will have improved XN2 O data.\n680\n\nFor GGG2020, we elected to choose the XN2 O in situ correction as the value of the fit in Fig. 14c at 310 K potential\ntemperature. This is consistent with the choice of ADCF values at the same temperature (§7.1). The value of 0.9822 is very\nclose to the mean TCCON/in situ ratio using the 8 true in situ profiles in Fig. 14b. That both methods agree gives us confidence\nthat this is a reasonable value to use for the in situ correction. We are also investigating applying the slope from Fig. 14c to\nTCCON XN2 O as a temperature-based bias correction. Figure 15 demonstrates the difference this correction would make, both\n\n685\n\nin comparison to the in situ data (Fig. 15a,b) and to the column-average dry mole fractions themsleves (Fig. 15c).\n\n33\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nXgas product\n\nCorrection factor\n\nCF error\n\nCalibration scale\n\nN\n\nfO2\n\nXCO2\n\n1.0101\n\n0.0005\n\nWMO X2007\n\n67\n\nFixed\n\nXCO2 _x2019\n\n1.0090\n\n0.0005\n\nWMO X2019\n\n70\n\nVar.\n\nXwCO2\n\n1.0008\n\n0.0005\n\nWMO X2007\n\n67\n\nFixed\n\nXwCO2 _x2019\n\n0.9996\n\n0.0005\n\nWMO X2019\n\n69\n\nVar.\n\nXlCO2\n\n1.0014\n\n0.0007\n\nWMO X2007\n\n67\n\nFixed\n\nXlCO2 _x2019\n\n1.0006\n\n0.0007\n\nWMO X2019\n\n69\n\nVar.\n\nXCH4\n\n1.0031\n\n0.0014\n\nWMO X2004\n\n40\n\nFixed\n\nXN2 O\n\n0.9821\n\n0.0098\n\nNOAA 2006A\n\nN/A\n\nFixed\n\nXCO\n\n1.000\n\n0.0526\n\nN/A\n\n31\n\nFixed\n\nXH2 O\n\n0.9883\n\n0.0157\n\nARM Radiosondes\n\n94\n\nFixed\n\nTable 2. In situ correction factors and their errors for each Xgas product evaluated against in situ data. The “Calibration scale” column\nindicates which scale or source these data are tied to by the AICFs. The N column indicates how many profiles are used to calculate the\nAICF for that gas. The fO2 column indicates what O2 mole fraction was used in the column density to column-average mole fraction\nconversion: “Fixed” means fO2 = 0.2095 in Eq. (1) and “Var.” means that the variable mole fraction described in §7.3.2 was used.\n\n7.3.4\n\nIn situ bias correction summary\n\nA summary of the in situ correction factors, their errors, and what in situ calibration scales each product is tied to are given\nin Table 2. Because these correction factors are the mean TCCON/in situ ratio, dividing the airmass-corrected and windowaveraged values by these correction factors removes the mean TCCON-in situ bias.\n690\n\nIn the TCCON data, users will find two sets of XCO2 variables. Those with the _x2019 suffix (xwco2_experimental_x2019,\nxlco2_experimental_x2019, and xco2_x2019) are those tied to the WMO X2019 CO2 scale and which use the variable O2 mole fraction. Those CO2 variables without the _x2019 suffix remain tied to the WMO X2007 CO2 scale and still\nuse the fixed O2 mole fraction. All other gases (xch4, xco, etc.) also still use the fixed O2 mole fraction.\nReleasing the rescaled XCO2 as new variables, rather than creating a new TCCON data version with the existing variables\n\n695\n\nrescaled, was chosen for several reasons. First, it is logistically simpler, allowing us to provide this update more quickly.\nSecond, during this transitional period when existing CO2 data is available on both the X2007 and X2019 scales, having\nboth X2007 and X2019 XCO2 allows users to switch back and forth easily if they need to match up with other datasets on\na mix of both scales. Third, this approach provides for release of more recent TCCON data without disrupting existing users\nworkflows—users do not have to worry about existing variables changing, but can switch their analyses to use the updated\n\n700\n\nXCO2 variables if and when they wish. Incorporating the variable O2 mole fraction for all gases is planned for an upcoming\nminor revision of the TCCON data (tentatively called “GGG2020.1”). Likewise, a temperature-corrected XN2 O product will\nbe included in GGG2020.1 or the follow on GGG2020.2, depending on development time.\n\n34\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n6000\n\n90\n\n40\n\n80\n\n30\n\n5000\n\n-20\n\n20\n\n60\n10\n50\n\n3000\n40\n2000\n\nSZA ( °)\n\nX H O (ppm)\n2\n\n-10\n\n°C)\n\n4000\n\nSurface temperature (\n\n70\n\n0\n\n30\n20\n\n1000\n\n0\nJan Feb Mar Apr May Jun Jul Aug\n\n10\n\n-30\n\n0\n\n-40\n\n2019\nFigure 16. The three dates chosen for the error budget calculations are from East Trout Lake on February 18 (blue), June 11 (red), and July\n23 (yellow), 2019. These dates were chosen to span a range of water vapor, solar zenith angle, and surface temperature. In the left panel, the\nblack data points show the full East Trout Lake record between Jan and Aug 2019 for reference.\n\n8 Uncertainty budget\nTo calculate an uncertainty in the GGG2020 dataset, we selected three days from the East Trout Lake dataset spanning a\n705\n\nrange of atmospheric water vapor, surface temperature and solar zenith angle (Figure 16). Each known source of uncertainty is\nmodeled or perturbed by a realistic amount in the GFIT forward model (the quantitative amounts are described in the following\nparagraphs), and we compute the percent fractional difference in Xgas between the perturbed and unperturbed value. The total\nuncertainty is computed as the sum in quadrature of the individual uncertainties. For each gas, we have plotted the contributions\nof each source as a function of solar zenith angle for the June 11, 2019 date in Figures 18–20. The same figures for cold, dry\n\n710\n\nFebruary 18 are in the Appendix in Figures B1–B3, and for warm, wet July 23 are in Figures B4–B6. The sum in quadrature\nof all the sources of error for each gas are plotted for the three days together in Figures 21–23. Each source of uncertainty\nincluded in our error budget is described below.\nField of view\nThe field of view (FOV) is the maximum solid angle viewed by the detector element, and its value is set by the field stop\n\n715\n\ndiameter inside the instrument. It is an important parameter in the GFIT forward model because it defines the extent of off-axis\nrays that pass through the interferometer, ultimately limiting the spectral resolution of a spectrum. The field stop diameter is\n\n35\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nset by a physical pinhole ranging from 0.5-1.3 mm drilled into a thin plate within the instrument, and its size can be in error by\na few percent. Here, we increase FOV by 7% to reflect any uncertainty in the field stop diameter.\nContinuum basis functions\n720\n\nIn GGG2020, the number of continuum basis functions has been optimized to improve the spectral fits without over fitting the\ndata (see §6). Here, we increase the number of continuum basis functions fitted by 1 in all windows that have widths >5 cm−1\nto assess the sensitivity of our choice of the number of basis functions to the retrieved Xgas value. The gases excluded from\nthis test because of their fitting window widths are HF, HCl, and some H2 O and HDO windows.\nSolar pointing\n\n725\n\nThe observer-sun Doppler stretch (OSDS) is a calculation made by GFIT based on the Earth-Sun radial velocity and the\nEarth’s rotational velocity component, under the assumption that the solar tracker is imaging the centre of the Sun. It defines\nthe Doppler stretch of the solar absorption lines relative to the telluric (atmospheric) absorption lines. If the solar tracker is not\nimaging the exact centre of the Sun, the solar lines may be Doppler-shifted relative to the telluric lines, creating systematic\nresiduals in the spectral fits. Here we increase the OSDS by 2 ppm to assess the sensitivity of the retrievals to a small pointing\n\n730\n\nerror from the Doppler stretch component alone. This error affects carbon monoxide more than the other gases because for\nevery telluric CO line in the spectrum, there is also a solar CO absorption line beneath, making it difficult to distinguish solar\nfrom telluric CO absorption. In GGG2014 and previous versions, this was a particular problem, because the pointing was\nassumed to be in the centre of the solar disk. In GGG2020, however, the solar-gas stretches are now fitted, reducing the impact\nof an OSDS error on the CO retrievals (see Wunch et al., 2015, Fig. 13).\n\n735\n\nSolar tracker pointing offsets also affect the ray tracing in GFIT, causing errors in the airmasses calculated for a given\nspectrum. This error impacts all gas retrievals, but should mostly cancel in the ratio between the gas of interest and oxygen.\nHere, we add a 0.05 degree pointing offset (poff), which represents a pointing error of about 20% of the solar radius.\nPrior\nWe modify the priors in several ways to estimate the uncertainties caused by various errors in the a priori profiles.\n\n740\n\n– A priori pressure profile (prior pressure). We multiplied the pressure at each atmospheric level in the prior by 1.002 to\nscale up the pressure by 0.2% at all altitudes. For the HCl cell pressure error, we added 0.14 hPa (0.138 atm) to the cell\npressure, following the “pessimistic” uncertainty budget in Hase et al. (2013, P3565). (The purpose of the HCl cells will\nbe described in §8.10.)\n– A priori temperature profile (prior temperature). We added 1 K to each atmospheric level in the prior.\n\n745\n\n– A priori profile shape (prior shift). We shifted the a priori profiles down by one atmospheric level. In GGG2014, we\nshifted the priors down by 1 km, so this is a slightly different approach, but the level spacing is about 1 km in altitude\nnear the tropopause, where this shift is most important for well-mixed tropospheric gases like N2 O and CH4 , and HF, a\nstratospheric gas. H2 O and HDO are not shifted as part of this process, but are modified in an independent test.\n\n36\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n– A priori boundary layer CO (prior CO enhanced). The GEOS FP-IT CO profiles are created using an old emission\ninventory, and tend to significantly overestimate emissions in urban regions that have reduced their emissions over time\n\n750\n\n(e.g., Los Angeles). However, because of the coarse spatial resolution of GEOS FP-IT, sites that are located near to an\nurban centre can be affected by the urban enhancements in the model. We therefore add an additional test that affects\nonly the CO error budget, in which we add 25 ppb to the altitudes below 2 km to estimate the uncertainty caused by the\nincorrect lower atmosphere shape in the GGG2020 CO prior profiles.\n755\n\n– A priori H2 O and HDO (prior h2o/hdo). We modified the water and HDO profiles by reducing the values in the first\n1 km by 50%.\nSurface pressure\nThe surface pressure measurements we collect as part of our on-site meteorological data are important for calculating the total\ncolumn of air overhead. The largest surface pressure uncertainty permitted by the TCCON data protocol is 0.3 hPa, but we\n\n760\n\nhave seen these instruments drift by up to 1 hPa. Here, we add 1 hPa to the surface pressure (pout) to calculate the sensitivity\nof the retrievals to this error.\nNonlinearity\nDetector nonlinearities, described in §5.1, cause a discrepancy between the low-resolution spectral envelope and the high\nresolution spectral lines, resulting in an offset at zero in the spectrum. These zero level offsets are most readily observed in\n\n765\n\nregions of the spectrum where strong absorption lines absorb all the incident light (Abrams et al., 1994). Here, we add 0.001\n(0.1%) to the zero level offset (ZLO) parameter in GFIT, a large ZLO observed in the network.\nInstrument line shape\nThe instrument line shape (ILS) of a Fourier transform spectrometer quantifies the optical alignment of the instrument, and is\nindependent of the alignment of the solar image. The ILS is characterized by two parameters: the modulation efficiency and\n\n770\n\nphase error. The modulation efficiency is the broadening or narrowing of the ideal spectral line width in the instrument, and the\nphase error is the asymmetrical component of the spectral line that is caused by the misalignment. It is not currently possible\nto model phase error within GFIT, but we can model imperfect modulation efficiency. The TCCON data protocol requires that\nthe instrument modulation efficiencies must be within 5% of a perfect alignment. The modulation efficiency of a perfectly\naligned interferometer is defined as a value of 1.0 at all optical path differences, taking self-apodization into account, and\n\n775\n\ntherefore the maximum and minimum modulation efficiency acceptable in the network is 1.05 and 0.95, respectively. Here we\nmodel two cases: a “shear” misalignment, where the modulation efficiency of the spectrometer increases linearly to 1.05 as a\nfunction of optical path difference, and an “angular” misalignment, where the modulation efficiency drops linearly to 0.95 as a\nfunction of optical path difference. We confirmed the misalignment by passing synthetic spectra generated by GFIT with these\nmisalignments through LINEFIT (v14.8 Hase et al., 1999), a program designed to assess instrument line shapes (see Figure\n\n780\n\n17).\nBecause GGG2020 cannot model phase errors, these sensitivity studies are likely to underestimate the full effect of ILS\nerrors, and therefore we include both the “shear” and “angular” misalignment in the sum.\n37\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nFigure 17. Synthetic spectra were generated using GFIT to simulate shear and angular misalignment with 5% change from the ideal line\nshape at a maximum optical path difference of 45 cm. These spectra were then passed through LINEFIT 14.8 to confirm that the modulation\nefficiency and phase errors were as expected.\n\n8.1\n\nGeneral comments on the results\n\nThe results of this error budget analysis only account for changes using a single instrument, and therefore cannot assess\n785\n\nimprovements to GGG2020 that affect inter-instrument precision, such as consistent continuum fitting across the network,\nchannel fringe fitting when needed, a priori shape improvements, and so on. Site-to-site variability have been assessed in\nsections §7.1–§7.3. The results in this section quantify the errors incurred by uncertainties in a single instrument setup.\nThe method of simulating modulation efficiency errors in GGG2014 (Wunch et al., 2015) was incorrect, resulting in an\ninferred uncertainty from ILS errors that is too large, likely by about a factor of 2 (see Appendix B1 for details). The change\n\n790\n\nfrom the errant ILS modeling to our current model, on its own, will produce an apparent overall uncertainty reduction for\nGGG2020 when compared with GGG2014, but there have been no improvements in GGG2020 with respect to fitting imperfect\nILS. However, there are several other improvements in GGG2020 that have resulted in systematic reductions in the uncertainty,\nincluding higher order continuum fitting (§6), solar-gas stretch fitting (§8), and gas-specific spectroscopy (§3.1) and line shape\nfitting improvements (§3.2).\n\n795\n\nIn GGG2014, our retrievals were performed on a 1 km grid, and we shifted the profiles down by 1 level (or 1 km at all\naltitudes). In GGG2020, our retrievals are on a grid that increases in spacing with altitude, and a shift down by 1 level is\n\n38\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxco2 - 20190611\n\nxluft - 20190611\n0.25\n\n1\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.6\n\n%\n\n0.4\n\n0.2\n\n0\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.2\n0.15\n0.1\n\n%\n\n0.8\n\n0.05\n0\n-0.05\n\n-0.2\n\n-0.1\n-0.15\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nxco - 20190611\n\nxch4 - 20190611\n2.5\n\n0.5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.3\n0.2\n\n%\n\n0.1\n0\n-0.1\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n2\n\n1.5\n\n1\n\n%\n\n0.4\n\n0.5\n\n0\n\n-0.2\n\n-0.5\n\n-0.3\n\n-1\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure 18. June 11, 2019 error budget from East Trout Lake. The figures show the percent difference between the perturbed test and the\nstandard retrieval plotted as a function of solar zenith angle. “Sum” in the legend means the quadrature sum of the other terms. The retrievals\nplotted here are Xluft , XCO2 , XCH4 , and XCO .\n\n39\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxh2o - 20190611\n\nxhdo - 20190611\n4\n\n2\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n1\n\n%\n\n0.5\n0\n-0.5\n\n3\n\n2\n\n1\n\n%\n\n1.5\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0\n\n-1\n\n-1\n\n-2\n\n-1.5\n-2\n\n-3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\nxn2o - 20190611\n\n50\n\n60\n\n70\n\n80\n\n90\n\n70\n\n80\n\n90\n\n°)\n\nxhf - 20190611\n\n1.2\n\n5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.8\n0.6\n0.4\n0.2\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n4\n3\n2\n\n%\n\n1\n\n%\n\n40\n\nSolar Zenith Angle (\n\n°)\n\n1\n0\n\n0\n\n-1\n\n-0.2\n\n-2\n\n-0.4\n\n-3\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n°)\n\nFigure 19. As in Figure 18, but for XH2 O , XHDO , XN2 O , and XHF .\n\nroughly 1 km at the tropopause, but smaller below and larger above. This change is most likely to affect the retrievals of gases\nfor which there is a rapid change in abundance near the tropopause and above: N2 O, CH4 , and HF. Therefore, our shift for the\nGGG2020 error budget represents a larger perturbation to the a prior shape for these gases, which will cause larger errors in\n800\n\nretrievals. However, because HF is a species found primarily in the stratosphere, and N2 O and CH4 are species found primarily\nin the troposphere, retrievals of HF can be used to diagnose and reduce the impact of the profile shift errors on XN2 O and XCH4\n(e.g., Washenfelder et al., 2003; Saad et al., 2014, 2016; Wang et al., 2014).\nIn each section below, we will discuss the results for each gas, keeping in mind the reductions in error from the ILS model,\nand the inflation of error from the prior shifts.\n\n40\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxwco2 - 20190611\n\nxlco2 - 20190611\n0.6\n\n0.4\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.2\n\n%\n\n0.1\n\n0\n\n-0.1\n\n0.5\n0.4\n0.3\n0.2\n\n%\n\n0.3\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.1\n0\n-0.1\n-0.2\n\n-0.2\n\n-0.3\n-0.4\n\n-0.3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nvsf_hcl - 20190611\n4\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n3\n\n%\n\n2\n\n1\n\n0\n\n-1\n\n-2\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure 20. As in Figure 18, but for XlCO2 , XwCO2 , and HCl scale factors (vsf_hcl).\n805\n\n8.2\n\nXluft\n\nXluft is the column-averaged amount of dry air, and is equivalent to the parameter Xair in GGG2014. The error budget for\nXluft (Figures 18 and 21) is very similar to that of Xair in GGG2014, with uncertainties smaller than 0.7% for all solar zenith\nangles less than 82◦ . The error is dominated by pointing offsets at large solar zenith angles, and zero level offsets contribute\nsignificantly to the error at all solar zenith angles.\n810\n\n8.3\n\nXCO2\n\nThe XCO2 error budget is smaller than for GGG2014 (Wunch et al., 2015), mostly from the reduced continuum fitting errors.\nThe GGG2020 errors are below 0.16% (∼0.6 ppm) for solar zenith angles less than 82◦ , though if extrapolated linearly to\n41\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nsmaller solar zenith angles, the error could become larger than 0.15% at 0 degrees (Figures 18 and 21). The largest sources\nof error at lower solar zenith angles are from prior pressure offsets and misalignment. At larger solar zenith angles, the error\n815\n\nbecomes dominated by prior temperature errors and zero level offsets.\n8.4\n\nXCH4\n\nThe XCH4 error budget is smaller than for GGG2014 (Wunch et al., 2015). There is a significant reduction in the errors\nassociated with observer-sun Doppler stretch (OSDS) offsets and continuum fitting errors. The GGG2020 errors are below\n0.4% (∼7 ppb) for solar zenith angles less than 82◦ (Figures 18 and 21). The largest sources of error at lower solar zenith\n820\n\nangles are from prior profile shifts and prior pressure errors. At larger solar zenith angles, the error is dominated by prior\nprofile shifts. Errors caused by profile shifts can be mitigated by extracting the tropospheric partial column of XCH4 using the\nSaad et al. (2014) or Wang et al. (2014) methods.\n8.5\n\nXCO\n\nThe XCO spectral fitting has been substantially improved in GGG2020, largely because of our reduced sensitivity to errors in\n825\n\nthe observer-sun Doppler stretch (OSDS), and also because we removed one of the fitted windows from our standard analysis\nin GGG2020 that had relatively poorer spectral fits. The GGG2020 errors are below 2% (∼ 2 ppb assuming a 100 ppb column)\nfor all SZA < 82◦ . The largest sources of error are the prior CO enhancement, the prior shift, prior temperature, and shear\nmisalignment (Figures 18 and 21).\n8.6\n\n830\n\nXH2 O and XHDO\n\nThe error budget for water and HDO is roughly the same as for GGG2014 and earlier, with total errors under 2% in XH2 O and\n3% in XHDO over all solar zenith angles less than 82◦ . The largest component of the error budget for water vapor and HDO is\nthe shape of the a priori profile, which dominates the error budget for all solar zenith angles below 75◦ for water, and over all\nsolar zenith angles below 82◦ for HDO (Figures 19 and 22).\n8.7\n\n835\n\nXN2 O\n\nThe XN2 O error budget is roughly the same as in GGG2014, with total errors less than 1.25% (∼4 ppb) over all solar zenith\nangles. The largest source of error is the prior shift, which is not surprising, given the rapid chemical destruction of N2 O above\nthe tropopause, though the magnitude of the error is about twice as large as it was for GGG2014. As discussed above, this\nis likely caused by differences in the way we shift the profile, and could be mitigated by extracting the tropospheric partial\ncolumn by adapting the Saad et al. (2014) approach. Other contributors to the total error include the prior pressure, and shear\n\n840\n\nand angular misalignments (Figures 19 and 22).\n\n42\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n8.8\n\nXHF\n\nHF has only a single absorption line (4038.96 cm−1 ) that is located on the wing of a strong water absorption feature, so the\nretrievals tend to be noisy, especially at high solar zenith angles and under wet conditions. The XHF error budget has reduced\nin GGG2020 compared with GGG2014, with total errors now less than 5% over all solar zenith angles. In GGG2014, the errors\n845\n\nwere typically below 8%, but that error was dominated by the much larger shear misalignment. The largest source of error in\nGGG2020 is the prior shift, followed closely by shear misalignment (Figures 19 and 22).\n8.9\n\nXlCO2 and XwCO2\n\nIn GGG2014 and previous versions, we did not retrieve strong (“lCO2 ”) and weak (“wCO2 ”) CO2 bands. The strong CO2\nretrieval errors are dominated by prior temperature errors, and the weak CO2 errors are dominated by both shear and angular\n850\n\nmisalignments, errors in the prior pressure, adjustments to the continuum curvature, and zero level offsets (Figures 20 and 23).\nThe strong lCO2 retrieval errors are less than 0.3% over all solar zenith angles, and the weak wCO2 retrievals have around\n0.5% errors at all solar zenith angles, declining slightly at higher angles.\n8.10\n\nVSF HCl\n\nIn this error budget, we have included the scale factors retrieved for HCl (vsf_hcl in Figs. 20 and 23). In the East Trout Lake\n855\n\ninstrument and most others in the network, a sealed HCl cell filled with a known quantity of gas (Hase et al., 2013) is placed\npermanently in the solar beam inside the evacuated spectrometer to monitor long-term changes in ILS. Because the quantity\nof gas in the cell is significantly larger than the atmospheric abundance, the atmospheric component is negligible and largely\nindependent of surface pressure or other atmospheric adjustments. To assess the HCl retrieval sensitivity to changes in ILS and\nother parameters, we include the HCl scale factors in our error budget.\n\n860\n\nThe retrieval errors in the scaling factors retrieved for HCl in a sealed cell are dominated by errors in the instrument line\nshape with no significant solar zenith angle dependence. This is a comforting result, showing that our HCl retrievals are a good\ndiagnostic for instrument line shape drift. The HCl retrievals are not included in the standard public data files as they are used\nprimarily for diagnostic purposes.\n8.11\n\n865\n\nUncertainty estimate comparison\n\nFor six products (XCO2 , XwCO2 , XlCO2 , XCH4 , XCO , and XH2 O ) we can compare the uncertainty estimates derived from the\nerror budgets with those computed from in situ comparisons similar to those in §7.3 but with one difference: the comparisons\nin §7.3 use the in situ vertical profiles as the prior trace gas profiles in the TCCON retrievals; the in situ comparisons in this\nsection use standard TCCON GGG2020 prior profiles. For the in situ uncertainty, we use the median absolute deviation of the\nTCCON Xgas values from the in situ Xgas values after removing the mean bias for each Xgas (i.e. the correction factor in\n\n870\n\nTable 2). To convert the percent error from the error budget into a column-average mole fraction, we use the mean total percent\nerror across all three days used in the error budget (18 Feb, 11 June, and 23 July 2019) binned by SZA in 5° increments. We\n43\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxco2\n\nxluft\n0.16\n\n0.7\n20190218\n20190611\n20190723\n\n0.65\n\n20190218\n20190611\n20190723\n\n0.15\n\n0.6\n\n0.14\n\n0.55\n\n%\n\n%\n\n0.5\n\n0.13\n\n0.45\n\n0.12\n\n0.4\n0.35\n\n0.11\n0.3\n\n0.1\n\n0.25\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n70\n\n80\n\n90\n\n°)\n\nxco\n\nxch4\n\n2\n\n0.34\n20190218\n20190611\n20190723\n\n0.32\n\n10\n\n°)\n\n20190218\n20190611\n20190723\n\n1.9\n\n0.3\n\n1.8\n\n0.28\n\n1.7\n\n0.26\n\n%\n\n%\n\n1.6\n0.24\n\n1.5\n0.22\n\n1.4\n0.2\n\n1.3\n\n0.18\n\n1.2\n\n0.16\n\n1.1\n\n0.14\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n°)\n\nFigure 21. These figures show the sum in quadrature of all the errors plotted in Figure 18 for all three dates. The errors plotted here are for\nXluft , XCO2 , XCH4 , and XCO .\n\n44\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxh2o\n\nxhdo\n\n1.8\n\n3\n20190218\n20190611\n20190723\n\n1.6\n\n20190218\n20190611\n20190723\n\n2.8\n2.6\n\n1.4\n2.4\n2.2\n\n%\n\n%\n\n1.2\n1\n\n2\n1.8\n\n0.8\n\n1.6\n0.6\n1.4\n0.4\n\n1.2\n\n0.2\n\n1\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\n40\n\nxn2o\n1.2\n20190218\n20190611\n20190723\n\n60\n\n70\n\n80\n\n90\n\n70\n\n80\n\n90\n\n°)\n\nxhf\n\n4.4\n\n1.15\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n20190218\n20190611\n20190723\n\n4.2\n4\n\n1.1\n3.8\n3.6\n\n1\n\n%\n\n%\n\n1.05\n\n3.4\n3.2\n\n0.95\n\n3\n\n0.9\n2.8\n\n0.85\n\n2.6\n\n0.8\n\n2.4\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n°)\n\nFigure 22. As in Figure 21, but for XH2 O , XHDO , XN2 O , and XHF . XHF values above 68° SZA are not available on 2019-07-23 because\nthe HF lines were blacked out by H2 O absorbance.\n\n45\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxwco2\n\nxlco2\n0.48\n\n0.3\n20190218\n20190611\n20190723\n\n0.28\n\n20190218\n20190611\n20190723\n\n0.47\n0.46\n\n0.26\n\n0.45\n0.44\n\n%\n\n%\n\n0.24\n0.22\n\n0.43\n0.42\n\n0.2\n\n0.41\n0.18\n\n0.4\n0.16\n\n0.39\n0.38\n\n0.14\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nvsf_hcl\n2.77\n20190218\n20190611\n20190723\n\n2.76\n2.75\n2.74\n\n%\n\n2.73\n2.72\n2.71\n2.7\n2.69\n2.68\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure 23. As in Figure 21, but for XlCO2 , XwCO2 , and HCl scale factors (vsf_hcl).\n\ninterpolate this to the mean SZA of all spectra used in the in situ comparison for that gas and multiply this interpolated mean\npercentage by the mean TCCON Xgas value across all the in situ comparisons. The results are presented in Table 3.\nIt is important to acknowledge that the error amounts calculated from the in situ comparison are (for most gases) conserva875\n\ntive, for several reasons. First, in situ profiles are usually taken when the target TCCON station is near optimal performance, so\nthose comparisons are unlikely to capture the full range of error sources. Second, the in situ profiles are heavily concentrated\nover certain TCCON sites, also limiting how representative they are. Finally, the TCCON Xgas values compared against the\nin situ values are averaged over a minimum of 2 hours. This will reduce sources of random error. However, we believe this\nis still a worthwhile evaluation of measurement accuracy because (a) there is real physical variation in the atmosphere during\n\n880\n\nthe in situ profile, and the time averaging is necessary to account for that and (b) many of the factors considered in the error\n\n46\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nGas\n\nSZA\n\nMean abs. dev.\n\nError budget\n\n\u000fin situ\n\n\u000fmeas\n\n\u000fFT\n\n\u000fstrat\n\nXCO2\n\n46°\n\n0.42 ppm\n\n0.47 ppm\n\n0.053 (0.30) ppm\n\n0.033 (0.16) ppm\n\n0.032 (0.12) ppm\n\n0.061 (0.072) ppm\n\nXwCO2\n\n46°\n\n0.43 ppm\n\n1.8 ppm\n\n0.062 (0.36) ppm\n\n0.037 (0.16) ppm\n\n0.038 (0.15) ppm\n\n0.075 (0.10) ppm\n\nXlCO2\n\n46°\n\n0.75 ppm\n\n0.66 ppm\n\n0.038 (0.24) ppm\n\n0.025 (0.14) ppm\n\n0.020 (0.067) ppm\n\n0.057 (0.060) ppm\n\nXCH4\n\n46°\n\n4.9 ppb\n\n3.9 ppb\n\n2.0 (9.6) ppb\n\n0.65 (3.1) ppb\n\n0.19 (0.49) ppb\n\n3.4 (6.3) ppb\n\nXCO\n\n43°\n\n8.1 ppb\n\n1.7 ppb\n\n2.8 (14.0) ppb\n\n1.9 (9.3) ppb\n\n0.13 (0.39) ppb\n\n0.24 (4.8) ppb\n\nXH2 O\n\n52°\n\n140 ppm\n\n33 ppm\n\n100 (950) ppm\n\n100 (950) ppm\n\n0 (0) ppm\n\n0 (0) ppm\n\nTable 3. A comparison of typical errors calculated from the differences between TCCON and in situ Xgas values (“Mean abs. dev.” in the\ntable) and errors calculated from the error budget (“Error budget” in the table). The text gives details on how each error metric was computed.\n“SZA” gives the solar zenith angle for which the error budget percent was taken to calculate the “Error budget” column. The remaining four\ncolumns give the total 2σ uncertainty on the in situ data (\u000fin situ ), followed by the 2σ uncertainty components coming from the in situ measurement itself (\u000fmeas ), the unmeasured free troposphere (\u000fFT ), and the unmeasured stratosphere (\u000fstrat ). The last two components are 0 for\nXH2 O because the radiosonde measurements used always cover the free troposphere, and we assume that error in the meteorological model\nused to obtain the stratospheric H2 O profile is negligible. The parenthetical numbers give the mean value per TCCON/in situ comparison\nfor each uncertainty component; the non-parenthetical errors are smaller because they are calculated by formally propagating the error from\n√\nindividual comparisons to the mean absolute deviation, thus reducing by n. Appendix C6 describes how the uncertainty components from\nthe last 3 columns are calculated and combined to give \u000fin situ in the fifth column.\n\nbudget will not average out over the coincidence window. For example, angular or shear misalignment of the instrument would\nbe essentially constant over an entire day.\nFor three Xgas products (XCO2 , XlCO2 , and XCH4 ) the in situ and error budget estimates are similar, which gives us\nconfidence in the error budget estimates. For XwCO2 , the error budget estimate is much larger than the in situ error estimate.\n885\n\nIt may be that the error budget tested larger errors in the stratosphere temperature or VMR prior profile than were observed\nduring the in situ comparisons, as the XwCO2 product is more sensitive to the upper atmosphere than the other CO2 products\nin GGG2020. (Pressure errors could be another source of the overestimate, but the pressure perturbation test was designed to\navoid introducing an overly large perturbation to the stratosphere.) As we treat the in situ-derived errors as conservative, this\nsituation is acceptable, but will be investigated in the future.\n\n890\n\nBoth XCO and XH2 O had larger errors in comparison with in situ data than through the error budget. For XCO , the difference\nin error estimates is 6.4 ppb. Almost half of that is attributed to uncertainty in the in situ measurements. The uncertainty in\nindividual comparisons (the parenthetical numbers in Table 3) is quite a bit larger; if part of this error is systematic (such as\nfrom drift in calibration tanks, e.g., Andrews, 2019), that could explain the remaining difference. For XH2 O , this is because of\nuncertainty in the radiosondes used to compare against. The radiosondes used at ARM have a 4 or 5% uncertainty in relative\n\n895\n\nhumidity (https://www.arm.gov/publications/tech_reports/handbooks/sonde_handbook.pdf, last accessed 10 Apr 2023). When\nwe propagate this uncertainty to the mean absolute deviation, it works out to 103 ppm—very nearly the missing 110 ppm\nbetween the two error estimates.\n47\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n9\n\nMiscellaneous changes\n\n9.1\n900\n\nAK binning\n\nThe public GGG2020 TCCON files now include one averaging kernel (AK) per observation. This is a change from GGG2014,\nwhere the public files included a table of canonical AKs for a limited set of SZAs, and users were required to interpolate the\nAKs to the SZA of each spectrum. This was done in response to user requests to simplify the use of the averaging kernels. This\ndoes not mean that averaging kernels are computed by GGG for every TCCON observation (they are not). Internally, we still\nuse a table of precomputed AKs, which are interpolated as needed to provide per-spectrum AKs in the public files. This affords\n\n905\n\nsignificant saving in data storage, as the files GGG requires for AK calculation are very large.\nThough users of public TCCON data no longer need to know how the AK tables work, there are two changes from GGG2014\nthat we wish to document here.\nFirst, in GGG2020, the bin coordinate has changed from solar zenith angle (SZA) to “slant Xgas ,” which is defined as:\n\nSlant Xgas = airmass · Xgas\n910\n\n(11)\n\nwhere “airmass” is the airmass calculated by GGG in the O2 window and “Xgas ” is the column average mole fraction of\nthe gas of interest. Using slant Xgas as the bin coordinate correctly accounts for cases where the dynamic range of a gas’s\nconcentrations is large enough to change the AK at a single SZA. This can be seen in Fig. 24. For CO2 (Fig. 24a,b), the AKs\nvary smoothly and monotonically with either SZA or slant XCO2 . However, for H2 O, the AKs do not vary monotonically with\nSZA (Fig. 24c) but do with slant XH2 O (Fig. 24d). Therefore, slant Xgas was adopted as the binning coordinate for all AKs for\n\n915\n\nconsistency.\nSecond, in order to provide per-spectrum AKs in the public TCCON data files without significantly increasing the file size,\nit was necessary to ensure that observations with similar slant Xgas values had identical AKs so that the netCDF compression\nalgorithm could operate effectively. We achieved this by “quantizing” the slant Xgas values that we interpolated the AKs to;\nthat is, we select 500 slant Xgas values that cover the expected range of slant Xgas , plus 50 additional points to cover extreme\n\n920\n\nvalues. Each observation then uses the AK corresponding to the one of those 550 slant Xgas values closest to its true slant Xgas\nvalue. This scheme keeps the difference between the quantized and full resolution AKs to < 1% in 90% of observations while\nonly increasing file size by ∼ 20%.\n9.2\n\nA priori profiles and AK corrections\n\nAs described in §4.3, the a priori profiles reported in the published GGG2020 netCDF files are in wet mole fraction. When\n925\n\napplying an averaging kernel correction to calculate the Xgas value that would be retrieved by TCCON for an arbitrary gas\nprofile, that gas profile must be converted into wet mole fraction. This can be done using either the TCCON H2 O a priori\nprofile provided or an H2 O profile measured or modeled coincidentally with the gas profile for which an Xgas value is desired.\n\n48\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n90\n\n0.0\n\nlog10(XCO2 airmass)\n\n50\n\n2.8\n\nSZA\n\nPressure (atm)\n\n2.6\n\n60\n0.4\n\n40\n\n0.6\n\n3.0\n\n30\n\n0.8\n\n20\n\n3.2\n\n10\n\n1.0\n0.2\n\n0.4\n\n0.6 0.8 1.0\nCO2 Column AK\n\n1.2\n\n1.4\n\n0\n\n0.2\n\n90\n\n0.0\n\n0.4\n\n0.6 0.8 1.0\nCO2 Column AK\n\n1.2\n\n1.4\n\n(d)\n\n1.2\n\n80\n\n1.4\n\n70\n\n0.2\n\n1.6\n\n60\n0.4\n\n50\n\n1.8\n\n40\n\n2.0\n\n30\n\n2.2\n\nSZA\n\nPressure (atm)\n\n2.4\n\n70\n\n0.2\n\n(c)\n\n(b)\n\n80\n\nlog10(XH2O airmass)\n\n(a)\n\n0.6\n0.8\n\n20\n\n2.4\n\n10\n\n1.0\n0.2\n\n0.4\n\n0.6\n0.8\nH2O Column AK\n\n1.0\n\n1.2\n\n2.6\n\n0\n\n0.2\n\n0.4\n\n0.6\n0.8\nH2O Column AK\n\n1.0\n\n1.2\n\nFigure 24. CO2 and H2 O AKs from four days’ measurements at the TCCON site in Lamont, OK, USA. (a) CO2 AKs binned by SZA. (b)\nCO2 AKs binned by slant XCO2 . (c) H2 O AKs binned by SZA. (d) H2 O AKs binned by slant XH2 O .\n\nUsers who are unsure which is appropriate for their application are encouraged to reach out to the TCCON network chairs\n(listed at https://tccon-wiki.caltech.edu/Main/SteeringCommitteeMembership) for assistance.\n930\n\n9.3\n\nChanges to quality flags\n\nAs in GGG2014, a spectrum is flagged as being poor quality if any of the retrieved Xgas or Xgas error values, or ancillary\nvariables pertaining to instrument operation or local observation conditions are outside of expected ranges. Such spectra are\nnot included in the public data files. In GGG2020, spectra may also be flagged as poor quality and withheld if:\n– the staff at the TCCON site identify a hardware issue affecting that spectrum\n935\n\n– during pre-release data review, a time period containing that spectrum is identified as out-of-family for TCCON data.\nThe latter case focuses on a smoothed timeseries of Xluft and DIP. As shown in §7.3 and §8, deviation of Xluft from the\nnetwork median correlate with bias in the other Xgas products. (See §3.3 for a definition of Xluft .) Therefore, when a 500spectrum rolling median of Xluft falls consistently outside the nominal range of 0.995 to 1.003, that time period is rejected,\nas the Xgas products will likely have biases exceeding the expected TCCON accuracy. Likewise, DIP is a measure of detector\n\n940\n\nnonlinearity (§5.1), and testing has shown that increasing magnitude of DIP increases bias in XCO2 (Fig. 26). Thus, data where\nDIP consistently exceeds ±5 × 10−4 are removed in order to keep the XCO2 bias less than 0.25 ppm.\n49\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n104\n\n0.2\n\n0.4\n\n0.6 0.8 1.0 1.2\nXCO2 column AK (unitless)\n\n1.4\n\n104\n\n400\n\n103\n\n600\n800\n\n102\n\n0.00 0.25 0.50 0.75 1.00 1.25 1.50 1.75\nXlCO2 column AK (unitless)\n\n104\n103\n\n400\n600\n\n102\n\n800\n0.0\n\n0.2\n\n0.4 0.6 0.8 1.0\nXHF column AK (unitless)\n\n1.2\n\n1.4\n\n104\n\n200\nSlant XN2O\n\nPressure (hPa)\n\n(g) 0\n400\n\n103\n\n600\n800\n1000\n\n0.50 0.75 1.00 1.25 1.50 1.75 2.00 2.25 2.50\nXN2O column AK (unitless)\n\nSlant XH2O\n\nPressure (hPa)\n\n400\n\n104\n\n600\n800\n1000\n\n0.2\n\n0.4 0.6 0.8 1.0 1.2\nXH2O column AK (unitless)\n\n1.4\n\nSlant XwCO2\n\n800\n0.5\n\n0.6\n\n0.7 0.8 0.9 1.0 1.1\nXCH4 column AK (unitless)\n\n1.2\n\n107\n\n400\n\n106\n\n600\n800\n0.00 0.25 0.50 0.75 1.00 1.25 1.50 1.75\nXO2 column AK (unitless)\n\n105\n104\n\n200\n\n103\n\n400\n600\n\n102\n\n800\n0.6\n\n0.8\n\n1.0 1.2 1.4 1.6 1.8\nXCO column AK (unitless)\n\n101\n\n2.0\n\n105\n\n(j) 0\n200\n400\n\n104\n\n600\n800\n1000\n\n103\n\n103\n\n200\n\n1000\n\n102\n\n200\n\n104\n\n600\n\n(h) 0\n\n105\n\n(i) 0\n\n400\n\n1000\n\n101\n\nPressure (hPa)\n\n1000\n\n105\n\n(f) 0\nPressure (hPa)\n\n200\n\nSlant XHF\n\nPressure (hPa)\n\n(e) 0\n\n102\n\n200\n\n1000\n\nPressure (hPa)\n\n1000\n\n0.50 0.75 1.00 1.25 1.50 1.75 2.00 2.25\nXwCO2 column AK (unitless)\n\n(d) 0\nPressure (hPa)\n\n200\nSlant XlCO2\n\nPressure (hPa)\n\n(c) 0\n\n800\n1000\n\n102\n\n103\n\n600\n\nSlant XCH4\n\n800\n1000\n\n400\n\nSlant XO2\n\n600\n\n200\n\nSlant XCO\n\n103\n\nSlant XHDO\n\n400\n\n104\n\n(b) 0\nPressure (hPa)\n\n200\nSlant XCO2\n\nPressure (hPa)\n\n(a) 0\n\n1.0\n\n1.2\n1.4\n1.6\n1.8\nXHDO column AK (unitless)\n\n2.0\n\n103\n\nFigure 25. Precomputed column AKs for TCCON Xgas products: (a) XCO2 , (b) XwCO2 , (c) XlCO2 , (d) XCH4 , (e) XHF , (f) XO2 , (g)\nXN2 O , (h) XCO , (i) XH2 O , and (j) XHDO .\n\n50\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nFigure 26. Detector nonlinearity can cause a bias in XCO2 . This figure shows an example of the difference between the XCO2 retrieved after\ncorrecting the nonlinearity and prior to the nonlinearity correction as a function of the DIP parameter, that is a proxy for nonlinearity. Prior\nto correction, the Indianapolis data had DIP values that were almost exclusively negative. To limit the XCO2 bias caused by nonlinearity to\nless than 0.25 ppm, the absolute value of the DIP must be smaller than 0.5×10−3 .\n\n10\n\nConclusions\n\nThe GGG2020 TCCON data product incorporate numerous improvements to the GGG retrieval, based both on first-principle\nunderstanding and empirical evaluation. To review:\n945\n\n– The interferogram-to-spectrum conversion has added checks and diagnostics for detector nonlinearity or saturation, as\nwell as a modification to the phase correction that reduces bias between forward and reverse scans of the interferometer.\n– The solar and telluric spectroscopic linelists used in the GGG forward model have been updated to reflect new laboratory\nand atmospheric/solar observing studies, to include non-Voigt lineshapes, and to reduce an observed temperature and\nwater dependence in the O2 column amounts.\n\n950\n\n– The a priori inputs of atmospheric state (temperature, pressure, and composition) have increased temporal resolution and\nthe trace gas profiles have been updated to better reflect both atmospheric growth rates of key species and gradients in\ntheir mixing ratios across the tropopause.\n– Improvements to fitting the continuum and channel fringes in the spectra.\n– A more flexible airmass correction applied to Xgas value from individual spectral windows, rather than multi-window\n\n955\n\naverages of said values.\n– A change to how retrieved Xgas values from multiple spectral windows measuring the same gas are averaged together\nthat eliminates a dependence on how many observations were averaged at once.\n51\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n– An updated in situ correction factor that increases the number of profiles used to tie TCCON to the calibration scales\nused by in situ GHG measurements.\n– Improvements to user-friendliness in how AKs and prior profiles are reported in public files.\n\n960\n\nThere remains work to be done to further improve the TCCON data product. Implementing the capability in GGG to account\nfor errors in ILS remains a high priority. This was planned for inclusion in GGG2020, but could not be completed in time. It\nis expected that this capability will be an important tool to eliminate the XCO2 bias seen in comparison with in situ profiles\nas Xluft deviates from its nominal 0.999 value. A second high priority objective is to investigate the temperature dependence\n965\n\nseen in the N2 O and (to a much lesser extent) CH4 data and correct the underlying spectroscopic terms.\nWe currently plan to develop a minor release, GGG2020.1, within the next several years that will include additional postprocessing bias corrections to address the bias of XCO2 versus Xluft and XN2 O and XCH4 versus temperature. We expect these\nwill allow us to release data from the early years of several sites, which is currently flagged as poor quality due to out-of-bounds\nXluft as well as improve the XN2 O data substantially. As this would be a post-processing-only update, the reprocessing could\n\n970\n\nbe completed very rapidly.\nAt time of writing, 26 TCCON sites have reprocessed their existing data with GGG2020. Several sites are still in the process\nof carrying out this reprocessing, in many cases to improve the data quality based on new diagnostics available in GGG2020.\nWork is ongoing towards completing these sites’ reprocessing. Extensions to the existing data records will be released monthly\ngoing forward.\n\n975\n\n11\n\nCode and data availability\n\nAll TCCON GGG2020 data is linked through tccondata.org and stored as DOI-tagged datasets on CaltechDATA (data.caltech.\nedu). Each TCCON site has a separate repository and DOI on CaltechDATA; these are listed in Table 1. If a future correction\nrequires a revision of previously published data, that revision will receive a new DOI. Users are encouraged to check tccondata.\norg for the latest revisions of data rather than relying on Table 1. A repository containing the full set of TCCON GGG2020\n980\n\ndata is also available on CaltechDATA with the DOI 10.14291/TCCON.GGG2020 (Total Carbon Column Observing Network\n(TCCON) Team, 2022). Users are asked to cite the individual sites’ data records rather than the combined record as this\nhelps track usage of site data and thus support the ongoing operation of these sites. We provide a citation generator at https:\n//tccondata.org/metadata/siteinfo/genbib/. All data is provided in netCDF format, and additional documentation for the data is\navailable at https://tccon-wiki.caltech.edu/. The GGG2020 retrieval software is archived on CaltechDATA (Toon, 2023) as well\n\n985\n\nas publicly available through GitHub at https://github.com/TCCON/GGG.\nAppendix A: Abbreviations\nAbbreviations used in this paper are listed in Table A1.\n\n52\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nAbbreviation\n\nMeaning\n\nNotes\n\nADCF\n\nAirmass dependent correction factor\n\nSee SZA note\n\nAICF\n\nAirmass independent correction factor\n\nAlso call the “in situ correction factor”\n\nAK\n\nAveraging Kernel\n\nRefers to column averaging kernels unless otherwise indicated\n\nCBF\n\nContinuum basis function\n\nFT\n\nFree troposphere\n\nFFT\n\nFast Fourier transform\n\nFOV\n\nField of view\n\nFTIR\n\nFourier transform infrared\n\nFTS\n\nFourier transform spectrometer\n\nFVSI\n\nFraction variation in solar intensity\n\nILS\n\nInstrument line shape\n\nIR\n\nInfrared\n\nGGG\n\n-\n\nGHG\n\nGreenhouse gas\n\nLM\n\nLine mixing\n\nMIR\n\nMid infrared\n\nMOPD\n\nMaximum optical path difference\n\nMOPITT\n\nMeasurements of Pollution in the Troposphere\n\nNDIR\n\nNondispersive infrared\n\nNIR\n\nNear infrared\n\nOSDS\n\nObserver-sun Doppler stretch\n\nRH\n\nRelative humidity\n\nRMS\n\nRoot mean square/squared\n\nqSDV\n\nQuadratice speed-dependent Voigt\n\nSZA\n\nSolar zenith angle\n\nTCCON\n\nTotal Carbon Column Observing Network\n\nUTC\n\nCoordinated Universal Time\n\nVMR\n\nVolume mixing ratio\n\nVSF\n\nVMR scale factor\n\nXgas\n\nColumn-average mole fraction\n\nZLO\n\nZero level offset\n\nZPD\n\nZero path difference\n\nThe name of the retrieval, not an abbreviation\n\nAn instrument on the Terra satellite\n\n“SZA-” and “airmass-dependence” are used equivalently\n\n“Xgas ” is generic; “XCO2 ”, “XCH4 ”, etc. are specific\n\nTable A1. Abbreviations used in this paper.\n\n53\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxco2 - 20190218\n\nxluft - 20190218\n0.25\n\n1\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.6\n\n%\n\n0.4\n\n0.2\n\n0\n\n0.2\n0.15\n0.1\n\n%\n\n0.8\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.05\n0\n-0.05\n\n-0.2\n\n-0.1\n-0.15\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nxco - 20190218\n\nxch4 - 20190218\n2.5\n\n0.5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.3\n0.2\n\n%\n\n0.1\n0\n-0.1\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n2\n\n1.5\n\n1\n\n%\n\n0.4\n\n0.5\n\n0\n\n-0.2\n\n-0.5\n\n-0.3\n\n-1\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure B1. February 18, 2019 error budget from East Trout Lake. The figures show the percent difference between the perturbed test and the\nstandard retrieval plotted as a function of solar zenith angle. The retrievals plotted here are Xluft , XCO2 , XCH4 , and XCO .\n\nAppendix B: Error budget\nFor completeness, we include the error budget figures equivalent to Figures 18–20 for February and July at East Trout Lake in\n990\n\nFigs. B1 to B6. February is extremely cold (-30 to -15◦ C) and dry (<500 ppm XH2 O ), with short days and large solar zenith\nangles. July is warm (20 to 30◦ C) and humid (3000 to 4500 ppm XH2 O ), causing the HF absorption feature to be blacked out\nby adjacent H2 O lines at higher solar zenith angles, causing unreliable retrievals of HF.\n\n54\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxh2o - 20190218\n\nxhdo - 20190218\n4\n\n2\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n1\n\n%\n\n0.5\n0\n-0.5\n\n3\n\n2\n\n1\n\n%\n\n1.5\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0\n\n-1\n\n-1\n\n-2\n\n-1.5\n-2\n\n-3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\nxn2o - 20190218\n\n50\n\n60\n\n70\n\n80\n\n90\n\n70\n\n80\n\n90\n\n°)\n\nxhf - 20190218\n\n1.2\n\n5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.8\n0.6\n0.4\n0.2\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n4\n3\n2\n\n%\n\n1\n\n%\n\n40\n\nSolar Zenith Angle (\n\n°)\n\n1\n0\n\n0\n\n-1\n\n-0.2\n\n-2\n\n-0.4\n\n-3\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n°)\n\nFigure B2. As in Figure B1, but for XH2 O , XHDO , XN2 O , and XHF .\n\nB1\n\nILS\n\nWe created synthetic spectra in GGG2020 with different ILS errors, following the formulation for the “shear” and “angular”\n995\n\nmisalignments tested for the GGG2014 error budget, and for the new formulation in GGG2020. We then passed these synthetic\nspectra through an ILS quantification program called LINEFIT (v14.8) (Hase et al., 1999), which calculates the modulation\nefficiency and phase error of the spectra. Here, we plot the LINEFIT-derived modulation efficiencies for these four cases\nin Figure B7. The GGG2020 shear and angular misalignments represent a ramp-up and ramp-down from 1.0 at zero path\ndifference to 5% offsets at 45 cm optical path difference, as expected. Unfortunately, the GGG2014 “shear” and “angular”\n\n1000\n\nmisalignments both model shear misalignments of different magnitudes. The GGG2014 “shear” case is, in fact, more like a\n\n55\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxwco2 - 20190218\n\nxlco2 - 20190218\n0.6\n\n0.4\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.2\n\n%\n\n0.1\n\n0\n\n-0.1\n\n0.5\n0.4\n0.3\n0.2\n\n%\n\n0.3\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.1\n0\n-0.1\n-0.2\n\n-0.2\n\n-0.3\n-0.4\n\n-0.3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nvsf_hcl - 20190218\n4\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n3\n\n%\n\n2\n\n1\n\n0\n\n-1\n\n-2\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure B3. As in Figure B1, but for XlCO2 , XwCO2 , and HCl scale factors (vsf_hcl).\n\n15% ramp up as a function of optical path difference, and the GGG2014 “angular” case is more like a 3% ramp up. This will\nessentially double the inferred error from the ILS in GGG2014, when compared with GGG2020.\nAppendix C: AICF profile selection\nC1\n1005\n\nCO2 , CH4 , CO\n\nIn situ profiles for CO2 , CH4 , and CO were drawn primarily from the NOAA CO2 ObsPack (Cooperative Global Atmospheric\nData Integration Project, 2019), NOAA CH4 ObsPack (Cooperative Global Atmospheric Data Integration Project, 2020),\nNOAA AirCore dataset (Baier et al., 2021), additional AirCore launches at the Sodanklyä and Nicosia TCCON sites, the\n\n56\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxco2 - 20190723\n\nxluft - 20190723\n0.25\n\n1\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.6\n\n%\n\n0.4\n\n0.2\n\n0\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.2\n0.15\n0.1\n\n%\n\n0.8\n\n0.05\n0\n-0.05\n\n-0.2\n\n-0.1\n-0.15\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nxco - 20190723\n\nxch4 - 20190723\n2.5\n\n0.5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.3\n0.2\n\n%\n\n0.1\n0\n-0.1\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n2\n\n1.5\n\n1\n\n%\n\n0.4\n\n0.5\n\n0\n\n-0.2\n\n-0.5\n\n-0.3\n\n-1\n\n-0.4\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure B4. July 23, 2019 error budget from East Trout Lake. The figures show the percent difference between the perturbed test and the\nstandard retrieval plotted as a function of solar zenith angle. The retrievals plotted here are Xluft , XCO2 , XCH4 , and XCO .\n\n57\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxh2o - 20190723\n\nxhdo - 20190723\n4\n\n2\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n1\n\n%\n\n0.5\n0\n-0.5\n\n3\n\n2\n\n1\n\n%\n\n1.5\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0\n\n-1\n\n-1\n\n-2\n\n-1.5\n-2\n\n-3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\nxn2o - 20190723\n\n50\n\n60\n\n70\n\n80\n\n90\n\n70\n\n80\n\n90\n\n°)\n\nxhf - 20190723\n\n1.2\n\n5\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.8\n0.6\n0.4\n0.2\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n4\n3\n2\n\n%\n\n1\n\n%\n\n40\n\nSolar Zenith Angle (\n\n°)\n\n1\n0\n\n0\n\n-1\n\n-0.2\n\n-2\n\n-0.4\n\n-3\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n°)\n\nFigure B5. As in Figure 18, but for XH2 O , XHDO , XN2 O , and XHF .\n\nInfrastructure for Measurement of the European Carbon Cycle (IMECC) campaign, and the GO-AMAZON campaign. The\nObsPack contains data from numerous providers across different institutions; Tables C1 and C2 provide a detailed breakdown.\n1010\n\nFor the NOAA ObsPack Aircraft and AirCore profiles, the procedure used to match these data to TCCON sites will be detailed\nin the following subsections. For the remaining sources, the profiles were already associated with specific TCCON sites, so no\ncolocation was required.\nAll airborne data sources used for these profiles are listed in Tables C1 and C2. Ground data used to extend some of the\nprofiles to the surface are listed in Table C3.\n\n58\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nxwco2 - 20190723\n\nxlco2 - 20190723\n0.6\n\n0.4\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.2\n\n%\n\n0.1\n\n0\n\n-0.1\n\n0.5\n0.4\n0.3\n0.2\n\n%\n\n0.3\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n0.1\n0\n-0.1\n-0.2\n\n-0.2\n\n-0.3\n-0.4\n\n-0.3\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n0\n\n90\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n°)\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nvsf_hcl - 20190723\n4\n\nfov\ncontinuum\nosds\npointing offset\nprior co enhanced\nprior h2o/hdo\nprior pressure\nprior shift\nprior temperature\npsurf\nangular\nshear\nzlo\nsum\n\n3\n\n%\n\n2\n\n1\n\n0\n\n-1\n\n-2\n0\n\n10\n\n20\n\n30\n\n40\n\n50\n\nSolar Zenith Angle (\n\n60\n\n70\n\n80\n\n90\n\n°)\n\nFigure B6. As in Figure B4, but for XlCO2 , XwCO2 , and HCl scale factors (vsf_hcl).\n1015\n\nC1.1\n\nObsPack\n\nThe ObsPack data is provided as a single time series per measurement campaign or similar source. To extract individual profiles\nfrom these files, we:\n1. Scan all files for data points within 2° (total distance) of an active TCCON site. When one is found, we store the list of\ndata points surrounding it in time that fall a box 10° longitude width and 5° latitude tall centered on the TCCON site as\n1020\n\na “chunk.” A chunk extends forward and backward in time from the point closest to the TCCON site and stops at the\nfirst data point in each direction that is outside the 10◦ × 5◦ box. Any profiles derived from this chunk are assigned to\n\nthe TCCON station it passes closest to.\n\n59\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nFigure B7. The modulation efficiencies tested in GGG2014 and GGG2020.\n\n2. Further filter the chunks based on the lowest altitude, highest altitude, number of data points, and minimum distance to\na TCCON site. This step was done interactively to find the filtering criteria that gave the best balance between number\n1025\n\nof chunks retained and the usefulness of the profile(s) within the chunk. The final criteria used were:\n– Minimum altitude below 2000 m\n– Maximum altitude above 7500 m\n– At least 20 data points\n– Approached within 0.1° of a TCCON station\n\n1030\n\n3. These filtered chunks were then individually evaluated and specific data points within them chosen by hand to use as\nprofiles. In this process, we considered the latitude/longitude position of the aircraft, the profile of altitude versus time,\nand the profile of CO2 or CH4 versus altitude. We generally selected as profiles times when the aircraft was consistently\nascending or descending, and excluded times of level flight. However, this had to be handled on a case-by-case basis to\nallow for profiles with a period of level flight in between two legs of an ascent or descent. If a chunk contained multiple\n\n1035\n\nascending/descending legs, we would split them if:\n– there was a clear separation in time, or\n– the legs measured different airmasses (evidenced by different CO2 or CH4 mole fractions)\n4. For each profile, we check for ground data in the ObsPack that can be used to extend the profile to the surface. We\nidentified which ground files in the ObsPack are near which TCCON sites by hand. We interpolate any data within 4\n60\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nTable C1. Airborne profile data used in the AICF calculation. “CO2 Obspack” is the CO2 GLOBALVIEWplus v5.0 ObsPack (Cooperative\nGlobal Atmospheric Data Integration Project, 2019) and “CH4 ObsPack” the CH4 GLOBALVIEWplus v2.0 ObsPack (Cooperative Global\nAtmospheric Data Integration Project, 2020). The “TCCON sites” column indicates at which sites profiles were used; the IDs are mapped\nto locations in Table 1 and numbers of profiles per site are given in Tables C4 and C5. In the “Providers” column, affiliations are given\nin parentheses. If only one affiliation is listed, it applies to all individuals named. Abbrevations: NASA = National Aeronautics and Space\nAdministration; LaRC = Langley Research Center; Harvard U. = Harvard University; CSUSB = California State University San Bernadino;\nGSFC = Goddard Space Flight Center; NCAR = National Center for Atmospheric Research; NOAA = National Oceanic and Atmospheric\nAdministration; GML = Global Monitoring Laboratory; FMI = Finnish Meteorological Institure; CARE-C = Climate and Atmosphere Research Center; LSCE/IPSL = Laboratoire des Sciences du Climat et de l’Environnement.\nSource\n\nCampaign or ID\n\nProviders\n\nTCCON sites\n\nCO2 ObsPack\n\nCO2 Budget and Regional Airborne Study -\n\nSteve Wofsy (Harvard U.)\n\npa\n\nDeep Convective Clouds & Chemistry\n\nAndreas Beyersdorf (CSUSB) & Yonghoon\n\noc\n\n(DC3), DC8 aircraft\n\nChoi (SSAI)\n\nCO2 ObsPack\n\nGoddard Space Flight Center (GSFC)\n\nStephan Randolph Kawa, James Brice Ab-\n\nCO2 ObsPack\n\nHIAPER\n\nMaine (COB2004)\nCO2 ObsPack\n\ndf, pa\n\nshire, & Haris Riris (NASA GSFC)\n\nCO2 ObsPack\nCO2 ObsPack\nCO2 ObsPack\n\nPole-to-Pole\n\nObservations\n\nSteve Wofsy (Harvard U.), & Britton\n\n(HIPPO)\n\nStephens (NCAR)\n\nIntercontinental Chemical Transport Exper-\n\nStephanie A. Vay (NASA LaRC) &\n\niment - North America (INTEX-NA)\n\nYonghoon Choi (SSAI)\n\nKorea-United States Air Quality Study\n\nJoshua P. DiGangi, & Yonghoon Choi\n\n(KORUS-AQ)\n\n(SSAI)\n\nO2 /N2 Ratio and CO2 Airborne Southern\n\nBritton Stephens (NCAR), Colm Sweeney\n\nOcean Study (ORCAS)\n\n(NOAA GML), Kathryn McKain (NOAA\n\nll, wg\npa\nan, df, rj\noc\n\nGML), Eric Kort (U. Michigan)\nCO2 ObsPack\n\nStudies of Emissions and Atmospheric\n\nSteve Wofsy (Harvard U.)\n\ndf\n\nStudies of Emissions and Atmospheric\n\nAndreas Beyersdorf (CSUSB) & Yonghoon\n\noc\n\nComposition, Clouds and Climate Coupling\n\nChoi (SSAI)\n\nComposition, Clouds and Climate Coupling\nby Regional Surveys (SEAC4RS), ER-2 aircraft\nCO2 ObsPack\n\nby Regional Surveys (SEAC4RS), DC8 aircraft\n\n1040\n\nhours of the lowest altitude measurement in a profile to the time of the lowest altitude profile measurement. In cases\n\n61\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nTable C2. Table C1, continued. ARM = Atmospheric Radiation Monitoring facility.\nSource\n\nCampaign or ID\n\nProviders\n\nTCCON sites\n\nCO2 ObsPack\n\nStratosphere-Troposphere Analyses of\n\nSteve Wofsy (Harvard U.)\n\npa\n\nKathryn McKain (NOAA GML), Colm\n\nae, df, eu, ll, oc,\n\nSweeney (NOAA GML), Steve Wofsy\n\npa\n\nRegional Transport (START-08)\nCO2 ObsPack\n\nAtmospheric\n\nTomography\n\nMission\n\n(ATom)\n\n(Harvard U.), Bruce Daube (Harvard\nU.), Roisin Commane (Harvard U.)\nOther CO2\n\nNOAA Manaus\n\nJohn Miller (NOAA GML)\n\nma\n\nCH4 ObsPack\n\nHIAPER Pole-to-Pole Observations\n\nSteve Wofsy, Greg Santoni, & Jasna\n\nll,oc,pa,wg\n\n(HIPPO)\n\nPittman (Harvard U.)\n\nStratosphere-Troposphere Analyses of\n\nSteve Wofsy (Harvard U.)\n\npa\n\nKathryn McKain & Colm Sweeney\n\nae,ci,df,eu,ll,oc,pa\n\nCH4 ObsPack\n\nRegional Transport (START08)\nCH4 ObsPack\nIMECC\n\nAtmospheric\n\nRepository\n\nTomography\n\nMission\n\n(ATom)\n\n(NOAA GML)\n\nInfrastructure for Measurement of the\n\nVarious\n\nbi,br,gm,je,ka,or\n\nBianca Baier & Colm Sweeney (NOAA\n\ndf,oc,pa,so\n\n(CO2 , CH4 , CO)\n\nEuropean Carbon Cycle (IMECC)\n\nNOAA AirCores (CO2 ,\n\nN/A\n\nCH4 , CO)\nSodankylä\n\nGML)\nAirCores\n\nN/A\n\nHuilin Chen (RUG) & Rigel Kivi (FMI)\n\nso\n\nN/A\n\nPierre-Yves Quéhé (CARE-C, Cyl) &\n\nni\n\n(CO2 , CH4 , CO)\nNicosia AirCores (CO2 ,\nCH4 , CO)\nRadiosondes (H2 O)\n\nThomas Laemmel (LSCE/IPSL)\nSouthern Great Plains (SGP) Lamont\nCentral Facility and Tropical Western\nPacific (TWP) Darwin Facility\n\n62\n\nARM\n\ndb, oc\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nwhere ground data is only available before or after the lowest profile measurement, we use the closest ground data in\ntime.\nC1.2\n\nAirCore\n\nAs AirCore data intrinsically provides discrete profile, matching these data to TCCON sites was much simpler. For NOAA\n1045\n\nAirCores, we search all files for those where the mean latitude and longitude of the profile were within 1° (total distance) of\na TCCON site. We use a looser distance compared to the aircraft as it is unlikely that an AirCore would be within 1° of a\nTCCON site by happenstance if it was not intended to match with that TCCON. However, since it is possible that the balloon\ntrajectory drifted significantly depending on the winds, we use the looser distance criterion to allow for that.\nC2\n\n1050\n\nH2 O\n\nProfiles for the H2 O AICF come from radiosonde data provided by the Department of Energy Atmospheric Radiation Measurement (ARM) facility (Keeler and Burk). The data were downloaded from https://adc.arm.gov/discovery/#/results/instrument_\nclass_code::sonde%2Fprimary_meas_type_code::atmtemp in March 2021. Two ARM sites are close enough to TCCON locations to be useful: the Southern Great Plains (SGP) site’s Central Facility (facility code C1) is near the Lamont, OK, USA\nTCCON site, and the Tropical Western Pacific (TWP) site’s Darwin facility (code C3) is near the Darwin, Australia TCCON\n\n1055\n\nsite.\nThese facilities produce more radiosonde observations than we can feasibly use in the AICF calculation, so we must choose\na subset. We use the following steps for each site:\n1. Identify radiosonde profiles that are coincident with another trace gas profile (CO2 , CO, CH4 , or N2 O).\n\n1060\n\n2. Identify radiosonde profiles not in the set identified in Step 1 that have at least 30 TCCON spectra within ±3 hours of\nthe time of the profile’s lowest altitude measurement and\n\n3. Combine the profiles from step 1 with randomly selected profiles from step 2 to collect 50 total profiles. (We use a seed\nof 42—chosen in reference to “The Hitchhiker’s Guide to the Galaxy”—to ensure repeatability across runs.)\n4. Finally, remove any profiles from this set of 50 that have a maximum altitude < 15 km.\nOnce we have assembled a pool of radiosonde profiles, we convert the relative humidity (RH) values stored in the files to\n1065\n\nwater mole fractions. Based on the convention described in Miloshevich et al. (2006), we assume that the definition of RH\nis the ratio of water vapor pressure to the saturation water vapor pressure over liquid water and calculate the H2 O dry mole\nfraction as\nRH · SVP\np\nfH2 O,wet\nfH2 O,dry =\n1 − fH2 O,wet\n\nfH2 O,wet =\n\n(C1)\n(C2)\n\n63\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n1070\n\nwhere RH is the relative humidity as a fraction (i.e. 0 to 1), SVP is the saturation vapor pressure of water over liquid water\ncalculated using Eq. 6 of Miloshevich et al. (2004) (see also Eq. 15 of Wexler, 1976), and p is the atmospheric pressure (in the\nsame units as SVP).\nC3 Constructing full profiles\nIn order to ensure a proper comparison between the in situ and TCCON column amounts, the in situ profiles must extend to the\n\n1075\n\ntop of the TCCON retrieval altitude grid, 70 km. No aircraft or balloon-borne profile reaches this altitude, therefore, similarly\nto Wunch et al. (2010), we extend the in situ profiles using the GGG2020 prior profiles (Laughner et al., 2023).\nThe differences between Wunch et al. (2010) and our approach stem from (1) the GGG2020 priors do a better job of\nrepresenting trace gas profiles in the stratosphere and (2) we have enough additional profiles over TCCON sites to be selective\nabout which ones we use. This is why we filtered the ObsPack data to “chunks” that have data up to at least 7500 m altitude\n\n1080\n\n(§C1.1), to limit the altitude that needs to be filled in above the top of the profile.\nThere are three ways that profiles are extended up to 70 km altitude, depending on their top altitude:\n1. If the profile’s top is above 380 K potential temperature (i.e. reaches the stratospheric overworld), then we append the\nGGG2020 priors for levels above the profile top.\n2. If the profile’s top is below 380 K potential temperature but at or above 7.5 km, then the in situ profile’s values are\n\n1085\n\nbinned to the same altitude grid (see below) and then we do a constant value extrapolation of the top binned value up\nto the tropopause altitude. We use the GGG2020 prior above 380 K potential temperature again, and connect the two\nparts of the profile by linearly interpolating the trace gas mole fractions with respect to potential temperature between\nthe tropopause and 380 K. This case covers profiles where the top of the measured profile is expected to be a better\nrepresentation of the unmeasured free troposphere than the GGG2020 priors.\n\n1090\n\n3. If the profile’s top is below 7.5 km, then we use the GGG2020 priors for all levels above the profile top. The case assumes\nthat profiles that do not reach above 7.5 km do not constrain the free troposphere well enough to supplant the GGG2020\npriors. While we filtered the ObsPack data for “chunks” that have data above 7.5 km, we still have a few profiles with\nceilings below 7.5 km from chunks that needed to be split into multiple profiles.\nFor #2, we calculate the binned in situ profile values for the highest altitude of the GGG retrieval grid below the in situ\n\n1095\n\nprofile’s ceiling (zGGG,k ) as:\nPnobs\nwf\nPnobsi obs,i\nf obs = i=1\ni=1 wi\n\n\n\n(zobs,i − zGGG,k−1 )/(zGGG,k − zGGG,k−1 ) if zGGG,k−1 ≤ zobs,i < zGGG,k\nwi = (zGGG,k+1 − zobs,i )/(zGGG,k+1 − zGGG,k ) if zGGG,k ≤ zobs,i < zGGG,k+1\n\n\n\n0\notherwise\n64\n\n(C3)\n\n(C4)\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n5000\n\nGGG altitude grid level\nObservation weighting\n\nAltitude (km)\n\n4000\n3000\n2000\n1000\n0.0\n\n0.1\n\n0.2\n0.3\nWeight\n\n0.4\n\n0.5\n\n0.6\n\nFigure C1. An example of the weighting functions from Eq. (C4). Lines indicate the weights applied to the observed mole fractions and\ncircles indicate the GGG altitude grid levels that correspond to those weights—like colors match.\n\nFigure C1 shows an example of the weights for one short profile at the Armstrong TCCON site.\nThere is a special case for CH4 applied when integrating the in situ profile to calculate the in situ-derived XCH4 . Previous\n1100\n\nwork (e.g. Washenfelder et al., 2003; Saad et al., 2014, 2016) established that there is a strong correlation between CH4 and\nHF in the stratosphere. Since this correlation is encoded into the GGG2020 priors (Laughner et al., 2023), we can use the\ndifference between the prior and posterior HF column (which is almost entirely found in the stratosphere) from the TCCON\nretrievals to adjust the levels in the in situ CH4 profiles that use the GGG2020 profiles.\nSpecifically, when calculating the in situ XCH4 , we get the slope of CH4 vs. HF mixing ratios used by the GGG2020 priors\n\n1105\n\nfor the year and region (tropics, midlatitudes, or polar vortex) of the profile (see §3.5 and Fig. 11 of Laughner et al., 2023). We\nthen multiply this slope by the difference between the prior and median posterior HF profile of all the TCCON observations\nmatched with the in situ profile in question in order to get the expected change in the CH4 priors to better match the true\nstratospheric profile. Finally, we multiply this profile difference by the TCCON AK and integrate only the levels in the total in\nsitu profile obtained from the GGG2020 priors. The integration uses Eq. (8) and add the integrated change to the in situ XCH4\n\n1110\n\nas a posterior adjustment.\nAgain, note that this correction is only applied when integrating the in situ profiles to obtain the true XCH4 value to compare\nthe TCCON retrievals against. When using the in situ profiles as priors in the TCCON retrievals, the levels taken from the\nGGG2020 priors are not adjusted in this fashion.\nC4 Grouping temporally proximate profiles\n\n1115\n\nThere are several cases where multiple profiles are available within a short time of each other (such as different legs of a\nmissed approach or duplicate AirCore launches). Because we use the observed profiles as the prior in the TCCON retrievals\nfrom which the AICF is derived, this presents a technical challenge. Ideally, we want to use the same prior for all retrievals\nmatched up with a given profile for comparison. Our temporal coincidence criterion can be up to ±3 hours, therefore, in cases\n65\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nwith two or more profiles within a few hours, if for each TCCON retrieval we used the observed priors closest in time to it, this\n1120\n\nwould result in a change of prior partway through our coincidence window.\nOur solution was to merge profiles close enough in time for this to occur, but only for use as priors. Each individual observed\nprofile still contributes one point on Fig. 11. This does mean that the prior will not exactly match any of the observed profiles\nthose retrievals are compared against, but we consider that an acceptable error, given that we do apply an AK correction to the\nintegrated in situ profile.\n\n1125\n\nTo find profiles that need to be merged, we first identify which TCCON observations would match with that profile. We ignore\nthe quality filtering criteria from §7.3.1 during this step, and only try to find the time window (± 1, 2, or 3 hours) necessary\nto match at least 30 TCCON observations to each profile. If any two profiles from the same TCCON site are matched to any\nof the same TCCON observations, they are grouped together in the list of profiles, to be averaged together when creating the\ncustom priors in §C5. This initial list is written out to a text file so that it can be modified by hand later, as needed.\n\n1130\n\nC5 Running custom TCCON retrievals\nAs mentioned in §7.3, when we run the TCCON retrievals for the AICF calculation, we use as custom priors the in situ profiles\nthat a given TCCON observation will be compared against. This reduces error in the TCCON Xgas value that arises from an\nincorrect prior profile and thus improves the accuracy of the AICF. There are several technical considerations in how we handle\nthis matching. In order to make those considerations clear, let us first describe how the GGG retrieval accepts inputs describing\n\n1135\n\nboth the prior profiles and the TCCON observations to retrieve on.\nGGG takes a list of TCCON spectra to retrieve as input in the “runlog” file. This lists each spectrum on which to run the\nretrieval in order. For the AICF retrievals, we combined all the spectra from all the relevant TCCON sites into a single runlog.\nThe priors (including temperature and pressure as well as trace gas mixing ratios) are written to a “.mav” file. This file is\norganized into blocks. Each block indicates the first spectrum from the runlog which the priors contained in the .mav block\n\n1140\n\napply to. During the retrieval, GGG iterates through the spectra contained in the runlog. When it reaches the spectrum defined\nas the first spectrum of the next block in the .mav file, it loads the priors from that block before continuing.\nIn inserting the in situ profiles into the .mav file as priors, we had three objectives:\n1. Retain the standard priors for gases and times that we did not have in situ profiles available.\n2. Ensure that the in situ profiles were used as priors for any spectra that they might be compared against.\n\n1145\n\n3. Ensure that any in situ profiles were only applied to the TCCON site where and day when they were measured.\nTo meet these objectives, our approach to inserting the in situ profiles as priors was:\n– Divide the runlog into chunks by site and day, so that each chunk only has spectra from one site on one day.\n– For each unique site/day chunk, collect all the in situ profiles from that day.\n\n66\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n– Average together any in situ profiles grouped together in the list created in §C4. For this, we used an approach that\nconsiders whether each in situ profile contributed observations to a given level in the regridded profile. For a level on the\n\n1150\n\nretrieval grid where none of the in situ profiles provided any data points (i.e. the observed profiles were extrapolated or\nhad the GGG2020 prior appended to it), both profiles are weighted equally. For a level where at least one of the in situ\nprofiles had observed data, each profile is weighted by the fraction of data for that level that came from observations.\n– For gases that only have one profile (after averaging) for that site/day, assign that profile to all the .mav blocks for that\nsite/day.\n\n1155\n\n– For gases that have multiple profiles that are not merged together (§C4), use the first profile in the day for all .mav blocks\nup until the first spectrum that could be compared with the second profile in the day (for our coincidence criteria, this\nwill be the spectra 3 hours before the floor time of the second profile). Introduce a new .mav block on that profile that\nswitches to the second profile. Repeat for third, fourth, etc. profiles if present. Assign the last profile to cover all .mav\nblocks through the end of the day.\n\n1160\n\nOnce the profiles are assigned to their .mav blocks, they must be averaged from their native vertical resolution to the GGG\nretrieval altitude grid and, if multiple profiles for the same gas were present for the same block, they must be averaged together.\nFor the vertical regridding, we use the same approach as described in §C3 where we do a weighted average of the observed\nmixing ratios, where the weights are maximized when the observed altitude equals the altitude of the GGG retrieval level they\n1165\n\nare being averaged to, and which decrease linearly to the adjacent GGG retrieval levels (Fig. C1, Eq. C4).\nWe found that it is crucial that we use geopotential height as the altitude for the regridding, as that did a better job ensuring\nthat the observed profiles followed hydrostatic balance. To compute geopotential height for the in situ profiles, we take pressure\nand geopotential height from the two GEOS FP-IT files (Lucchesi, 2015) that bound the profile’s lowest altitude in time and\naverage the GEOS FP-IT data, and weight each by the time difference between the GEOS FP-IT profile and the time of the\n\n1170\n\nlowest altitude measurement in the in situ profile, giving greater weight to profiles nearer in time to the in situ profile. We then\ninterpolate the GEOS FP-IT geopotential altitude on the logarithm of pressure to the pressures in the in situ profile.\nThe final consideration in preparing the custom priors is that we always retain the pressure and temperature profiles from\nthe standard GEOS FP-IT priors used in GGG2020. This is because our testing found it very difficult to maintain hydrostatic\nbalance if we used the observed pressure and temperature. This, in turn, caused greater error in the retrieved Xgas values, as\n\n1175\n\nthe air column would be incorrect.\nOnce the custom priors were generated, the TCCON retrievals could be run as normal. The standard post processing corrections for airmass dependence (§7.1) and window-to-window averaging (§7.2) were applied as well. AKs were calculated for\neach spectrum retrieved as used to smooth the in situ profiles and account for the TCCON vertical sensitivity (§7.3).\nC6\n\n1180\n\nUncertainty in TCCON/in situ comparisons\n\nFor the TCCON/in situ ratios in §7.3, we considered five sources of uncertainty for the comparisons:\n\n67\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n1. In situ measurement error (\u000fmeas ): This accounts for the error in individual in situ measurements that make up the\nprofiles. To be conservative, we assume the worst-case scenario with 100% correlated error at all levels. The uncertainty in\nXgas is then calculated as:\nZ\nZ\n\u000fmeas = c(p) + 2σ(p) dp − c(p) dp\n1185\n\n(C5)\n\nwhere c(p) is the measured mixing ratio and σ(p) the uncertainty at each level. The integrals represent the pressure-weighted\nintegration, Eq. (8). The uncertainty values are those reported in the original data files where available or a typical value chosen\nin consultation with the data providers.\n2. Unmeasured free troposphere (\u000fFT ): This accounts for uncertainty due to the portion of the free troposphere not measured by a given profile. For each profile, we first calculate σobs,FT , the standard deviation of measurements above 750 hPa\n\n1190\n\nand below the tropopause (as determined by GEOS FP-IT meteorology). We then create a perturbed profile,\n\nc(p) + 2σ\nobs,FT if interp/extrap at p\nc0 (p) =\n\nc(p)\notherwise\n\n(C6)\n\nwhich adds this standard deviation to interpolated or extrapolated levels above the top of the measured profile. The uncertainty\nin Xgas is calculated as:\nZ\nZ\n\u000fFT = c0 (p) dp − c(p) dp\n\n1195\n\n(C7)\n\nThis error will be zero for profiles that do not require extrapolation or interpolation to reach the stratospheric overworld (i.e.\naltitudes with potential temperature ≥ 380 K).\n\n3. Bias in stratospheric prior (\u000fstrat ): This represents expected bias in the column from the use of GGG2020 priors for\n\nlevels in the stratosphere. This uses the retrieved vs. prior HF column as a proxy for error in the stratospheric prior. As discussed\nin §7.3.3, HF is predominately found in the stratosphere, so the difference between the retrieved and prior HF columns gives\n1200\n\ninformation about whether the stratospheric profile was biased high or low. We calculate the bias as:\n\u000fstrat = 2 · (XHF,post − XHF,prior ) ·\n\n∂Xgas\n∂XHF\n\n(C8)\n\nThe derivative ∂Xgas /∂XHF has to be calculated for each gas. For CO2 we use 8.09×103 , which was derived from East Trout\nLake TCCON data by comparing prior and posterior wCO2 and HF columns. (East Trout Lake is positioned to see significant\nstratospheric variability due to the polar vortex, and wCO2 is the GGG2020 CO2 product with enhanced sensitivity to the\n1205\n\nstratosphere.) For CH4 , this is drawn from the CH4 :HF slopes used in the GGG2020 priors (Laughner et al., 2023).\nAirCore profiles are treated specially, as they always reach into the stratosphere. For these profiles, we create a perturbed\nprofile, c0 (p), where the levels in the stratosphere filled by the GGG2020 priors have the difference between the top of the\nAirCore profile and the corresponding level in the prior added to them. The difference between the integral of these profiles\n\n68\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nbecome the stratospheric error. Mathematically, that is\n\nc(p) + 2[c\nprior (pobs. top ) − cAirCore (pobs. top )]\n1210\nc0 (p) =\n\nc(p)\nZ\nZ\n\u000fstrat,AirCore = c0 (p) dp − c(p) dp\n\nif using prior at p\n\n(C9)\n\notherwise\n\n(C10)\n\n4. Random error in TCCON Xgas value (\u000fstd. xgas ): This represents random error in the TCCON observations. Because we\nrequire at least 30 TCCON observations coincident with a profile for a valid comparison, we use twice the standard deviation\namong those coincident observations as the metric of random error. The coincidence windows vary between 2 and 6 hours\n1215\n\nwide, so the standard deviation likely includes some true change in the data, and can therefore be considered conservative.\n5. Bias in TCCON derived from Xluft (\u000fXluft ): This represents bias in retrieved Xgas values resulting from instrument\nhardware issues diagnosed from deviations in Xluft from the nominal network value (0.999, see §7.3). The bias is calculated\nas:\n\u000fXluft =\n\n1220\n\n∂r\n· (Xluft,median − 0.999) · Xgas,median\n∂Xluft\n\n(C11)\n\nHere, Xluft,median and Xgas,median are the median values of TCCON Xluft and the target Xgas across the 30+ coincident\nobservations for the comparison. 0.999 is the nominal value of Xluft that represents a well-operating instrument. The ∂r/∂Xluft\nvalue is how the TCCON/in situ ratio changes with Xluft , and was derived for XCO2 , XwCO2 , XlCO2 , and XCH4 by an\nunweighted robust fit through similar plots of TCCON/in situ ratio vs. Xluft as Fig. 11, but with TCCON retrievals that used\nthe standard trace gas priors instead of custom ones built from the in situ profiles. The values used are given in Table C6.\n\n1225\n\nFull error calculation: As the error terms include a mix of random (\u000fmeas , \u000fFT , \u000fstd. xgas ) and systematic (\u000fstrat , \u000fXluft )\nerrors, the in situ and TCCON total errors are calculated as:\nq\n\u000fin situ = \u000f2meas + \u000f2FT + |\u000fstrat |\nq\n\u000fTCCON = \u000f2std. xgas + |\u000fXluft |\n\n(C12)\n(C13)\n\nThe first term in the second equation is written as a root of a square to indicate that if additional random TCCON error terms\n1230\n\nwere to be added in the future, they should add in quadrature. The uncertainty in the TCCON/in situ ratio (Xgas,TCCON /Xgas,in situ )\nP\nfollows standard error propagation (\u000ftotal = i (σx · ∂f (x)/∂x)2 ):\n\u000ftotal =\n\n2\n\u000f2TCCON \u000f2in situ Xgas,TCCON\n+\n\u000f2in situ\n\u000f4in situ\n\n(C14)\n\nNote that Eq. (C12) is applied to each individual TCCON/in situ comparison, while the statistics in Table 3 are averaged\nover all the comparisons for a given gas. Therefore, the values of \u000fin situ , \u000fmeas , \u000fFT , and \u000fstrat in Table 3 do not directly relate\n1235\n\nto each other through Eq. (C12). As noted in the caption for Table 3, the non-parenthetical values in the last four columns\n\n69\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nformally propagate the error from the individual comparisons, such that the values shown in the table (which we will denote\ngenerally as \u000fformal ) are calculated from the individual comparisons’ values with\n\n\u000f2formal =\n\nn \u0012\nX\n1\ni=1\n\nn\n\n\u000findiv,i\n\n\u00132\n\n(C15)\n\nwhere \u000findiv,i denotes individual comparisons’ error values and n is the number of individual observations. Conversely, the\n1240\n\nparenthetical numbers in Table 3 give the simple mean, i.e.:\nn\n\n1X\n\u000fmean =\n\u000findiv,i\nn i=1\n\n(C16)\n\nAppendix D: Comparison between TCCON and NOAA surface N2 O\nFor Fig. 14, we constructed N2 O profiles to compare TCCON XN2 O against using NOAA surface data. This approach takes\nadvantage of how well-mixed N2 O is in the troposphere to build a large set of comparison. The approach, in detail, is as\n1245\n\nfollows.\nThe TCCON vs. in situ comparison shown in Fig. 14 calculates an in situ XN2 O from N2 O profiles using Eq. (7) as with the\nother Xgas quantities in §7.3. These N2 O profiles are constructed using the NOAA surface N2 O VMR from the surface to the\ntropopause, the GGG2020 N2 O prior for levels with potential temperature greater than 380 K, and linearly interpolating the\nN2 O VMR with respect to potential temperature between the tropopause and 380 K level.\n\n1250\n\nFor the tropospheric N2 O VMRs, we obtained monthly average NOAA global N2 O data from https://gml.noaa.gov/hats/\ncombined/N2O.html (last access 10 May 2021). For sites at latitudes north of 23◦ N or south of 23◦ S, we use the northern and southern hemispheric averages, respectively (GML_NH_N2O and GML_SH_N2O in the combined NOAA N2 O file).\nFor equatorial latitudes between 23◦ S and 23◦ N, we used the average of the Mauna Loa and American Samoa N2 O data\n(GML_mlo_N2O and GML_smo_N2O in the combined file). For each comparison point in Fig. 14, we used the N2 O VMR\n\n1255\n\nfrom that month as the tropospheric VMR of the profile.\nThe comparisons selected for Fig. 14 meet the following criteria:\n– The difference between the prior and posterior HF column must be < 2 × 1014 molec. cm−2 in magnitude. Since HF is\n\nalmost entirely in the stratosphere, this limits the comparisons to cases where the GGG2020 prior stratospheric profiles\nare reasonably accurate, thus limiting error in the in situ XN2 O from an incorrect assumed stratosphere\n\n1260\n\n– Xluft must be in the range [0.996, 1.002). This ensures we are considering data when the TCCON instrument was well\naligned, as discussed in §7.3.1\n– FVSI must be ≤ 0.05. This limits the comparison to mostly cloud-free observations.\n\n70\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nAppendix E: Variable O2 mole fraction derivations\nE1\n1265\n\nTrends in O2 mole fraction from trends in XCO2\n\nThe derivation of Eq. (10) begins from the definition of fO2 :\n\nfO2 =\n\nNO2\nN + NO2 + NCO2\n\n(E1)\n\nwhere:\n– NO2 and NCO2 are the number of moles of O2 and CO2 , respectively,\n– N is the number of moles of gases other than O2 or CO2 in H2 O-free air, and\n– Ntot (used below) is N + NO2 + NCO2\n\n1270\n\nDefining α = ∂NO2 /∂NCO2 , taking the derivative of fO2 with respect to NCO2 , and simplifying gives:\n∂fO2\n=\n∂NCO2\n\n\u0012\n\nα(N + NCO2 ) NO2\n−\nNtot\nNtot\n\n\u0013\n\n·\n\n1\nNtot\n\n(E2)\n\nRecognizing that NO2 /Ntot = fO2 and (N + NCO2 )/Ntot = 1 − fO2 as well as converting the derivative to a ratio of small\n\nbut finite differences (represented by δ in place of ∂) gives:\n\n1275\n\n1\nδfO2\n= (α − α · fO2 − fO2 ) ·\nδNCO2\nNtot\nδNCO2\n⇒ δfO2 = (α − α · fO2 − fO2 ) ·\nNtot\n\n(E3)\n(E4)\n\nFinally, to convert δNCO2 /Ntot into terms of XCO2 and XCO2 ,ref , we start by defining:\n\nXCO2 ,ref =\n\nNCO2\nNtot\n\n(E5)\n\nand\n1280\n\nXCO2 =\n\nNCO2 + δNCO2\nNtot + δNCO2 + δNO2\n\n(E6)\n\nas well as δNO2 = α · δNCO2 . Substituting this and NCO2 = XCO2 ,ref · Ntot from Eq. (E5) in Eq. (E6) and rearranging gives:\nXCO2 − XCO2,ref\nδNCO2\n=\nNtot\n1 − XCO2 − α · XCO2\n\n(E7)\n\nSubstituting Eq. (E7) in Eq. (E4) yields the final version of Eq. (10).\n71\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nE2\n1285\n\nO2 mole fraction from O2 /N2 data\n\nMeasurements of atmospheric O2 concentration are commonly reported as 10−6 relative deviations in the O2 /N2 ratio (denoted\nδ(O2 /N2 ) and given in units of per meg) to avoid the complexities of diluation effects from changes in CO2 and other trace\nspecies on the O2 mole fraction. To convert from available measurements of trends in δ(O2 /N2 ), we must convert to units of\nppm and account for the diluting effect of trends in CO2 . The equation for the black line in Fig. 13, based on Scripps δ(O2 /N2 )\nand NOAA global mean CO2 data, is slightly different from Eq. (10). As above, the derivation starts with Eq. (E1), but now\n\n1290\n\nsince we have measured values for the change in NO2 and NCO2 , our change in fO2 will instead be:\n\nδfO2 =\n\n∂fO2\n∂fO2\n· δNO2 +\n· δNCO2\n∂NO2\n∂NCO2\n\n(E8)\n\nIn this case, both ∂NO2 /∂NCO2 and ∂NCO2 /∂NO2 are 0, since we have measurements of both O2 and CO2 and therefore\ncan treat their changes as orthogonal. That leads to the following expressions for the derivatives in Eq. (E8):\n\n1295\n\n1 − fO2,ref\n∂fO2\n=\n∂NO2\nNtot\nf\n∂fO2\nO\n= − 2,ref\n∂NCO2\nNtot\n\n(E9)\n(E10)\n\nInserting these into Eq. (E8) gives:\n\nδfO2 = (1 − fO2,ref ) ·\n\nδNCO2\nδNO2\n− fO2,ref ·\nNtot\nNtot\n\n(E11)\n\nδNO2 /Ntot can be expressed in terms of δ(O2 /N2 ) values by using the definition of δ(O2 /N2 ) (Keeling et al., 1998):\nδ(O2 /N2 ) =\n1300\n\n(O2 /N2 )sample\n−1\n(O2 /N2 )reference\n\n(E12)\n\nand assuming that the amount of N2 in the atmosphere does not change. Multiplying this definition by fO2,ref gives:\n\nδ(O2 /N2 ) · fO2,ref\n\n\u0014\n\n\u0015\n(NO2 + δNO2 )/NN2\nNO2\n=\n−1 ·\nNO2 /NN2\nNtot\nδNO2\n=\nNtot\n\n(E13)\n(E14)\n\nδNCO2 /Ntot can be expressed as in Eq. (E7) except with α = 0 (again, this is because we have measurements of mole\nfractions of CO2 and O2 ). The final equation used for the “best estimate” line in Fig. 13 is therefore:\n\n1305\n\nfO2 ,ref + δfO2 = fO2 ,ref + (1 − fO2 ,ref ) · δ(O2 /N2 ) · fO2 ,ref −\n\nXCO2 − XCO2 ,ref\n· fO2 ,ref\n1 − XCO2\n\n72\n\n(E15)\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nwhere fO2 ,ref is the 0.209341 value obtained in §7.3.2 by adjusting Aoki et al. (2019). As noted in §7.3.2, the δ(O2 /N2 ) data\nused is a weighted average of the ALT, LJO, and CGO sites with weights of 41 , 14 , and 12 , respectively. Note that the NOAA\nglobal mean CO2 (rather than TCCON XCO2 ) is used for XCO2 and XCO2 ,ref in this equation.\n\nAuthor contributions. J.L. Laughner led the development of the new airmass correction (§7.1), window-to-window averaging (§7.2), in situ\n1310\n\nscaling (§7.3), and miscellaneous changes in §9. G.C. Toon is the main developer of GGG. J. Mendonca developed the non-Voigt treatment\nof the spectral line shape (§3.2). C. Petri contributed to the development of the phase correction update (§5.2). S. Roche developed the new\nretrieval grid (§4.1), meteorological resampler (§4.2), and netCDF writer. D. Wunch carried out the sensitivity tests (§8). D. Wunch, C.M.\nRoehl, G.C. Toon, P.O. Wennberg, and J.L. Laughner conducted the O2 study in §3.3. J.-F. Blavier is a key developer of I2S. D.W.T. Griffith\ncontributed to various aspects of GGG2020 development. P. Heikkinen, R. Kivi, and M.K. Sha first diagnosed the nonlinearity issue from\n\n1315\n\n§5.1 and developed a correction methodology. R.F. Keeling and B.B. Stephens consulted on the approaches to parameterize the change in O2\nmole fraction (§7.3.2). M. Kiel performed tests of the phase correction threshold (§5.2) and choices of NCBFs (§6) C.M. Roehl, N. Deutscher,\nP. Jeseck, D. Pollard, M. Rettinger, S. Roche, M.K. Sha, Y. Té and D. Wunch all participated in a beta test of GGG2020. N.M. Deutscher,\nJ. Gross, B. Herkommer, P. Jeseck, I. Morino, H. Ohyama, C. Petri, J. Notholt, D. Pollard, M. Rettinger, S. Roche, E. McGee, K. Strong,\nC.M. Roehl, M.K. Sha, K. Shiomi, R. Sussmann, Y. Té, V. Velazco, D. Wunch, and M. Zhou provided data used to derive the corrections in\n\n1320\n\n§7.1 and §7.2. B.C. Baier, B.B. Stephens, H. Chen, Y. Choi, X. Lan, T. Laemmel, K. McKain, J. Miller, H. Riris, C. Rousogenous, and S.C.\nWofsy provided in situ data used in §7.3. P.O. Wennberg provided input to all elements of this work. All authors reviewed the manuscript.\n\nCompeting interests. The authors declare no competing interests.\n\nAcknowledgements. The authors gratefully acknowledge the use of GNU Parallel (Tange, 2011) in the GGG processing. The authors also\nthank James Abshire for providing CO2 data used in deriving the in situ correction (§7.3). A portion of this research was carried out\n1325\n\nat the Jet Propulsion Laboratory (JPL), California Institute of Technology, under a contract with NASA (80NM0018D0004). Government\nsponsorship is acknowledged. Support for Caltech TCCON sites and partial support for JLL, MK, CMR, and POW provided by NASA grants\nNNX17AE15G and 80NSSC22K1066. Material from BBS and RFK is based upon work supported by the National Center for Atmospheric\nResearch, which is a major facility sponsored by the National Science Foundation under Cooperative Agreement No. 1852977.\nMR and RS acknowledge funding by the German Helmholtz Research Program “Changing Earth – Sustaining our Future” within the\n\n1330\n\nResearch Field “Earth and Environment”. The Paris TCCON site has received funding from Sorbonne Université, the French research center\nCNRS and the French space agency CNES. The Cyprus TCCON site and AirCore flights have received funding from the European Union’s\nHorizon 2020 research and innovation programme under grant agreement No. 856612 and the Cyprus Government. The TCCON site at\nRéunion Island has been operated by the Royal Belgian Institute for Space Aeronomy with financial support since 2014 by the EU project\nICOS-INIWRE (Grant agreement ID: 313169), the ministerial decree for ICOS (FR/35/IC1 to FR/35/C6), ESFRI-FED ICOS-BE project\n\n1335\n\n(EF/211/ICOS-BE) and local activities supported by LACy/UMR8105 and by OSU-R/UMS3365 – Université de La Réunion. The Eureka\nTCCON measurements were made at the Polar Environment Atmospheric Research Laboratory (PEARL) by the Canadian Network for the\n\n73\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nDetection of Atmospheric Change (CANDAC), primarily supported by the Natural Sciences and Engineering Research Council of Canada,\nEnvironment and Climate Change Canada, and the Canadian Space Agency. TCCON sites at Tsukuba, Rikubetsu and Burgos are supported\nin part by the GOSAT series project. Burgos is supported in part by the Energy Development Corporation Philippines.\n\n74\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n1340\n\nReferences\nAbrams, M. C., Toon, G. C., and Schindler, R. A.: Practical example of the correction of Fourier-transform spectra for detector nonlinearity,\nAppl. Opt., 33, 6307–6314, https://doi.org/10.1364/AO.33.006307, 1994.\nAllen, D. 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T., Hase, F., Heikkinen, P., Hermans, C.,\n\n1565\n\nHoffmann, A., Huebner, M., Jones, N., Kivi, R., Langerock, B., Petri, C., Scolas, F., Tu, Q., and Weidmann, D.: Intercomparison of lowand high-resolution infrared spectrometers for ground-based solar remote sensing measurements of total column concentrations of CO2 ,\nCH4 , and CO, Atmospheric Measurement Techniques, 13, 4791–4839, https://doi.org/10.5194/amt-13-4791-2020, 2020.\nSherlock, V., Connor, B., Robinson, J., Shiona, H., Smale, D., and Pollard, D.: TCCON data from Lauder, New Zealand, 120HR,\nRelease GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A.,\n\n1570\n\nhttps://doi.org/10.14291/tccon.ggg2020.lauder01.R0, 2022a.\nSherlock, V., Connor, B., Robinson, J., Shiona, H., Smale, D., and Pollard, D.: TCCON data from Lauder, New Zealand, 125HR,\nRelease GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A.,\nhttps://doi.org/10.14291/tccon.ggg2020.lauder02.R0, 2022b.\nShiomi, K., Kawakami, S., Ohyama, H., Arai, K., Okumura, H., Ikegami, H., and Usami, M.: TCCON data from Saga, Japan,\n\n1575\n\nRelease GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A.,\nhttps://doi.org/10.14291/tccon.ggg2020.saga01.R0, 2022.\nStrong, K., Roche, S., Franklin, J., Mendonca, J., Lutsch, E., Weaver, D., Fogal, P., Drummond, J., Batchelor, R., and Lindenmaier, R.: TCCON data from Eureka, Canada, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology,\nPasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.eureka01.R0, 2022.\n\n1580\n\nSussmann, R. and Rettinger, M.: TCCON data from Garmisch, Germany, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.garmisch01.R0, 2017a.\nSussmann, R. and Rettinger, M.: TCCON data from Zugspitze, Germany, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.zugspitze01.R0, 2017b.\nSweeney, C., McKain, K., Higgs, J., Wolter, S., Crotwell, A., Neff, D., Dlugokencky, E., Lang, P., Novelli, P., Mund, J., Moglia,\n\n1585\n\nE., and Crotwell, M.: NOAA Carbon Cycle and Greenhouse Gases Group aircraft-based measurements of CO2 , CH4 , CO,\nN2 O, H2\n\nSF6 in flask-air samples taken since 1992. NOAA Earth System Research Laboratory, Global Monitoring Division.,\n\nhttps://doi.org/10.7289/V5N58JMF, 2018.\nTange, O.: GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February, 42–47, 2011.\nTans, P.: System and method for providing vertical profile measurements of atmospheric gases., U.S. Patent 7,597,014, filed 15 Aug 2006,\n1590\n\nissued 6 Oct 2009, 2009.\nTe, Y., Jeseck, P., and Janssen, C.: TCCON data from Paris, France, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA,\nCalifornia Institute of Technology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.paris01.R0, 2022.\nToon, G.: Atmospheric Non-Voigt Line List for the TCCON 2020 Data Release (GGG2020.R0) [Data set]. CaltechDATA,\nhttps://doi.org/10.14291/TCCON.GGG2020.ATMNV.R0, 2022a.\n\n1595\n\nToon,\n\nG.:\n\nSolar\n\nLine\n\nList\n\nfor\n\nthe\n\nTCCON\n\n2020\n\nhttps://doi.org/TCCON.GGG2020.SOLAR.R0, 2022b.\n\n81\n\nData\n\nRelease\n\n(GGG2020.R0)\n\n[Data\n\nset].\n\nCaltechDATA,\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nToon, G.: Atmospheric Voigt Line List for the TCCON 2020 Data Release (GGG2020.R0) [Data set]. CaltechDATA,\nhttps://doi.org/10.14291/TCCON.GGG2020.ATM.R0, 2022c.\nToon, G.: TCCON/GGG – GGG2020, https://doi.org/10.14291/tccon.ggg2020.stable.R0, 2023.\n1600\n\nTotal\n\nCarbon\n\nColumn\n\nObserving\n\nNetwork\n\n(TCCON)\n\nTeam:\n\n2020\n\nTCCON\n\nData\n\nRelease\n\n(GGG2020),\n\nhttps://doi.org/10.14291/TCCON.GGG2020, 2022.\nTran, D., Delahaye, T., Armante, R., Hartmann, J.-M., Mondelain, D., Campargue, A., Fleurbaey, H., Hodges, J., and Tran, H.: Validation of\nspectroscopic data in the 1.27 µm spectral region by comparisons with ground-based atmospheric measurements, Journal of Quantitative\nSpectroscopy and Radiative Transfer, 261, 107 495, 2021.\n1605\n\nTran, D. D., Tran, H., Vasilchenko, S., Kassi, S., Campargue, A., and Mondelain, D.: High sensitivity spectroscopy of the O2 band at 1.27\nµm:(II) air-broadened line profile parameters, Journal of Quantitative Spectroscopy and Radiative Transfer, 240, 106 673, 2020.\nTran, H., Ngo, N. H., and Hartmann, J.-M.: Efficient computation of some speed-dependent isolated line profiles, Journal of Quantitative\nSpectroscopy and Radiative Transfer, 129, 199–203, 2013.\nWang, Z., Deutscher, N., Warneke, T., Notholt, J., Dils, B., Griffith, D. W., Schmidt, M., Ramonet, M., and Gerbig, C.: Retrieval of tropo-\n\n1610\n\nspheric column-averaged CH 4 mole fraction by solar absorption FTIR-spectrometry using N 2 O as a proxy, Atmospheric Measurement\nTechniques, 7, 3295–3305, 2014.\nWarneke, T., Messerschmidt, J., Notholt, J., Weinzierl, C., Deutscher, N., Petri, C., Grupe, P., Vuillemin, C., Truong, F., Schmidt, M., Ramonet, M., and Parmentier, E.: TCCON data from Orleans, France, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA,\nCalifornia Institute of Technology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.orleans01.R0, 2022.\n\n1615\n\nWashenfelder, R. A., Wennberg, P. O., and Toon, G. C.: Tropospheric methane retrieved from ground-based near-IR solar absorption spectra,\nGeophys. Res. Lett., 30, https://doi.org/10.1029/2003GL017969, 2003.\nWeidmann, D., Brownsword, R., and Doniki, S.: TCCON data from Harwell, Oxfordshire (UK), Release GGG2020.R0,\nhttps://doi.org/10.14291/tccon.ggg2020.harwell01.R0, 2023.\nWennberg, P. O., Roehl, C., Blavier, J.-F., Wunch, D., Landeros, J., and Allen, N.: TCCON data from Jet Propulsion Laboratory, Pasadena,\n\n1620\n\nCalifornia, USA, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology, Pasadena, CA,\nU.S.A., https://doi.org/10.14291/tccon.ggg2020.jpl02.R0, 2022a.\nWennberg, P. O., Roehl, C., Wunch, D., Toon, G. C., Blavier, J.-F., Washenfelder, R., Keppel-Aleks, G., Allen, N., and Ayers, J.: TCCON\ndata from Park Falls, Wisconsin, USA, Release GGG2020R1. TCCON data archive, hosted by CaltechDATA, California Institute of\nTechnology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.parkfalls01.R1, 2022b.\n\n1625\n\nWennberg, P. O., Wunch, D., Roehl, C., Blavier, J.-F., Toon, G. C., and Allen, N.: TCCON data from California Institute of Technology,\nPasadena, California, USA, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology,\nPasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.pasadena01.R0, 2022c.\nWennberg, P. O., Wunch, D., Roehl, C., Blavier, J.-F., Toon, G. C., Allen, N., Dowell, P., Teske, K., Martin, C., and Martin, J.: TCCON data\nfrom Lamont, Oklahoma, USA, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of Technology,\n\n1630\n\nPasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.lamont01.R0, 2022d.\nWennberg, P. O., Wunch, D., Yavin, Y., Toon, G. C., Blavier, J.-F., Allen, N., and Keppel-Aleks, G.: TCCON data from Jet Propulsion\nLaboratory, Pasadena, California, USA, Release GGG2020R0. TCCON data archive, hosted by CaltechDATA, California Institute of\nTechnology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.jpl01.R0, 2022e.\n\n82\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nWexler, A.: Vapor Pressure Formulation for Water in Range 0 to 100◦ C. A Revision, J. Res. Nat. Bur. Stand. A Phys. Chem., 80A,\n1635\n\nhttps://doi.org/10.6028/jres.080A.071, 1976.\nWunch, D., Toon, G. C., Wennberg, P. O., Wofsy, S. C., Stephens, B. B., Fischer, M. L., Uchino, O., Abshire, J. B., Bernath, P., Biraud,\nS. C., Blavier, J.-F. L., Boone, C., Bowman, K. P., Browell, E. V., Campos, T., Connor, B. J., Daube, B. C., Deutscher, N. M., Diao,\nM., Elkins, J. W., Gerbig, C., Gottlieb, E., Griffith, D. W. T., Hurst, D. F., Jiménez, R., Keppel-Aleks, G., Kort, E. A., Macatangay, R.,\nMachida, T., Matsueda, H., Moore, F., Morino, I., Park, S., Robinson, J., Roehl, C. M., Sawa, Y., Sherlock, V., Sweeney, C., Tanaka,\n\n1640\n\nT., and Zondlo, M. A.: Calibration of the Total Carbon Column Observing Network using aircraft profile data, Atmos. Meas. Tech., 3,\n1351–1362, https://doi.org/10.5194/amt-3-1351-2010, 2010.\nWunch, D., Toon, G. C., Blavier, J.-F. L., Washenfelder, R. A., Notholt, J., Connor, B. J., Griffith, D. W., Sherlock, V., and Wennberg,\nP. O.: The Total Carbon Column Observing Network, Philosophical Transactions of the Royal Society A: Mathematical, Physical and\nEngineering Sciences, 369, 2087–2112, https://doi.org/10.1098/rsta.2010.0240, 2011.\n\n1645\n\nWunch, D., Toon, G. C., Sherlock, V., Deutscher, N. M., Liu, C., Feist, D. G., and Wennberg, P. O.: Documentation for the 2014 TCCON\nData Release, https://doi.org/10.14291/TCCON.GGG2014.DOCUMENTATION.R0/1221662, 2015.\nWunch, D., Wennberg, P. O., Osterman, G., Fisher, B., Naylor, B., Roehl, C. M., O'Dell, C., Mandrake, L., Viatte, C., Kiel, M., Griffith, D.\nW. T., Deutscher, N. M., Velazco, V. A., Notholt, J., Warneke, T., Petri, C., Maziere, M. D., Sha, M. K., Sussmann, R., Rettinger, M.,\nPollard, D., Robinson, J., Morino, I., Uchino, O., Hase, F., Blumenstock, T., Feist, D. G., Arnold, S. G., Strong, K., Mendonca, J., Kivi,\n\n1650\n\nR., Heikkinen, P., Iraci, L., Podolske, J., Hillyard, P. W., Kawakami, S., Dubey, M. K., Parker, H. A., Sepulveda, E., García, O. E., Te, Y.,\nJeseck, P., Gunson, M. R., Crisp, D., and Eldering, A.: Comparisons of the Orbiting Carbon Observatory-2 (OCO-2) XCO2 measurements\nwith TCCON, Atmospheric Measurement Techniques, 10, 2209–2238, https://doi.org/10.5194/amt-10-2209-2017, 2017.\nWunch, D., Mendonca, J., Colebatch, O., Allen, N., Blavier, J.-F. L., Kunz, K., Roche, S., Hedelius, J., Neufeld, G., Springett, S., Worthy, D., Kessler, R., and Strong, K.: TCCON data from East Trout Lake, Canada, Release GGG2020R0. TCCON data archive, hosted\n\n1655\n\nby CaltechDATA, California Institute of Technology, Pasadena, CA, U.S.A., https://doi.org/10.14291/tccon.ggg2020.easttroutlake01.R0,\n2022.\nZhou, M., Wang, P., Nan, W., Yang, Y., Kumps, N., Hermans, C., and De Mazière, M.: TCCON data from Xianghe,\nhttps://doi.org/10.14291/tccon.ggg2020.xianghe01.R0, 2022.\n\n83\n\n\f84\n\nCRDS on tower\n\nFlask\n\nCRDS on tower\n\nLicor 7000 NDIR (CO2 ), in situ GHG FTS\n\nCH4 ObsPack\n\nCH4 ObsPack\n\nCH4 ObsPack\n\nNIWA (direct)\n\n(CH4 )\n\nProgrammable flask packages\n\nCH4 ObsPack\n\nLi-cor NDIR on tower\n\nCO2 ObsPack\n\nCRDS on tower\n\nProgrammable flask packages\n\nCO2 ObsPack\n\nCO2 ObsPack\n\nMeasurement type\n\nSource\n\nNIWA = National Institute of Water & Atmospheric Research Ltd.\n\nGreat\n\nDan Smale (NIWA)\n\nGreat\n\nPlains\n\nPlains\n\nPlains\n\nLauder, New Zealand\n\nARM site, OK, USA\n\nSouthern\n\nARM site, OK, USA\n\nBiraud (LBNL), & Margaret Torn (LBNL)\nSebastien Biraud & Margaret Torn (LBNL)\n\nSouthern\n\nGreat\n\nPark Falls, WI, USA\n\nPark Falls, WI, USA\n\nARM site, OK, USA\n\nSouthern\n\nPark Falls, WI, USA\n\nPark Falls, WI, USA\n\nLocation\n\nEd Dlugokencky (NOAA GML), Sebastien\n\nsai (U. of WI), & Dan Baumann (USGS)\n\nArlyn Andrews (NOAA GML), Ankur De-\n\nWI), & Dan Baumann (USGS)\n\nkencky (NOAA GML), Ankur Desai (U. of\n\nArlyn Andrews (NOAA GML), Ed Dlugo-\n\nSebastien Biraud & Margaret Torn (LBNL)\n\n(USGS)\n\nAnkur Desai (U. of WI), & Dan Baumann\n\nkencky (NOAA GML), Ken Davis (PSU),\n\nArlyn Andrews (NOAA GML), Ed Dlugo-\n\nWI), & Dan Baumann (USGS)\n\nwin, Ken Davis (PSU), Ankur Desai (U. of\n\nArlyn Andrews (NOAA GML), Peter Bak-\n\nProviders/partners\n\nll\n\noc\n\noc\n\npa\n\npa\n\noc\n\npa\n\npa\n\nTCCON site\n\nGeological Survey; LBNL = Lawrence Berkeley National Laboratory; ARM = Atmospheric Radiation Measurement; CRDS = cavity ring-down spectroscopy;\n\nand Atmospheric Administration Global Monitoring Laboratory; PSU = Pennsylvania State University; U. of WI = University of Wisconsin; USGS = United States\n\nparentheses. If only one affiliation is listed, it applies to all individuals named. Abbrevations: NDIR = Nondispersive infrared; NOAA GML = National Oceanic\n\n“TCCON sites” column indicates which sites profile were used at, the IDs are mapped to locations in Table 1. In the “Providers” column, affiliations are given in\n\nIntegration Project, 2019) and “CH4 ObsPack” the CH4 GLOBALVIEWplus v2.0 ObsPack (Cooperative Global Atmospheric Data Integration Project, 2020). The\n\nTable C3. Ground in situ data used in validating the priors. “CO2 Obspack” is the CO2 GLOBALVIEWplus v5.0 ObsPack (Cooperative Global Atmospheric Data\n\nhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nTable C4. The number of profiles in the CO2 in situ correction from each campaign or other data source identified and used for each TCCON\nsite. The “Found” column gives the number of profiles identified for that campaign & site, the “Used” column gives the number of those\nprofiles which could be used in the in situ comparison after matching with TCCON data. The definitions of the site IDs can be found in Table\n1; “we” refers to an instrument in Jena, Germany for which GGG2020 data is not available at time of writing.\nCampaign\n\nSite\n\nFound\n\nUsed\n\nCampaign\n\nSite\n\nATom\n\nae\n\n4\n\ndf\neu\n\nFound\n\nUsed\n\n0\n\nINTEX-NA\n\npa\n\n3\n\n3\n\n1\n\n1\n\nKORUS-AQ\n\n2\n\n0\n\nan\n\n1\n\n1\n\ndf\n\n1\n\n1\n\nll\n\n4\n\n4\n\nrj\n\n2\n\n2\n\noc\n\n1\n\n0\n\nORCAS\n\noc\n\n1\n\n1\n\npa\n\n1\n\n1\n\nSEAC4RS\n\ndf\n\n1\n\n1\n\nCOB2004\n\npa\n\n5\n\n4\n\noc\n\n2\n\n0\n\nDC3\n\noc\n\n3\n\n2\n\nSTART-08\n\npa\n\n2\n\n0\n\nGO-Amazon\n\nma\n\n2\n\n1\n\nAirCore\n\ndf\n\n3\n\n3\n\nGSFC\n\ndf\n\n8\n\n7\n\nni\n\n3\n\n2\n\npa\n\n2\n\n2\n\noc\n\n19\n\n13\n\nll\n\n7\n\n5\n\npa\n\n2\n\n2\n\nwg\n\n1\n\n0\n\nso\n\n16\n\n9\n\nbi\n\n2\n\n2\n\nbr\n\n2\n\n0\n\ngm\n\n1\n\n1\n\nje\n\n1\n\n0\n\nka\n\n1\n\n0\n\nor\n\n2\n\n0\n\nHIPPO\nIMECC\n\n85\n\n\fhttps://doi.org/10.5194/essd-2023-331\nPreprint. Discussion started: 24 August 2023\nc Author(s) 2023. CC BY 4.0 License.\n\nTable C5. Same as Table C4 but for the CH4 in situ correction.\nCampaign\n\nSite\n\nATom\n\nae\n\nHIPPO\n\nFound\n\nUsed\n\n4\n\n0\n\nCampaign\n\nSite\n\nFound\n\nUsed\n\nIMECC\n\nbi\n\n2\n\n2\n\nci\n\n2\n\n1\n\nbr\n\n2\n\n0\n\ndf\n\n1\n\n1\n\ngm\n\n1\n\n0\n\neu\n\n1\n\n0\n\nje\n\n1\n\n0\n\nll\n\n1\n\n1\n\nka\n\n1\n\n0\n\noc\n\n1\n\n0\n\nor\n\n2\n\n0\n\npa\n\n1\n\n1\n\nSTART-08\n\npa\n\n2\n\n1\n\nll\n\n5\n\n3\n\nAirCore\n\ndf\n\n3\n\n3\n\noc\n\n4\n\n1\n\nni\n\n3\n\n2\n\npa\n\n1\n\n0\n\noc\n\n19\n\n13\n\nwg\n\n1\n\n0\n\npa\n\n2\n\n2\n\nso\n\n16\n\n9\n\nTable C6. Values of ∂r/∂Xluft in Eq. (C11). Gases not listed here use 0 for ∂r/∂Xluft .\nGas\n\n∂r/∂Xluft\n\nCO2\n\n0.363\n\nwCO2\n\n0.206\n\nlCO2\n\n0.928\n\nCH4\n\n0.0609\n\n86\n\n\f"
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English
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Three TF Co-expression Modules Regulate Pressure-Overload Cardiac Hypertrophy in Male Mice
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Three TF Co-expression Modules Regulate Pressure-Overload Cardiac Hypertrophy in Male Mice Yao-Ming Chang   1, Li Ling2, Ya-Ting Chang2, Yu-Wang Chang2, Wen-Hsiung Li1,3, Arthur Chun-Chieh Shih4 & Chien-Chang Chen2 Received: 20 March 2017 Accepted: 3 July 2017 Published: xx xx xxxx Received: 20 March 2017 Accepted: 3 July 2017 Published: xx xx xxxx Yao-Ming Chang   1, Li Ling2, Ya-Ting Chang2, Yu-Wang Chang2, Wen-Hsiung Li1,3, Arthu Chun-Chieh Shih4 & Chien-Chang Chen2 Pathological cardiac hypertrophy, a dynamic remodeling process, is a major risk factor for heart failure. Although a number of key regulators and related genes have been identified, how the transcription factors (TFs) dynamically regulate the associated genes and control the morphological and electrophysiological changes during the hypertrophic process are still largely unknown. In this study, we obtained the time-course transcriptomes at five time points in four weeks from male murine hearts subjected to transverse aorta banding surgery. From a series of computational analyses, we identified three major co-expression modules of TF genes that may regulate the gene expression changes during the development of cardiac hypertrophy in mice. After pressure overload, the TF genes in Module 1 were up-regulated before the occurrence of significant morphological changes and one week later were down-regulated gradually, while those in Modules 2 and 3 took over the regulation as the heart size increased. Our analyses revealed that the TF genes up-regulated at the early stages likely initiated the cascading regulation and most of the well-known cardiac miRNAs were up-regulated at later stages for suppression. In addition, the constructed time-dependent regulatory network reveals some TFs including Egr2 as new candidate key regulators of cardiovascular-associated (CV) genes. Many heart related diseases, such as ischemic heart disease, hypertension, heart failure, and valvular heart dis- ease, are accompanied by cardiac hypertrophy1. This type of cardiac hypertrophy, also called pathological hyper- trophy, is associated with altered cardiac gene expression, fibrosis, and cardiac dysfunction and can progress to heart failure eventually. In contrast, the other type of cardiac hypertrophy is physiological and occurs in response to chronic exercise training that is reversible and characterized by normal cardiac morphology without fibrosis or apoptosis2. The gene regulation network involved in the hypertrophic process is still largely unknown. Studies using animal models have identified a few genes and regulators and verified some of their specific roles in cardiac hypertrophy3–13. The development of cardiac hypertrophy is a dynamic process, and a few studies have taken this fact into consideration14–16. www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports Results Animal model of cardiac hypertrophy, experimental design, and transcriptome data process- ing. Adult male C57BL/6 J mice were anaesthetized and subjected to pressure overload by transverse aortic banding (TAB) according to the method described previously18, 19. The RNAs of cardiac tissues were taken from the left ventricles of mouse hearts subjected to TAB or sham operation at days 3, 5, 7, 14, and 28 after surgery (Suppl. Fig. S1). The expression changes of mRNAs and miRNAs were measured by cDNA and miRNA microar- rays, respectively. After the data processing and within and between sample normalizations (see Methods), the total numbers of genes and miRNAs for this study are 16,152 and 928, respectively. The expression fold-changes of each gene and miRNA at each time point were separately calculated by the log2 ratio of the normalized inten- sity values with and without the pressure overload treatment (Suppl. File S1). Day 5 is the major transitional stage of transcriptome expression after pressure overload in mouse hearts. We first calculated the Pearson correlation coefficient (PCC) of gene expressions between sham and TAB at different time points. To reduce the bias that might arise from extremely high or low gene expression levels, those genes with expression intensity values above the top 1% or below the bottom 1% of all expressed genes at any time point were removed. Furthermore, to avoid the PCC being dominated by genes inde- pendent of the TAB treatment, the genes with expression differences between the two conditions that were not greater than one standard deviation in all time points were removed as well. Then, the PCCs of the total intensity values of the filtered non-TF genes (6,579 genes) between two different conditions were calculated for each time point (Suppl. Fig. S2). The same procedure was applied to 928 miRNAs and 606 TF genes to calculate their PCCs. For non-TF genes, the PCC between sham and TAB decreased from day 3 (0.77) to the minimum (0.68) at day 5 (blue line in Fig. 1). After day 5, the PCC increased from 0.78 at day 7, to 0.86 at day 14, and to 0.92 at day 28. The PCCs for TF genes showed similar tendencies: they were 0.84, 0.71, 0.86, 0.91, and 0.96 for days 3, 5, 7, 14, and 28, respectively (red line in Fig. 1). www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 1. Pearson correlation coefficients (PCCs) of the expression intensity values of filtered non-TF genes (with expressional differences greater than 1 standard deviation but excluding those at the top and bottom 1% intensity values), TF genes, and microRNAs between with and without pressure overload in the cardiac samples at days 3, 5, 7, 14, and 28. The blue, red, and green lines represent the PCCs for filtered non-TF genes, TF genes, and microRNAs, respectively. Figure 1. Pearson correlation coefficients (PCCs) of the expression intensity values of filtered non-TF genes (with expressional differences greater than 1 standard deviation but excluding those at the top and bottom 1% intensity values), TF genes, and microRNAs between with and without pressure overload in the cardiac samples at days 3, 5, 7, 14, and 28. The blue, red, and green lines represent the PCCs for filtered non-TF genes, TF genes, and microRNAs, respectively. modularized? (3) What roles do these TFs or miRNAs play in stress-induced cardiac hypertrophy? To answer these questions, we first conducted a time course experiments to collect mRNA and miRNA expression data at five different time points from thoracic aortic banding (TAB)- and sham-operated (control) mouse hearts. Then, we analyzed the time-course transcriptome data and integrated them with the regulatory information from public bioinformatics databases. Based on the results, we attempted to answer the above questions one by one and iden- tified the candidate TFs and miRNAs at different stages of cardiac hypertrophy. Three TF Co-expression Modules Regulate Pressure-Overload Cardiac Hypertrophy in Male Mice Yao-Ming Chang   1, Li Ling2, Ya-Ting Chang2, Yu-Wang Chang2, Wen-Hsiung Li1,3, Arthur Chun-Chieh Shih4 & Chien-Chang Chen2 For example, Friddle et al.14 conducted a time course experiment, taking a total RNA sample from heart tissue of the drug-induced cardiac hypertrophy each day in two weeks, and identified dozens of genes associated with cardiac hypertrophy. Van den Bosch et al.16 conducted another time course experiment from aortic banding-induced cardiac hypertrophy at five time points in 8 weeks and found many differentially expressed genes associated with metabolic activity for compensated hypertrophy. In addition, Sheehy et al.15 com- pared the temporal change of transcriptomes measured in hearts subjected to either exercise-induced or aortic banding–induced hypertrophy at different time points. As most studies took cardiac samples only at few time points, a comprehensive study of how the transcription factors (TFs) dynamically regulate the associated genes during the hypertrophic process is still lacking. Noting that heart undergoes morphological and electrophysiological changes to overcome a pressure over- load, Meerson and colleagues divided cardiac remodeling into three stages: developing hypertrophy, compensa- tory hypertrophy, and overt heart failure1, 17. However, how these morphological and electrophysiological changes are regulated is still largely unknown. In this study, we raised three questions: (1) Which genes are involved in the hypertrophic process, from developing hypertrophy to compensatory hypertrophy and to overt heart failure stages? (2) Which TFs or miRNAs are responsible for inducing these changes and are they co-regulated and 1Biodiversity Research Center, Academia Sinica, Taipei, Taiwan. 2Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan. 3Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA. 4Institute of Information Science, Academia Sinica, Taipei, Taiwan. Correspondence and requests for materials should be addressed to A.C.-C.S. (email: arthur@iis.sinica.edu.tw) or C.-C.C. (email: ccchen@ibms.sinica.edu.tw) SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 1 1 SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 Results For miRNAs, the PCCs also decreased from day 3 (0.95) to day 5 (0.87), then slowly increased from 0.91 at day 7 to 0.93 at day 14, but decreased to 0.86 at day 28, which was similar to that for day 5 (green line in Fig. 1). Anatomically, the morphology of the heart after pressure overload still appeared normally at day 3. The heart size started to increase from day 5 to day 7 and became significantly larger in the TAB group (Suppl. Fig. S3A). The ratio of heart weight over body weight (HW/BW, an index of cardiac hypertrophy) remained similar between the TAB and sham groups at day 3 after surgery in mice and started to increase from day 5 to day 7 and reached a stable level at day 14 in TAB mice20, 21 (Suppl. Fig. S3B).i y y y pp g In summary, we made three observations (Fig. 1): (1) the PCCs for filtered non-TF genes and TF genes in murine hearts after pressure overload decreased from day 3 and reached the lowest at day 5. Then, the PCCs slowly returned to the same level as in the case without pressure overload. Therefore, day 5 is the critical transi- tional stage of gene regulation during the process of TAB-induced cardiac hypertrophy in male murine hearts. This observation is consistent with the result that most genes within the process of compensated hypertrophy returned to basal expression levels one week after TAB16. (2) The PCCs for all filtered non-TF genes and for TF genes showed similar tendencies of change, indicating that most non-TF gene expression changes may be directly or indirectly regulated by TFs. (3) For miRNAs, its PCC after day 5 did not return to the normal level as those for filtered non-TF genes and TF genes, but had a significant change at day 28. It seems that after day 5 the miRNA expression may have different regulatory mechanisms than those for filtered non-TF genes and TF genes. SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 2 www.nature.com/scientificreports/ Figure 2. Proportions of differentially expressed (DE) genes and miRNAs and the number of enriched GO terms for DE genes at different time points. (A) Proportions of DE genes (blue bars) and miRNAs (red bars) that first time occurred at a time point. (B) Number of enriched GO terms for DE genes at a time point. Results We confirmed some of the DE genes using quanti- tative real-time RT-PCR and the results showed that Egr1, Egr2 and cMyc are indeed differentially expressed after TAB surgery at different time points (Suppl. Fig. S5).ii f Next, we inferred the enriched functions for identified DE genes. Using all identified DE genes as the queries and all expressed genes as the background (see Methods), we found 76, 30, and 15 enriched GO terms belonging to 20, 10, and 9 similar groups in the categories of biological process (BP), molecular function (MF), and cellular component (CC), respectively (Suppl. Table S1). The enriched functions for the up-regulated DE genes, includ- ing stimulus receptor on membrane, intracellular signal transduction, inflammatory response, and so on. These observations are mostly consistent with previous studies22, 23. y However, the numbers of enriched GO terms at different time points were not evenly distributed. We used the DE genes identified at each time point and inferred their enriched GO functions. After collecting the GO categories, we found 78, 426, 308, 46, and 25 GO terms enriched at days 3, 5, 7, 14, and 28, respectively (Fig. 2B). The numbers of enriched GO terms at days 5 and 7 were several times higher than those for the other three time points, although the numbers of DE genes between different time points did not differ significantly (Suppl. Fig. S4A and C). This result indicates that the DE genes at days 5 and 7 had more enriched functions related to pressure-overload induced cardiac hypertrophy. We then asked whether the enriched functions were derived from the DE genes that were already up-regulated before or at that time point. We divided the up-regulated DE genes at a time point into two sets: (1) up-regulated for the first time at that time point; these genes were classified in the New+ set (purple bars in Fig. 2C) and (2) already up-regulated at a previous time point(s); these genes were classified in the Old+ set (orange bars in Fig. 2C). After the functional enrichment analysis, we found that the total numbers of enriched GO terms for the DE genes in the New+ and Old+ sets were almost the same in day 5, but those for day 7 were mostly from the Old+ set (Fig. 2D). Results (C) Numbers of up-regulated DE genes with first time up-regulation (New+ set; purple bars) at a time point and DE genes up-regulated at a previous time point (Old+ set; orange bars). (D) Numbers of enriched GO terms for DE genes from the New+ set (purple bars) and DE genes from the Old+ set (orange bars) at a time point. Figure 2. Proportions of differentially expressed (DE) genes and miRNAs and the number of enriched GO terms for DE genes at different time points. (A) Proportions of DE genes (blue bars) and miRNAs (red bars) that first time occurred at a time point. (B) Number of enriched GO terms for DE genes at a time point. (C) Numbers of up-regulated DE genes with first time up-regulation (New+ set; purple bars) at a time point and DE genes up-regulated at a previous time point (Old+ set; orange bars). (D) Numbers of enriched GO terms for DE genes from the New+ set (purple bars) and DE genes from the Old+ set (orange bars) at a time point. Functional enrichments of genes and miRNAs differentially expressed at early stages. The genes and miRNAs whose expression levels differed significantly between sham and TAB at least at one time point were defined as differentially expressed (DE) genes and miRNAs, respectively. We identified the DE genes and miRNAs from the whole transcriptome data for each time point and used the DE genes to predict their potential functions by Gene Ontology (GO) term enrichment analysis (see Methods).ih y gy y We identified 2,853 DE genes and 148 DE miRNAs. There were 851, 917, 911, 908, and 948 genes and 64, 61, 67, 48, and 63 miRNAs differentially expressed at days 3, 5, 7, 14, and 28, respectively (Suppl. Fig. S4). There was no significant difference in the numbers of either DE genes or DE miRNAs between different time points. However, if we only considered the DE genes and miRNAs that were either up- or down-regulated for the first time at a specific time point, the proportions were 30%, 20%, 15%, 17%, and 18% of DE genes and 43%, 23%, 7%, 18%, and 9% of DE miRNAs at days 3, 5, 7, 14, and 28, respectively (Fig. 2A). Thus, half of DE genes and more than half of DE miRNAs arose for the first time at day 3 or 5. Results That is, the number of up-regulated TF genes in Module 1 increased from day 3 to day 7 and then decreased, while those in Module 2 increased from day 14 to day 28 (Fig. 3C). For down-regulated TF genes, in contrast, the number in Module 1 increased from day 7 to day 14, while that in Module 2 decreased from day 3 to day 7 and that in Module 3 increased at day 7 and then decreased (Fig. 3D). Next, the enriched functions for the TF genes and their coexpressed DE genes in each module were predicted. We first defined a DE gene as coexpressed with a TF gene if its intensity profile was positively correlated with that of the TF gene (PCC ≥ 0.9). After identifying the coexpressed genes, we conducted a functional enrichment analysis with GO-Slims, a cut-down version of the GO ontologies, for the three modules at each time point. We found 8, 28, 14, 11, and 14 GO-Slim terms enriched for days 3, 5, 7, 14, and 28, respectively, so the maximum number of enriched functions occurred at day 5 (Suppl. Fig. S7). The coexpressed DE genes in Module 1 had more enriched GO-Slim terms than those in the other two modules. Moreover, most of the GO-Slim terms for day 5 covered more than 75% of the total enriched functions for all time points. This result indicates that the DE genes coexpressed with the TF genes in Module 1, particularly those at day 5, may play a broader role than those in other modules during the hypertrophic process. We also checked the enriched functions of TFs themselves for each module at each time point. To identify enriched functions of a TF in the network, we applied the GO-Slim enrichment analysis using all expressed genes as the background but excluding those genes related to fundamental transcriptional molecular-level functions (see Methods). For the TF genes in Module 1, the enriched functions, particularly for those up-regulated at day 3, included skeletal system, nervous system, and muscle organ development, segment specification, pattern spec- ification process, and cell cycle (Fig. 4). However, only skeletal system, muscle organ, system development, and cell cycle can be found at the later time points in the same module and the enriched functions of digestive tract mesoderm development were found at day 14 only. Results In contrast, we could not find any enriched functions for the down-regulated TF genes in Module 1 from day 3 to day 7. In addition, almost all enriched functions found for up-regulated TF genes in Module 1 from day 3 to day 14 were also enriched for down-regulated TF genes at day 28 (Fig. 4), indicating that these enriched functions were up-regulated mostly at day 3 or at days 5, 7, and 14 but were all down-regulated at day 28. The transition in enriched functions from day 14 to day 28 could be explained by switching from up- to down-regulated TF genes in Module 1 (Fig. 3). For the up-regulated TF genes in Module 2, only the function of biosynthesis process was enriched at day 5 but many important functions were enriched at day 28, including ectoderm, nervous system, muscle organ, embryo, and mesoderm development (Fig. 4). For the down-regulated TF genes in Module 2, most enriched functions were found at days 3 and 14 (Fig. 4). In contrast to Module 1, most of the up-regulated TF genes in Module 2 did not have enriched functions until day 28. At day 28, many enriched functions for down-regulated TF genes in Module 1 were also found for up-regulated TFs in Module 2, indicating that TF genes in Module 2 were recruited to regulate these functions in the later stage of pressure overload. For TF genes in Module 3, we found no enriched function for the up-regulated TF genes at any time point, while many functions for down-regulated TF genes were found at day 7 (Fig. 4). Th b l l h h d TF M d l d l l h The above results reveal that the coexpressed TF genes in Modules 1 and 2 successively regulate the important functions associated with the cardiac hypertrophy. The TF genes in Module 1 probably responded to the pressure overload stimulus at the early stage (day 3) and continuously regulated some developmental functions until day 14. Then, the TF genes in Module 2 took over most of the functions and had four extra enriched functions at day 28. Finally, the TF genes in Module 3 had a few enriched functions from days 7 to 28. MiRNAs may suppress the expression of TF genes at different stages. Results That is, most of the enriched functions at day 7 were derived from the DE genes up-regulated at either day 3 or day 5 and those first up-regulated at day 7 did not seem to have strong functional preference. SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 3 www.nature.com/scientificreports/ Thus, the DE genes that were up-regulated at an early time point (day 3 or 5) likely play a more specific role than those upregulated at a later stage in the process of TAB-induced cardiac hypertrophy in mice. Three TF coexpression modules regulate the genes with enriched functions related to cardiac hypertrophy. We used all DE TF genes and their expression profiles in TAB to construct a coexpression network in which each node represents a DE TF gene and an edge between two nodes represents a positive correlation (PCC ≥ 0.9) between the two DE TF genes. In the network, there were 206 DE TF genes each with at least one edge and the total number of edges was 670 (Fig. 3A). The network could be partitioned by a modified bridge-finding algorithm into three major modules, Modules 1, 2, and 3, which included 94, 79, and 33 TF genes, respectively (Fig. 3A; see Methods). In addition, there were 8 DE TF genes that had no connection with any TF gene in the first three modules; they were assigned to Module 4 and were ignored in the subsequent analysis. d h d d l f h h d l d i We integrated the up and down regulation information at each time point into the modules (Fig. 3B), and found that Modules 1, 2 and 3 showed distinct gene up- and down-regulation patterns (numbers shown in Fig. 3C and D and proportions shown in Suppl. Fig. S6). In Module 1, most of the TF genes were up-regulated from days 3 to 7 and half of them were down-regulated after day 7 (Suppl. Fig. S6A). In Module 2, most of the TF genes were down-regulated at days 3 and 5 (Fig. 3D), but they began to be up-regulated after day 5 (Suppl. Fig. S6B). In Module 3, over half of the TF genes were down-regulated at day 7 (Suppl. Fig. S6C), while a few of the TF genes were up-regulated at other time points (Fig. 3C). Results We defined that a DE miRNA putatively suppresses the expression of a TF gene at a time point if the following three conditions are satisfied: (1) at least one binding site of the DE miRNA is found in the 3′UTR of the TF gene, (2) the miRNA is up-regulated at the time point, and (3) the TF gene is not up-regulated at that time point. According to this definition, we found that 69 miRNAs might down-regulate the expression of 130 TF genes at any of the five time points (Suppl. File S2). The numbers of the suppressing miRNAs and corresponding TF targets are 28, 37, 31, 22, and 44, and 93, 79, 87, 68, and 92 at days 3, 5, 7, 14, and 28, respectively (Suppl. Fig. S8). Because a miRNA can suppress multiple TF genes and a TF gene can be targeted by multiple miRNAs, the relationships of suppression from miRNAs to TF genes can be many-to-many. SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 4 www.nature.com/scientificreports/ Figure 3. A positive gene coexpression network for differentially expressed (DE) TF genes under the TAB condition. (A) The four modules of TF genes in the network. (B) TF genes in Modules 1, 2 and 3 have different patterns of differential expression at each time point. The red and green nodes, respectively, indicate the up- and down-regulated TF genes at the time point. The line charts represent the numbers of (C) up-regulated and (D) down-regulated DE TF genes in Modules 1, 2 and 3 at different time points. Figure 3. A positive gene coexpression network for differentially expressed (DE) TF genes under the TAB condition. (A) The four modules of TF genes in the network. (B) TF genes in Modules 1, 2 and 3 have different patterns of differential expression at each time point. The red and green nodes, respectively, indicate the up- and down-regulated TF genes at the time point. The line charts represent the numbers of (C) up-regulated and (D) down-regulated DE TF genes in Modules 1, 2 and 3 at different time points. We found that the up-down trend for the numbers of suppressing DE miRNAs was opposite to that for the number of suppressed TF gene targets at Day3 and day 5, but the same after day 7 (Suppl. Fig. S8). Results Based on this observation, we combined the analysis from the TF gene coexpression network of TF genes and miRNAs and hypothesized that the functions related to cardiac hypertrophy were induced by the up-regulated TF genes in Module 1 at days 3 and 5 but suppressed by some miRNAs after day 7. Runt related transcription factor 1 (Runx1), for example, in Module 1 is a key regulator of heart post-myocardial infarction24 and was up-regulated from day 3 to day 14 and likely suppressed by some known cardiac miRNAs, such as miR-126–5p, miR-195, miR-208b, and SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 5 www.nature.com/scientificreports/ Figure 4. The enriched GO-Slim terms of TFs in the three modules at each time point. The major columns on left represent the five time points from day 3 to day 28 and the three sub-columns within each major column represent Modules 1, 2, and 3. The rows give the GO-Slim descriptions. The up and down arrows represent the GO Slim in the row enriched (FDR<0 05) for up and down regulated DE TF genes of the modules at the time Figure 4. The enriched GO-Slim terms of TFs in the three modules at each time point. The major columns on left represent the five time points from day 3 to day 28 and the three sub-columns within each major column represent Modules 1, 2, and 3. The rows give the GO-Slim descriptions. The up and down arrows represent the GO-Slim in the row enriched (FDR < 0.05) for up- and down-regulated DE TF genes of the modules at the time point. miR-21 at day 28 (Suppl. File S2). As another example, Cyclin E1 (Ccne1), a regulator related to defective cardi- ovascular development25, also in Module 1, was up-regulated at days 3, 7, and 14 and likely suppressed by miR- 26b and miR-107 at day 28. Moreover, Toll-like receptor 2 (Tlr2), a regulator involved in the signaling pathway of cardiomyocyte dysfunction and inflammatory responses26, also in Module 1, was up-regulated at day 7 and then likely suppressed by miR-208b at days 14 and 28. Gene Regulatory Network for Pressure Overload Cardiac Hypertrophy. Integrating our data with the target pair information from several interactome databases (see Methods), we constructed the regulatory relationships of DE genes by DE TF genes and DE miRNAs for pressure overload cardiac hypertrophy. Results The three relationships considered in this network were: (1) the regulatory pair of TF gene and target gene, (2) the regula- tory pair of miRNA and target gene, and (3) the coexpressed pair of TF gene and miRNA (see Methods). In the last relationship, we did not consider the regulatory pair of TF gene and miRNA because only a few of the regula- tory relationships have been identified so far. We identified 207 TF genes, 148 miRNAs, and 1,080 non-TF genes with the regulatory or coexpressed relationships in TAB. For the target DE genes, we analyzed their enriched functions and found 220 more enriched GO terms in addition to those for all DE genes (Suppl. File S3). Moreover, we also found that the proportion of cardiovascular-associated (CV) genes among the target genes (25%) was sig- nificantly higher than those among total DE genes (20%) and among all expressed genes (20%) (p < 0.01). These 6 SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 www.nature.com/scientificreports/ Figure 5. The gene regulatory network in TAB. (A) Network for all TF genes (red nodes), non-TF genes (green nodes), and miRNAs (purple nodes) and the edges of positive (orange) and negative (blue) regulations in TAB. (B) A schematic gene regulatory network for a TF gene, a miRNA, and a non-TF gene. (C) A sub-network centered at the TF Egr2 gene to its direct targets, where genes with red name represent the cardiovascular- associated (CV) genes. Figure 5. The gene regulatory network in TAB. (A) Network for all TF genes (red nodes), non-TF genes (green nodes), and miRNAs (purple nodes) and the edges of positive (orange) and negative (blue) regulations in TAB. (B) A schematic gene regulatory network for a TF gene, a miRNA, and a non-TF gene. (C) A sub-network centered at the TF Egr2 gene to its direct targets, where genes with red name represent the cardiovascular- associated (CV) genes. esults suggest that the identified target DE genes in TAB and the associated regulators (TFs and miRNAs) likely lay an important role for the induction of cardiac hypertrophy by pressure overload. In addition, we integrated these relationships together and constructed a regulatory/coexpressed network. In the network, each node represents a gene, a TF gene, or a miRNA (Fig. 5A) and each edge represents one type of the three relationships between two nodes (Fig. 5B). www.nature.com/scientificreports/ www.nature.com/scientificreports/ CV gene TF Name Number of edges Outward (+, −) Inward (+, −) D3 D5 D7 D14 D28 1 Runx1 64 53 (43, 10) 11 (5, 6) 1 1 1 1 1 Il6 41 37 (29, 8) 4 (3, 1) 1 1 1 1 Egr2 34 32 (24, 8) 2 (2, 0) 1 1 1 1 1 Sox9 24 24 (19, 5) 0 (0, 0) 1 1 1 1 1 Tlx1 21 21 (7, 14) 0 (0, 0) −1 −1 Pou2f2 82 80 (64, 16) 2 (1, 1) 1 1 1 Batf 37 34 (30, 4) 3 (1, 2) 1 1 1 Mxi1 19 18 (7, 11) 1 (0, 1) −1 Sox10 15 15 (13, 2) 0 (0, 0) 1 Tgif1 20 14 (13, 1) 6 (2, 4) 1 1 1 Vdr 55 52 (43, 9) 3 (2, 1) 1 1 Irf7 36 34 (33, 1) 2 (2, 0) 1 1 Pou2af1 17 17 (11, 6) 0 (0, 0) 1 1 Rest 17 17 (8, 9) 0 (0, 0) −1 1 Nfe2 14 13 (9, 4) 1 (0, 1) 1 E2f1 153 152 (127, 25) 1 (0, 1) 1 1 Egr1 128 124 (99, 25) 4 (3, 1) −1 1 Fos 92 92 (80, 12) 0 (0, 0) −1 Rfx4 19 18 (15, 3) 1 (1, 0) −1 −1 1 Rel 19 17 (17, 0) 2 (0, 2) −1 −1 1 Gata1 35 34 (30, 4) 1 (0, 1) −1 Gli1 39 34 (16, 18) 5 (0, 5) −1 Zfp354c 13 12 (8, 4) 1 (0, 1) −1 1 Egr3 9 9 (8, 1) 0 (0, 0) 1 Prdm1 9 6 (5, 1) 3 (1, 2) 1 miRNA ID Number of edges Outward Inward D3 D5 D7 D14 D28 mmu-miR-26b 78 70 8 1 1 1 mmu-miR-23b 60 54 6 1 1 1 1 1 mmu-miR-98 54 44 10 1 1 1 1 1 mmu-let-7b/g/e 46 37 9 1 1 mmu-miR-146a/b 22 18 4 1 1 mmu-miR-130a 23 14 9 1 1 mmu-miR-3963 14 10 4 1 mmu-miR-125a-5p 14 6 8 1 1 mmu-miR-1224 9 7 2 −1 mmu-miR-208b 47 39 8 1 1 mmu-miR-126-5p 42 31 11 1 1 mmu-miR-130b 27 21 6 1 mmu-miR-497 58 48 10 1 mmu-miR-499 45 36 9 1 mmu-miR-152 34 29 5 1 Table 1. List of hubs in TAB-preferential regulatory network for each time point. www.nature.com/scientificreports/ (A) Top 5 TF genes (upp table) and (B) Top 3 miRNAs (lower table) with highest total degrees that first emerged at each time point Table 1. List of hubs in TAB-preferential regulatory network for each time point. (A) Top 5 TF genes (upper table) and (B) Top 3 miRNAs (lower table) with highest total degrees that first emerged at each time point. The values 1 and −1 in the five right most columns represent up- and down-regulated differential expression, respectively, from day 3 to day 28. Table 1. List of hubs in TAB-preferential regulatory network for each time point. (A) Top 5 TF genes (upper table) and (B) Top 3 miRNAs (lower table) with highest total degrees that first emerged at each time point. The values 1 and −1 in the five right most columns represent up- and down-regulated differential expression, respectively, from day 3 to day 28. 41, 34, 24, and 21, respectively (Table 1A). Three of them, Runx1, Il6, and Sox9, have been reported as CV genes in previous studies24, 27, 28. In addition, at the same time point three first emerged miRNAs with the three largest numbers of connecting edges were miR-26b, miR-23b, and miR-98 (Table 1B), which all have been reported as relevant miRNAs in cardiac hypertrophy29–31. Results For each pair of TF gene and target gene, the edge represents the positive or negative regulation from the TF gene to the target gene. For each pair of miRNA and gene, the edge represents the negative regulation from the miRNA to the target gene. For each pair of TF gene and miRNA, the edges from miRNA to TF gene and from TF gene to miRNA represent the negative regulation and positive coex- pression, respectively. Egr2, an example shown in Fig. 5C, was one of the key regulators in TAB and had 30 target genes, including two TF genes, and was coexpressed with one miRNA. In addition, ~75% of the target genes were positively coexpressed with Egr2, indicating that Egr2 is a positive regulator for most target genes. To identify important regulators at each time point, we calculated the numbers of inward and outward edges and their sum for each regulator node. Then, the regulator nodes that first emerged at that time point were selected and sorted by the numbers of connecting edges. Table 1A and B show the connection and merged infor- mation for top 5 selected TF genes and top 3 selected miRNAs, respectively, at each time point. For example, Runx1, Interleukin 6 (Il6), Early growth factor 2 (Egr2), Sex determining region y-box 9 (Sox9), and T-cell leukemia homeobox 1 (Tlx1) were the top 5 TF genes that first emerged at day 3 and their total numbers of edges are 64, SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 7 www.nature.com/scientificreports/ In addition, many enriched GO groups were also associated with the event of hypertrophic stimulus response22, such as detection of stimulus (GO:0051606), response to stimulus (GO:0050896), sensory perception of chemical stimulus (GO:0007606), positive regula- tion of response to external stimulus (GO:0032103) in BP category, receptor activity (GO:0004872), ion channel activity (GO:0005216) in MF category and membrane part (GO:0044425), extracellular matrix (GO:0031012) in CC category. For the event of intracellular signaling, the GO similar groups such as G-protein-coupled receptor signaling pathway (GO:0007186) in the BP category, cytokine activity (GO:0005125), and molecular transducer activity (GO:0060089) in the MF category were overrepresented. Moreover, other GO groups regarding the gene regulation were enriched in our analysis, such as negative regulation of peptidase activity (GO:0010466), positive regulation of behavior (GO:0048520), cell proliferation (GO:0008284), immune system process (GO:0002684), and multicellular organismal process (GO:0051240) in BP category (Suppl. Table 1).i g p ( ) g y ( pp ) In term of specific genes as hypertrophic markers32, 33, some immediate-early genes, such as Fos and Egr1, and fetal genes, such as Atrial natriuretic factor (Nppa), Beta-myosin heavy chain (Myh7), and Skeletal alpha actin (Acta1) were also differentially expressed. However, many of these genes were not up-regulated or down-regulated at all time points. For example, Myh7 was up-regulated at all time points except day 14, whereas Egr1, a TF, was down-regulated only at day 14. Thus, our data suggest that cardiac samples should be taken at several different time points over the time course in order, to have a reliable view of the gene expression profile over the time course.h The dynamic change of individual gene revealed in this study suggests critical time point of each gene play- ing its role to affect the progression of cardiac hypertrophy (Suppl. File. S1). For example, Fkbp1b modulates the calcium release from sarcoplasmic reticulum in cardiomyocyte and disruption of Fkbp1b results in cardiac hypertrophy in male mice34. In our results, during the developing stage, Fkbp1b was downregulated only before the hypertrophic growth of myocardium (day 3) and this suggests that downregulation of Fkbp1b at day 3 may be important to trigger the hypertrophic growth of heart. In contrast, expression pattern of Egr1 was upregulated and reached maximal level in the early stage (day 5) and downregulated at day 14. www.nature.com/scientificreports/ coexpression network was constructed. Based on these results, we made the following observations that may answer questions related to the gene regulation in cardiac hypertrophy.i q g g yp p y First, the PCCs for filtered non-TF genes, TF genes, and miRNAs between TAB and sham decreased from day 3, reached the lowest at day 5, and then returned to the same level at days 7 and 14 (Fig. 1). The global expression change was likely caused by many genes and miRNAs simultaneously in response to the pressure overload stimuli in the early stage, consistent with the previous study of pressure overload induced cardiac hypertrophy in mice16. Second, for miRNAs a globally significant transition occurred at day 28 (Fig. 1), indicating that miRNAs may play a regulatory role in cardiac hypertrophy at day 28. Third, the number of changes between suppressing DE miRNAs and that of suppressed DE TF gene targets showed the same trend only after day 7. We speculated that many DE TF genes were regulated by DE miRNAs in the later stages (Suppl. Fig. S8). Fourth, many CV TF genes in Module 1 were up-regulated at the early stages but down-regulated by miRNAs later (Suppl. File S2). Fifth, many functions related to cardiac hypertrophy were enriched in up-regulated DE TF genes in the early stages but enriched in down-regulated DE TF genes in the later stages (Fig. 4). From the last three observations, we may speculate that these functions were probably suppressed by DE miRNAs. Therefore, we hypothesize that TFs reg- ulate genes and miRNAs in responding to the pressure overload stimuli in the early stages, and then miRNAs may regulate TF genes in a feedback way for maintaining the tissue homeostasis in the hypertrophic process. g g y g yp p p In term of enriched GO functions for the DE genes, we found that the GO groups were mostly consistent with the general diagram of events found in the process of cardiomyocyte hypertrophy22, including hypertrophic stim- ulus response, intracellular signaling, and change in gene expression. www.nature.com/scientificreports/ Our finding suggests that Egr1 participates in developing stage of cardiac hypertrophy but may not be required for the compensatory stage of hypertrophy. This may be reflected by the reduced cardiac hypertrophy in the Egr1 knockout mice35. In addition, we found expression of Gli1 was upregulated only at the late stage of cardiac hypertrophy (day 28). Gli1 is a marker of perivascular mesenchymal stem cells and contributes to injury-induced organ fibrosis36. Removal of Gli1 + cells reduces the pressure overload-induced cardiac hypertrophy and cardiac fibrosis36. The late induction of Gli1 may reflect organ damage accumulated after long-term chronic pressure stress and also a hint of initiation of decompensation. Overall, our time domain-based quantification results can compensate the functional infor- mation derived from genetic modified mice studies. gi Based on the targeting and coexpression relationships, we constructed a TF-miRNA-gene regulation and coexpression network and identified the hubs as potential candidates of essential regulators for cardiac hyper- trophy (Table 1). Among the 25 TF candidates, 13 (~52%) of them are CV genes, which is significantly higher than the CV gene proportion in all expressed TF genes (22%), indicating that these detected TF genes are likely related to cardiac hypertrophy (Table 1A). For example, Egr2, not annotated as a CV gene yet, was differentially expressed at the beginning of TAB-induced cardiac hypertrophy and ~42% of its targets are CV genes, two of which, Fibroblast growth factor 8 (Fgf8) and Noggin (Nog), have been reported to negatively regulate cardiac mus- cle tissue development37, 38. As Egr1 and Egr3, two paralogous genes of Egr2, are both CV genes, and Egr2 is likely a CV gene and an essential regulator for TAB-induced cardiac hypertrophy. Discussion In this study, we analyzed the murine heart transcriptome data obtained at days 3, 5, 7, 14, and 28 under two conditions: with and without pressure overload. The expression levels were calculated for all expressed genes and miRNAs under the two conditions at the five time points and differentially expressed genes and miRNAs were identified. In addition, the expression profiles of the DE TF genes in TAB were used to infer their coexpression modules and predict potential functions. According to the targeting and coexpression information, the potential targets of the miRNAs and TF gene targets were identified and, finally, a TF gene-miRNA-gene regulation and 8 SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 www.nature.com/scientificreports/ www.nature.com/scientificreports/ p g y p p p p p Fluorescent targets were prepared from 2.5 µg total RNA samples using miRNA ULSTM Labeling Kit (Kreatech Diagnostics. USA) and then were hybridized to the Mouse & Rat miRNA OneArray® with Phalanx hybridization buffer using OneArray® Hybridization Chamber. After 16 hrs hybridization, non-specific binding targets were washed away. The slides were scanned using a DNA Microarray Scanner (Model 4000B, Molecular Devices, Sunnyvale, CA, USA). The Cy5 fluorescent intensities of each spot were analyzed by GenePix 4.1 soft- ware (Molecular Devices). The microarray data have been submitted to the National Center for Biotechnology Information Gene Expression Omnibus database under accession number GSE99460. Quantitative Real-time RT-PCR. The first-strand cDNA was synthesized from 1 μg of total RNA using the SuperScript III Reverse-Transcriptase Kit (Invitrogen). Real-time PCR reactions were performed in trip- licate in 96-well plates with use of an ABI 7500 Real-Time PCR System instrument (Applied Biosystems). cDNA was amplified by the SYBR green PCR method (Kapa Biosystems). The relative expressions of Egr1, Egr2 and cMyc genes were quantified by the comparative cycle threshold (Ct) method (∆∆Ct), with GAPDH as an endogenous control and normalized to day 3 sham. Sequences for primers were for mouse egr1, sense, 5′-TACGAGCACCTGACCACAGAGT-3′ and antisense, 5′-GCTGGGATAACTTGTCTCCACC-3′; egr2, sense, 5′-GTTGTGCGAGGAGCAAATGA-3′ and antisense, 5′-GCGAAGCTACTCGGATACGG -3′; cmyc, sense, 5′-AGCAGCGACTCTGAAGAAGAG-3′ and antisense, 5′-GAGACGTGGCACCTCTTGAG-3′; and for GAPDH, sense, 5′-CTTCACCACCATGGAGAAGG-3′ and antisense, 5′-GGCATGGACTGTGGTCATGAG-3′. cDNA and miRNA microarray data processing and normalization. For each cDNA array, the inten- sities were firstly normalized by median scaling normalization method, then taken the average of repeated data from the same sample. The whole data for a probe were removed if the intensity values were negative or less than one in any of the five time points. The remaining probe number was 20,021. The quantile approach was applied for the between-sample normalization. For each time point and condition data set, the intensity values were first sorted from the highest to the lowest. Second, for each condition the medium values of all intensity values at the same order positions were calculated. Finally, the normalized intensity values of each data set were re-assigned by the medium values of each corresponding sorted order position. If a gene had multiple probe sets, only that with the totally maximum absolute fold changes among all time points was selected to represent the expression profile of this gene. The final gene number for the analysis was 16,152. www.nature.com/scientificreports/ www.nature.com/scientificreports/ ventricles of Sham- and TAB-operated mice at 3, 5, 7, 14, and 28 days after surgery. Then, the expression changes of mRNAs and miRNAs were estimated by cDNA microarrays and miRNA arrays, respectively. ventricles of Sham- and TAB-operated mice at 3, 5, 7, 14, and 28 days after surgery. Then, the expression changes of mRNAs and miRNAs were estimated by cDNA microarrays and miRNA arrays, respectively. ventricles of Sham- and TAB-operated mice at 3, 5, 7, 14, and 28 days after surgery. Then, the expression changes of mRNAs and miRNAs were estimated by cDNA microarrays and miRNA arrays, respectively. Whole Genome OneArray® and miRNA OneArray®. Total RNA Isolation. Total RNA was extracted using the TRIzol® Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. The concentration and purity of the RNA was measured by NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific). Purity was checked by the ratio of the OD260/OD280 and OD260/OD230. The quality of total RNA was accessed using Agilent 2100 Bioanalyzer (Aglient Technologies, Santa Clara, CA, USA). Mouse OneArray®. The Mouse Whole Genome OneArray® v2 (Phalanx Biotech Group, Taiwan) contains 27,307 DNA oligonucleotide probes, and each probe is a 60-mer designed in the sense direction. Among the probes, 26,423 probes correspond to the annotated genes in RefSeq v51 and Ensembl v65 database and the other 884 probes are used for control. The detailed descriptions of the gene array list are available at http://www.pha- lanx.com.tw/products/MOA.php. Fluorescent RNA targets were prepared from 1 µg total RNA samples using OneArray® Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dye (GE Healthcare). They were then hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization, non-specific binding targets were washed away. The slides were scanned using a DNA microarray Scanner (Model G2505C, Agilent Technologies). The Cy5 Fluorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices). Mouse & Rat miRNA OneArray®. Mouse & Rat miRNA OneArray® v3 (Phalanx Biotech Group, Taiwan) con- tains triplicate 1086 unique miRNA probes from Mouse (miRBase Release 17) and 676 unique miRNA probes from Rat (miRBase Release 17). In addition, it also contains 144 experimental control probes. The detailed descriptions of the gene array list are available at http://www.phalanx.com.tw/products/MRmiOA_Probe.php. Materials and Methods Animal model of cardiac hypertrophy and experimental design. Eight-week-old adult male mice (C57BL/6 J) weighing 20–25 g were anaesthetized (vaporized 1% isoflurane) and subjected to pressure overload by transverse aortic banding (TAB) according to the method described previously18, 19. Animals were kept under specific pathogen-free conditions, and all procedures performed were approved by the Institutional Animal Care and Use Committee (IACUC) of Academia Sinica, Taiwan. All experimental procedures were carried out in accordance with approved guidelines of the IACUC. The RNAs of cardiac tissues were taken from the left SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 9 www.nature.com/scientificreports/ The species Mus musculus was selected and the false discovery rate (FDR) threshold was set to 0.05. The functional analysis tool used for the TFs themselves in the network was PANTHER against the background set of all expressed genes with the FDR threshold of 0.05 by the Benjamini-Hochberg procedure. Partition for the constructed TF coexpression network. An iterated bisection clustering method was applied to divide a connected network into multiple partitions step-by-step. First, all the bridges in the network were identified by a bridge-finding algorithm40. A bridge is an edge that when it is removed from a connected network, the network is divided into two separate networks. Second, the balancing values for the bridges with the size (number of nodes in the network) of the larger partition were calculated. Third, the bridge with smallest balancing value was selected as the cutting edge to divide the network into two partitions. Then the largest one from all partitions was chosen and divided further by repeating the method until no partition with size greater than 10 can be obtained, which is too few to do the functional enrichment test. Target gene prediction for TF and miRNA. The TF-target interaction data were integrated from two different sets: one predicted by Ernst et al.41, which had 468,319 interactions, and the other by Gerstein et al.42, which had 538,949 interactions. The original data of these two sets were both predicted in human. Using the ort- holog mapping, both human data sets had been transferred as the mouse data set already41, 42. The two transferred mouse datasets were combined together. The miRNA-target interaction data was integrated from one experimen- tal, miRTarBase (http://mirtarbase.mbc.nctu.edu.tw/), and two predicted datasets, TargetScanMouse Release 6.2 (http://www.targetscan.org/mmu_61/) and miRanda August 2010 release (http://www.microrna.org/microrna/). In miRTarBase Release 4.5, the number of miRNA-target interaction pairs for human was 38,113, where the numbers of miRNAs and target genes were 587 and 12,194, respectively. In contrast, the interaction number for mouse was only 9,378 where the numbers of miRNAs and target genes were 217 and 4,443, respectively. Using a similar procedure, the human data were converted to the mouse data by the ortholog mapping approach. If the miRNA and targets were both conserved in mouse, the pairs were also applied to the mouse analysis. In total, 48,466 miRNA-target pairs were collected from this data set. www.nature.com/scientificreports/ The Scatter Plots between TAB and sham gene expression levels at different time points were shown in Suppl. Fig. S2.li pf p pp g For the miRNA array data, the miRNAs with flags <0 within repeated probes and all chips were filtered out first. Then, the intensity values from repeated probes within one chip were combined by median. Then the com- bined values were normalized by a quantile normalized method within technical replicate. The processed data were provided by Phalanx Biotech Group, Taiwan. The number of remaining miRNAs was 928. The procedure for between-sample normalization is the same as that for cDNA array data39. TF and cardiovascular-associated gene information. The mouse TFs, transcription co-factors, and chromatin remodeling factors were collected from AnimalTFDB (http://www.bioguo.org/AnimalTFDB/) includ- ing 1,457 TFs of 71 families, 107 chromatin remodeling factors, and 279 transcription co-factors. Ignoring those without gene symbols, the final list included 1,740 TFs, transcription co-factors, and chromatin remodeling fac- tors in total. The miRNA information was downloaded from miRBase (http://www.mirbase.org/) and the version was release 17. The cardiovascular GO Annotation Initiative gene list (comprising 4,054 genes) was assembled by SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 10 www.nature.com/scientificreports/ merging 3 existing cardiovascular-associated (CV) gene lists (http://www.ebi.ac.uk/GOA/CVI) and downloaded from (ftp://ftp.ebi.ac.uk/pub/databases/). merging 3 existing cardiovascular-associated (CV) gene lists (http://www.ebi.ac.uk/GOA/CVI) and downloaded rom (ftp://ftp.ebi.ac.uk/pub/databases/). Identification of differentially expressed (DE) genes and miRNAs. For each time point, the fold-change of a gene was calculated by the log2 ratio of the intensity values measured from TAB-operated hearts over that measured from sham hearts. Then, the average and standard deviation of the total fold-change ratios for each time point were calculated. A differentially expressed (DE) gene was defined that its fold change was posi- tively higher or negatively lower than two times of the standard deviation in any of the five time points. The same procedure was also applied to the miRNA array data. Correlation, statistical test, and functional enrichment analysis. The correlations of two intensity expression profiles were measured by Pearson correlation coefficient. The functional analysis tool used for the DE genes and genes coexpressed with DE TF genes in the network were GOrilla (http://cbl-gorilla.cs.technion.ac.il/) and PANTHER (http://www.pantherdb.org) that can identify enriched Gene Ontology (GO) and GO-Slim terms in ranked lists of genes against the background set of all expressed genes in this study. www.nature.com/scientificreports/ In the miRanda data set, 246,504 mouse miRNA-gene interactions had been predicted and were directly downloaded from the microcosm website (http:// www.ebi.ac.uk/enright-srv/microcosm/) with p-value < 0.01, including 568 miRNAs and 19,183 target genes. In the TargetScanMouse dataset, both the conserved and non-conserved target site predictions were downloaded and the conserved predictions had 774 miRNAs and 11,828 genes and the non-conserved ones had 779 miRNAs and 18,249 genes. Finally, these three datasets were combined together and only the pairs of DE miRNAs and DE target genes were selected. TF-miRNA-gene regulatory and coexpression network construction. The TF-miRNA-gene net- work was constructed by considering the following three relationships: (1) the regulatory pair of TF gene and tar- get gene, (2) the regulatory pair of miRNA and target gene, and (3) the coexpressed pair of TF gene and miRNA. For the first relationship, if a DE gene not only was coexpressed, either positively or negatively, with a DE TF gene in TAB but also had one or more of the DE TF gene predicted binding sites in the promoter region, they were defined as a regulatory pair of TF gene and target gene. For the second relationship, a regulatory pair of miRNA and target gene was defined as a DE gene that was not only negatively coexpressed with the DE miRNA in TAB but also a predicted target of that miRNA. 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Downregulation of miR-199a derepresses hypoxia-inducible factor-1alpha and Sirtuin 1 and recapitulate preconditioning in cardiac m oc tes Circ Res 104 879 886 doi 10 1161/CIRCRESAHA 108 193102 (2009) 13. Rane, S. et al. Downregulation of miR-199a derepresses hypoxia-inducible factor-1alpha and Sirtuin 1 and recapitulates hypoxia preconditioning in cardiac myocytes. Circ Res 104, 879–886, doi:10.1161/CIRCRESAHA.108.193102 (2009).i p g y y 14. Friddle, C. J., Koga, T., Rubin, E. M. & Bristow, J. Expression profiling reveals distinct sets of genes altered during induction regression of cardiac hypertrophy Proc Natl Acad Sci USA 97 6745 6750 doi:10 1073/pnas 100127897 (2000) p g y y 14. Friddle, C. J., Koga, T., Rubin, E. M. & Bristow, J. Expression profiling reveals distinct sets of genes altered during induction and regression of cardiac hypertrophy. Proc Natl Acad Sci USA 97, 6745–6750, doi:10.1073/pnas.100127897 (2000). 14. Friddle, C. J., Koga, T., Rubin, E. M. & Bristow, J. Expression profiling reveals distinct sets of genes altered during induction and regression of cardiac hypertrophy. Proc Natl Acad Sci USA 97, 6745–6750, doi:10.1073/pnas.100127897 (2000). g yp p y p 15. Sheehy, S. P., Huang, S. & Parker, K. K. Author Contributions C.-C.C. and A.C.-C.S. directed the project and designed the study. L.L., Y.-T.C. and C.-C.C. performed experiments. Y.-M.C., A.C.-C.S. and C.-C.C. analyzed the data. Y.-M.C., Y.-W.C., W.-H.L., A.C.-C.S. and C.-C.C. wrote the manuscript. Acknowledgements g We thank Chih-Hao Chang, Han-Chu Hsu, and Shih-Ying Wu for excellent technical assistance. The work was supported by the Ministry of Science and Technology, Taiwan (102-2320-B-001-012-MY3 and 105-2320-B-001- 020 -MY3 to C.-C.C. and 103-2221-E-001-025-MY2 and 105-2221-E-001-026-MY3 to A.C.-C.S.). SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 12 www.nature.com/scientificreports/ SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 Additional Information Supplementary information accompanies this paper at doi:10.1038/s41598-017-07981-4h Competing Interests: The authors declare that they have no competing interests. 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 Cre- ative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not per- mitted 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 license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2017 SCIenTIfIC RePOrTS | 7: 7560 | DOI:10.1038/s41598-017-07981-4 13
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To cite this version: Amir Semmo, Tobias Isenberg, Jürgen Döllner. Neural Style Transfer: A Paradigm Shift for Image- based Artistic Rendering?. NPAR 2017 - Proceedings of the International Symposium on Non- Photorealistic Animation and Rendering (NPAR as part of Expressive), ACM, Jul 2017, Los Angleles, United States. pp.5:1-5:13, ￿10.1145/3092919.3092920￿. ￿hal-01527495v3￿ This is the authors’ version of the work. It is posted here for your personal use. Not for redistribution. The defnitive version will be published in Proceedings of Non- Photorealistic Animation and Rendering (NPAR ’17). http://dx.doi.org/10.1145/3092919.3092920. NPAR’17, Los Angeles, CA, USA © 2017 Copyright held by the owner/author(s). Publication rights licensed to ACM. 978-1-4503-5081-5/17/07...$$15.00 DOI: 10.1145/3092919.3092920 ACM Reference format: ACM Reference format: Amir Semmo, Tobias Isenberg, and Jürgen Döllner. 2017. Neural Style Trans- fer: A Paradigm Shift for Image-based Artistic Rendering? In Proceedings of Expressive, Los Angeles, CA, USA, July 28-29, 2017 (NPAR’17), 13 pages. DOI: 10.1145/3092919.3092920 Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? Amir Semmo Hasso-Plattner-Institut, Faculty of Digital Engineering, University of Potsdam, Germany amir.semmo@hpi.uni-potsdam.de Tobias Isenberg Inria & Université Paris-Saclay France tobias.isenberg@inria.fr Jürgen Döllner Hasso-Plattner-Institut, Faculty of Digital Engineering, University of Potsdam, Germany doellner@hpi.uni-potsdam.de Input ‘Mosaic’ ‘Udnie’ ‘La Muse’ / Oil Paint ‘The Scream’ / Watercolor Neural Style Transfer Neural Style Transfer with Filtering Figure 1: Outputs of a feed-forward NST using CNNs for image processing (Johnson et al. 2016a,b). The potentials and impact of NST on IB-AR and its combinations with paradigms such as image fltering (here: oil paint, watercolor) are discussed in this paper. “Brooklyn Bridge” by Curtis MacNewton is licensed under CC BY-SA 2.0;1 derivatives implicate style variants. Amir Semmo Hasso-Plattner-Institut, Faculty of Digital Engineering, University of Potsdam, Germany amir.semmo@hpi.uni-potsdam.de Jürgen Döllner Hasso-Plattner-Institut, Faculty of Digital Engineering, University of Potsdam, Germany doellner@hpi.uni-potsdam.de Jürgen Döllner Hasso-Plattner-Institut, Faculty of Digital Engineering, University of Potsdam, Germany doellner@hpi.uni-potsdam.de Tobias Isenberg Inria & Université Paris-Saclay France tobias.isenberg@inria.fr Tobias Isenberg Inria & Université Paris-Saclay France tobias.isenberg@inria.fr Neural Style Transfer with Filtering ‘Udnie’ Input ‘The Scream’ / Watercolor ‘La Muse’ / Oil Paint Neural Style Transfer with Filtering ‘Mosaic’ Neural Style Transfer ‘Udnie’ ‘Mosaic’ ‘La Muse’ / Oil Paint ‘Udnie’ ‘La Muse’ / Oil Paint Input ‘The Scream’ / Watercolor Input Figure 1: Outputs of a feed-forward NST using CNNs for image processing (Johnson et al. 2016a,b). The potentials and impact of NST on IB-AR and its combinations with paradigms such as image fltering (here: oil paint, watercolor) are discussed in this paper. “Brooklyn Bridge” by Curtis MacNewton is licensed under CC BY-SA 2.0;1 derivatives implicate style variants. • Computing methodologies →Non-photorealistic render- ing; Image processing; In this meta paper we discuss image-based artistic rendering (IB-AR) based on neural style transfer (NST) and argue, while NST may represent a paradigm shift for IB-AR, that it also has to evolve as an interactive tool that considers the design aspects and mecha- nisms of artwork production. IB-AR received signifcant attention in the past decades for visual communication, covering a plethora of techniques to mimic the appeal of artistic media. Example-based rendering represents one the most promising paradigms in IB-AR to (semi-)automatically simulate artistic media with high fdelity, but so far has been limited because it relies on pre-defned image pairs for training or informs only low-level image features for texture transfers. Advancements in deep learning showed to alleviate these limitations by matching content and style statistics via activations of neural network layers, thus making a generalized style trans- fer practicable. We categorize style transfers within the taxonomy of IB-AR, then propose a semiotic structure to derive a technical research agenda for NSTs with respect to the grand challenges of NPAR. We fnally discuss the potentials of NSTs, thereby identifying applications such as casual creativity and art production. • Computing methodologies →Non-photorealistic render- ing; Image processing; 1CC BY-SA 2.0 license: http://creativecommons.org/licenses/by-sa/2.0 KEYWORDS style transfer, stylization, convolutional neural networks, image- based artistic rendering, image processing, semiotics HAL Id: hal-01527495 https://inria.hal.science/hal-01527495v3 Submitted on 7 Jun 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. 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. Copyright 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. Copy Copyright 1 INTRODUCTION Non-photorealistic rendering (NPR) constitutes a highly active re- search domain of computer graphics that deals with the expres- sion, recognition, and communication of complex image contents by means of information abstraction and highlighting (DeCarlo and Santella 2002; Gooch 2010; Hertzmann 2010; Lansdown and Schofeld 1995). In particular, image-based artistic rendering (IB-AR) enjoys a growing popularity in mobile expressive rendering (Dev 2013; Winnemöller 2013) to simulate the appeal of traditional artis- tic styles and media for visual communication (Kyprianidis et al. 2013; Rosin and Collomosse 2013) such as pencil, pen-and-ink, oil paint, and watercolor. Classical IB-AR techniques typically model the design aspects that are involved with these artistic styles, i. e., to direct the smoothing and contour highlighting of image fltering, NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Semmo et al. Semmo et al. Style Content Texture Transfer / Risser et al. (2017) Style Content Color Transfer / Gatys et al. (2016b) Style Content Portrait Stylization / Selim et al. (2016) Frame i+1 Frame i Frame i+2 Frame i+3 Video Stylization / Johnson et al. (2016a; 2016b) Casual Creativity / Prisma (iOS) Content / Style Mask Casual Creativity / likemo.net Figure 2: Overview of NST techniques and applications. Previous works used implementations of NSTs to perform general- ized color and texture transfers, stylize videos, and provide means for casual creativity in mobile expressive rendering. Im- ages © Risser et al. (2017), from Gatys et al. (2016b) © IEEE, from Selim et al. (2016) © ACM, all used with permission. Style Content Portrait Stylization / Selim et al. (2016) Portrait Stylization / Selim et al. (2016) Content / Style Mask Casual Creativity / likemo.net Frame i+1 Frame i Frame i+2 Frame i+3 Video Stylization / Johnson et al. (2016a; 2016b) Casual Creativity / Prisma (iOS) Casual Creativity / Prisma (iOS) Video Stylization / Johnson et al. (2016a; 2016b) Casual Creativity / likemo.net Figure 2: Overview of NST techniques and applications. Previous works used implementations of NSTs to perform general- ized color and texture transfers, stylize videos, and provide means for casual creativity in mobile expressive rendering. Im- ages © Risser et al. (2017), from Gatys et al. (2016b) © IEEE, from Selim et al. (2016) © ACM, all used with permission. In this paper we discuss the potentials and challenges of NST for IB- AR. 1 INTRODUCTION In the following section, we frst provide a conceptual overview for (neural) style transfer and show how the design process dif- fers from classical IB-AR paradigms (Section 2). Next, we provide a semiotic structure for IB-AR that combines design aspects and mechanisms of artwork production with well-established design principles of NPAR (Section 3). We then use this structure to cat- egorize current (neural) style-transfer techniques (Section 4) and derive a technical research agenda for NST (Section 5) including potential mutual inclusions with other IB-AR paradigms such as image fltering (Figure 1). With this research agenda we shed light on how NSTs may contribute to deal with the grand challenges of NPAR put forth by Salesin (2002) and revisited by Gooch et al. (2010), and how they can be evolved as interactive tools that consider mechanisms of artwork production. Finally, we identify potential future applications such as casual creativity (Section 6). the approximation of image contents via rendering primitives (e. g., brush strokes, stipples), or an image segmentation. A more gener- alized approach has been introduced by example-based rendering (EBR), which employs machine learning or statistical models to em- ulate characteristics of artistic styles from visual examples (Kypri- anidis et al. 2013). Previous techniques in EBR, however, typically require analogous style and content pairs for training (Hertzmann et al. 2001) or only inform low-level image features for texture transfers, thus limiting its application and creative control over the design aspects. Advancements in deep learning and convolu- tional neural networks (CNNs) demonstrated that these technical limitations can be alleviated as follows: (1) Deep CNNs are able to accurately classify high-level im- age contents across generalized data sets (Simonyan and Zisserman 2015). (2) Layers of pre-trained deep CNNs can be activated to match content and style statistics, and thus perform a neural style transfer (NST) between arbitrary images (Gatys et al. 2016b) (Figure 1). 2 ARTISTIC STYLE TRANSFER WITHIN THE TAXONOMY OF IB-AR TECHNIQUES Style Transfer using Neural Networks: Techniques that employ neural networks to separate and recombine the content and style of arbitrary inputs. Typically, loss func- tions are minimized iteratively to balance the components of style and content in the output (Gatys et al. 2016b), or train feed-forward neural networks for linear image trans- formation (Johnson et al. 2016a,b). III. Style Transfer using Neural Networks: Techniques that employ neural networks to separate and recombine the content and style of arbitrary inputs. Typically, loss func- tions are minimized iteratively to balance the components of style and content in the output (Gatys et al. 2016b), or train feed-forward neural networks for linear image trans- formation (Johnson et al. 2016a,b). (1) Heuristics-based Algorithms: Paradigms that are based on rendering functions, which are implemented by a do- main expert who explicitly models individual artistic styles and its correspondent design aspects or mechanisms. This group basically comprises stroke-based rendering, region- based techniques, image processing and fltering, and may also account for physically-based simulations. We believe this classifcation helps to organize EBR techniques by their technical foundation and underpins the maturation from application-specifc (e. g., color transfers) towards generalized style transfers. In the following section, we defne design aspects and mechanisms important for implementing these three concepts. We believe this classifcation helps to organize EBR techniques by their technical foundation and underpins the maturation from application-specifc (e. g., color transfers) towards generalized style transfers. In the following section, we defne design aspects and mechanisms important for implementing these three concepts. (2) Style Transfer Algorithms: Example-based rendering which is directed to learn or reproduce artistic styles from visual examples (ground-truth data sets). This type often comprises statistical models and optimization schemes to balance aspects of content and style in the stylized output. 2 ARTISTIC STYLE TRANSFER WITHIN THE TAXONOMY OF IB-AR TECHNIQUES To this end, we argue that deep learning denotes a key technique in the chronology of IB-AR (Kyprianidis et al. 2013), as it makes— for the frst time—a generalized style transfer practicable. First applications demonstrate this process using the example of color and texture transfers as well as casual creativity systems and ser- vices (Figure 2). To provide a sophisticated paradigm shift for IB-AR, however, we believe that NSTs need to mature from color and tex- ture transfers to interactive tools that consider the design aspects and mechanisms involved in artwork production, i. e., to ease the visual expression of artists, non-artists (i. e., general public), and scientists (Gooch et al. 2010; Isenberg 2016; Salesin 2002). IB-AR is related to the processes of visual abstraction that are in- volved in the creation of general artworks (Hertzmann 2010; Ma 2002) and used to express uncertainty, communicate abstract ideas, and evoke the imagination (Gooch et al. 2010) by addressing the ra- tional, emotional, and cognitive qualities of the human mind (Halper et al. 2003; Hertzmann 2010). For an efective visual abstraction, the separation of content from style is thus considered to be a key factor to allow us to distinguish between the mechanisms used for captur- ing the essence of an image, on the one side, and the design aspects that drive the aesthetic appeal to stimulate human senses (Gooch et al. 2010; Salesin 2002), on the other side. To this end, research in Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? NPAR’17, July 28-29, 2017, Los Angeles, CA, USA ... Neural Style Transfer Content Image Output Image Loss Network (DNN) Loss Functions Minimization λ Style Image ... Image Statistics-/Analogies-based Style Transfer Input Image Output Image Matching Pipeline Optimization Functions Content Image Style Image ... Heuristics-based Algorithms Artistic Styles Input Image Output Image Rendering Pipeline Artworks Rendering Functions Training Data Processing Pipeline Processing Functions Image Data Texture-Transfer-Only Data/Functions Manual Modeling Effort Figure 3: Overview of style transfer concepts, which difer in the way artistic styles are modeled or transferred: heuristics- based algorithms (left) and style transfers based on image statistics or analogies (middle) require explicit modeling or training phases prior to application, whereas NSTs (right) combine both aspects in a single phase. 2 ARTISTIC STYLE TRANSFER WITHIN THE TAXONOMY OF IB-AR TECHNIQUES Loss Functions Texture-Transfer-Only Data/Functions Manual Modeling Effort Image Data Texture-Transfer-Only Data/Functions Manual Modeling Effort Processing Pipeline Figure 3: Overview of style transfer concepts, which difer in the way artistic styles are modeled or transferred: heuristics- based algorithms (left) and style transfers based on image statistics or analogies (middle) require explicit modeling or training phases prior to application, whereas NSTs (right) combine both aspects in a single phase. the feld of IB-AR has been devoted to deduce the design aspects of an artistic style that are involved in artwork production: color transfers that equalize the mean and variance be- tween content and style images (Neumann and Neumann 2005; Reinhard et al. 2001). Defnition “Artistic Style”: The constant form—and some- times the constant elements, qualities, and expression—in Defnition “Artistic Style”: The constant form—and some- times the constant elements, qualities, and expression—in Defnition “Artistic Style”: The constant form—and some- times the constant elements, qualities, and expression—in the art of an individual or a group. II. Style Transfer using Image Analogies: Techniques that use image pairs for training—a source image and an artistic depiction of this image—i. e., to learn an analogous trans- formation such that content images can be transformed into an artistic rendering of similar visual style (Hertzmann et al. 2001). II. Style Transfer using Image Analogies: Techniques that use image pairs for training—a source image and an artistic depiction of this image—i. e., to learn an analogous trans- formation such that content images can be transformed into an artistic rendering of similar visual style (Hertzmann et al. 2001). the art of an individual or a group. the art of an individual or a group. — Meyer Schapiro (Schapiro 1994) — Meyer Schapiro (Schapiro 1994) IB-AR implementations typically require programmers to model the design space as well as the defning and distinguishing charac- teristics of an artistic style. Here, we see two general approaches which align with Kyprianidis et al.’s (2013) taxonomy as follows: III. Style Transfer using Neural Networks: Techniques that employ neural networks to separate and recombine the content and style of arbitrary inputs. Typically, loss func- tions are minimized iteratively to balance the components of style and content in the output (Gatys et al. 2016b), or train feed-forward neural networks for linear image trans- formation (Johnson et al. 2016a,b). III. 3 A SEMIOTIC STRUCTURE FOR ARTISTIC STYLE TRANSFER Prominent examples of heuristics-based algorithms are the stroke- based rendering approach of Hertzmann (1998), the cartoon pipeline of Winnemöller et al. (2006), and the watercolor system of Bousseau et al. (2006). For style transfer algorithms, by contrast, the litera- ture primarily distinguishes between EBR techniques that transfer color or texture (Kyprianidis et al. 2013). However—with the matu- ration of machine learning—we believe that this strict separation is no longer practicable because color and texture represent only two out of many variables to defne the composition of artistic styles, and deep learning enables NSTs to abstract from applica- tions (e. g., color/texture transfer). To this end, we conjecture that it is worthwile to provide a process-oriented taxonomy for EBR that refects how artistic style transfers are modeled or technically implemented. Given artistic works as ground-truth data, we ar- gue that three concepts may distinguish current and future EBR techniques (Figure 3): Semiotics deals with the study of symbols and how they commu- nicate image contents or information in a meaningful way (Bertin 2010). In artwork production, elements of design are considered to be fundamental aspects of pictorial semiotics (Rudner 1951), whose mutual impact defne the “composition” of an artwork, and thus its artistic style. Therefore, we believe that the transfer of proven design aspects and mechanisms of artwork production to modern media and imaging technologies, and the development of new artis- tic styles are key challenges for current and future research. In IB-AR theory (Hertzmann 2010), a semiotic structure that considers these design aspects and the mechanisms of interactive NPAR has not been formulated yet. We believe, however, that such a structure is essential to provide developers of NPAR techniques with the con- ceptual means to help them compose and extend artistic styles as well as evolve (neural) style transfers as interactive tools that ease the visual expression of artists, non-artists and scientists for illus- trative visualization (Gooch et al. 2010; Isenberg 2016; Salesin 2002). We thus formulate a semiotic structure that is based on graphic I. Style Transfer using Image Statistics: Techniques that balance content and style of two separate inputs using sta- tistical models. Prominent examples are histogram-based I. Style Transfer using Image Statistics: Techniques that balance content and style of two separate inputs using sta- tistical models. Prominent examples are histogram-based NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Semmo et al. 3 A SEMIOTIC STRUCTURE FOR ARTISTIC STYLE TRANSFER (2005) × × Pouli & Reinhard (2011) × × × Reinhard et al. (2001) × × Wu et al. (2013) × × × Xiao & Ma (2009) × × × Yang et al. (2017) × × × Image Statistics Ashikhmin (2003) × × × × Bénard et al. (2013) × × × × × × × × × × × Berger et al. (2013) × × × × Efros & Freeman (2001) × × Fiser et al. (2016) × × × × × × Hashimoto et al. (2003) × × × × Hertzmann (2001) × × Hertzmann et al. (2002) × × × × Lee et al. (2011) × × × × Image Analogies Wang et al. (2013) × × × Zhao & Zhu (2011) × × × × Anderson et al. (2016) × × × × Champandard (2016) × × × × × Chen & Schmidt (2016) × × Dumoulin et al. (2017) × × Gatys et al. (2016a) × × × Gatys et al. (2016b) × × × Gatys et al. (2016c; 2017) × × × × × × Gupta et al. (2017) × × × × Huang & Belongie (2017) × × × Iizuka et al. (2016) × × × Johnson et al. (2016a) × × × Li & Wand (2016) × × Liu et al. (2017) × × × × × Risser et al. (2017) × × × × × Ruder et al. (2016) × × × × Selim et al. (2016) × × × × × × Taigman et al. (2016) × × Ulyanov et al. (2016a) × × Neural Networks Ulyanov et al. (2017a) × × × × Ulyanov et al. (2016b) × × 1. Modeling Aspects: They deal with encoding real-world phenomena as color maps, and complementary information as feature maps (e. g., results of an image segmentation, saliency analysis, optical fow estimation) and geometry maps (e. g., depth). 1. Modeling Aspects: They deal with encoding real-world phenomena as color maps, and complementary information as feature maps (e. g., results of an image segmentation, saliency analysis, optical fow estimation) and geometry maps (e. g., depth). 2. Filtering Aspects: They are used to select and apply dif- ferent confgurations of composition variables according to image location, color, or feature. Filtering aspects should provide efective control to globally and locally adjust the level of abstraction. Examples are the luminance-based placement of stipples (Martín et al. 3 A SEMIOTIC STRUCTURE FOR ARTISTIC STYLE TRANSFER Input Images Reality / Virtuality Output Image Modeling 1. Modeling Aspects Color Maps Feature Maps Geometry Maps Perceives Location Color Feature 2. Filtering Aspects Implements Techniques Parameterizes Techniques Composition Variables Engineer / Domain Expert Consumer / Artist 5. Design Mechanisms Space / Texture Transparency Orientation Shading Shadows Crispness Resolution 4. Graphical Variables Form Shape Size Color 3. Graphical Elements Point Line Area 2D Element System / Design Instance 6. Perceptional Aspects Flatness Motion Coherence Temporal Continuity Pictorial Cues Configures / Controls Figure 4: Semiotic structure comprising graphical core variables and mechanisms that may be considered for style transfers. Engineer / Domain Expert Reality / Virtuality igure 4: Semiotic structure comprising graphical core variables and mechanisms that may be consi comprising graphical core variables and mechanisms that may be considered for style transfers. Figure 4: Semiotic structure comprising graphical core variables and mechanisms that may be considered for style transfers. Table 1: Overview of image-based artistic style transfer tech- niques and how they relate to semiotic aspects. Current NST techniques apparently lack to model graphical ele- ments/variables and provide interactive (creative) control. semiology principles of Bertin (2010) and MacEachren et al. (2012) that provide a theoretical foundation to visualization (Figure 4). The visual variables described by Bertin (2010) and MacEachren et al. (2012), however, cannot fully express the unique requirements of interactive media and systems (e. g., animation, video, interac- tive parameterizations). We thus extend the classifcation by the concepts of fltering and perception to consider interactivity, level of abstraction, and coherence/continuity issues of NPAR as well. This way, user involvement can be considered as a key mechanism for maintaining an iterative feedback loop between a system—as design instance implementing NPAR techniques—and the user’s requirements—as consumer/artist. In particular, it is directed to interactively adjust the semiotic structure that defnes aspects of modeling, fltering, composition and perception (Figure 4): Publication Color Maps Feature Maps Geometry Maps Location-based Filtering Color-based Filtering Feature-based Filtering Point / Line / Area Color / Brightness Form / Shape / Size Space / Texture Transparency Orientation Shading / Shadows Crispness / Resolution Coherence / Continuity Pictorial Cues User Interaction Arbelot et al. (2016) × × × × × × × Chang et al. (2015) × × × × × Kim et al. (2009) × × × × × × × × Maciejewski et al. (2008) × × × × × × × × Martín et al. 3 A SEMIOTIC STRUCTURE FOR ARTISTIC STYLE TRANSFER (2011) × × × × × × × × × Neumann Broth. (2005) × × Pouli & Reinhard (2011) × × × Reinhard et al. (2001) × × Wu et al. (2013) × × × Xiao & Ma (2009) × × × Yang et al. (2017) × × × Image Statistics Ashikhmin (2003) × × × × Bénard et al. (2013) × × × × × × × × × × × Berger et al. (2013) × × × × Efros & Freeman (2001) × × Fiser et al. (2016) × × × × × × Hashimoto et al. (2003) × × × × Hertzmann (2001) × × Hertzmann et al. (2002) × × × × Lee et al. (2011) × × × × Image Analogies Wang et al. (2013) × × × Zhao & Zhu (2011) × × × × Anderson et al. (2016) × × × × Champandard (2016) × × × × × Chen & Schmidt (2016) × × Dumoulin et al. (2017) × × Gatys et al. (2016a) × × × Gatys et al. (2016b) × × × Gatys et al. (2016c; 2017) × × × × × × Gupta et al. (2017) × × × × Huang & Belongie (2017) × × × Iizuka et al. (2016) × × × Johnson et al. (2016a) × × × Li & Wand (2016) × × Liu et al. (2017) × × × × × Risser et al. (2017) × × × × × Ruder et al. (2016) × × × × Selim et al. (2016) × × × × × × Taigman et al. (2016) × × Ulyanov et al. (2016a) × × Neural Networks Ulyanov et al. (2017a) × × × × Ulyanov et al. (2016b) × × Publication Color Maps Feature Maps Geometry Maps Location-based Filtering Color-based Filtering Feature-based Filtering Point / Line / Area Color / Brightness Form / Shape / Size Space / Texture Transparency Orientation Shading / Shadows Crispness / Resolution Coherence / Continuity Pictorial Cues User Interaction Arbelot et al. (2016) × × × × × × × Chang et al. (2015) × × × × × Kim et al. (2009) × × × × × × × × Maciejewski et al. (2008) × × × × × × × × Martín et al. (2011) × × × × × × × × × Neumann Broth. 4.1 Style Transfer using Image Statistics color blending via overdraw or layering, the orientation of graphical elements, the shading and lighting conditions, and the crispness/resolution of image features. Previous works deal with mechanisms for stylized shadows (DeCoro et al. 2007), the orientation and layering of curved brush strokes (Hertzmann 1998), and low-pass image flters. color blending via overdraw or layering, the orientation of graphical elements, the shading and lighting conditions, and the crispness/resolution of image features. Previous works deal with mechanisms for stylized shadows (DeCoro et al. 2007), the orientation and layering of curved brush strokes (Hertzmann 1998), and low-pass image flters. Most techniques using image statistics are designed to perform color transfers. Here we can only mention the most representative works and refer to Faridul et al.’s (2014) survey for a comprehensive overview. The majority of techniques equalizes the mean and vari- ance of a style and content image to control color distributions via luminance-based (Reinhard et al. 2001) or HSL-based (Neumann and Neumann 2005) histograms. Extensions integrate feature maps to consider local information as well, such as image segmentation (Wu et al. 2013; Xiao and Ma 2009), edge-aware texture descriptors (Arbe- lot et al. 2016), and semantics (Yang et al. 2017) to colorize grayscale images. With interactive methods it is also possible to maintain control over a set of colors that is involved in palette-based color transfers (Chang et al. 2015; Pouli and Reinhard 2011). 6. Perceptional Aspects: IB-AR typically aims to reproduce a hand-drawn look, where “distracting fickering and slid- ing artifacts” for animated scenes (e. g., virtual environ- ments, video) should be minimized (Bénard et al. 2011). Bénard et al. (2011) propose this challenge to be a concur- rent fulfllment of three goals: fatness, motion coherence, and temporal continuity. In addition, we conjecture that pictorial cues are important perceptional aspects because artists often carefully consider linear perspective, occlu- sion, and texture gradients to infer depth in their artworks. Another classical application for image statistics can be found in image stippling (Martín et al. 2017). Here, patterns are learned and applied through example using statistical texture measures (Kim et al. 2009; Maciejewski et al. 2008), modeling aspects such as the location of points (stipples), texture, shading, and resolution, which should depend on the spatial size of the output image. Martín et al. 4.1 Style Transfer using Image Statistics (2011) evolve these methods towards a “scale-dependent, example- based stippling technique that supports both low-level stipple place- ment and high-level interaction with the stipple illustration.” These methods are prime examples for how style transfers can be im- plemented on a primitive level, considering graphical elements explicitly rather than texture patches. The mutual impact of these aspects defne the individual artistic style and composition, and thus should be considered when design- ing and implementing style transfers. In particular, we argue that color and texture are only two semiotic aspects most techniques cur- rently serve. By contrast, a “successful” modeling approach should consider the distinctive design aspects and mechanisms involved in a particular artistic style, i. e., with respect to the rendering func- tions, optimization functions for image statistics and analogies, or loss functions for neural networks (Section 2). 2The overview gives a non-exhaustive general picture of how semiotics are considered in current research, we expect it to be extended with future research. 3 A SEMIOTIC STRUCTURE FOR ARTISTIC STYLE TRANSFER 2015), the location- dependent placement of contour lines (Cole et al. 2008), and feature-guided image fltering using orientation infor- mation (Kyprianidis and Döllner 2008). 3. Graphical Elements: These elements comprise rendering primitives such as points, lines, areas, and generalized 2D elements. They may also defne rendering paths or loca- tions for texturing, e. g., stippling, contour-lining, and the decoration of image segments. 4. Graphical Variables: They refer to the illusion of physical mass and density (form), image regions with well-defned boundaries (shape), the size of graphical elements, and color including brightness as phenomena of light and human vi- sual perception. Prominent examples refer to rendering with reduced color palettes and at multiple scales (Kypri- anidis et al. 2013). 5. Design Mechanisms: They deal with the surface charac- ter and relationships among image features with respect to position and direction (space/texture), transparency to infer Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Conv1_1 Conv4_1 Content Image Style Image Conv2_1 10 -4 10 -4 10 -5 10 -3 10 -2 Conv3_1 Conv2_1 Figure 5: Adjusting the level of abstraction: (top) using diferent relative weightings between content/style reconstruction, (bottom) matching the style representation with layer subsets of the VGG-Network. Images from Gatys et al. (2016b), © IEEE, used with permission. Style image by Wassily Kandinsky is in the public domain (source: Google Art Project). 10 -3 Content Image 10 -2 g Style Image C 2 1 Conv1 1 Conv4_1 Conv3_1 Conv2_1 Conv4_1 Conv1_1 Style Image Figure 5: Adjusting the level of abstraction: (top) using diferent relative weightings between content/style reconstruction, (bottom) matching the style representation with layer subsets of the VGG-Network. Images from Gatys et al. (2016b), © IEEE, used with permission. Style image by Wassily Kandinsky is in the public domain (source: Google Art Project). 4.3 Style Transfer using Neural Networks To discuss this subfeld, we draw on Gatys et al. (2016b) defnition of NSTs. Given a style image, a content image and a loss network, e. g., VVG-16 (Simonyan and Zisserman 2015), that is used to defne several loss functions to measure the diference between the output image and a target image, one can compute an output image by minimizing a weighted combination of the loss functions. Gatys et al. (2016b) initially defne perceptual loss functions that control fea- ture and style reconstructions to balance the components of content and style, and control spatial smoothness by regularizing the total variation, then solve the optimization problem using L-BFGS (Fig- ure 5). Besides texture transfers, this approach can be employed to perform sophisticated color transfers as well, e. g., to colorize grayscale images (Iizuka et al. 2016). Because this generalized style transfer employs back-propagation and combines learning and ap- plication in a single phase, we denote it as an iterative approach and distinguish it from the approach that separates learning from application to train a feed-forward neural network. Feed-forward Approaches. The solving of NSTs optimization prob- lems is computationally extensive. Some approaches thus provide approximations by computing the weights of a feed-forward neural network. Here, test images sets, e. g., ImageNet (Krizhevsky et al. 2012) or MS-COCO (Lin et al. 2014), are often used in a training phase performed once per artistic style, after which the obtained generative convolutional networks are used for linear image trans- formation (Johnson et al. 2016a,b; Ulyanov et al. 2016a, 2017a,b). Johnson et al. (2016a; 2016b) and Ulyanov et al. (2016a) showed that these networks can be three orders of magnitude faster than the iterative approach. The output quality of these approaches can be further improved by employing network layers for (adaptive) instance normalization (Huang and Belongie 2017; Ulyanov et al. 2016b) that align the mean and variance of features of the con- tent and style images. Conceptual limitations of these approaches, however, lie in the limited level of detail: style characteristics are generalized and not balanced for a unique style/content image pair (Figure 7). Alternative approaches either employ simpler loss functions with only local matching constraints, e. g., using a single layer of a pre-trained loss network (Chen and Schmidt 2016), or learn multiple styles or generative networks at once (Dumoulin et al. 2017; Zhang and Dana 2017) to improve versatility. Iterative Approaches. 4.2 Style Transfer using Image Analogies Most style transfer techniques defned by image analogies are based on texture transfers. Its basic idea is to copy image patches from a style image to a content image in a way that locally shares and minimizes pixel diferences in the content image, thereby using a smoothness constraint to provide similarity with adjacent tex- tures (Efros and Freeman 2001). Hertzmann (2001) defnes this as an optimization problem by learning the analogous transformation of a style/ground-truth image pair (A,A′) and applying it to a content image B to obtain a stylized output B′ such that A : A′ :: B : B′. In this section we now provide an overview2 of existing techniques with respect to the three concepts of style transfer and show how they consider aspects of the semiotic structure (Figure 4). We pro- vide a summary of this discussion in Table 1. NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Semmo et al. Color Control Size Control Input with Feature Map Location-based Style Control Figure 6: Adjustments of loss functions for NST to control graphical variables of the semiotic structure. Images © Gatys et al. (2016c), used with permission. Location-based Style Control Input with Feature Map Ashikhmin (2003) provides conditions for how to integrate user- defned feature maps to adjust parameter values of the texture trans- fer. The approach can also be used to learn stroke placements for contour-lining (Hertzmann et al. 2002) in domains such as portrait sketches using templates (Zhao and Zhu 2011) and modeling image features at multiple scales for level of abstraction rendering (Berger et al. 2013). Further extensions use edge and orientation information encoded in feature maps to control the placement of texture patches (Lee et al. 2011) and individual brush strokes (Wang et al. 2013), learn multiple styles and stroke patterns for portrait sketching and painting (Berger et al. 2013; Zhao and Zhu 2011), and estimate mo- tion using fow felds to stabilize temporal coherence (Hashimoto et al. 2003). Bénard et al. (2013) propose a sophisticated system for artists that performs style transfers for animations using orienta- tion, velocity, and geometry information of 3D models to direct the transfer with shading and lighting conditions, and to ensure tem- poral and style continuity. In addition, they support overdraw and partial transparency using a layering approach explicitly defned by the artist. 4.3 Style Transfer using Neural Networks Extensions of Gatys et al.’s (2016b) work primarily defne additional loss functions to control the output’s composition. MRFs loss functions, for instance, can be used as a local constraint to provide a more accurate texture patch matching and blending (Li and Wand 2016), histogram losses may produce outputs that statistically match style images more accurately (Risser et al. 2017), and a depth loss function to consider the spatial distribution of image features (Liu et al. 2017). Further, a temporal loss function based on optical fow can be used to stabilize temporal coherence when applied on a per-frame basis to video (Anderson et al. 2016; Gupta et al. 2017; Ruder et al. 2016; Selim et al. 2016). A few works controlled perceptual factors locally by considering feature maps using semantics-based image segmentation, such as to subdivide the optimization problem of NST to local image regions (Champandard 2016) or facial regions of portrait images (Selim et al. 2016) to 4.2 Style Transfer using Image Analogies Most of these works, however, typically consider only luminance- or color-guidance texture transfers, yet other informa- tion may be considered as well such as illumination as shown by Fišer et al. (2016) for stylized 3D models. Input with Feature Map Location-based Style Control Size Control Color Control Size Control Color Control Figure 6: Adjustments of loss functions for NST to control graphical variables of the semiotic structure. Images © Gatys et al. (2016c), used with permission. provide semantically more accurate transfers. Some enhancements also considered composition variables of the semiotic structure such as color, size, and location-based fltering by introducing control measures (Gatys et al. 2016a,c, 2017) (Figure 6). We see these works as a starting point to evolve NSTs as interactive tools for IB-AR that facilitate creative expression, which we discuss below. 5 A TECHNICAL RESEARCH AGENDA FOR NEURAL STYLE TRANSFER NST is a relatively new feld of research but has already shown promising results for generalized style transfers. We believe its future directions can be defned in the context of some of the grand challenges of NPAR (Gooch et al. 2010; Isenberg 2016; Salesin 2002), Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Input Image (Content) Style Image deepart.io Pikazo Ulyanov et al. (2017b) / BN Ulyanov et al. (2017b) / IN Figure 7: Comparison of iterative approaches for NST (deepart.io and Pikazo) with feed-forward approaches (BN: batch nor- malization, IN: instance normalization). Images © Ulyanov et al. (2017b), used with permission. Style Image Style Image Ulyanov et al. (2017b) / IN deepart.io Input Image (Content) Figure 7: Comparison of iterative approaches for NST (deepart.io and Pikazo) with feed-forward approaches (BN: batch nor- malization, IN: instance normalization). Images © Ulyanov et al. (2017b), used with permission. Figure 7: Comparison of iterative approaches for NST (deepart.io and Pikazo) with feed-forward malization, IN: instance normalization). Images © Ulyanov et al. (2017b), used with permission. of its analogy to patch-based texturing, divisionism can be modeled quite accurately by current loss functions. i. e., its combination with other IB-AR paradigms for providing algorithmic aesthetics, improving the fdelity in reproducing and extending artistic styles towards new forms of art, and its parama- terization to evolve as interactive tools that “support full design cycle” (Salesin 2002) and ease visualization tasks. With these chal- lenges and semiotics-oriented overview of Section 4 in mind, we thus propose the following technical research agenda. i. e., its combination with other IB-AR paradigms for providing algorithmic aesthetics, improving the fdelity in reproducing and extending artistic styles towards new forms of art, and its parama- terization to evolve as interactive tools that “support full design cycle” (Salesin 2002) and ease visualization tasks. With these chal- lenges and semiotics-oriented overview of Section 4 in mind, we thus propose the following technical research agenda. • Cubism depicts subjects using simplifed shapes and forms for composition, which are often portrayed using multiple perspectives. Here, NST techniques would need to infer geometric transformations and match geometric represen- tations, e. g., as practiced by Mital et al. (2013), in corre- spondence with the color similarity. • Pop Art typically composes images by thick outlines, bold solid colors and Ben-Day dots. Proposal 1: Semiotics-based Loss Functions Current NST techniques primarily depend on color statistics for style transfer, but model color as a mutual inclusion and efect of multiple composition variables. However, we believe that loss functions need to be defned for individual composition variables and controlled fltering-wise by providing modeling information that, e. g., encode how the size, shape, orientation, transparency, shading, and shadows are aligned with the contents of a style image. For instance, stroke-based rendering models the image composi- tion by placing, orienting, and layering individual brush strokes as graphical elements (Kyprianidis et al. 2013). Typically, techniques estimate image fow (Wang et al. 2004; Yan et al. 2008; Zeng et al. 2009) or derive local surface properties (Sloan et al. 2001) to guide brush strokes with the orientation of image features or the shading and lighting conditions (Fišer et al. 2016). Together with texture layering, e. g., of painterly art maps or dictionaries (Yan et al. 2008; Zeng et al. 2009), they provide better quality in preserving fne texture details and modeling style characteristics induced by form, shape, and orientation. For the latter, we believe a similar loss used for temporal consistency (Gupta et al. 2017; Ruder et al. 2016)—but based on image orientation information—could help guide the tex- ture transfer. There is also demand to explicitly model semiotic aspects that consider feature semantics. Here, Figure 8 exemplifes some limitations that NSTs currently face for three artistic styles: The examples of cubism and pop art demonstrate that the coupling of individual semiotic aspects with the semantics of content and style images requires sophisticated rule-based algorithms. Eventu- ally, this would lead to couple feature-level engineering with the architecture engineering approach of deep learning. 5 A TECHNICAL RESEARCH AGENDA FOR NEURAL STYLE TRANSFER Here, current NST tech- niques face multiple limitations in reproducing shape, pre- serving the semantic composition, and style characteristics such as the regularity and color inversion of halftoning. Proposal 2: Combination with IB-AR Paradigms Local efects and phenomena of traditional artistic media such as oilpaint, pencil, or watercolor at high-fdelity and resolution are still hard to reproduce by NSTs. Here, we believe that NSTs may be used as one of multiple processing stages in IB-AR, and combined with the knowledge and algorithms of other paradigms. NSTs would thus not operate at the lowest level of detail, but as a frst stage that introduces higher-level abstractions—to be followed by a low-level, established technique to simulate drawing media and their interplay with substrates. For instance, specialized line drawing algorithms can be used to detect and stylize (salient) edges, e. g., via diference-of-Gaussians (Winnemöller et al. 2012), edge- preserving fltering for noise reduction (Kyprianidis et al. 2013), and the constraints of stroke-based rendering to control the placement of graphical elements, e. g, based on luminance to direct (tonal) art maps for pencil rendering (Lee et al. 2006; Praun et al. 2001) or structure grids for feature-guided stippling (Son et al. 2011) to • Divisionism represents images by regularly aligned ren- dering primitives, e. g., brush strokes that optically com- pose image features when viewed from distance. Because • Divisionism represents images by regularly aligned ren- dering primitives, e. g., brush strokes that optically com- pose image features when viewed from distance. Because NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Semmo et al. Content Image Style Image / Divisionism Neural Style Transfer Style Image / Cubism Neural Style Transfer Style Image / Pop Art Neural Style Transfer Figure 8: Limitations of current NSTs for simulating artistic styles. Style images of Robert Delaunay and Juan Gris are in the public domain (source: Wikimedia Commons). Content image from Son et al. (2011) © Elsevier Inc, used with permission. Style Image / Pop Art Neural Style Transfer Neural Style Transfer Style Image / Divisionism Neural Style Transfer Style Image / Divisionism Style Image / Cubism Neural Style Transfer Style Image / Cubism Style Image / Pop Art Neural Style Transfer Style Image / Pop Art Content Image Content Image Figure 8: Limitations of current NSTs for simulating artistic styles. Style images of Robert Delaunay and Juan Gris are in the public domain (source: Wikimedia Commons). Content image from Son et al. (2011) © Elsevier Inc, used with permission. Content Image Style Image [Randy Glass] Neural Style Transfer Son et al. Proposal 2: Combination with IB-AR Paradigms (2011) Style Image [Igor Lukyanov] Neural Style Transfer Praun et al. (2001) / Lee et al. (2006) Figure 9: Comparison of NSTs with heuristics-based algorithms for stippling and hatching. Content image and stippling from Son et al. (2011) © Elsevier Inc, style images © Randy Glass and © Igor Lukyanov, all used with permission. Style Image [Igor Lukyanov] Neural Style Transfer Style Image [Igor Lukyanov] Neural Style Transfer Style Image [Randy Glass] Content Image Style Image [Randy Glass] Neural Style Transfer Son et al. (2011) Style Image [Igor Lukyanov] Neural St Figure 9: Comparison of NSTs with heuristics-based algorithms for stippling and hatching. C from Son et al. (2011) © Elsevier Inc, style images © Randy Glass and © Igor Lukyanov, all used wi Content Image Praun et al. (2001) / Lee et al. (2006) Proposal 4: Providing Interactivity avoid the artifacts from pure NSTs shown in Figure 9. In Figure 10 we show results of a case study, where image fltering is employed in a post-processing stage to NST to simulate local efects such as edge darkening, pigment density variation, and wet-in-wet of watercolors quite accurately (Bousseau et al. 2006; Wang et al. 2014), whereas fow-based Gaussian fltering with Phong shading is used to flter low-level noise and create smooth continuous oilpaint-like texture efects (Hertzmann 2002; Semmo et al. 2016b) In both cases we used the abstract style of Pablo Picasso’s “La Muse” to generate an efect of higher-level abstraction, before adding mentioned flters to simulate the respective low-level, local paint characteristics. Recently, Isenberg (2016) argued that EBR approaches have the potential to enable users to provide “both higher-level interaction and low-level control”—suggesting that this allows us to create both interaction environments for artists who need a wide range of low-level to high-level control and for non-artists whose inter- action needs are likely easier satisfed with high-level interactions such as the application of flters. Many traditional EBR approaches, however, have relied on a close relationship between input style and input context, e. g., for hatching (Gerl and Isenberg 2013). NSTs have the potential to address this very problem: styles are more easy to capture and thus the interactive application of stye becomes easier. So far, however, NST are typically treated like a “black box”, supporting only the high-level application of a captured style. To enable the interaction spectrum that Isenberg (2016) calls for, it would be necessary to integrate more local control. Artists need to be able to afect the result on a semantic level: controlling how larger regions are treated, change groups of marks, and even adjust a single mark. One approach could be to provide loss functions that operate on primitive-level and single design aspects as well, e. g., graphical elements such as brush strokes in a style image. For example, Figure 9 demonstrates how a purely global NST approach fails in several regions, and local control such as the change of an underlying directional feld, e. g., as practiced by (Salisbury et al. 1994), seems to be missing. Proposal 5: Supporting Visualization Tasks With respect to aesthetic evaluation, Salesin (2002) and Gooch et al. (2010) raised the issue of a “Turing Test” that determines if CG imagery can be indistinguishable from imagery produced by humans. While the utility of such a test is being debated (Hall and Lehmann 2013), some authors have included respective questions in their evaluations (Gatys et al. 2016b; Isenberg et al. 2006). Gatys et al. for instance, evaluated their NST technique (2016b) in a preliminary choice experiment, asking participants to fnd the hand-painted images in a set of 10 hand-painted/NST image pairs. The average of their 45,000 participants answered 6.1 image pairs correctly.3 With the further consideration of semiotic aspects, in particular fltering that includes semantics to resolve incoherences in color transfers, it would be great to gather more information such as response time and eye fxations to determine apparent locations or aspects of style incoherence—information that may be injected into the learning phase for improving a style transfer. Semiotics are inherently linked with the theory of (information) visualization (Bertin 2010). In particular, style transfers have been commonly used in illustrative visualization (Rautek et al. 2008), e. g., for the stylization of lines to depict fow (Everts et al. 2015), to make phenomena—hidden in complex data sets—visible to the human mind. However, efective visualization must also “enable analysis of the supplied information, while easing the cognitive burden of a user” (Gooch et al. 2010). NSTs based on deep CNNs emulate functionalities of the visual cortex by solving tasks through hierar- chical processing (DiCarlo et al. 2012), but need to be performed in a context-dependent manner, e. g., with respect to a user’s task and data domain, for efective visualization. Here, we imagine the development of toolboxes or palettes of illustration styles that can be interactively applied by professional illustrators, in a way that considers an interaction spectrum from low-level to high-level con- trols (Isenberg 2016). For example, a palette for computer-supported hatching and stippling could be provided that alleviates some of the tediousness of manual processes, but that includes support for higher-level illustration processes, e. g., (Martín et al. 2011), where NSTs could suggest regions to be fltered or regions to be contrast- adjusted. The layers of deep CNNs that capture multiple levels of abstraction could be interactively used for this purpose to direct the interactive visualization/illustration process. Proposal 3: New Forms of Styles Gooch et al. (Gooch et al. 2010) provided an overview of NPAR re- search through Heinlein’s maturation model, and argue that NPAR has left the frst stage—emulating and imitating artistic styles—, evolved towards the second stage by optimizing the performance of the (used) technology, and is about to move towards the last stage, where the technology becomes seamless and almost transparent. In this respect, we believe that NST provides new opportunities for the frst two stages, but needs to “incorporate elements such as interac- tion, collaboration, human perception and cognition” (Gooch et al. 2010) to approach the third stage. In particular, here we see two potential use cases for NST. First, modifying learned artistic styles by providing mechanisms to specify transfer or loss functions that change particular design aspects or variables. Second, performing a style transfer by taking rule-based algorithms into account, i. e., to learn styles not only from style images but also a set of descriptions how an artistic style should look like, which makes new forms of styles—that have never been seen before—practicable. Moreover, it is important to consider the input from several style images, which is technically demonstrated by Johnson et al. (2016a; 2016b) for blending multiple styles. This could be extended to either learn a particular technique/style or even an artist’s design prin- ciples more reliably, or it could be used to combine two diferent NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? Neural Style Transfer Neural Style Transfer with Post-process Watercolor Rendering Neural Style Transfer with Post-process Oilpaint Filtering Content Image Figure 10: Post-process image fltering to reduce low-level noise and inject paint characteristics. NST results are combined with watercolor rendering (Bousseau et al. 2006; Wang et al. 2014) and oilpaint fltering (Semmo et al. 2016b). Content image by Frank Köhntopp is in the public domain. Figure 10: Post-process image fltering to reduce low-level noise and inject paint characteristics. NST results are combined with watercolor rendering (Bousseau et al. 2006; Wang et al. 2014) and oilpaint fltering (Semmo et al. 2016b). Content image by Frank Köhntopp is in the public domain. for portrait images (Selim et al. 2016)), and data-domain specifc design mechanisms such as generalization (MacEachren 1995). styles in the same target image. Proposal 3: New Forms of Styles For example for the latter, illustra- tions that combine diferent depiction styles to steer attention and create focus and context view would be an important application domain. Such an approach, however, would need local control or a semantic/semiotic processing of the content image by the NST algorithm, e. g., as is partially practiced by Gatys et al. (2016c; 2017) using feature maps, and interactive performance for immediate vi- sual feedback, but which is currently a strong limitation of iterative NST techniques. 3According to Leon Gatys in his talk at CVPR 2016 on “Image Style Transfer Using Convolutional Neural Networks” (Gatys et al. 2016b). Proposal 6: Evaluation The evaluation of aesthetics and practical benefts for illustration or visualization tasks remains an important issue in IB-AR (Gooch 2010; Hall and Lehmann 2013; Hertzmann 2010; Isenberg 2013). For efective comparison of NST techniques, we believe there is demand for a standardized benchmark image set such as the general NPAR set provided by Mould and Rosin (2016). 5Tate IK Prize 2016. http://www.tate.org.uk/about/projects/ik-prize-2016. Last fol- lowed: 04/09/2017. 6Adobe Artistic Eye. http://blogs.adobe.com/conversations/2017/03/ de-youngsters-photos-get-the-look-of-masterpieces.html. Last followed: 04/09/2017. 4Stephen Merity. 2016. In deep learning, architecture engineering is the new feature engineering. http://smerity.com/articles/2016/architectures_are_the_new_feature_ engineering.html. Last followed: 04/09/2017. Proposal 5: Supporting Visualization Tasks Finally, we believe that, with the generalized application of NSTs, more complex artis- tic styles of several visualization domains could be served, such as medical imaging or cartography, but which requires NSTs to consider the semantics of style and content images (e. g., as shown With respect to task efciency, studies are required to determine if NSTs only copy low-level style aspects or if they also maintain higher-level semantics of image contents. These studies could also be used to determine to what degree NSTs introduce abstraction, whether the degree of abstraction can be intentionally controlled, and how it can be seamlessly interpolated for an interactive appli- cation as discussed above. In particular, the meaningful interaction with NSTs as tools for artists or scientists (e. g., with respect to illustrative visualization) requires investigation. NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Semmo et al. Painting from ‘Loving Vincent’ Content Style transfer from deepart.io Style Figure 11: Comparison between emulating an artistic style via painting (oil on canvas) and a NST. Results from “Loving Vincent” © BreakThru Films, used with permission. Style image by Vincent van Gogh is in the public domain. Style transfer from deepart.io Style Painting from ‘Loving Vincent’ Content 6 APPLICATIONS The shift from feature engineering towards architecture engineer- ing4 of deep learning enables IB-AR to abstract from input data, and thus increase the general applicability in highly dynamic envi- ronments. Here, we see the following potentials for using NSTs. 7 CONCLUSION Deep learning has opened new possibilities for IB-AR to make a gen- eralized style transfer practicable. On the one hand, NSTs provide new potentials for using IB-AR in context-sensitive and creative application domains, such as casual creativity apps for mobile ex- pressive rendering and production tools for feature flms. On the other hand, NSTs currently provide only “black box” solutions from a HCI point-of-view: research (so far) has mainly focused on tuning hyperparameters of deep neural networks. To this end, we propose a semiotic structure to provide developers of NST techniques with the conceptual means of artworks production to help them compose and extend artistic styles, as well as consider design aspects and mechanisms for evolving NSTs as interactive tools. In particular, we hope that this structure helps researchers to identify requirements for semiotics-based loss functions, combine NSTs with the knowl- edge of other IB-AR paradigms, promote completely new artistic styles, and assist applications in illustrative visualization. Casual Creativity NSTs have particularly enriched casual creativity applications (Win- nemöller 2013) in ubiquitous environments such as mobile comput- ing. This domain has largely been devoted to image fltering and processing to date, providing only constrained efects (Dev 2013). Prominent examples are the web service deepart.io and the iOS app Prisma—attracting 60 million users in three weeks—, which also started to establish their own social media communities for sharing and commenting on stylized outputs. We believe, how- ever, that these apps have to evolve from “black box” solutions towards user-centric tools (Winnemöller 2013) to further promote visual expression. Here, a metaphor for on-screen parameter paint- ing (Semmo et al. 2016a) may be used to tune hyperparameters of neural networks, while hiding the computational complexity. Style transfer from deepart.io Painting from ‘Loving Vincent’ Painting from ‘Loving Vincent’ Figure 11: Comparison between emulating an artistic style via painting (oil on canvas) and a NST. Results from “Loving Vincent” © BreakThru Films, used with permission. Style image by Vincent van Gogh is in the public domain. Art Production Machine learning has gathered particular interest as an interactive component of exhibition and art installations, e. g., Tate Modern’s IK Prize 2016 winner Recognition5 uses pattern recognition to compare art to photojournalism. For instance, Adobe’s Artistic Eye6 uses NSTs to enable children transform their self-portraits into artistic renditions in the style of a museum’s exhibits, while Becattini et al. (2016) combined NSTs with art explorations, allowing users to scan exhibits and transfer their style to user-defned images. Salesin (2002) had envisioned the support of artists to be a major goal of NPAR, i. e., developing tools that make their life easier but that do not constrain their capabilities in visual expression (Isen- berg 2016). We discussed in Section 5 that this requires NSTs to evolve as interactive tools. One example is the system by Fišer et al. (2016) in which artists are able to draw over a printed stencil, while their individual style is transferred in real-time onto 3D mod- els, dealing with proper light propagation and auto-completion. Another example is the system for watercolor rendering with art- directed control of Montesdeoca et al. (2016; 2017), where the efects shown in Figure 10 (among others) can be controlled via on-screen painting. Here, a long-term goal would be to integrate NSTs in the production pipeline of feature flms, e. g., as evaluated by Joshi et al. (2017) for Come Swim, reaching a quality level to assist the laborious production of fully painted animated flms such as Loving Vincent (Mackiewicz and Melendez 2016) (Figure 11), e. g., with respect to temporal coherence and the placement of graphical ele- ments such as brush strokes. Style Transfer using Image Statistics Benoit Arbelot, Romain Vergne, Thomas Hurtut, and Joëlle Thollot. 2016. Automatic Texture Guided Color Transfer and Colorization. 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State of the “Art”: A Taxonomy of Artistic Stylization Techniques for Images and Video. IEEE Transactions on Visualization and Computer Graphics 19, 5 (May 2013), 866–885. doi: 10.1109/TVCG.2012.160 Teaching Art Classes We see potentials to use NSTs for teaching purposes, i. e., to help study and explore artistic styles of famous artists or epochs. In particular, we consider semiotics-oriented loss functions (Section 5) as a key goal for providing algorithmic support at a high-level (e. g., texture transfer) and low-level (e. g., primitive-level transfer). This way, interactive art explorations could be feasible for children using (semi-)automatic transfers, e. g., using the semantics of two- bit doodles (Champandard 2016). A similar scenario can also be created for adults who could explore, e. g., the modeling, painting, and mixing of style invariances (e. g., brush size, pattern, etc.). Finally, we argue that semiotics can be considered for defning artistic style and used to systematically evaluate NST techniques. Eventually, this evaluation should also account for the application space, level of interactivity, and audience including the user’s con- text and environment, skills and competence, and the purpose of NPAR’17, July 28-29, 2017, Los Angeles, CA, USA NPAR’17, July 28-29, 2017, Los Angeles, CA, USA Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? Neural Style Transfer: A Paradigm Shif for Image-based Artistic Rendering? artistic rendering, e. g., the user’s task—conditions that afect the “success” of a NST. 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Qeios · Definition, February 2, 2020 Open Peer Review on Qeios Body Weight Gain Reason Not Done National Cancer Institute National Cancer Institute Qeios ID: 6PM4KG · https://doi.org/10.32388/6PM4KG Source National Cancer Institute. Body Weight Gain Reason Not Done. NCI Thesaurus. Code C119770. The explanation given as to why body weight gain was not assessed. Qeios ID: 6PM4KG · https://doi.org/10.32388/6PM4KG 1/1
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Retinal Layers Changes in Human Preclinical and Early Clinical Diabetic Retinopathy Support Early Retinal Neuronal and Müller Cells Alterations
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Hindawi Publishing Corporation Journal of Diabetes Research Volume 2013, Article ID 905058, 8 pages http://dx.doi.org/10.1155/2013/905058 Hindawi Publishing Corporation Journal of Diabetes Research Volume 2013, Article ID 905058, 8 pages http://dx.doi.org/10.1155/2013/905058 Hindawi Publishing Corporation Journal of Diabetes Research Volume 2013, Article ID 905058, 8 pages http://dx.doi.org/10.1155/2013/905058 Stela Vujosevic1 and Edoardo Midena1,2 1 Department of Ophthalmology, University of Padova, Via Giustiniani 2, 35128 Padova, Italy 2 Fondazione G. B. Bietti, Via Livenza 3, 00198 Roma, Italy 1 Department of Ophthalmology, University of Padova, Via Giustiniani 2, 35128 Padova, Italy 2 Fondazione G. B. Bietti, Via Livenza 3, 00198 Roma, Italy Correspondence should be addressed to Edoardo Midena; edoardo.midena@unipd.it Received 8 March 2013; Revised 17 May 2013; Accepted 20 May 2013 Academic Editor: Ahmed M. Abu El-Asrar Copyright © 2013 S. Vujosevic and E. Midena. 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. Purpose. To evaluate the changes in thickness of individual inner and outer macular and peripapillary retinal layers in diabetes. Methods. 124 subjects (124 eyes) were enrolled: 74 diabetics and 50 controls. Macular edema, proliferative diabetic retinopathy (DR), any intraocular treatment and refractive error > 6 diopters were the main exclusion criteria. Full ophthalmic examination, stereoscopic fundus photography, and spectral domain-OCT were performed. After automatic retinal segmentation (layering) in 5 layers, the thickness of each layer was calculated, and values compared among groups. Results. Thirty patients had no DR, 44 patients had non proliferative DR. A significant increase of inner plexiform and nuclear layers was found in DR eyes versus controls (𝑃< 0.001). A significant decrease (𝑃< 0.01) of retinal nerve fiber layer (RNFL) and at specific sites of retinal ganglion cell layer (𝑃= 0.02) was documented in the macula. In the peripapillary area there were no differences between diabetics and controls. Conclusions. Decreased RNFL thickness and increased INL/OPL thickness in diabetics without DR or with initial DR suggest early alterations in the inner retina. On the contrary, the outer retina seems not to be affected at early stages of DM. Automatic intraretinal layering by SD-OCT may be a useful tool to diagnose and monitor early intraretinal changes in DR. 1. Introduction according to which neurodegeneration precedes the vas- cular one is confirmed by some electrophysiological and psychophysical studies, which show that the alterations are present even before the microvascular damage becomes ophthalmoscopically or angiographically visible. Such retinal function alterations mainly consist in contrast sensitivity loss, altered color perception, and failure of retinal recovery time [5, 6]. Moreover, it has been observed that in diabetic mice the oscillatory potentials of the electroretinogram (ERG) have increased peak latencies and/or reduced amplitudes, suggesting a compromised inner retinal function secondary to neuronal transmission alterations or to the combined loss of amacrine and ganglion cells [7]. Diabetic retinopathy (DR) is the first cause of visual impair- ment and blindness in the adult working-age population [1]. For a long period of time, DR has been considered primarily a retinal microvascular disorder caused by the direct effects of hyperglycemia and by the metabolic path- ways it activates [2]. Nevertheless, some recent studies have demonstrated that retinal neurodegeneration (the result of a negative balance between neurotoxic and neuroprotective factors) is present even before the development of clinically detectable microvascular damage. Retinal neurodegeneration may therefore represent an early event in the pathophysiol- ogy of DR and may anticipate the onset of microvascular changes [2–4]. The term neurodegeneration used in this paper encompasses pathologic phenomena affecting both the pure neuronal component and the glial one. The hypothesis During the course of DR, apoptotic cells have been observed in all retinal layers, suggesting the involvement of different types of neurons [8]. Numerous studies have evidenced that diabetes, through the alteration of different 2 Journal of Diabetes Research Journal of Diabetes Research 2.1.2. Fundus Photography. Color stereoscopic fundus pho- tographs (7 ETDRS fields) were taken after an adequate dilatation by a trained photographer using the same TOP- CON TRC 50IA 35 degree fundus camera (TOPCON, Tokyo, Japan). Diabetic retinopathy was graded as no DR and as nonproliferative DR mild or moderate DR (NPDR) by two independent graders experienced in grading DR. metabolic pathways, induces functional deficits and even the loss of different types of retinal cells which cover from the inner to the outer retinal cells: ganglion cells, bipolar cells, amacrine cells, horizontal cells, and eventually photorecep- tors [9]. Different authors reported a decrease in retinal thickness in diabetic eyes with or without clinical signs of DR com- pared to normal subjects [10–13]. Biallosterski et al. 1. Introduction found a significant reduction in pericentral macular thickness in 53 diabetic patients with mild nonproliferative DR [10]. Van Dijk et al. have demonstrated by spectral domain optical coherence tomography (SD-OCT) a decrease in the inner retinal thickness in the macula in diabetics with mild DR, suggesting that this phenomenon might be firstly due to ganglion cells loss in the pericentral areas and secondly to retinal nerve fiber layer (RNFL) thinning in the peripheral macula [14, 15].h 2.1.3. Spectral Domain OCT. All eyes were examined with spectral domain optical coherence tomography (SD-OCT, RS-3000, NIDEK, Gamagori, Japan). This instrument has a light source of 880 nm wavelength. Each eye was exam- ined, after pupillary dilation, both in the macula and the peripapillary area. The following scanning protocols were used: “Macula Map” in the macula and “Disc Circle” in the peripapillary area.h y The Macula Map scan pattern evaluates 6 × 6 mm area centered on the fovea with 64 horizontal B-scan lines, each consisting of 1024 A-scans per line. For each SD-OCT linear scan, an automatic algorithm has individuated 5 different retinal layers based on the different shades of gray corre- sponding to the reflectivity indexes of each layer, which include from inside to outside the following: inner limiting membrane + nerve fiber layer (ILM + RNFL); ganglion cell layer + inner plexiform layer (GCL + IPL); inner nuclear layer + outer plexiform layer (INL + OPL); outer nuclear layer + external limiting membrane (ONL + ELM); and inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE). Retinal thickness was automatically calculated in the 9 ETDRS areas (consisting in a central circular zone with a 1-mm diameter, representing the foveal area and inner and outer rings of 3 and 6 mm diameter, resp.). The inner and the outer rings are divided into four quadrants: superior, nasal, inferior, and temporal. Mean retinal thickness and mean thickness of each of the five retinal layers in each of the nine ETDRS subfields were recorded (Figures 1(a) and 1(b)). The main purpose of this study was to identify in vivo, by SD-OCT, the changes in thickness of selected retinal layers both in the macula and the peripapillary area in diabetic patients without DR or with early stages of DR (mild and moderate nonproliferative DR) versus normal subjects. 2. Material and Methods One hundred twenty-four subjects (74 diabetic patients and 50 normal subjects) were included in this study. One eye of each subject was used for the spectral domain optical coherence tomography (SD-OCT) analysis. The exclusion criteria were as follows: proliferative DR, macular edema, any type of previous retinal treatment (macular laser photocoagu- lation, vitrectomy, intravitreal steroids, and/or antiangiogenic drugs), any intraocular surgery, refractive error > 6D, previ- ous diagnosis of glaucoma, ocular hypertension, uveitis, other retinal diseases, neurodegenerative disease (e.g., Alzheimer’s, Parkinson’s, and dementia), and significant media opacities that precluded fundus examination or imaging. A written consent form was obtained from all patients as well as the approval from our institutional ethics committee. The study was conducted in accordance with the tenets of the Declaration of Helsinki. In the peripapillary area, a circle scan centered on the optic disc (3.46 mm diameter, “Disc Circle” option) was used. Peripapillary retinal thickness was automatically measured by the instrument in the temporal, superior, nasal, and inferior quadrants (Figure 1(c)). Each subject underwent a complete ophthalmic examina- tion, with determination of best corrected visual acuity, ante- rior segment examination, Goldman applanation tonometry, indirect ophthalmoscopy, and 90D lens biomicroscopy. Then, SD-OCT and fundus photography were obtained. If any instrument error in the automatic segmentation of retinal layers was documented, the manual correction con- sisted in the repositioning into proper place of the incorrectly placed points (using high magnification images), in order to redefine the retinal profile. Each grader was blinded to clinical data of all examined eyes. 2.1. Study Procedures 2.1.4. Statistics. Age, spherical equivalent, IOP, and visual acuity were compared among groups by means of analysis of variance (ANOVA); The mean values of retinal layers’ thickness in each group, both in macula and peripapillary area, were confronted using the repeated measures analysis of variances (ANOVA-RM). In cases of significant results (𝑃< 0.05), the ANOVA-RM was followed by the Bonferroni multiple comparisons post hoc test. All statistical analyses 2.1.1. Visual Acuity. Best corrected distance visual acuity (BCVA) for each eye was measured by a trained examiner using standard Early Treatment Diabetic Retinopathy Study (ETDRS) protocol at 4-meter distance with a modified ETDRS distance chart transilluminated with a chart illumi- nator (Precision Vision) [16]. Visual acuity was scored as the total number of letters read correctly and converted to the logarithm of the minimum angle of resolution (logMar). 2.1.1. Visual Acuity. Best corrected distance visual acuity (BCVA) for each eye was measured by a trained examiner using standard Early Treatment Diabetic Retinopathy Study (ETDRS) protocol at 4-meter distance with a modified ETDRS distance chart transilluminated with a chart illumi- nator (Precision Vision) [16]. Visual acuity was scored as the total number of letters read correctly and converted to the logarithm of the minimum angle of resolution (logMar). 2.1.4. Statistics. Age, spherical equivalent, IOP, and visual acuity were compared among groups by means of analysis of variance (ANOVA); The mean values of retinal layers’ thickness in each group, both in macula and peripapillary area, were confronted using the repeated measures analysis of variances (ANOVA-RM). In cases of significant results (𝑃< 0.05), the ANOVA-RM was followed by the Bonferroni multiple comparisons post hoc test. All statistical analyses 3 3 Journal of Diabetes Research (b) ILM NFL/GCL IPL-INL OPL-ONL IS/OS RPE-BM RNFL GCL IPL INL OPL ONL IS/OS RPE ELM (a) (c) 90∘ Figure 1: Spectral domain OCT automatic segmentation of retinal layers in the macula ((a) and (b)) and in the peripapillary area (c). In the macula the segmentation is performed on the linear scan (b) and in the peripapillary area on the circular scan around the optic disc (c). were performed with SAS 9.2 for Windows, SAS (Cary, NC, USA). were performed with SAS 9.2 for Windows, SAS (Cary, NC, USA). were performed with SAS 9.2 for Windows, SAS (Cary, NC, USA). and inferior inner quadrant (IIM, 𝑃= 0.01) in no DR group versus controls. RNFL thickness was significantly decreased in the SOM (𝑃< 0.0001), NOM (𝑃= 0.0003), IOM (𝑃= 0.001), TOM (𝑃= 0.01), and SIM (𝑃= 0.003), in the NPDR group versus controls (Figure 2(a)).i 2.1. Study Procedures Six lines determine 5 retinal layers which from inside out are as follows: inner limiting membrane + nerve fibre layer (ILM + RNFL); ganglion cell layer + inner plexiform layer (GCL + IPL); inner nuclear layer + outer plexiform layer (INL + OPL); outer nuclear layer + external limiting membrane (ONL + ELM); and inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE) (a). (b) (c) 90∘ ILM NFL/GCL IPL-INL OPL-ONL IS/OS RPE-BM RNFL GCL IPL INL OPL ONL IS/OS RPE ELM (a) 90∘ (b) (a) (c) Figure 1: Spectral domain OCT automatic segmentation of retinal layers in the macula ((a) and (b)) and in the peripapillary area (c). In the macula the segmentation is performed on the linear scan (b) and in the peripapillary area on the circular scan around the optic disc (c). Six lines determine 5 retinal layers which from inside out are as follows: inner limiting membrane + nerve fibre layer (ILM + RNFL); ganglion cell layer + inner plexiform layer (GCL + IPL); inner nuclear layer + outer plexiform layer (INL + OPL); outer nuclear layer + external limiting membrane (ONL + ELM); and inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE) (a). Table 1: Demographic characteristics of the patients. Control Diabetic Grade of DR No DR NPDR Patients, number 50 74 30 44 Mean age, yrs (SD) 55.8 (13.0) 56.4 (12.7) 56.1 (12.8) 55.9 (12.6) Mean diabetes duration, yrs (SD) — 5.9 (4.1) 18.6 (10.3) Mean HbA1c % (SD) — 8.1 (1.4) 7.8 (0.8) 8.2 (1.5) Visual acuity, logMAR (SD) 0.003 (0.020) 0.011 (0.039) 0.024 (0.066) IOP, mmHg (SD) 15.3 (1.9) 16.1 (3.4) 16.8 (3.2) SE, (SD) −0.04 (1.5) 0.46 (1.1) 0.42 (1.0) SD: standard deviation; No DR: diabetic patients without retinopathy; NPDR: non proliferative diabetic retinopathy; IOP: intraocular pressure; SE: spherical equivalent. Table 1: Demographic characteristics of the patients. 3. Results In the macula, ILM + RNFL thickness was significantly decreased in the superior outer quadrant (SOM, 𝑃< 0.0001), inferior outer quadrant (IOM, 𝑃< 0.0001), temporal outer quadrant (TOM, 𝑃= 0.01), nasal outer quadrant (NOM, 𝑃= 0.0003), superior inner quadrant (SIM, 𝑃= 0.0003), INL/OPL thickness was significantly increased in the central OCT subfield (CSF, 𝑃= 0.004), SIM (𝑃= 0.003), NIM (𝑃= 0.04), TIM (𝑃= 0.0018), SOM (𝑃= 0.002), IOM (𝑃= 0.04), and TOM (𝑃= 0.001) in the NPDR group versus controls (Figure 2(c)).hf There was no difference in the ONL/ELM and IS/OS – RPE thickness between diabetics with and without DR and controls (Figures 2(d) and 2(e)).i In the peripapillary area, retinal thickness was signifi- cantly decreased with increasing age (𝑃= 0.0021) and in 4 Journal of Diabetes Research 30 40 50 60 70 80 90 100 CSF SIM NIM IIM TIM SOM NOM IOM TOM CSF SIM NIM IIM TIM SOM NOM IOM TOM CSF SIM NIM IIM TIM SOM NOM IOM TOM Control No DR NPDR 30 40 50 60 70 80 90 100 110 Control (C) No DR (ND) NPDR (DR) 20 30 40 50 60 70 80 Control (C) No DR (ND) NPDR (DR) (𝜇) (𝜇) (𝜇) (b) (d) (e) ∗= P < 0.05 Inner ring Outer ring Inner ring Outer ring Inner ring Outer ring GCL + IPL ONL + ELM IS/OS + RPE control), diabetics without retinopathy (no DR), and dia by spectral domain OCT in 9 ETDRS areas in the macu l layer + inner plexiform layer (GCL + IPL); (c) inner nu miting membrane (ONL + ELM); and (e) inner segment/ ) indicates statistically significant values; CSF: central su quadrant; IIM: inferior inner quadrant; TIM: temporal uadrant; IOM: inferior outer quadrant; TOM: temporal 30 40 50 60 70 80 90 100 CSF SIM NIM IIM TIM SOM NOM IOM TOM (𝜇) Inner ring Outer ring GCL + IPL 30 40 50 60 70 CSF SIM NIM IIM TIM SOM NOM IOM TOM CSF SIM NIM IIM TIM SOM NOM IOM TOM CSF SIM NIM IIM TIM SOM NOM IOM TOM Control No DR NPDR 30 40 50 60 70 80 90 CSF SIM NIM IIM TIM SOM NOM IOM TOM Control (C) No DR (ND) NPDR (DR) 0 10 20 30 40 50 60 CSF SIM NIM IIM TIM SOM NOM IOM TOM Control (C) No DR (ND) NPDR (DR) 30 40 50 60 70 80 90 100 110 Control (C) No DR (ND) NPDR (DR) 20 30 40 50 60 70 80 Control (C) No DR (ND) NPDR (DR) (𝜇) (𝜇) (𝜇) (𝜇) (𝜇) (a) (c) (b) (d) (e) ∗= P < 0.05 ∗= P < 0.05 ∗= P < 0.05 ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ C-DR C-ND C-DR C-ND C-DR C-ND C-DR C-ND C-ND C-ND Inner ring Inner ring Outer ring Outer ring Inner ring Outer ring Inner ring Outer ring Inner ring Outer ring ILM + RNFL INL + OPL C-DR C-DR C-DR C-DR C-DR C-DR C-DR ND-DR ONL + ELM IS/OS + RPE Figure 2: Graphs showing specific retinal layer thickness in normal subjects (control), diabetics without retinopathy (no DR), and diabetics with nonproliferative diabetic retinopathy (NPDR) determined automatically by spectral domain OCT in 9 ETDRS areas in the macula. 3. Results (a) Inner limiting membrane + nerve fibre layer (ILM + RNFL); (b) ganglion cell layer + inner plexiform layer (GCL + IPL); (c) inner nuclear layer + outer plexiform layer (INL + OPL); (d) outer nuclear layer + external limiting membrane (ONL + ELM); and (e) inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE). (∗) indicates statistically significant values; CSF: central subfield thickness; SIM: superior inner quadrant in the macula; NIM: nasal inner quadrant; IIM: inferior inner quadrant; TIM: temporal inner quadrant; SOM: superior outer quadrant in the macula; NOM: nasal outer quadrant; IOM: inferior outer quadrant; TOM: temporal outer quadrant. 3. Results 30 40 50 60 70 80 90 CSF SIM NIM IIM TIM SOM NOM IOM TOM Control (C) No DR (ND) NPDR (DR) 0 10 20 30 40 50 60 CSF SIM NIM IIM TIM SOM NOM IOM TOM Control (C) No DR (ND) NPDR (DR) (𝜇) (𝜇) (a) (c) ∗= P < 0.05 ∗= P < 0.05 ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ C-DR C-ND C-DR C-ND C-DR C-ND C-DR C-ND C-ND C-ND Inner ring Outer ring Inner ring Outer ring ILM + RNFL INL + OPL C-DR C-DR C-DR C-DR C-DR C-DR C-DR ND-DR 30 40 50 60 70 80 90 CSF SIM NIM IIM TIM SOM NOM IOM TOM Control (C) No DR (ND) NPDR (DR) 0 10 20 30 40 50 60 CSF SIM NIM IIM TIM SOM NOM IOM TOM Control (C) No DR (ND) NPDR (DR) (𝜇) (𝜇) (a) (c) ∗= P < 0.05 ∗= P < 0.05 ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ ∗ C-DR C-ND C-DR C-ND C-DR C-ND C-DR C-ND C-ND C-ND Inner ring Outer ring Inner ring Outer ring ILM + RNFL INL + OPL C-DR C-DR C-DR C-DR C-DR C-DR C-DR ND-DR 0 10 20 30 40 50 60 CSF SIM NIM IIM TIM SOM NOM IOM TOM (𝜇) ∗= P < 0.05 ∗ ∗ ∗ ∗ ∗ ∗ C-DR C-ND C-DR C-ND C-DR C-ND C-DR C-ND C-ND C-ND Inner ring Outer ring ILM + RNFL CSF SIM NIM IIM TIM SOM NOM IOM TOM 30 40 50 60 70 80 90 100 110 (𝜇) (b) ∗= P < 0.05 Inner ring Outer ring ONL + ELM 30 40 50 60 70 80 90 CSF SIM NIM IIM TIM SOM NOM IOM TOM (𝜇) ∗= P < 0.05 ∗ ∗ ∗ ∗ ∗ ∗ ∗ Inner ring Outer ring INL + OPL C-DR C-DR C-DR C-DR C-DR C-DR C-DR ND-DR CSF SIM NIM IIM TIM SOM NOM IOM TOM 20 30 40 50 60 70 80 (𝜇) Inner ring Outer ring IS/OS + RPE (c) (e) Figure 2: Graphs showing specific retinal layer thickness in normal subjects (control), diabetics without retinopathy (no DR), and diabetics with nonproliferative diabetic retinopathy (NPDR) determined automatically by spectral domain OCT in 9 ETDRS areas in the macula. 3. Results GCL/IPL thickness was not statistically significantly dif- ferent between diabetics and controls, although there was a trend toward decreasing thickness in no DR group versus controls in the inner and outer rings’ quadrants. GCL/IPL thickness was significantly decreased only in the NOM and SOM (𝑃= 0.02, for both) in diabetics with no DR versus NPDR group (Figure 2(b)).i Of 124 enrolled subjects 74 were diabetics, (49 males and 25 females). Of 50 normal subjects, 21 were males and 29 females. Mean age of diabetics was 56.4 ± 12.7 years (range: 31–83 years); mean age of controls was 55.8 ± 13 years (range: 25–80 years). Thirty eyes were graded as no DR and 44 eyes as nonproliferative DR (NPDR). Eighteen patients (24.32%) had type 1 DM and 56 (75.68%) had type 2 DM. Mean HbA1c was 8.1% (range: 5.3%–11%). There was no significant difference in age (ANOVA, 𝑃= 0.98), spherical equivalent (ANOVA, 𝑃= 0.12), IOP (ANOVA, 𝑃= 0.4), and visual acuity (ANOVA, 𝑃= 0.5) among controls, no DR, and NPDR groups (Table 1). 3. Results (a) Inner limiting membrane + nerve fibre layer (ILM + RNFL); (b) ganglion cell layer + inner plexiform layer (GCL + IPL); (c) inner nuclear layer + outer plexiform layer (INL + OPL); (d) outer nuclear layer + external limiting membrane (ONL + ELM); and (e) inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE). (∗) indicates statistically significant values; CSF: central subfield thickness; SIM: superior inner quadrant in the macula; NIM: nasal inner quadrant; IIM: inferior inner quadrant; TIM: temporal inner quadrant; SOM: superior outer quadrant in the macula; NOM: nasal outer quadrant; IOM: inferior outer quadrant; TOM: temporal outer quadrant. Figure 2: Graphs showing specific retinal layer thickness in normal subjects (control), diabetics without retinopathy (no DR), and diabetics with nonproliferative diabetic retinopathy (NPDR) determined automatically by spectral domain OCT in 9 ETDRS areas in the macula. (a) Inner limiting membrane + nerve fibre layer (ILM + RNFL); (b) ganglion cell layer + inner plexiform layer (GCL + IPL); (c) inner nuclear layer + outer plexiform layer (INL + OPL); (d) outer nuclear layer + external limiting membrane (ONL + ELM); and (e) inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE). (∗) indicates statistically significant values; CSF: central subfield thickness; SIM: superior inner quadrant in the macula; NIM: nasal inner quadrant; IIM: inferior inner quadrant; TIM: temporal inner quadrant; SOM: superior outer quadrant in the macula; NOM: nasal outer quadrant; IOM: inferior outer quadrant; TOM: temporal outer quadrant. 3. Results Journal of Diabetes Research 5 60 70 80 90 100 110 120 130 140 ILM + RNFL Control No DR NPDR Temporal Superior Nasal Inferior (𝜇) (a) 0 10 20 30 40 50 60 70 80 GCL + IPL Control No DR NPDR Temporal Superior Nasal Inferior (𝜇) (b) 0 10 20 30 40 50 60 70 80 INL + OPL Control No DR NPDR Temporal Superior Nasal Inferior (𝜇) (c) 0 10 20 30 40 50 60 70 80 ONL + ELM Control No DR NPDR Temporal Superior Nasal Inferior (𝜇) (d) 20 30 40 50 60 70 80 90 100 IS/OS + RPE Control No DR NPDR Temporal Superior Nasal Inferior (𝜇) (e) igure 3: Graphs showing specific retinal layer thickness in normal subjects (control), diabetics without retinopathy (no DR), and diabetics with nonproliferative diabetic retinopathy (NPDR) determined automatically by spectral domain OCT in 4 peripapillary areas (temporal, uperior, nasal, and inferior). (a) Inner limiting membrane + nerve fibre layer (ILM + RNFL); (b) ganglion cell layer + inner plexiform layer GCL + IPL); (c) inner nuclear layer + outer plexiform layer (INL + OPL); (d) outer nuclear layer + external limiting membrane (ONL + ELM); nd (e) inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE). There is no significant difference in he retinal layer thickness among the controls, no DR, and NPDR groups. 3. Results 0 10 20 30 40 50 60 70 80 GCL + IPL Control No DR NPDR Temporal Superior Nasal Inferior (𝜇) 60 70 80 90 100 110 120 130 140 ILM + RNFL Temporal Superior Nasal Inferior (𝜇) (b) 20 30 40 50 60 70 80 90 100 IS/OS + RPE Control Temporal Superior Nasal Inferior (𝜇) (a) 0 10 20 30 40 50 60 70 80 INL + OPL Control No DR NPDR Temporal Superior Nasal Inferior (𝜇) (c) (a) 0 10 20 30 40 50 60 70 80 INL + OPL Temporal Superior Nasal Inferior (𝜇) 0 10 20 30 40 50 60 70 80 ONL + ELM Control No DR NPDR Temporal Superior Nasal Inferior (𝜇) (d) (b) 20 30 40 50 60 70 80 90 100 IS/OS + RPE Control No DR NPDR Temporal Superior Nasal Inferior (𝜇) (e) (c) (e) (d) Figure 3: Graphs showing specific retinal layer thickness in normal subjects (control), diabetics without retinopathy (no DR), and diabetics with nonproliferative diabetic retinopathy (NPDR) determined automatically by spectral domain OCT in 4 peripapillary areas (temporal, superior, nasal, and inferior). (a) Inner limiting membrane + nerve fibre layer (ILM + RNFL); (b) ganglion cell layer + inner plexiform layer (GCL + IPL); (c) inner nuclear layer + outer plexiform layer (INL + OPL); (d) outer nuclear layer + external limiting membrane (ONL + ELM); and (e) inner segment/outer segment photoreceptor layer + retinal pigment epithelium (IS/OS + RPE). There is no significant difference in the retinal layer thickness among the controls, no DR, and NPDR groups. males versus females (𝑃= 0.0004) in both controls and diabetics.if explained by progressive ganglion cells and astrocytes loss induced by diabetes. It may depend on a direct toxicity of hyperglycemia or on M¨uller cells dysfunction, which are unable to maintain an adequate osmotic equilibrium between the intra- and the extracellular matrices with consequent apoptosis of neuronal cells and progressive axonal degen- eration [2, 9, 17–20]. Different authors have reported the thinning of RNFL and, in some cases, of the GCL + IPL complex, suggesting that retinal neurodegeneration is an early event in diabetes mellitus, representing a preclinical stage of DR [15, 21, 22]. In fact, the decrease of RNFL thickness in the superior macular region in diabetics without DR or with minimal signs of DR has been documented in vivo [23– 26]. Lonneville et al. 3. Results have demonstrated that RNFL thickness decreases with poor metabolic control in diabetics with or ILM + RNFL thickness was significantly different in 4 quadrants, thicker in the superior and inner quadrants, and thinner in the nasal and temporal quadrants. There was no significant difference in the ILM + RNFL, GCL/IPL, INL/OPL, ONL/ELM, and IS/OS −RPE thickness between controls and diabetics (Figure 3). 4. Discussion Moreover, as inner and outer retinas appear differently affected, it seems crucial to have the possibility to evaluate the different retinal layers separately. (c) Figure 4: Spectral domain OCT linear scans in the macula of (a) normal subject, (b) diabetic patient without retinopathy, and (c) diabetic patient with mild nonproliferative diabetic retinopathy. The arrows indicate a progressive thinning of the retinal nerve fiber layer in diabetics (without and with retinopathy) versus normal subjects. without clinically detectable DR [27]. In this study, we did not find significant difference in RNFL thickness between diabetics without DR and with NPDR. This is probably due to the fact that all our patients were at early stages of DR and had quite good metabolic control. In this study we did not find statistically significant difference in the thickness of GCL/IPL between diabetics and controls, although there was a trend of decreasing GCL/IPL thickness in diabetics without DR versus controls in the pericentral macula. This may be due to the small differences in the specific layer thickness, thus suggesting a more numerous study population.h f In conclusion, the thinning of the inner neural retina in diabetic patients without clinically detectable retinopathy and with mild and moderate nonproliferative retinopathy without macular edema is confirmed in vivo using SD-OCT. Retinal thinning is mainly due to the selective thinning of inner retinal layers in the central retina, strongly suggesting an early neuronal loss in DR. The neuronal loss is accompanied (or induced) by M¨uller cells activation, with increasing thickness in the INL. Automatic intraretinal layering by SD-OCT may be a useful tool to diagnose and monitor early intraretinal changes in diabetic retinopathy. gg g y p p The INL and the OPL showed increased thickness in diabetic patients with NPDR versus controls in this study. The INL is mainly formed by the nuclei of bipolar and M¨uller cells and by the association of horizontal and amacrine cells. Different experimental studies have reported an activation of M¨uller cells with consequent hypertrophy in the earlier stages of diabetic retinopathy [28–32]. No histopathologic studies have reported changes in OPL thickness in the early stages of diabetes mellitus. Therefore, the INL/OPL thickening would be mostly due to the changes in INL thickness. INL thicken- ing, never previously reported in vivo, may represent a sign of M¨uller cells activation which is represented by significant hypertrophy of these cells. 4. Discussion In this study we report a decrease in RNFL thickness in the macula of diabetic eyes even without any clinical sign of retinopathy (Figure 4). Reduced RNFL thickness may be Journal of Diabetes Research 6 (a) (b) (c) Figure 4: Spectral domain OCT linear scans in the macula of (a) normal subject, (b) diabetic patient without retinopathy, and (c) diabetic patient with mild nonproliferative diabetic retinopathy. The arrows indicate a progressive thinning of the retinal nerve fiber layer in diabetics (without and with retinopathy) versus normal subjects. (a) microvascular lesions, although it is still not known which one of these two events appears first [39, 40]. M¨uller cells become hyperplastic in DM, with an increasing number of nuclei, as histopathologically demonstrated. In fact, the number of cell nuclei is increased in the INL and reaches a multiplication factor of 1.6 times, at 20 weeks of DM [28].hif (a) There was not a significant difference in ONL/ELM thickness between diabetics without DR and normal subjects. In diabetics with retinopathy the ONL/ELM was reduced just in the superior macular quadrants. The photoreceptor/RPE layer was not different in thickness between diabetics and normal subjects. Therefore, it seems that outer retina is not significantly influenced by diabetes at least in the early stages of disease whereas the inner retina is precociously affected (b) (b) (c) il of disease, whereas the inner retina is precociously affected. In the peripapillary area, although RNFL thickness was reduced in diabetics versus controls, it did not reach statistical and clinical significance, probably due to the fact that in this area small changes are more difficult to be clinically detected because of the high density of retinal nerve fibers [41]. The automatic segmentation of SD-OCT used in this study, although not able to identify any single retinal layer, but rather layers by couple, can be easily used in both the macula and the peripapillary region for the inner and outer retinal thickness analysis in normal subjects and in diabetic eyes. Its use in a more advanced cases of diabetic retinopathy, mostly in macular edema, needs to be further validated. A detection of retina layer thickness changes in diabetic patients without retinopathy or at early stages of retinopathy may also help in the early diagnosis of retinal tissue loss in DM and to better elucidate the pathophysiology of this severe chronic disease. This study was supported by grant from the 7th Framework Programme (EUROCONDOR. FP7-278040). This study was supported by grant from the 7th Framework Programme (EUROCONDOR. FP7-278040). 4. Discussion M¨uller cells are particularly sus- ceptible to hyperglycemia and are recognized as key elements in the onset and the progression of retinal damage induced by hyperglycemia [33]. Diabetes induces hypertrophy (swelling) of M¨uller cells with a limited impact on the apoptotic cascade [34, 35]. Metabolic and morphological alterations of M¨uller cells induce secondary progressive neuronal loss, due to the crucial role of M¨uller cells in mediating relationship between retinal vessels and neurons [36–38]. Carrasco et al. have proven that both apoptosis and glial activation precede References [1] A. Girach, D. Manner, and M. Porta, “Diabetic microvascular complications: can patients at risk be identified? 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Lin, “Nerve fibre layer thinning in patients with preclinical retinopathy,” Canadian Journal of Ophthalmology, vol. 44, no. 4, pp. 417–422, 2009. [27] Y. H. Lonneville, S. C. Ozdek, M. Onol, I. Yetkin, G. G¨urelik, and B. Hasanreiso˘glu, “The effect of blood glucose regulation on retinal nerve fiber layer thickness in diabetic patients,” Ophthalmologica, vol. 217, pp. 347–350, 2003. [11] D. J. Browning, C. M. Fraser, and S. Clark, “The relationship of macular thickness to clinically graded diabetic retinopathy severity in eyes without clinically detected diabetic macular edema,” Ophthalmology, vol. 115, no. 3, pp. 533–539, 2008. [28] E. Rungger-Br¨andle, A. A. Dosso, and P. M. Leuenberger, “Glial reactivity, an early feature of diabetic retinopathy,” Investigative Ophthalmology & Visual Science, vol. 41, pp. 1971–1980, 2000. [12] M. Nilsson, G. Von Wendt, P. Wanger, and L. Martin, “Early detection of macular changes in patients with diabetes using Rarebit Fovea Test and optical coherence tomography,” British Journal of Ophthalmology, vol. 91, no. 12, pp. 1596–1598, 2007. [29] Q. Li and D. G. Puro, “Diabetes-induced dysfunction of the glutamate transporter in retinal M¨uller cells,” Investigative Ophthalmology & Visual Science, vol. 43, pp. References 3109–3116, 2002. [13] T. Oshitari, K. Hanawa, and E. Adachi-Usami, “Changes of macular and RNFL thicknesses measured by Stratus OCT in patients with early stage diabetes,” Eye, vol. 23, no. 4, pp. 884– 889, 2009. [30] E. Lieth, A. J. Barber, B. Xu et al., “Glial reactivity and impaired glutamate metabolism in short- term experimental diabetic retinopathy,” Diabetes, vol. 47, no. 7, pp. 815–820, 1998. [31] M. Mizutani, C. Gerhardinger, and M. Lorenzi, “Muller cell changes in human diabetic retinopathy,” Diabetes, vol. 47, no. 3, pp. 445–449, 1998. [14] H. W. Van Dijk, F. D. Verbraak, P. H. B. 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Sim´o, “Lowered cortistatin expression is an early event in the human diabetic retina and is associated with apoptosis and glial activation,” Molecular Vision, vol. 14, pp. 1496–1502, 2008. [41] B. Fortune, H. Yang, N. G. Strouthidis et al., “The effect of acute intraocular pressure elevation on peripapillary retinal thickness, retinal nerve fiber layer thickness, and retardance,” Investigative Ophthalmology and Visual Science, vol. 50, no. 10, pp. 4719–4726, 2009.
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https://figshare.com/articles/journal_contribution/Supplementary_Figure_Legends_from_PI3_-Kinase_Inhibition_Forestalls_the_Onset_of_MEK1_2_Inhibitor_Resistance_in_i_BRAF_i_-Mutated_Melanoma/22530428/1/files/39993551.pdf
English
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PI3′-Kinase Inhibition Forestalls the Onset of MEK1/2 Inhibitor Resistance in <i>BRAF</i>-Mutated Melanoma
Cancer discovery
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SUPPLEMENTARY FIGURE LEGENDS Figure S1: BP2C mouse melanoma-derived cells are sensitive to PI3Kα-selective inhibition Figure S1: BP2C mouse melanoma-derived cells are sensitive to PI3Kα-selective inhibition (A) BP2C melanoma cells were cultured in the presence of the indicated concentrations of BYL719 for 72 hours before being fixed and stained with Crystal Violet. Crystal Violet staining was quantified as described above. Values are normalized to DMSO control and error bars represent SEM. (B) BP2C melanoma cells were cultured in the presence of the indicated concentrations of BYL719 with cells counted every 24 hours for a total period of 72 hours. Cell counts are indicated as change in cell number relative to the number of cells at the initiation of drug treatment and error bars represent SEM. (C) Lysates of BP2C melanoma cells cells treated for 6 hours with DMSO, LGX818 (100nM), BYL719 (5μM) or the combination of both agents were analyzed by immunoblotting. (D) Mice bearing BRAFV600E/PIK3CAH1047R melanoma were dosed with a single dose of BYL719 (50mg/kg) and sacrificed at the indicated times post dose. Lysates of melanomas that had been snap frozen in liquid nitrogen were analyzed by immunoblotting. Figure S3: PI3Kβ-sparing PI3K inhibition enhances the effects of MEK inhibition on BRAFV600E/ PTENNull melanoma-derived cells Figure S2: BRAFV600E/PTENNull melanoma-derived cells are sensitive to PI3Kβ-sparing PI3’ kinase inhibition (A) M233 or M249 melanoma cells were cultured in the presence of the indicated concentrations of KIN193 or GSK771 for 72 hours before being fixed and stained with Crystal Violet. Crystal Violet staining was quantified as described above. Values indicated are normalized to DMSO control and error bars represent SEM. (B) Lysates of 1205Lu, WM793, M233, M249, B10C, or BPC melanoma cells treated for 24 hours with the indicated concentrations of KIN193 or GSK771 were analyzed by immunoblotting. (C) M233 or M249 melanoma cells were cultured in the presence of the indicated concentrations of GDC-0032 (blue) or GDC-0941 (pink) for 72 hours prior to fixation and staining with Crystal Violet. Crystal Violet staining was quantified as described above. Values indicated are normalized to DMSO control and error bars represent SEM. (D) Lysates of 1205Lu, WM793, M233 or M249 melanoma cells treated for 24 hours with DMSO or GDC-0941 or GDC-0032 (with drug treatment applied from 10μM to 31.25 nM in two-fold dilution series as indicated) were analyzed by immunoblotting. (E) Lysates of 1205Lu melanoma cells treated for treated for 24 hours with DMSO, GDC-0032 (0032), BYL719 (BYL), IPI145 (IPI) or BYL719+IPI145 (BYL+IPI) (all at 5μM) were analyzed by immunoblotting. Figure S3: PI3Kβ-sparing PI3K inhibition enhances the effects of MEK inhibition on BRAFV600E/ PTENNull melanoma-derived cells (A) Lysates of B10C, M233 or M249 melanoma cells treated for 6 hours with GDC-0973 (1μM), GDC-0032 (5μM) or GDC-0973 plus GDC-0032 were analyzed by immunoblotting. (A) Lysates of B10C, M233 or M249 melanoma cells treated for 6 hours with GDC-0973 (1μM), GDC-0032 (5μM) or GDC-0973 plus GDC-0032 were analyzed by immunoblotting. (A) Lysates of B10C, M233 or M249 melanoma cells treated for 6 hours with GDC-0973 (1μM), GDC-0032 (5μM) or GDC-0973 plus GDC-0032 were analyzed by immunoblotting. (B) B10C, M233 or M249 melanoma cells were cultured in the presence of GDC-0032 (5μM), GDC-0973 (1μM) or GDC-0973 plus GDC-0032 with cells fixed and stained with Crystal Violet every 24 hours for of 72 hours. Crystal Violet staining was quantified as described above. Error bars represent SEM. Asterisks indicate significant difference between combination drug treatment and single agent drug treatment (2-way ANOVA, p<0.0001). Figure S4: BRAFV600E/PTENWT melanoma cells are sensitive to PI3Kβ-sparing PI3’-kinase inhibition, and PI3Kβ-sparing PI3K inhibition enhances the effects of MEK inhibition on BRAFV600E/ PTENWT melanoma cells (A) SK-MEL-239 melanoma cells were cultured in the presence of the indicated concentrations of KIN193 or GSK771 for 72 hours before being fixed and stained with Crystal Violet. Crystal Violet staining was quantified as described above. Values indicated are normalized to DMSO control and error bars represent SEM. (B) Lysates of SK-MEL-239 melanoma cells treated for 24 hours with the indicated concentrations of KIN193 or GSK771 were analyzed by immunoblotting. (C) SK-MEL-239 melanoma cells were cultured in the presence of the indicated concentrations of GDC-0941 or GDC-0032 for 72 hours before being fixed and stained with Crystal Violet. Crystal Violet staining was quantified as described above. Values indicated are normalized to DMSO control and error bars represent SEM. (D) Lysates of SK-MEL-239 melanoma cells treated for 6 hours with GDC-0973 (1μM), GDC- 0032 (5μM) or GDC-0973 plus GDC-0032 were analyzed by immunoblotting.
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https://europepmc.org/articles/pmc6681330?pdf=render
English
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Expression of miR159 Is Altered in Tomato Plants Undergoing Drought Stress
Plants
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8,943
Received: 27 May 2019; Accepted: 27 June 2019; Published: 2 July 2019 Abstract: In a scenario of global climate change, water scarcity is a major threat for agriculture, severely limiting crop yields. Therefore, alternatives are urgently needed for improving plant adaptation to drought stress. Among them, gene expression reprogramming by microRNAs (miRNAs) might offer a biotechnologically sound strategy. Drought-responsive miRNAs have been reported in many plant species, and some of them are known to participate in complex regulatory networks via their regulation of transcription factors involved in water stress signaling. We explored the role of miR159 in the response of Solanum lycopersicum Mill. plants to drought stress by analyzing the expression of sly-miR159 and its target SlMYB transcription factor genes in tomato plants of cv. Ailsa Craig grown in deprived water conditions or in response to mechanical damage caused by the Colorado potato beetle, a devastating insect pest of Solanaceae plants. Results showed that sly-miR159 regulatory function in the tomato plants response to distinct stresses might be mediated by differential stress-specific MYB transcription factor targeting. sly-miR159 targeting of SlMYB33 transcription factor transcript correlated with accumulation of the osmoprotective compounds proline and putrescine, which promote drought tolerance. This highlights the potential role of sly-miR159 in tomato plants’ adaptation to water deficit conditions. Expression of miR159 Is Altered in Tomato Plants Undergoing Drought Stress María José López-Galiano 1, Inmaculada García-Robles 1 , Ana I. González-Hernández 2 Gemma Camañes 2 , Begonya Vicedo 2, M. Dolores Real 1 and Carolina Rausell 1,* Gemma Camañes , Begonya Vicedo , M. Dolores Real and Carolina Rausell 1 Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain 2 Plant Physiology Area, Biochemistry and Biotechnology Group, Department CAMN, University Jaume I, 12071 Castellón, Spain * C d li ll@ T l 34 96 354 3397 * Correspondence: carolina.rausell@uv.es; Tel.: +34-96-354-3397 * Correspondence: carolina.rausell@uv.es; Tel.: +34-96-354-3397 * Correspondence: carolina.rausell@uv.es; Tel.: +34-96-354-3397 Plants 2019, 8, 201; doi:10.3390/plants8070201 plants plants 1. Introduction Climate change due to increasing concentration of CO2 in the atmosphere is leading to rising temperatures, altered rainfall patterns, and more frequent and severe drought episodes [1], which negatively impact crop production. Therefore, gaining knowledge about how plants regulate their adaptation to stress is critical to find ways to enhance plant performance in eventually drier environments. To cope with drought, plants activate a complex cascade of events at the cellular level that include extensive metabolic and gene transcriptional reprogramming to protect cells from osmotic stress, and limit water loss. The response of plants to drought stress involves genes related to diverse functional categories such as genes encoding proteins participating in the direct protection of essential proteins and membranes (osmoprotectants, free radical scavengers, etc.), genes encoding membrane transporters and ion channels that promote water uptake, and genes encoding stress related regulatory proteins such as kinases and transcription factors belonging to the V-myb myeloblastosis viral oncogene homolog (MYB), basic-helix-loop-helix (bHLH), basic region/leucine zipper (bZIP), NAM, ATAF1/2, and CUC (NAC), and APETALA2/ethylene-responsive element binding protein (AP2/EREBP) families [2]. Plants 2019, 8, 201; doi:10.3390/plants8070201 www.mdpi.com/journal/plants Plants 2019, 8, 201 2 of 11 The phytohormone Abscisic acid (ABA) coordinates the plant’s response to reduced water availability by modulating the expression of some of the drought responsive genes [3]. Interestingly, microRNAs (miRNAs) have been recently reported to mediate drought tolerance by post-transcriptionally regulating drought-responsive genes, some of which are known to be controlled by ABA signaling pathways [4]. An example of such intricate regulatory network is provided by miR159, which in Arabidopsis germinating seeds, has been reported to be induced by ABA and drought treatments, and promote transcript cleavage of the ABA positive regulators MYB33 and MYB101 transcription factors, thereby playing a key role in ABA response [5]. The miR159 family is highly conserved among monocot and dicot plants, but in plants undergoing drought, miR159’s relative abundance varies in a tissue- and species-specific manner. For instance, miR159 was reported to be up-regulated by drought stress in Arabidopsis [6], and maize [7], but down-regulated in cotton [8], and potato [9], whereas in barley and alfalfa, miR159 was down-regulated in roots and up-regulated in leaves in response to drought stress [10,11]. Pegler et al. 1. Introduction [12] proposed that the differential miRNA abundance across species following drought or salt stress exposure might be in part due to differential distribution of regulatory transcription factor binding sites within the putative promoter region of the miRNA gene, which encodes the highly conserved, stress-responsive miRNA. To expand our knowledge on the miR159 regulatory network involved in tomato plants’ response to drought stress, in the present work we analyzed the expression of miR159 and its predicted target genes in tomato plants of Solanum lycopersicum Mill. cv. Ailsa Craig undergoing drought stress, in which we previously reported that ABA hormone is accumulated after water deprivation [13]. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress To assess miR159 expression in tomato plants of Solanum lycopersicum Mill. cv. Ailsa Craig following a seven-day water deprivation, we analyzed sly-miR159 (GenBank: 102464332) transcript levels by RT-qPCR in control tomato plants and plants undergoing drought stress. Results showed significantly reduced expression of sly-miR159 in response to stress (Figure 1A). However, in recent high-throughput sequencing studies performed by Liu et al. [14,15], miR159 was not found among the miRNAs differentially expressed after 10 days of drought stress in a sensitive and a tolerant tomato cultivar. This apparent discrepancy with our results might be due to the differential experimental conditions or techniques used to measure miRNA expression, but is most probably due to the fact that the tomato cultivars were different, since it has been reported that miRNAs respond to environmental stresses in a genotype-dependent manner [16]. As in plants, most miRNAs negatively regulate their target genes, we hypothesized that sly-miR159 gene targets that are upregulated in tomato plants grown in water-limited conditions in our experimental conditions may play beneficial roles in the adaptive responses to drought stress. In Arabidopsis, a clade of seven closely related GAMYB-like genes (MYB33, MYB101, MYB65, MYB81, MYB97, MYB104, and MYB120) share a conserved putative miR159-binding site [17]. The GAMYB-like genes encode a highly conserved family of R2R3-type MYB domain transcription factors that are regulated by Gibberellic acid (GA) and ABA and participate in the GA signaling pathway [18]. Recent studies in potato plants highlight the involvement of miR159 and its targets GAMYB-like genes in the response of this species to water stress [9]. Using psRNATarget software [19] we identified the following putative GAMYB-like transcription factor genes that are sly-miR159 targets in tomato: SlMYB33 (Solyc01g009070.2.1), SlMYB65 (Solyc06g073640.2.1), SlMYB104 (Solyc11g072060.1.1), SlMYB97 (Solyc10g019260.1.1), and SlMYB120 (Solyc01g090530.1.1). Figure 1B shows the nucleotide sequence of the sly-miR159-binding sites in the tomato SlMYB transcripts identified, which strongly resemble those found in AtMYB transcripts targeted by miR159 in Arabidopsis [20]. 3 of 11 express Plants 2019, 8, 201 water stres [22] Figure 1. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato pla undergoing drought stress. (A) RT-qPCR analysis of sly-miR159 expression in control tomato pla and tomato plants following 7-day water deprivation. (B) Nucleotide sequence of sly-miR159-bind sites in tomato GAMYB-like transcripts. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress (A) RT-qPCR analysis of sly-miR159 expression in control tomato pla and tomato plants following 7-day water deprivation. (B) Nucleotide sequence of sly-miR159-bind sites in tomato GAMYB-like transcripts. Nucleotides in the cleavage site are underlined, lower-c red letters indicate mismatches to sly-miR159, and G:U pairing is shown in uppercase green lett (C) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104, SlMYB97, and SlMYB120 genes express in control tomato plants and tomato plants following 7-day water deprivation. In panels (A) and ( data shown are the mean of three independent experiments ± standard error (SE). Asterisk indica that differences between means of control and undergoing drought stress tomato plants w statistically significant (Student’s t-test, p < 0.05). Figure 1. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plants undergoing drought stress. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants and tomato plants following 7-day water deprivation. (B) Nucleotide sequence of sly-miR159-binding sites in tomato GAMYB-like transcripts. Nucleotides in the cleavage site are underlined, lower-case red letters indicate mismatches to sly-miR159, and G:U pairing is shown in uppercase green letters. (C) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104, SlMYB97, and SlMYB120 genes expression in control tomato plants and tomato plants following 7-day water deprivation. In panels (A) and (C), data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato plants were statistically significant (Student’s t-test, p < 0.05). To further assess the involvement of sly-miR159 in the regulation of SlMYB33 gene express under drought stress, we aimed at analyzing SlMYB33 cleavage fragments. We designed two p of primers to amplify SlMYB33 mRNA fragments in small RNA samples isolated from total RNA Li et al. [21] identified 127 MYB genes in the tomato genome and classified the corresponding proteins into 18 subgroups based on domain similarity and phylogenetic topology, and suggested that conserved motifs outside the MYB domain might reflect their functional conservation. SlMYB33, SlMYB65, and SlMYB104 proteins cluster in subgroup 12, in which the three of them are the only ones (out of the thirteen subgroup members) sharing the conserved motifs 14 and 15 outside the MYB domain. SlMYB97 and SlMYB120 proteins constitute subgroup 15, which is composed only by these two MYB proteins that have no conserved motifs outside the MYB domain. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress Nucleotides in the cleavage site are underlined, lower-c red letters indicate mismatches to sly-miR159, and G:U pairing is shown in uppercase green lett (C) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104, SlMYB97, and SlMYB120 genes express in control tomato plants and tomato plants following 7-day water deprivation. In panels (A) and data shown are the mean of three independent experiments ± standard error (SE). Asterisk indica that differences between means of control and undergoing drought stress tomato plants w statistically significant (Student’s t-test, p < 0.05). B sly-miR159 AUCUCGAGGGAAGUUAGGUUU-5’ SlMYB33 UGGAGCUCCCUUCAcUCCAAA-3’ SlMYB65 UcGAGCUCCCUUCAcUCCAAA-3’ SlMYB104 UGGAGCUCCCUUCuuUCCAAA-3’ SlMYB97 UGGAGCUCCaUUCGAUCCAAA-3’ SlMYB120 UGGAGCUCCaUUCGAUCCAAA-3’ 0.0E+00 2.0E-06 4.0E-06 6.0E-06 8.0E-06 1.0E-05 1.2E-05 SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120 Relative number of molecules (N0) Control Drought C * 0 1.2x10-5 1.0x10-5 8.0x10-6 6.0x10-6 4.0x10-6 2.0x10-6 0 0 0.5 1 1.5 2 2.5 sly-miR159 relative number of molecules (N0) A * 2.5 2.0 1.5 1.0 0.5 0 Figure 1. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plants undergoing drought stress. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants and tomato plants following 7-day water deprivation. (B) Nucleotide sequence of sly-miR159-binding sites in tomato GAMYB-like transcripts. Nucleotides in the cleavage site are underlined, lower-case red letters indicate mismatches to sly-miR159, and G:U pairing is shown in uppercase green letters. (C) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104, SlMYB97, and SlMYB120 genes expression in control tomato plants and tomato plants following 7-day water deprivation. In panels (A) and (C), data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato plants were statistically significant (Student’s t-test, p < 0.05). B sly-miR159 AUCUCGAGGGAAGUUAGGUUU-5’ SlMYB33 UGGAGCUCCCUUCAcUCCAAA-3’ SlMYB65 UcGAGCUCCCUUCAcUCCAAA-3’ SlMYB104 UGGAGCUCCCUUCuuUCCAAA-3’ SlMYB97 UGGAGCUCCaUUCGAUCCAAA-3’ SlMYB120 UGGAGCUCCaUUCGAUCCAAA-3’ 0.0E+00 2.0E-06 4.0E-06 6.0E-06 8.0E-06 1.0E-05 1.2E-05 SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120 Relative number of molecules (N0) Control Drought C * 0 1.2x10-5 1.0x10-5 8.0x10-6 6.0x10-6 4.0x10-6 2.0x10-6 0 B 0 0.5 1 1.5 2 2.5 sly-miR159 relative number of molecules (N0) A * 2.5 2.0 1.5 1.0 0.5 0 A 0.0E+00 2.0E-06 4.0E-06 6.0E-06 8.0E-06 1.0E-05 1.2E-05 SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120 Relative number of molecules (N0) Control Drought C * 0 1.2x10-5 1.0x10-5 8.0x10-6 6.0x10-6 4.0x10-6 2.0x10-6 0 C SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120 SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120 Figure 1. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato pla undergoing drought stress. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress RT-PCR amplification of SlMYB33 mRNA fragments. (A) Nucleotide sequence of sly- iR159-binding sites in SlMYB33 transcripts. Bar in red depicts the putative cleavage site and arrows dicate the annealing positions of primer pair OFw and ORv, outside the sly-miR159-binding region, d primer pair FFw and FRv, flanking the putative cleavage site in sly-miR159-binding region. (B) T-PCR analysis of SlMYB33 small RNA fragments in control tomato plants and tomato plants llowing 7-day water deprivation using primers OFw and ORv, or FFw and FRv. RPS18 gene pression was used as normalization control. For each sample, three biological replicates were ooled and analyzed. Figure 2. RT-PCR amplification of SlMYB33 mRNA fragments. (A) Nucleotide sequence of sly-miR159-binding sites in SlMYB33 transcripts. Bar in red depicts the putative cleavage site and arrows indicate the annealing positions of primer pair OFw and ORv, outside the sly-miR159-binding region, and primer pair FFw and FRv, flanking the putative cleavage site in sly-miR159-binding region. (B) RT-PCR analysis of SlMYB33 small RNA fragments in control tomato plants and tomato plants following 7-day water deprivation using primers OFw and ORv, or FFw and FRv. RPS18 gene expression was used as normalization control. For each sample, three biological replicates were pooled and analyzed. Interestingly, Qin et al. [23] proposed that MYB33 transcription factor may enhance drought erance by means of promoting osmotic pressure balance reconstruction and reactive oxidative ecies (ROS) scavenging, since ectopic over-expression of wheat MYB33 gene in Arabidopsis induced e expression of AtP5CS and AtZAT12 genes involved in proline synthesis and ascorbate peroxidase nthesis, respectively. Accordingly, we observed an induction of SlP5CS gene expression and a markable increase in proline levels relative to other amino acids in tomato plants grown in water- ortage conditions compared to irrigated control plants (Figure 3A,B), suggesting that sly-miR159 ght participate in the tomato plants’ adaptive response to drought stress via induction of SlMYB33 nscription factor gene expression. Nevertheless, further research is needed to demonstrate hether the sly-miR159-SlMYB33 pathway is necessary for drought tolerance in the tomato cultivar lsa Craig. T l [24] d b li di i b l i d li Interestingly, Qin et al. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress We analyzed the expression of sly-miR159 MYB predicted targets in control tomato plants and plants undergoing drought stress by RT-qPCR (Figure 1C). Only SlMYB33 gene showed statistically significant induction in water-stressed tomato plants, exhibiting an opposite pattern of expression relative to that of sly-miR159, which suggests that this MYB gene may be regulated by sly-miR159 in tomato plants in response to drought stress. In line with this hypothesis, in potato plants in which the CBP80 gene encoding a protein involved in RNA processing was silenced, improved tolerance to water stress was correlated with decreased levels of miR159 and enhanced MYB33 gene expression [22]. To further assess the involvement of sly-miR159 in the regulation of SlMYB33 gene expression under drought stress, we aimed at analyzing SlMYB33 cleavage fragments. We designed two pairs of primers to amplify SlMYB33 mRNA fragments in small RNA samples isolated from total RNA of control tomato plants and tomato plants following a seven-day water deprivation (Materials and Methods, Section 4.3). Figure 2A shows the annealing positions of both pairs of PCR primers. The primer pair 4 of 11 nd Plants 2019, 8, 201 l l OFw and ORv anneals to sequences within a SlMYB33 mRNA region downstream of the predicted sly-miR159-binding site, yielding a 199 bp SlMYB33 amplification product. The primer pair FFw and FRv anneals to sequences flanking the putative cleavage site in the predicted sly-miR159-binding region, yielding a 200 bp SlMYB33 amplification product only when the SlMYB33 mRNA is not cleaved at the sly-miR159 cleavage site. Therefore, we hypothesized that if sly-miR159 is not involved in the regulation of SlMYB33 gene expression of the same amplification patterns of control vs. drought, then small RNA samples with both primer pairs would be expected. Figure 2B shows the results obtained in the RT-PCR amplifications using the two pairs of primers. Lower amounts of amplification products were obtained using primers OFw and ORv in tomato plants grown under water scarcity compared to control plants. In contrast, higher amount of PCR amplified product was observed in drought-stressed tomato plants than in control tomato plants using primers FFw and FRv. Collectively, these results support targeted cleavage of SlMYB33 transcripts by sly-miR159 that might participate in the transcriptional regulation of the tomato plants’ response to drought stress. ethods, Section 4.3). Figure 2A shows the annealing positions of both pairs of PCR primers. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress The mer pair OFw and ORv anneals to sequences within a SlMYB33 mRNA region downstream of the edicted sly-miR159-binding site, yielding a 199 bp SlMYB33 amplification product. The primer pair w and FRv anneals to sequences flanking the putative cleavage site in the predicted sly-miR159- nding region, yielding a 200 bp SlMYB33 amplification product only when the SlMYB33 mRNA is t cleaved at the sly-miR159 cleavage site. Therefore, we hypothesized that if sly-miR159 is not volved in the regulation of SlMYB33 gene expression of the same amplification patterns of control drought, then small RNA samples with both primer pairs would be expected. Figure 2B shows e results obtained in the RT-PCR amplifications using the two pairs of primers. Lower amounts of mplification products were obtained using primers OFw and ORv in tomato plants grown under water arcity compared to control plants. In contrast, higher amount of PCR amplified product was served in drought-stressed tomato plants than in control tomato plants using primers FFw and FRv. llectively, these results support targeted cleavage of SlMYB33 transcripts by sly-miR159 that might rticipate in the transcriptional regulation of the tomato plants’ response to drought stress. Figure 2. RT-PCR amplification of SlMYB33 mRNA fragments. (A) Nucleotide sequence of sly- miR159-binding sites in SlMYB33 transcripts. Bar in red depicts the putative cleavage site and arrows indicate the annealing positions of primer pair OFw and ORv, outside the sly-miR159-binding region, and primer pair FFw and FRv, flanking the putative cleavage site in sly-miR159-binding region. (B) RT-PCR analysis of SlMYB33 small RNA fragments in control tomato plants and tomato plants following 7-day water deprivation using primers OFw and ORv, or FFw and FRv. RPS18 gene expression was used as normalization control. For each sample, three biological replicates were pooled and analyzed. Figure 2. RT-PCR amplification of SlMYB33 mRNA fragments. (A) Nucleotide sequence of sly-miR159-binding sites in SlMYB33 transcripts. Bar in red depicts the putative cleavage site and arrows indicate the annealing positions of primer pair OFw and ORv, outside the sly-miR159-binding region, and primer pair FFw and FRv, flanking the putative cleavage site in sly-miR159-binding region. (B) RT-PCR analysis of SlMYB33 small RNA fragments in control tomato plants and tomato plants following 7-day water deprivation using primers OFw and ORv, or FFw and FRv. RPS18 gene expression was used as normalization control. For each sample, three biological replicates were pooled and analyzed. gure 2. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress [23] proposed that MYB33 transcription factor may enhance drought tolerance by means of promoting osmotic pressure balance reconstruction and reactive oxidative species (ROS) scavenging, since ectopic over-expression of wheat MYB33 gene in Arabidopsis induced the expression of AtP5CS and AtZAT12 genes involved in proline synthesis and ascorbate peroxidase synthesis, respectively. Accordingly, we observed an induction of SlP5CS gene expression and a remarkable increase in proline levels relative to other amino acids in tomato plants grown in water-shortage conditions compared to irrigated control plants (Figure 3A,B), suggesting that sly-miR159 might participate in the tomato plants’ adaptive response to drought stress via induction of SlMYB33 transcription factor gene expression. Nevertheless, further research is needed to demonstrate whether the sly-miR159-SlMYB33 pathway is necessary for drought tolerance in the tomato cultivar Ailsa Craig. Tonon et al. [24] proposed a strong metabolic coordination between polyamines and proline thways in response to osmotic stresses. Therefore, we analyzed polyamine levels in tomato plants dergoing drought stress and non-stressed control plants (Figure 3C), and results showed increased cumulation of putrescine a polyamine reported to have a role in protecting plants during water Tonon et al. [24] proposed a strong metabolic coordination between polyamines and proline pathways in response to osmotic stresses. Therefore, we analyzed polyamine levels in tomato plants undergoing drought stress and non-stressed control plants (Figure 3C), and results showed 5 of 11 Plants 2019, 8, 201 increased accumulation of putrescine, a polyamine reported to have a role in protecting plants during water-deficient conditions, as well as oxidative stress [25]. In wheat, Pál et al. [26] recently described that ABA pre-treatments induced the expression of P5CS gene and enhanced the accumulation of putrescine. Authors suggested that the connection between polyamine metabolism and ABA signaling may control the regulation and maintenance of polyamine and proline levels under osmotic stress conditions in wheat seedlings. , , deficient conditions, as well as oxidative stress [25]. In wheat, Pál et al. [26] recently described that ABA pre-treatments induced the expression of P5CS gene and enhanced the accumulation of putrescine. Authors suggested that the connection between polyamine metabolism and ABA signaling may control the regulation and maintenance of polyamine and proline levels under osmotic stress conditions in wheat seedlings. Figure 3. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants undergoing drought stress. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and tomato plants following 7-day water deprivation. (B) Amino acids levels upon drought treatment. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon drought treatment. Polyamines levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Tomato leaves were collected from plants that were properly irrigated (Control) or deprived of water 1 week (Drought). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato plants were statistically significant (Student’s t-test, p < 0.05). C 0 5 10 15 20 25 30 35 40 45 50 Put Spd Spn Polyamines (μg/g) Control Drought * -20 0 20 40 60 80 100 120 140 160 180 200 Ala Asp Glu Gln His Lys Met Phe Pro Ser Thr Trp Tyr Val Amino acids (μg/g) Control Drought B * * * * 0.0E+00 5.0E-05 1.0E-04 1.5E-04 2.0E-04 2.5E-04 SlP5CS relative number of molecules (N0) A * 2.5x10-4 2.0x10-4 1.5x10-4 1.0x10-4 5.0x10-5 0 Figure 3. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants undergoing drought stress. (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and tomato plants following 7-day water deprivation. (B) Amino acids levels upon drought treatment. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon drought treatment. Polyamines levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Tomato leaves were collected from plants that were properly irrigated (Control) or deprived of water 1 week (Drought). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato plants were statistically significant (Student’s t-test, p < 0.05). -20 0 20 40 60 80 100 120 140 160 180 200 Ala Asp Glu Gln His Lys Met Phe Pro Ser Thr Trp Tyr Val Amino acids (μg/g) Control Drought B * * * * 0.0E+00 5.0E-05 1.0E-04 1.5E-04 2.0E-04 2.5E-04 SlP5CS relative number of molecules (N0) A * 2.5x10-4 2.0x10-4 1.5x10-4 1.0x10-4 5.0x10-5 0 B Control Drought A 0 5 10 15 20 25 30 35 40 45 50 Put Spd Spn Polyamines (μg/g) Control Drought * C Control Drought Figure 3. 2.1. Expression of miR159 in Tomato Plants Undergoing Drought Stress Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants undergoing drought stress. (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and tomato plants following 7-day water deprivation. (B) Amino acids levels upon drought treatment. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon drought treatment. Polyamines levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Tomato leaves were collected from plants that were properly irrigated (Control) or deprived of water 1 week (Drought). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato plants were statistically significant (Student’s t-test, p < 0.05). Figure 3. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants undergoing drought stress. (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and tomato plants following 7-day water deprivation. (B) Amino acids levels upon drought treatment. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon drought treatment. Polyamines levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Tomato leaves were collected from plants that were properly irrigated (Control) or deprived of water 1 week (Drought). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato plants were statistically significant (Student’s t-test, p < 0.05). 2 2 Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 2.2. Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 f y p f g g f To ascertain whether SlMYB33 targeting by sly-miR159 is stress-specific, we analyzed the expression of sly-miR159 and its predicted MYB target genes in tomato plants attacked by the coleopteran insect pest Colorado potato beetle (CPB), in which we previously reported that, as opposed to tomato plants undergoing drought stress, ABA was not accumulated [13]. In the present work, neither SlP5CS gene expression were induced, nor were increased proline and putrescine levels observed in infested tomato plants compared to tomato control plants (Figure 4), corroborating that To ascertain whether SlMYB33 targeting by sly-miR159 is stress-specific, we analyzed the expression of sly-miR159 and its predicted MYB target genes in tomato plants attacked by the coleopteran insect pest Colorado potato beetle (CPB), in which we previously reported that, as opposed to tomato plants undergoing drought stress, ABA was not accumulated [13]. In the present work, neither SlP5CS gene expression were induced, nor were increased proline and putrescine levels observed in infested tomato plants compared to tomato control plants (Figure 4), corroborating that the plants’ response to this biotic stress is different from the plant response to water stress. Plants 2019, 8, 201 Plants 2019, 8, x FOR 6 of 11 6 of 11 he plants’ response to this biotic stress is different from the plant response to water stress. Figure 4. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants infested by Colorado potato beetle (CPB) larvae. (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and tomato plants infested by CPB larvae. (B) Amino acids levels upon CPB infestation. Tomato leaves were collected from non-infested plants (Control) or plants infested by CPB. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon CPB larvae infestation. Tomato leaves were collected from non-infested plants (Control) or plants infested by CPB. Polyamines levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato plants were statistically significant (Student´s t-test, p < 0.05). 2 2 Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 2.2. Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 0 10 20 30 40 50 60 Ala Asp Glu Gln His Lys Met Phe Pro Ser Thr Trp Tyr Val Amino acids (μg/g) Control CPB infestation * * * * * * * B C 0 5 10 15 20 25 30 35 40 45 50 Put Spd Spn Polyamines (μg/g) Control CPB infestation A 0.0E+00 5.0E-05 1.0E-04 1.5E-04 2.0E-04 2.5E-04 3.0E-04 SlP5CS relative number of molecules (N0) 0 3.0x10-4 2.5x10-4 2.0x10-4 1.5x10-4 1.0x10-4 5.0x10-5 0 Figure 4. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants infested by Colorado potato beetle (CPB) larvae. (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and tomato plants infested by CPB larvae. (B) Amino acids levels upon CPB infestation. Tomato leaves were collected from non-infested plants (Control) or plants infested by CPB. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon CPB larvae infestation. Tomato leaves were collected from non-infested plants (Control) or plants infested by CPB. Polyamines levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato plants were statistically significant (Student´s t-test, p < 0.05). otic stress is different from the plant response to water stress. 0 10 20 30 40 50 60 Ala Asp Glu Gln His Lys Met Phe Pro Ser Thr Trp Tyr Val Amino acids (μg/g) Control CPB infestation * * * * * * * B the plants response to this b A 0.0E+00 5.0E-05 1.0E-04 1.5E-04 2.0E-04 2.5E-04 3.0E-04 SlP5CS relative number of molecules (N0) 0 3.0x10-4 2.5x10-4 2.0x10-4 1.5x10-4 1.0x10-4 5.0x10-5 0 B B A A C p y p C 0 5 10 15 20 25 30 35 40 45 50 Put Spd Spn Polyamines (μg/g) Control CPB infestation Figure 4. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants infested by Colorado potato beetle (CPB) larvae. (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and tomato plants infested by CPB larvae. (B) Amino acids levels upon CPB infestation. Tomato leaves were collected from non-infested plants (Control) or plants infested by CPB. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon CPB larvae infestation. 2 2 Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 2.2. Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 Tomato leaves were collected from non-infested plants (Control) or plants infested by CPB. Polyamines levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato plants were statistically significant (Student´s t-test, p < 0.05). Figure 4. Analysis of SlP5CS gene expression, and amino acid and polyamines in tomato plants infested by Colorado potato beetle (CPB) larvae. (A) RT-qPCR analysis of SlP5CS expression in control tomato plants and tomato plants infested by CPB larvae. (B) Amino acids levels upon CPB infestation. Tomato leaves were collected from non-infested plants (Control) or plants infested by CPB. Amino acids levels are expressed in µg/g DW. (C) Polyamines levels upon CPB larvae infestation. Tomato leaves were collected from non-infested plants (Control) or plants infested by CPB. Polyamines levels are expressed in µg/g DW. Put (putrescine), Spd (Spermidine), Spn (Spermine). Data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control and undergoing drought stress tomato plants were statistically significant (Student´s t-test, p < 0.05). Intriguingly, as it was observed in plants deprived of water, in infested tomato plants, sly- miR159 was significantly down-regulated compared to non-infested control plants (Figure 5A). However, in plants attacked by CPB, among sly-miR159 putative MYB targets, only the SlMYB104 transcript factor gene was significantly up-regulated (Figure 5B), suggesting that sly-miR159 might be regulating this specific MYB transcription factor in response to CPB damage. Intriguingly, as it was observed in plants deprived of water, in infested tomato plants, sly-miR159 was significantly down-regulated compared to non-infested control plants (Figure 5A). However, in plants attacked by CPB, among sly-miR159 putative MYB targets, only the SlMYB104 transcript factor gene was significantly up-regulated (Figure 5B), suggesting that sly-miR159 might be regulating this specific MYB transcription factor in response to CPB damage. 7 of 11 7 of Plants 2019, 8, 201 l A 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 sly-miR159 relative number of molecules (N0) 1.6 1.4 1.2 1.0 0.8 0.6 0.4 0.2 0 * Figure 5. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plants infested by CPB larvae. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants and tomato plants infested by CPB larvae. 2 2 Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 2.2. Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 (B) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104, SlMYB97, and SlMYB120 genes expression in control tomato plants and tomato plants upon CPB larvae infestation. In panels (A) and (B), data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control tomato plants and tomato plants infested by CPB larvae were statistically significant (Student´s t-test, p < 0.05). B 0.0E+00 2.0E-07 4.0E-07 6.0E-07 8.0E-07 1.0E-06 1.2E-06 1.4E-06 1.6E-06 SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120 Relative number of molecules (N0) Control CPB infestation * 0 1.6 x10-6 1.4 x10-6 1.2 x10-6 1.0 x10-6 8.0 x10-7 6.0 x10-7 4.0 x10-7 2.0 x10-7 0 A 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 sly-miR159 relative number of molecules (N0) 1.6 1.4 1.2 1.0 0.8 0.6 0.4 0.2 0 * Figure 5. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plants infested by CPB larvae. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants and tomato plants infested by CPB larvae. (B) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104, SlMYB97, and SlMYB120 genes expression in control tomato plants and tomato plants upon CPB larvae infestation. In panels (A) and (B), data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control tomato plants and tomato plants infested by CPB larvae were statistically significant (Student´s t-test, p < 0.05). B 0.0E+00 2.0E-07 4.0E-07 6.0E-07 8.0E-07 1.0E-06 1.2E-06 1.4E-06 1.6E-06 SlMYB33 SlMYB65 SlMYB104 SlMYB97 SlMYB120 Relative number of molecules (N0) Control CPB infestation * 0 1.6 x10-6 1.4 x10-6 1.2 x10-6 1.0 x10-6 8.0 x10-7 6.0 x10-7 4.0 x10-7 2.0 x10-7 0 A B Figure 5. RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plant infested by CPB larvae. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants an tomato plants infested by CPB larvae. (B) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104 SlMYB97, and SlMYB120 genes expression in control tomato plants and tomato plants upon CP larvae infestation. In panels (A) and (B), data shown are the mean of three independent experiment ± standard error (SE). Asterisk indicates that differences between means of control tomato plants an tomato plants infested by CPB larvae were statistically significant (Student´s t-test, p < 0.05). Figure 5. 2 2 Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 2.2. Assessment of sly-miR159 Stress-Specific Targeting of SlMYB33 RT-qPCR analysis of sly-miR159 expression and its MYB predicted targets in tomato plants infested by CPB larvae. (A) RT-qPCR analysis of sly-miR159 expression in control tomato plants and tomato plants infested by CPB larvae. (B) RT-qPCR analysis of SlMYB33, SlMYB65, SlMYB104, SlMYB97, and SlMYB120 genes expression in control tomato plants and tomato plants upon CPB larvae infestation. In panels (A) and (B), data shown are the mean of three independent experiments ± standard error (SE). Asterisk indicates that differences between means of control tomato plants and tomato plants infested by CPB larvae were statistically significant (Student´s t-test, p < 0.05). In contrast, correlating with the lack of proline and putrescine accumulation, no variation w detected in SlMYB33 transcription factor gene expression. This suggests that the specificity of th stress response regulated by sly-miR159 might, at least in part, rely on the distinct MYB transcriptio factor transcript that the sly-miR159 sRNA specifically regulates under each stress condition. It h been proposed that additional factors other than complementarity and cleavage, such as targ accessibility and secondary structure, RNA binding proteins, and target site context may modula silencing efficiency [27], which might lie at the root of the stress specific miR159 regulation of MY transcription factors, and deserve further research. In contrast, correlating with the lack of proline and putrescine accumulation, no variation was detected in SlMYB33 transcription factor gene expression. This suggests that the specificity of the stress response regulated by sly-miR159 might, at least in part, rely on the distinct MYB transcription factor transcript that the sly-miR159 sRNA specifically regulates under each stress condition. It has been proposed that additional factors other than complementarity and cleavage, such as target accessibility and secondary structure, RNA binding proteins, and target site context may modulate silencing efficiency [27], which might lie at the root of the stress specific miR159 regulation of MYB transcription factors, and deserve further research. 3. Conclusio 3. Conclusions Overall, the results obtained in this work show the potential involvement of sly-miR159 in th tomato plants’ response to different stresses through stress-specific MYB transcription facto targeting. Under drought-stress, sly-miR159 targeting of SlMYB33 correlates with induction SlP5CS gene expression and accumulation of the osmoprotective compounds proline and putrescin pointing to the possible participation of this miR in the regulation of drought stress toleranc Understanding the regulatory network underlying drought stress response may provide ne biotechnological approaches to generate plants better adapted to dry environments. Our resul support that in addition to using SlMYB33 transcription factor as a biotechnological target fo metabolic engineering by ectopic expression, SlMYB33 gene expression reprogramming by sl miR159 might develop into a useful system to improve plant drought tolerance in tomato plants Overall, the results obtained in this work show the potential involvement of sly-miR159 in the tomato plants’ response to different stresses through stress-specific MYB transcription factor targeting. Under drought-stress, sly-miR159 targeting of SlMYB33 correlates with induction of SlP5CS gene expression and accumulation of the osmoprotective compounds proline and putrescine, pointing to the possible participation of this miR in the regulation of drought stress tolerance. Understanding the regulatory network underlying drought stress response may provide new biotechnological approaches to generate plants better adapted to dry environments. Our results support that in addition to using SlMYB33 transcription factor as a biotechnological target for metabolic engineering by ectopic expression, SlMYB33 gene expression reprogramming by sly-miR159 might develop into a useful system to improve plant drought tolerance in tomato plants. 4.2. Total RNA Isolation and RT-qPCR Analysis Total RNA was isolated from leaves of control tomato plants and plants undergoing drought stress or CPB infestation using RiboPure Kit (Ambion, Cat. No. AM1924), following the manufacturer’s protocol. TURBO DNA-free kit (Ambion, Cat. No. AM1907) was used to remove contaminating genomic DNA from RNA preparations and RNA quality was evaluated by 1% agarose gel electrophoresis and quantified spectrophotometrically (NanoDrop 2000, Thermo Scientific, Waltham, MA, USA). RT-qPCR amplification was performed using SYBR Premix Ex Taq II (Takara). For sly-miR159 amplification 1 µg of RNA was polyadenylated in a final volume of 10 µL, including 1 µL of 10x poly(A) polymerase buffer, 1 mM of ATP, and 1 unit of poly(A) polymerase (New England Biolabs, Ipswich, MA, USA), and incubated at 37 ◦C for 15 min and then at 65 ◦C for 20 min. Polyadenylated RNA was reverse transcribed to complementary DNA (cDNA) using the Universal RT-primer (Integrated DNA Technologies, Coralville, IA, USA) described in Balcells et al. [29] (5′-CAGGTCCAGTTTTTTTTTTTTTTTVN-3′, where V is A, C, and G, and N is A, C, G, and T). Reverse transcription reaction was performed using PrimeScript™RT reagent Kit (Takara) in a final volume of 10 µL, including 2 µL of 5X PrimeScript™Buffer, 0.5 µL of PrimeScript™RT Enzyme Mix I, and 1 µM of Universal RT-primer, and it was incubated at 37 ◦C for 15 min followed by enzyme inactivation at 85 ◦C for 5 s. Forward and reverse primers for miRNA RT-qPCR amplification were designed according to Balcells et al. [29] (Table 1). Table 1. Primers used to analyze by RT-qPCR sly-miR159, SlMYB, and SlP5CS gene expression in tomato plants. Gene Forward Primer (5′-3′) Reverse Primer (5′-3′) Product Size (bp) sly-miR159 CGCAGTTTGGATTGAAGGGAG CAGGTCCAGTTTTTTTTTTTTTTTTAGAG 50 SlMYB33 TATGGGCATCCAGTCTCTCC TGGGACTGGAAAAGATCGTC 199 SlMYB65 TCTGCTGCATCGGTGTTTAG TCTGGCCTGGGACAGATAAG 164 SlMYB104 TTTCGGAATTGTTTGGAAGC TGAAGAAGTTGCCGACAATG 110 SlMYB97 CATGTCCCCTTGGAAGATTTAG CTAGTGGCAAAGCAAAGTCATC 181 SlMYB120 CACATTCCAGTCCAAACCAAC CCTAGGTCGGAAGCACTGAG 116 SlP5CS TGCTCAACAGGCCGGATATG AAAGTGTGACCAAGGGGCTC 126 U6 snRNA GGGGACATCCGATAAAATTGGAAC TGGACCATTTCTCGATTTGTGC 88 RPS18 GGGCATTCGTATTTCATAGTCAGAG CGGTTCTTGATTAATGAAAACATCCT 105 Table 1. Primers used to analyze by RT-qPCR sly-miR159, SlMYB, and SlP5CS gene expression in tomato plants. For SlMYB33, SlMYB65, SlMYB104, SlMYB97, SlMYB120, and SlP5CS transcript amplification, the PrimeScript™RT reagent kit (Takara) was used for cDNA synthesis according to the manufacturer’s protocol using 50 ng/µL oligo(dT) (Promega), and 2.5 µM random hexamers (Applied Biosystems). Ten ng cDNA, and gene specific forward (F) and reverse (R) primers (Table 1), designed with PRIMER3PLUS software [30], were used. 4.1. Plants 4.1. Plants Thirty-day-old tomato plants of Solanum lycopersicum Mill. cv. Ailsa Craig (four-week-old) we grown from germinated seeds in a growth chamber under the following environmental condition 16/8 h light/night cycle 26/18 °C day/night temperature cycle and 60% relative humidity (RH) Seed Thirty-day-old tomato plants of Solanum lycopersicum Mill. cv. Ailsa Craig (four-week-old) were grown from germinated seeds in a growth chamber under the following environmental conditions: 16/8 h light/night cycle, 26/18 ◦C day/night temperature cycle, and 60% relative humidity (RH). Seeds Plants 2019, 8, 201 8 of 11 were irrigated twice a week with distilled water during the first week, and with Hoagland solution thereafter [28]. For drought stress experiments, thirty-day-old tomato plants were deprived of water for 7 days, and leaf tissue from 3rd and 4th leaves was collected, frozen in liquid nitrogen, and stored at −80 ◦C. Leaf tissue from 3rd and 4th leaves of irrigated plants was also collected as control. For Colorado potato beetle (CPB) infestation, 15 CPB larvae of different developmental stages were placed on the 3rd and 4th leaves of thirty-day-old tomato plants. When necessary, non-cooperative larvae (molting or not eating) were removed and substituted. Leaf tissue left after 3 h of CPB feeding and that of the non-infested control plants were harvested, frozen in liquid nitrogen, and stored at −80 ◦C. 4.2. Total RNA Isolation and RT-qPCR Analysis A StepOnePlus Real-Time PCR system (Applied Biosystems) was used, under the conditions recommended by the manufacturer, and the cycling parameters were: Initial polymerase activation step at 95 ◦C for 30 s, 40 cycles of denaturation at 95 ◦C for 5 s, annealing, and elongation at 60 ◦C 9 of 11 Plants 2019, 8, 201 for 30 s. For each sample, three biological replicates (with 3 technical replicates each) were analyzed. Relative-fold calculations were made using RPS18 (ribosomal protein S18, GeneBank: 3950409) gene to normalize gene expression, and U6 snRNA gene (GenBank: X51447.1) to normalize sly-miR159 expression (Table 1). LingReg software [31] was employed for the analysis of RT-qPCR experiments and data were analyzed by Student’s t-test for statistically significant differences (p < 0.05). Each biological sample from the 3rd and 4th leaves of plants undergoing drought stress and their corresponding controls consisted of a pool of total RNA from 25 plants. Biological samples in CPB infestation experiments and their corresponding controls also consisted of a pool of total RNA from 25 plants. 4.3. Small RNA Isolation and RT-PCR Analysis The small RNA fraction in total RNA samples of control tomato plants and tomato plants following 7-day water deprivation was isolated using Nucleospin® miRNA (Macherey-Nagel, Bethlehem, PA, USA) following the manufacturer’s instructions. For SlMYB33 small mRNA amplification, the PrimeScript™RT reagent kit (Takara, Shiga, Japan) was used for cDNA synthesis according to the manufacturer’s protocol using 50 ng/µL oligo(dT) (Promega, Madison, WI, USA) and 2.5 µM random hexamers (Applied Biosystems, Waltham, MA, USA), 10 ng cDNA, and gene specific forward (F) and reverse (R) primers (Table 2), designed with PRIMER3PLUS software [30]. RPS18 (ribosomal protein S18, GeneBank: 3950409) was used as a reference gene. Table 2. Primers used to analyze SlMYB33 small transcript fragments by RT-PCR in tomato plants annealing to a region outside the predicted sly-miR159 binding site in SlMYB33 mRNA (OFw, ORv) or flanking the putative cleavage site within the predicted sly-miR159 binding site in SlMYB33 mRNA (FFw, FRv). Table 2. Primers used to analyze SlMYB33 small transcript fragments by RT-PCR in tomato plants annealing to a region outside the predicted sly-miR159 binding site in SlMYB33 mRNA (OFw, ORv) or flanking the putative cleavage site within the predicted sly-miR159 binding site in SlMYB33 mRNA (FFw, FRv). Primer Pair Forward Primer (5′-3′) Reverse Primer (5′-3′) Product Size (bp) OFw, ORv TATGGGCATCCAGTCTCTCC TGGGACTGGAAAAGATCGTC 199 FFw, FRv ATGACGGTTCTTTGCTTGCT CTGTCTGGTTTTGGAGTGAAGG 200 RPS18FW, RPS18RV GGGCATTCGTATTTCATAGTCAGAG CGGTTCTTGATTAATGAAAACATCCT 105 The cycling parameters were as follows: Initial polymerase activation step at 95 ◦C for 30 s, 40 cycles of denaturation at 95 ◦C for 5 s, annealing, and elongation at 60 ◦C for 30 s. For each sample, three biological replicates were pooled and analyzed. Five microliters of the reaction volume were separated in a 3% agarose gel. 4.4. Amino Acids and Polyamines Quantification Leaves were recollected after stress condition and frozen in liquid N2, ground, and lyoph q 2 g y p For amino acids analysis, dry tissue (0.1 g) was homogenized with 800 µL of extraction solution: 400 µL of distilled water, 200 µL of chloroform, and 200 µL of methanol per sample. Moreover, a mixture of internal standards was added prior to extraction (100 ng of Phe 13C915N and 100 ng of Thr 13C415N). Samples were filtered, and a final concentration of 1 mM perfluoroheptanoic acid as ion-pairing reagent was added to each sample. A 20 µL aliquot was injected into a high-performance liquid chromatography system (HPLC) with an XSelect HSS C18 column (5 µm 2.1 × 100 mm) which was interfaced with a triple quadrupole mass spectrometer (TQD, Waters, Manchester, UK). Polyamine analysis was conducted according to the method described by Sánchez-López et al. [32], using as internal standards a mixture of [13C4]-putrescine and 1,7-diamineheptane. To analyze each condition, ten independent biological replicates per sample were generated and three independent experiments were conducted. 10 of 11 Plants 2019, 8, 201 10 of 11 Author Contributions: Conceptualization, I.G.-R., M.D.R. and C.R.; Funding acquisition, I.G.-R., G.C., B.V., M.D.R. and C.R.; investigation, M.J.L.-G., I.G.-R., A.I.G.-H. and G.C.; writing—original draft, M.D.R. and C.R.; writing—review and editing, M.J.L.-G., I.G.-R., G.C. and B.V. Funding: This work was supported by “MINECO” and “FEDER” (AGL2013-49023-C3-1,2,3-R; AGL2017-85987-C3-1,2-R). M.J. López-Galiano was awarded with a University of Valencia Ph. D. fellowship. Acknowledgments: We thank the Genomics, Proteomics and Greenhouse Facilities from the SCSIE of the University of Valencia and the SCIC from the University Jaume I. Conflicts of Interest: The authors declare no conflict of interest. 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Machine Learning for Prediction of Outcomes in Cardiogenic Shock
Frontiers in cardiovascular medicine
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ORIGINAL RESEARCH published: 06 May 2022 doi: 10.3389/fcvm.2022.849688 ORIGINAL RESEARCH published: 06 May 2022 doi: 10.3389/fcvm.2022.849688 Machine Learning for Prediction of Outcomes in Cardiogenic Shock Fangning Rong †, Huaqiang Xiang †, Lu Qian, Yangjing Xue, Kangting Ji* and Ripen Yin* Department of Cardiology, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China Objective: The management of cardiogenic shock (CS) in the elderly remains a major clinical challenge. Existing clinical prediction models have not performed well in assessing the prognosis of elderly patients with CS. This study aims to build a predictive model, which could better predict the 30-day mortality of elderly patients with CS. Keywords: cardiogenic shock, intensive care unit, machine learning, CoxBoost, predictive model Edited by: Francois Roubille, Université de Montpellier, France †These authors have contributed equally to this work Specialty section: This article was submitted to Heart Failure and Transplantation, a section of the journal Frontiers in Cardiovascular Medicine Received: 06 January 2022 Accepted: 07 March 2022 Published: 06 May 2022 Specialty section: This article was submitted to Heart Failure and Transplantation, a section of the journal Frontiers in Cardiovascular Medicine Received: 06 January 2022 Received: 06 January 2022 Accepted: 07 March 2022 Published: 06 May 2022 Edited by: Francois Roubille, Université de Montpellier, France Reviewed by: Ole Kristian Lerche Helgestad, Odense University Hospital, Denmark Haobo Li, China-Japan Friendship Hospital, China Dion Stub, The Alfred Hospital, Australia Zhongheng Zhang, Sir Run Run Shaw Hospital, China *Correspondence: Kangting Ji jikt@wmu.edu.cn Ripen Yin 15948657@qq.com †These authors have contributed equally to this work Edited by: Francois Roubille, Université de Montpellier, France Reviewed by: Ole Kristian Lerche Helgestad, Odense University Hospital, Denmark Haobo Li, China-Japan Friendship Hospital, China Dion Stub, The Alfred Hospital, Australia Zhongheng Zhang, Sir Run Run Shaw Hospital, China *Correspondence: Kangting Ji jikt@wmu.edu.cn Ripen Yin 15948657@qq.com †These authors have contributed equally to this work Edited by: Francois Roubille, Université de Montpellier, France Edited by: Francois Roubille, Université de Montpellier, France Methods: We extracted data from the Medical Information Mart for Intensive Care III version 1.4 (MIMIC-III) as the training set and the data of validation sets were collected from the Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University. Three models, including the cox regression model, the Least Absolute Shrinkage and Selection Operator (LASSO) regression model, and the CoxBoost model, were established using the training set. Through the comparison of area under the receiver operating characteristic (ROC) curve (AUC), C index, net reclassification improvement (NRI), integrated discrimination improvement (IDI), and median improvement in risk score, the best model was selected. Then for external validation, compared the best model with the simplified acute physiology score II (SAPSII) and the CardShock risk score. Reviewed by: Ole Kristian Lerche Helgestad, Odense University Hospital, Denmark Haobo Li, China-Japan Friendship Hospital, China Dion Stub, The Alfred Hospital, Australia Zhongheng Zhang, Sir Run Run Shaw Hospital, China Reviewed by: Ole Kristian Lerche Helgestad, Odense University Hospital, Denmark Haobo Li, China-Japan Friendship Hospital, China Dion Stub, The Alfred Hospital, Australia Zhongheng Zhang, Sir Run Run Shaw Hospital, China *Correspondence: Kangting Ji jikt@wmu.edu.cn Ripen Yin 15948657@qq.com Results: A total of 919 patients were included in the study, of which 804 patients were in the training set and 115 patients were in the verification set. Using the training set, we built three models: the cox regression model including 6 predictors, the LASSO regression model including 4 predictors, and the CoxBoost model including 16 predictors. Among them, the CoxBoost model had good discrimination [AUC: 0.730; C index: 0.6958 (0.6657, 0.7259)]. Compared with the CoxBoost model, the NRI, IDI, and median improvement in risk score of other models were all < 0. In the validation set, the CoxBoost model was also well-discriminated [AUC: 0.770; C index: 0.7713 (0.6751, 0.8675)]. Compared with the CoxBoost model, the NRI, IDI, and median improvement in risk score of SAPS II and the CardShock risk score were all < 0. And we constructed a dynamic nomogram to visually display the model. BACKGROUND Medical Center (Boston, MA) and the Massachusetts Institute of Technology (Cambridge, MA), IRB approval from our institution was exempted. Data of validation sets were collected from the patient data of ICU at the Second Affiliated Hospital and Yuying Children’s Hospital of WMU. The Medical Ethics Committee of the Second Affiliated Hospital and Yuying Children’s Hospital, WMU approved the use of the patient data of the Second Affiliated Hospital and Yuying Children’s Hospital (Ethical Review Number: 2021-K-71-01). Cardiogenic shock (CS) is an extremely serious clinical condition and occurs as a consequence of cardiac pump failure, which has a high mortality (1, 2). In recent decades, the prevalence of CS has increased from 4.1 to 7.7%, and the mortality rate is up to 40% (3– 5). Age itself increases the risk of CS associated with myocardial infarction, and advanced age itself is an independent risk factor for CS (6). This suggested that for the elderly, the risk of CS will be higher. The WHO defines the elderly as over 65 years old; as this aging population continues to grow, it is crucial to pay attention to issues related to this group. Therefore, the management of CS in the elderly is a huge clinical challenge (7, 8). Finding an efficient method to early evaluate the prognosis is helpful for clinicians to identify high-risk patients in time, and make better medical decisions in clinical practice. The inclusion criteria were as follows: (1) ICU admissions age ≥65 years; (2) CS patients in MIMIC-III database and the Second Affiliated Hospital and Yuying Children’s Hospital of WMU. Among them, patients from the MIMIC-III database were diagnosed according to the International Classification of Diseases, Ninth Revision (ICD-9) diagnostic code 785.51 or 998.01, and patients from the Second Affiliated Hospital and Yuying Children’s Hospital of WMU were selected by unified diagnostic criteria: minimum systolic blood pressure (SBP) <90 mmHg, or need of vasopressors therapy or signs of hypoperfusion. Only records of the first ICU visit were selected for analysis to eliminate duplicate data. The specific process was shown in Figure 1. However, in the elderly population, information on the prevalence, determinants, and prognostic factors of CS is scarce. Citation: Rong F, Xiang H, Qian L, Xue Y, Ji K and Yin R (2022) Machine Learning for Prediction of Outcomes in Cardiogenic Shock. Front. Cardiovasc. Med. 9:849688. doi: 10.3389/fcvm.2022.849688 Conclusion: In conclusion, this study showed that in predicting the 30-day mortality of elderly CS patients, the CoxBoost model was superior to the Cox regression model, LASSO regression model, SAPS II, and the CardShock risk score. May 2022 | Volume 9 | Article 849688 Frontiers in Cardiovascular Medicine | www.frontiersin.org Machine Learning Predicts Cardiogenic Shock Rong et al. METHODS Data Source and Research Population Data Source and Research Population We extracted data from MIMIC-III database version 1.4 as the training set, which is a public and free intensive care unit (ICU) database (20). Since the MIMIC-III database was approved by the Institutional Review Boards (IRB) of Beth Israel Deaconess Missing Data Variables with missing values ≥40% were excluded directly. We used multiple interpolations to deal with missing variables <40%. Patients with individual data missing by more than 10% or outliers [values above the mean of 3 standard deviations (SD)] were excluded. In the training set and the verification set, we carried out the above data processing respectively. Data Extraction and Outcome Data Extraction and Outcome We extracted the following information of patients on the first day of admission: (1) demographic information such as age, gender, ethnicity, and pathogeny; (2) vital sign data including heart rate, SBP, mean blood pressure (MBP), diastolic blood pressure (DBP), respiratory rate, temperature, and arterial oxygen saturation (SpO2); (3) laboratory data including white blood cell (WBC) count, red cell distribution width (RDW), hemoglobin, hematocrit, platelet, activated partial thromboplastin time (APTT), international normalized ratio (INR), prothrombin time (PT), anion gap, bicarbonate, glucose, blood lactic acid, serum creatinine, serum urea nitrogen, serum sodium, and serum potassium; (4) comorbidities including congestive heart failure, atrial fibrillation, coronary heart disease, renal failure, liver disease, stroke, tumor, chronic obstructive pulmonary disease (COPD), acute respiratory distress syndrome (ARDS), and pneumonia; (5) traditional severity scores including simplified acute physiology score II (SAPSII); (6) As well as ejection fraction and the use of the vasopressor. If multiple measurements were made in the first 24 h, the vital signs and the laboratory data were based on the results of the first examination. The endpoint was 30-day mortality. Compared with traditional forecasting methods, novel machine learning techniques can process high-dimensional data, identify complex relationships between variables and develop precise clinical prediction models, which have received more and more attention and recognition from clinicians (11, 12). There are many studies that apply machine learning to the evaluation of a variety of diseases and with good results (13–15). It has also been used in other medical auxiliary disciplines, such as imaging and anesthesiology (16, 17). Hou et al. (18) used XGboost machine learning to predict 30-days mortality of patients with sepsis. Weyer and Binder (19) developed a weighting approach for judging the effect of patient strata on high-dimensional risk prediction signatures using CoxBoost. Therefore, we hope to use the CoxBoost method to help us better predict the prognosis of elderly patients with CS. Based on the Medical Information Mart for Intensive Care III (MIMIC-III) database and the Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University (WMU), the goal of this study is to build a predictive model using CoxBoost machine learning, which can predict the 30-day mortality of elderly patients with CS. BACKGROUND Some researchers have constructed risk prediction models to facilitate risk assessment and predict the mortality of CS, such as the CardShock risk score (9, 10), but these models still have some shortcomings, such as the calculation methods are complicated, or the included predictors of some models are not all objective data. For example, in the CardShock risk score, the evaluation of the patients’ consciousness depends on the subjective judgment of clinicians. Besides, they are not completely built for the elderly population, the evaluation effect of the prognosis of the elderly needs further assessment. Baseline Characteristics After excluding the patients who did not meet the inclusion criteria, a total of 919 patients were included in this study. Among them, 804 were from the training set and 115 were from the verification set. We divided these patients into two groups based on their death or survival in 30-day. Table 1 summarizes the basic distribution of all the target patients’ baseline characteristics, vital signs, comorbidities, and other indicators. In the training set, the difference in age, SBP, MBP, DBP, respiratory rate, temperature, SpO2, WBC count, RDW, INR, PT, anion gap, bicarbonate, blood lactic acid, serum creatinine, serum urea nitrogen, serum potassium, tumor, SAPSII score, and length of stay in the hospital between the two groups was statistically significant. In the validation set, the difference in temperature, PT, bicarbonate, blood lactic acid, congestive heart failure, pneumonia, SAPSII score, and length of stay in hospital between the two groups was statistically significant. Statistical Analysis The continuous variables were expressed as mean ± SD of the normal distribution, while the non-normal continuous variables Frontiers in Cardiovascular Medicine | www.frontiersin.org May 2022 | Volume 9 | Article 849688 2 Rong et al. Machine Learning Predicts Cardiogenic Shock FIGURE 1 | Flowchart of patient selection. FIGURE 1 | Flowchart of patient selection. were expressed as median (interquartile range). Wilcoxon W test or Kruskal Wallis test was used to assess the differences among groups. The variance inflation factor (VIF) was calculated to verify whether multicollinearity existed. (IDI), and median improvement in risk score were used to choose the best model. In the validation set, AUC, C index, NRI, IDI, and median improvement in risk score were also used to evaluate the CoxBoost model, SAPSII score model, and the CardShock risk score model for external validation. We constructed a DynNom- based dynamic nomogram to visually display the final model. R software version 4.0.3 was used for all statistical analyses. P < 0.05 was considered statistically significant. y y In the model development stage, three models were established using the training set: the cox regression model, the Least Absolute Shrinkage and Selection Operator (LASSO) regression model, and the CoxBoost model. In the Cox regression model, we used the monofactor analysis to pick out targeted predictors and screened the predictors twice using multiple regression analysis. After two rounds of screening, the predictive factors were finally incorporated into the Cox regression model. The main idea of LASSO is to construct a first-order penalty function to obtain a refined model and to carry out feature screening by finally determining the coefficients of some variables to be 0. In the LASSO regression model, we determined the cutoffvalue based on ten-folds cross-validation to select the most useful predictive variables to form the LASSO regression model. CoxBoost (https://github.com/binderh/CoxBoost) is used to fit a Cox proportional hazards model by componentizing likelihood- based boosting, which is particularly suitable for models with a large number of predictors and allows for mandatory covariates with unpenalized parameter estimates. In contrast to gradient boosting, CoxBoost is not based on gradients of loss functions but adapts the offset-based boosting approach for estimating Cox proportional hazards models (21). According to the CoxBoost machine learning analysis of the importance of the predictors, we select targeted variables incorporated into the CoxBoost regression model. Frontiers in Cardiovascular Medicine | www.frontiersin.org Model Development These three models were evaluated together with the classic SAPSII score model. The area under receiver operating characteristic (ROC) curve (AUC), C index, net reclassification improvement (NRI), integrated discrimination improvement Based on the training set, we developed three models. In the traditional cox regression model, we first used the monofactor analysis to pick out 8 predictors (P < 0.05), May 2022 | Volume 9 | Article 849688 Frontiers in Cardiovascular Medicine | www.frontiersin.org 3 Machine Learning Predicts Cardiogenic Shock Rong et al. TABLE 1 | Baseline characteristics of the study population of 30-day all-cause death. Model Development Training set Validation set Survival in 30-day Death in 30-day P Survival in 30-day Death in 30-day P Number of patients 500 304 53 62 Pathogeny / 0.392 Acute coronary syndrome, n (%) / / 47 (88.68) 56 (90.32) Valvopathy, n (%) / / 2 (3.77) 1 (1.61) Cardiomyopathy, n (%) / / 2 (3.77) 4 (6.45) Heart failure, n (%) / / 0 (0.00) 1 (1.61) Atrial fibrillation, n (%) / / 2 (3.77) 0 (0.00) Clinical parameters Age, years 77.50 ± 7.39 80.01 ± 7.51 <0.001 76.28 ± 6.47 78.56 ± 7.62 0.089 Sex, n (%) 0.623 0.498 Female 223 (44.60) 141 (46.38) 24 (45.28) 32 (51.61) Male 277 (55.40) 163 (53.62) 29 (54.72) 30 (48.39) Ethnicity, n (%) 0.279 / White 346 (69.20) 217 (71.38) / / Black 31 (6.20) 11 (3.62) / / Others 123 (24.60) 76 (25.00) 53 (100) 62 (100) Vital signs Heart rate, beats/minute 87.09 ± 16.08 89.44 ± 17.29 0.051 99.75 ± 23.97 104.05 ± 19.98 0.299 SBP, mmHg 104.97 ± 13.53 100.44 ± 13.57 <0.001 124.58 ± 33.65 114.49 ± 28.03 0.083 MBP, mmHg 72.45 ± 8.99 69.70 ± 9.73 <0.001 89.36 ± 24.28 83.15 ± 21.53 0.150 DBP, mmHg 55.25 ± 8.85 53.21 ± 9.33 0.002 71.75 ± 21.96 67.48 ± 20.81 0.288 Respiratory rate, times/minute 19.50 ± 3.84 20.49 ± 4.27 <0.001 20.51 ± 6.11 23.02 ± 7.94 0.065 Temperature, ◦C 36.73 ± 0.76 36.53 ± 1.08 0.003 36.78 ± 0.88 36.40 ± 0.97 0.034 SpO2, % 96.69 ± 4.09 95.31 ± 6.78 <0.001 95.36 ± 8.62 94.48 ± 7.78 0.575 Laboratory parameters WBC count, 109/L 12.50 ± 5.69 14.20 ± 7.40 <0.001 15.03 ± 5.52 15.80 ± 5.63 0.466 RDW, % 15.07 ± 1.93 15.62 ± 2.57 <0.001 14.38 ± 1.72 14.03 ± 1.54 0.262 Hemoglobin, g/dl 11.07 ± 2.18 11.08 ± 2.02 0.944 11.71 ± 2.81 11.65 ± 2.14 0.904 Hematocrit, % 33.40 ± 6.37 33.58 ± 6.04 0.704 0.36 ± 0.08 0.36 ± 0.07 0.913 Platelet, 109/L 229.84 ± 110.60 223.86 ± 113.18 0.461 242.68 ± 93.47 210.02 ± 101.88 0.081 APTT, s 53.02 ± 35.10 58.47 ± 49.84 0.069 99.00 ± 65.95 94.00 ± 61.63 0.681 INR 1.78 ± 1.54 2.16 ± 2.20 0.004 1.54 ± 1.59 1.75 ± 1.03 0.403 PT, s 17.49 ± 9.65 20.11 ± 15.97 0.004 16.09 ± 3.00 19.31 ± 7.89 0.006 Anion gap, mmol/L 16.44 ± 4.47 18.84 ± 5.34 <0.001 15.99 ± 5.96 19.41 ± 6.41 0.070 Bicarbonate, mmol/L 22.11 ± 4.69 20.40 ± 6.08 <0.001 18.96 ± 5.20 15.67 ± 6.09 0.003 Glucose, mg/dl 181.99 ± 94.06 183.43 ± 106.79 0.842 181.27 ± 91.40 205.57 ± 71.03 0.212 Blood lactic acid, mmol/L 3.09 ± 2.68 4.27 ± 3.64 <0.001 4.34 ± 4.09 7.64 ± 5.73 <0.001 Serum creatinine, mg/dl 1.76 ± 1.39 2.14 ± 1.52 <0.001 1.67 ± 1.35 1.86 ± 1.20 0.420 Serum urea nitrogen, mg/dl 35.57 ± 21.61 43.71 ± 27.42 <0.001 31.51 ± 20.86 36.33 ± 23.95 0.262 Serum sodium, mg/dl 137.11 ± 4.81 136.97 ± 5.82 0.705 138.06 ± 7.44 138.96 ± 5.76 0.468 Serum potassium, mg/dl 4.32 ± 0.79 4.46 ± 1.05 0.039 6.09 ± 13.73 4.34 ± 0.78 0.319 Comorbidities Congestive heart failure, n (%) 109 (21.80) 70 (23.03) 0.685 3 (5.66) 14 (22.58) 0.011 Atrial fibrillation, n (%) 258 (51.60) 146 (48.03) 0.326 9 (16.98) 18 (29.03) 0.129 Coronary heart disease, n (%) 151 (30.20) 84 (27.63) 0.437 44 (83.02) 53 (85.48) 0.717 Renal failure, n (%) 118 (23.60) 77 (25.33) 0.579 19 (35.85) 27 (43.55) 0.401 Liver disease, n (%) 7 (1.40) 7 (2.30) 0.343 8 (15.09) 10 (16.13) 0.879 Stroke, n (%) 14 (2.80) 4 (1.32) 0.168 17 (32.08) 15 (24.19) 0.347 Tumor, n (%) 41 (8.20) 42 (13.82) 0.011 2 (3.77) 2 (3.23) 0.873 (Continued) TABLE 1 | Baseline characteristics of the study population of 30-day all-cause death. Model Development Pneumonia, n (%) 156 (31.20) 98 (32.24) 0.759 40 (75.47) 27 (43.55) <0.001 Ejection fraction, % / / / 41.74 ± 10.89 42.04 ± 13.93 0.905 Vasopressor, n (%) 416 (83.20) 266 (87.50) 0.099 50 (94.34) 58 (93.55) 0.860 Severity of illness SAPSII score 47.36 ± 13.29 55.61 ± 14.98 <0.001 42.13 ± 8.00 59.94 ± 15.07 <0.001 Length of stay in hospital, day 14.72 ± 12.54 6.89 ± 6.64 <0.001 21.12 ± 13.23 6.73 ± 11.01 <0.001 The data of the training set came from MIMIC-III database version 1.4; the data of validation set came from the patient data of ICU at the Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University. SBP, systolic blood pressure; DBP, diastolic blood pressure; MBP, mean blood pressure; SpO2, arterial oxygen saturation; WBC, white blood cell; RDW, red cell distribution width; APTT, activated partial thromboplastin time; INR, international normalized ratio; PT, prothrombin time; COPD, chronic obstructive pulmonary disease; ARDS, acute respiratory distress syndrome; SAPSII, simplified acute physiology score II. TABLE 2 | Cox regression model. TABLE 3 | LASSO regression model. TABLE 3 | LASSO regression model. HR (95%CI) P Clinical parameters Age 1.0386 (1.0231–1.0544) <0.0001 Vital signs SBP 0.9846 (0.9765–0.9928) 0.0002 Laboratory parameters Anion gap 1.0588 (1.0342–1.0840) <0.0001 Blood lactic acid 1.0433 (1.0050–1.0830) 0.0262 SBP, systolic blood pressure. TABLE 2 | Cox regression model. HR (95%CI) P Clinical parameters Age 1.0386 (1.0229–1.0545) <0.0001 Vital signs Heart rate 1.0118 (1.0047–1.0189) 0.0010 Temperature 0.7894 (0.6897–0.9036) 0.0006 Laboratory parameters WBC count 1.0281 (1.0110–1.0454) Anion gap 1.0580 (1.0332–1.0833) 0.0012 Blood lactic acid 1.0548 (1.0168–1.0943) <0.0001 WBC, white blood cell. TABLE 3 | LASSO regression model. model had good discrimination (AUC: 0.730) in the training set, which was better than others (Figure 2A). Besides, using the CoxBoost model as a reference, the Cox regression model, LASSO regression model, and SAPSII score model did worse in the C index (cox regression model: 0.6835; LASSO regression model: 0.6786; SAPSII: 0.6490), NRI (cox regression model: −0.0590; LASSO regression model: −0.1480; SAPSII: −0.1630), IDI (cox regression model: −0.0040; LASSO regression model: −0.0300; SAPSII: −0.0530), and median improvement in risk score (cox regression model: −0.0040; LASSO regression model:−0.0220; SAPSII: −0.0570) (Table 5). Therefore, we choose the CoxBoost model as the target model. the results are presented in Supplementary Table 1. Then, we screened the predictors twice using multiple regression analysis (Supplementary Table 2). Model Development The final Cox regression model was shown in Table 2, a total of 6 predictors including age, heart rate, temperature, WBC count, anion gap, and blood lactic acid. In the LASSO regression model, we determined the cutoff value based on the Loess smoothing function and the Youden index. In this way, 36 features were reduced to 4 potential predictors (Supplementary Table 3), including age, SBP, anion gap, and blood lactic acid (Table 3). According to the CoxBoost machine learning analysis of the importance of the predictors (Supplementary Table 4), we selected 17 predictors (P < 0.05) to construct the CoxBoost model, considering the existence of multicollinearity, we removed MBP. The final model was shown in Table 4, including age, heart rate, SBP, DBP, respiratory rate, temperature, SpO2, WBC count, RDW, INR, PT, anion gap, bicarbonate, blood lactic acid, serum urea nitrogen, and tumor. VIF proved there was no significant multicollinearity in all three models (VIF ≤3). Frontiers in Cardiovascular Medicine | www.frontiersin.org SBP, systolic blood pressure; DBP, diastolic blood pressure; MBP, mean blood pressure; SpO2, arterial oxygen saturation; WBC, white blood cell; RDW, red cell distribution width; APTT, activated partial thromboplastin time; INR, international normalized ratio; PT, prothrombin time; COPD, chronic obstructive pulmonary disease; ARDS, acute respiratory distress syndrome; SAPSII, simplified acute physiology score II. Model Development According to the CoxBoost machine learning analysis of the importance of the predictors (Supplementary Table 4), we selected 17 predictors (P < 0.05) to construct the CoxBoost model, considering the existence of multicollinearity, we removed MBP. The final model was shown TABLE 3 | LASSO regression model. HR (95%CI) P Clinical parameters Age 1.0386 (1.0231–1.0544) <0.0001 Vital signs SBP 0.9846 (0.9765–0.9928) 0.0002 Laboratory parameters Anion gap 1.0588 (1.0342–1.0840) <0.0001 Blood lactic acid 1.0433 (1.0050–1.0830) 0.0262 SBP, systolic blood pressure. model had good discrimination (AUC: 0.730) in the training set, which was better than others (Figure 2A). Besides, using the CoxBoost model as a reference, the Cox regression model, LASSO regression model, and SAPSII score model did worse in the C index (cox regression model: 0.6835; LASSO regression model: 0.6786; SAPSII: 0.6490), NRI (cox regression model: −0.0590; LASSO regression model: −0.1480; SAPSII: −0.1630), IDI (cox regression model: −0.0040; LASSO regression model: −0.0300; SAPSII: −0.0530), and median improvement in risk score (cox regression model: −0.0040; LASSO regression model:−0.0220; SAPSII: −0.0570) (Table 5). Therefore, we choose the CoxBoost model as the target model. Model Comparisons In the validation set, we further evaluated and validated the CoxBoost model. The CoxBoost model was well-discriminated TABLE 1 | Continued Training set Validation set Survival in 30-day Death in 30-day P Survival in 30-day Death in 30-day P COPD, n (%) 6 (1.20) 4 (1.32) 0.886 2 (3.77) 1 (1.61) 0.469 ARDS, n (%) 6 (1.20) 7 (2.30) 0.229 1 (1.89) 1 (1.61) 0.911 Pneumonia, n (%) 156 (31.20) 98 (32.24) 0.759 40 (75.47) 27 (43.55) <0.001 Ejection fraction, % / / / 41.74 ± 10.89 42.04 ± 13.93 0.905 Vasopressor, n (%) 416 (83.20) 266 (87.50) 0.099 50 (94.34) 58 (93.55) 0.860 Severity of illness SAPSII score 47.36 ± 13.29 55.61 ± 14.98 <0.001 42.13 ± 8.00 59.94 ± 15.07 <0.001 Length of stay in hospital, day 14.72 ± 12.54 6.89 ± 6.64 <0.001 21.12 ± 13.23 6.73 ± 11.01 <0.001 The data of the training set came from MIMIC-III database version 1.4; the data of validation set came from the patient data of ICU at the Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University. Model Development SBP systolic blood pressure; DBP diastolic blood pressure; MBP mean blood pressure; SpO2 arterial oxygen saturation; WBC white blood cell; RDW red cell distribution width; TABLE 1 | Continued Training set Validation set Survival in 30-day Death in 30-day P Survival in 30-day Death in 30-day P COPD, n (%) 6 (1.20) 4 (1.32) 0.886 2 (3.77) 1 (1.61) 0.469 ARDS, n (%) 6 (1.20) 7 (2.30) 0.229 1 (1.89) 1 (1.61) 0.911 Pneumonia, n (%) 156 (31.20) 98 (32.24) 0.759 40 (75.47) 27 (43.55) <0.001 Ejection fraction, % / / / 41.74 ± 10.89 42.04 ± 13.93 0.905 Vasopressor, n (%) 416 (83.20) 266 (87.50) 0.099 50 (94.34) 58 (93.55) 0.860 Severity of illness SAPSII score 47.36 ± 13.29 55.61 ± 14.98 <0.001 42.13 ± 8.00 59.94 ± 15.07 <0.001 Length of stay in hospital, day 14.72 ± 12.54 6.89 ± 6.64 <0.001 21.12 ± 13.23 6.73 ± 11.01 <0.001 The data of the training set came from MIMIC-III database version 1.4; the data of validation set came from the patient data of ICU at the Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University. SBP, systolic blood pressure; DBP, diastolic blood pressure; MBP, mean blood pressure; SpO2, arterial oxygen saturation; WBC, white blood cell; RDW, red cell distribution width; APTT, activated partial thromboplastin time; INR, international normalized ratio; PT, prothrombin time; COPD, chronic obstructive pulmonary disease; ARDS, acute respiratory distress syndrome; SAPSII, simplified acute physiology score II. TABLE 2 | Cox regression model. HR (95%CI) P Clinical parameters Age 1.0386 (1.0229–1.0545) <0.0001 Vital signs Heart rate 1.0118 (1.0047–1.0189) 0.0010 Temperature 0.7894 (0.6897–0.9036) 0.0006 Laboratory parameters WBC count 1.0281 (1.0110–1.0454) Anion gap 1.0580 (1.0332–1.0833) 0.0012 Blood lactic acid 1.0548 (1.0168–1.0943) <0.0001 WBC hit bl d ll TABLE 3 | LASSO regression model. HR (95%CI) P Clinical parameters Age 1.0386 (1.0231–1.0544) <0.0001 Vital signs SBP 0.9846 (0.9765–0.9928) 0.0002 Laboratory parameters Anion gap 1.0588 (1.0342–1.0840) <0.0001 Blood lactic acid 1.0433 (1.0050–1.0830) 0.0262 SBP, systolic blood pressure. Model Development May 2022 | Volume 9 | Article 849688 Frontiers in Cardiovascular Medicine | www.frontiersin.org 4 Machine Learning Predicts Cardiogenic Shock Rong et al. Rong et al. Machine Learning Predicts Cardiogenic Shock TABLE 1 | Continued Training set Validation set Survival in 30-day Death in 30-day P Survival in 30-day Death in 30-day P COPD, n (%) 6 (1.20) 4 (1.32) 0.886 2 (3.77) 1 (1.61) 0.469 ARDS, n (%) 6 (1.20) 7 (2.30) 0.229 1 (1.89) 1 (1.61) 0.911 Pneumonia, n (%) 156 (31.20) 98 (32.24) 0.759 40 (75.47) 27 (43.55) <0.001 Ejection fraction, % / / / 41.74 ± 10.89 42.04 ± 13.93 0.905 Vasopressor, n (%) 416 (83.20) 266 (87.50) 0.099 50 (94.34) 58 (93.55) 0.860 Severity of illness SAPSII score 47.36 ± 13.29 55.61 ± 14.98 <0.001 42.13 ± 8.00 59.94 ± 15.07 <0.001 Length of stay in hospital, day 14.72 ± 12.54 6.89 ± 6.64 <0.001 21.12 ± 13.23 6.73 ± 11.01 <0.001 The data of the training set came from MIMIC-III database version 1.4; the data of validation set came from the patient data of ICU at the Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University. SBP, systolic blood pressure; DBP, diastolic blood pressure; MBP, mean blood pressure; SpO2, arterial oxygen saturation; WBC, white blood cell; RDW, red cell distribution width; APTT, activated partial thromboplastin time; INR, international normalized ratio; PT, prothrombin time; COPD, chronic obstructive pulmonary disease; ARDS, acute respiratory distress syndrome; SAPSII, simplified acute physiology score II. TABLE 2 | Cox regression model. HR (95%CI) P Clinical parameters Age 1.0386 (1.0229–1.0545) <0.0001 Vital signs Heart rate 1.0118 (1.0047–1.0189) 0.0010 Temperature 0.7894 (0.6897–0.9036) 0.0006 Laboratory parameters WBC count 1.0281 (1.0110–1.0454) Anion gap 1.0580 (1.0332–1.0833) 0.0012 Blood lactic acid 1.0548 (1.0168–1.0943) <0.0001 WBC, white blood cell. the results are presented in Supplementary Table 1. Then, we screened the predictors twice using multiple regression analysis (Supplementary Table 2). The final Cox regression model was shown in Table 2, a total of 6 predictors including age, heart rate, temperature, WBC count, anion gap, and blood lactic acid. In the LASSO regression model, we determined the cutoff value based on the Loess smoothing function and the Youden index. In this way, 36 features were reduced to 4 potential predictors (Supplementary Table 3), including age, SBP, anion gap, and blood lactic acid (Table 3). Model Comparisons In the validation set, we further evaluated and validated the CoxBoost model. The CoxBoost model was well-discriminated in the external validation set (AUC: 0.770), which was greater than the SAPSII score model (AUC: 0.724) and the CardShock risk score (Supplementary Table 5) (AUC: 0.677) (Figure 2B). In the C index, the CoxBoost model has the best performance (C index: CoxBoost model 0.7713, SAPSII score model 0.7341, CardShock risk score 0.6628, Table 5). Using the CoxBoost model as a reference, the NRI of the SAPSII score model These three models were evaluated together with the classic SAPSII score model to choose the best one. The CoxBoost Frontiers in Cardiovascular Medicine | www.frontiersin.org May 2022 | Volume 9 | Article 849688 5 Machine Learning Predicts Cardiogenic Shock Rong et al. respectively (Table 5), all of which suggested that the CoxBoost model was better. and the CardShock risk score were −0.3620 and −0.3480, the IDI of the two models were −0.1740 and −0.2490, and the median improvement in risk scores were −0.2380 and −0.1910 median improvement in risk scores were −0.2380 and −0.1910 TABLE 4 | CoxBoost model. Variables P Clinical parameters Age <0.0001 Vital signs Heart rate 0.0224 SBP <0.0001 DBP 0.0204 Respiratory rate 0.0020 Temperature 0.0020 SpO2 <0.0001 Laboratory parameters WBC count <0.0001 RDW 0.0020 INR 0.0143 PT 0.0082 Anion gap <0.0001 Bicarbonate 0.0061 Blood lactic acid <0.0001 Serum urea nitrogen 0.0020 Comorbidities Tumor 0.0143 SBP, systolic blood pressure; DBP, diastolic blood pressure; SpO2, arterial oxygen saturation; WBC, white blood cell; RDW, red cell distribution width; INR, international normalized ratio; PT, prothrombin time. Model Presentation p TABLE 4 | CoxBoost model. Variables P Clinical parameters Age <0.0001 Vital signs Heart rate 0.0224 SBP <0.0001 DBP 0.0204 Respiratory rate 0.0020 Temperature 0.0020 SpO2 <0.0001 Laboratory parameters WBC count <0.0001 RDW 0.0020 INR 0.0143 PT 0.0082 Anion gap <0.0001 Bicarbonate 0.0061 Blood lactic acid <0.0001 Serum urea nitrogen 0.0020 Comorbidities Tumor 0.0143 SBP, systolic blood pressure; DBP, diastolic blood pressure; SpO2, arterial oxygen saturation; WBC, white blood cell; RDW, red cell distribution width; INR, international normalized ratio; PT, prothrombin time. We constructed a DynNom-based dynamic nomogram to visually display the final model (Table 4) (https://CoxBoost- model.shinyapps.io/DynNomapp/), which could directly obtain the patient’s in-hospital mortality by inputting the values of the relevant predictors. The final model formula and its regression coefficients was as follows: survival possibility in 30-day = 0.0339 ∗age + 0.0104 ∗heart rate – 0.0070 ∗SBP – 0.0127 ∗DBP + 0.0126 ∗respiratory rate – 0.1959 ∗temperature – 0.0112 ∗SpO2 + 0.0250 ∗WBC count + 0.0422 ∗RDW + 0.0176 ∗INR + 0.0021 ∗PT + 0.0355 ∗anion gap – 0.0055 ∗bicarbonate + 0.0463 ∗blood lactic acid + 0.0026 ∗serum urea nitrogen + 0.2125 ∗ (tumor = 1). DISCUSSION Based on the data of the training set, we developed three models altogether: the Cox regression model, the LASSO regression model, and the CoxBoost model. After extensive evaluation, the CoxBoost model was chosen as the best model. The model includes 16 predictors, which can simply and effectively predict the 30-day mortality of CS patients. In external validation, the discrimination of the CoxBoost model was better than the SAPSII and the CardShock risk score. And we developed a dynamic nomogram. Over the years, various scoring systems have been widely used in the ICU (22, 23). However, in order to be suitable for various types of critical patients, the sensitivity and specificity of SAPSII are low. And the accuracy of the results of the assessment SBP, systolic blood pressure; DBP, diastolic blood pressure; SpO2, arterial oxygen saturation; WBC, white blood cell; RDW, red cell distribution width; INR, international normalized ratio; PT, prothrombin time. FIGURE 2 | (A) Receiver operating characteristic (ROC) comparison of training set models. (B) ROC comparison of validation set models. | (A) Receiver operating characteristic (ROC) comparison of training set models. (B) ROC comparison of validation set models. Frontiers in Cardiovascular Medicine | www.frontiersin.org May 2022 | Volume 9 | Article 849688 Machine Learning Predicts Cardiogenic Shock Rong et al. TABLE 5 | Model comparison. Model C index (95%CI) NRI IDI Median improvement in risk score Training set CoxBoost model 0.6958 (0.6657, 0.7259) Cox regression model 0.6835 (0.6529, 0.7141)* −0.0590 −0.0040* −0.0040 LASSO regression model 0.6786 (0.6489, 0.7084)* −0.1480** −0.0300** −0.0220** SAPSII score model 0.6490 (0.6181, 0.6799)** −0.1630** −0.0530** −0.0570** Validation set CoxBoost model 0.7713 (0.6751, 0.8675) SAPSII score model 0.7341 (0.6448, 0.8234)* −0.3620* −0.1740 −0.2380 The CardShock risk Score model 0.6628 (0.5518, 0.7738)** −0.3480* −0.2490* −0.1910* *Compared with the CoxBoost model P < 0.05; **Compared with the CoxBoost model P < 0.0001. NRI, net reclassification improvement; IDI, integrated discrimination improvement. the anion gap was identified as a significant predictor of poor prognosis in patients with CS (34). It could be linked to lactic acid levels and keto, because elevated serum anion gap is usually associated with excess production of organic acid anions and reduced anion excretion (35). More experiments are needed to confirm this. system depends on the experience of practitioners. There are also some small studies that used SASPAII to predict the prognosis of patients with CS (24, 25). DISCUSSION But the integrated ICU severity score cannot accurately and reliably predict the mortality of elderly patients with CS. The CoxBoost model constructed in this study was targeted at elderly patients with CS, with higher sensitivity and specificity. In the results of our study, it can be found that the performance of the CoxBoost model was relatively better than SAPSII in the both training set and validation set. This research was a multi-center retrospective study, the main advantage was that the CoxBoost model was used for the first time to predict the 30-day mortality of elderly patients with CS. Multiple validation methods were used to compare the CoxBoost model with traditional regression analysis, LASSO regression analysis, and clinical scoring systems. The dynamic nomogram was developed to facilitate users. However, there are some limitations in this study: first, due to the relatively low incidence of CS, the sample size of patients selected in our study was relatively small. Second, there are potential differences between the training set and the validation set in terms of patient demography and research years. Third, the objective limitations of the database may produce bias. Such as the use of diagnostic codes to select patients may occur selective bias to a certain extent. Or cause a lack of potential predictors. Fourth, there was no further exploration of the database, which may make the model imperfect. We will expand the sample size and refine the sample data to conduct more in-depth research to validate our model. Overall, we believe that the model developed in this study may be useful in evaluating the prognosis of elderly patients with CS. g In recent years, models have been developed specifically to assess the prognosis of patients with CS, but also have some drawbacks (26, 27). For example, the IABP-SHOCK II study established a scoring system for predicting 30-day mortality in patients with CS (9), but it is more suitable for patients with CS after emergency percutaneous coronary intervention (PCI). The CardShock risk score (10) need complicated calculation and scoring when it is used and partly depend on the subjective judgment of clinicians. Hongisto et al. evaluated the prognostic ability of two models in elderly patients with CS and the results showed that the predictive power was not very good (28). CONCLUSION The 16 factors that made up the CoxBoost model included all the predictive factors in the cox model and LASSO model, which showed that the CoxBoost approach has better performance and accuracy. In the factors that made up the CoxBoost model, blood lactic acid, WBC count, and anion gap were the three most important laboratory indicators. Among them, blood lactate was recognized as an important independent prognostic factor for CS (29–31). WBC count could assess the prognosis of patients, which may be related to the systemic inflammatory response caused by hypoperfusion during CS (32, 33). But the mechanism for the anion gap’s prediction was unclear. Zhang et al. found that In conclusion, this study showed that in predicting the 30-day mortality of elderly patients with CS, the CoxBoost model was superior to the Cox regression model, LASSO regression model, SAPSII, and the CardShock risk score. It is a simple and objective score that can be applied in clinical practice. DISCUSSION The CoxBoost model was applicable to all types of elderly patients, and external verification showed that its prediction ability was better than the CardShock risk score. Last but not least, the CoxBoost model could evaluate the short-term prognosis of elderly CS patients by simply collecting patients’ vital signs, simple laboratory data, and relevant medical history at admission, all the selected predictors are objective data. The dynamic nomogram further simplified the use of the model through an easy-to-use web page. 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ACKNOWLEDGMENTS We thank for the Second Affiliated Hospital and Yuying Children’s Hospital of WMU for supporting our work. We thank for the Second Affiliated Hospital and Yuying Children’s Hospital of WMU for supporting our work. SUPPLEMENTARY MATERIAL KJ took responsibility for the content of the manuscript, including the data and analysis. FR had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis. The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fcvm. 2022.849688/full#supplementary-material ETHICS STATEMENT All authors contributed substantially to the study design, data analysis and interpretation, and the writing of the manuscript. All authors contributed to the article and approved the submitted version. 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(2007) 114:176–82. doi: 10.1016/j.ijcard.2006.01.024 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. 30. Attaná P, Lazzeri C, Chiostri M, Picariello C, Gensini GF, Valente S. Lactate clearance in cardiogenic shock following ST elevation myocardial infarction: a pilot study. Frontiers in Cardiovascular Medicine | www.frontiersin.org REFERENCES Acute Card Care. (2012) 14:20–6. doi: 10.3109/17482941.2011.655293 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. 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. 31. Li CL, Wang H, Jia M, Ma N, Meng X, Hou XT. The early dynamic behavior of lactate is linked to mortality in postcardiotomy patients with extracorporeal membrane oxygenation support: a retrospective observational study. J Thorac Cardiovasc Surg. (2015) 149:1445–50. doi: 10.1016/j.jtcvs.2014. 11.052 32. Kohsaka S, Menon V, Lowe AM, Lange M, Dzavik V, Sleeper LA, et al. Systemic inflammatory response syndrome after acute myocardial infarction complicated by cardiogenic shock. Arch Intern Med. (2005) 165:1643– 50. doi: 10.1001/archinte.165.14.1643 Copyright © 2022 Rong, Xiang, Qian, Xue, Ji and Yin. 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. 33. Stegman BM, Newby LK, Hochman JS, Ohman EM. Post-myocardial infarction cardiogenic shock is a systemic illness in need of systemic treatment: is therapeutic hypothermia one possibility? J Am Coll Cardiol. (2012) 59:644–7. doi: 10.1016/j.jacc.2011.11.010 May 2022 | Volume 9 | Article 849688 Frontiers in Cardiovascular Medicine | www.frontiersin.org 9
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Open Access 2007 Teschendorff et al. Volume 8, Issue 8, Article R157 Research An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer Andrew E Teschendorff*, Ahmad Miremadi†, Sarah E Pinder†, Ian O Ellis‡ and Carlos Caldas*† Addresses: *Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK. †Cambridge Breast Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK. ‡Histopathology, Nottingham City Hospital NHS Trust and Department of Pathology, University of Nottingham, Nottingham NG5 1PB, UK. Correspondence: Andrew E Teschendorff. Email: aet21@cam.ac.uk. Carlos Caldas. Email: cc234@cam.ac.uk Published: 2 August 2007 Genome Biology 2007, 8:R157 (doi:10.1186/gb-2007-8-8-r157) The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2007/8/8/R157 Published: 2 August 2007 Genome Biology 2007, 8:R157 (doi:10.1186/gb-2007-8-8-r157) Received: 14 March 2007 Revised: 25 June 2007 Accepted: 2 August 2007 © 2007 Teschendorff 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. Breast cancer prognosis <p>A feature selection method was used in an analysis of three major microarray expression datasets to identify molecular subclasses and prognostic markers in estrogen receptor negative breast cancer showing that it is a heterogeneous disease with at least four main sub types </p> Open Access 2007 Teschendorff et al. Volume 8, Issue 8, Article R157 Research An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer Andrew E Teschendorff*, Ahmad Miremadi†, Sarah E Pinder†, Ian O Ellis‡ and Carlos Caldas*† Addresses: *Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK. †Cambridge Breast Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK. ‡Histopathology, Nottingham City Hospital NHS Trust and Department of Pathology, University of Nottingham, Nottingham NG5 1PB, UK. Correspondence: Andrew E Teschendorff. Email: aet21@cam.ac.uk. Carlos Caldas. Email: cc234@cam.ac.uk © 2007 Teschendorff et al.; licensee BioMed Central Ltd. Published: 2 August 2007 Genome Biology 2007, 8:R157 (doi:10.1186/gb-2007-8-8-r157) Received: 14 March 2007 Revised: 25 June 2007 Accepted: 2 August 2007 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2007/8/8/R157 Open Access Open Access The FDR is higher in ER- breast cancer The FDR is higher in ER- breast cancer g To understand why in ER- breast cancer it has not been possi- ble to derive a validated prognostic signature using conven- tional approaches, we compared the FDR for ER+ and ER- disease. We used as cohorts integrated datasets obtained by merging together three of the largest profiled breast cancer cohorts [5,9,18] using the z-score transformation, a proce- dure that we validated previously [17]. Briefly, the z-score transformation shifts the mean of each gene expression vec- tor in each cohort to zero, while scaling its variance to unity. The transformed gene expression vectors are then merged across cohorts. This merging step resulted in integrated expression matrices of 186 ER- and 527 ER+ tumors profiled over a common set of 5,007 genes. To enable the comparison, we selected at random 186 ER+ tumors from the 527 available. We then used the univariate Cox proportional hazards model with time to distant metastasis (TTDM) and overall survival as end-points to obtain P values of significance for all the genes. Next, we estimated, for each choice of significance threshold, the number of false positives using the q-value approximation [20]. The numbers of significant genes and false positives as a function of the significance threshold were then plotted for ER+ and ER- breast cancer and for the two dif- ferent end-points used (Figure 1). We verified that the curves for ER+ breast cancer were robust to random selections of the 186 ER+ tumors. This showed that the FDR is much higher in ER- tumours and motivated us to develop a different feature selection approach based on a pattern recognition algorithm (PACK) [17]. In spite of these clinical advances, ER+ and ER- breast cancers remain heterogeneous diseases, and little is known regarding why patients with the same histopathologic characteristics may have widely different clinical outcomes [1]. This is partic- ularly true for the basal subtype of ER- breast cancer, which is commonly defined by over-expression of cytokeratin markers (CK 5/6 and CK 14) and which is often also HER2 negative (HER2-) [2]. Most recent efforts to obtain a molecular under- standing of the observed heterogeneity have focused on ER+ breast cancer, where gene expression signatures that are either prognostic or predictive of response to hormone ther- apy have been derived [3-10]. In contrast, few studies have thus far attempted to derive a prognostic signature within ER- breast cancer. Background ER- breast cancer and, if possible, to find different prognostic subclasses and the corresponding prognostic markers. g It is widely recognized that estrogen receptor (ER)-positive (ER+) and ER-negative (ER-) breast cancers are two different disease entities. Generally, ER- tumours tend to be of high grade, are more frequently p53 mutated, and have worse prognosis compared with ER+ disease. Moreover, while ER+ disease can be treated with hormone therapy, the only tar- geted therapy available for ER- patients is a monoclonal anti- body that binds to the ERBB2 receptor and that is effective only for those ER- tumours with HER2/ERBB2 over-expres- sion. Abstract Background: Estrogen receptor (ER)-negative breast cancer specimens are predominantly of high grade, have frequent p53 mutations, and are broadly divided into HER2-positive and basal subtypes. Although ER-negative disease has overall worse prognosis than does ER-positive breast cancer, not all ER-negative breast cancer patients have poor clinical outcome. Reliable identification of ER- negative tumors that have a good prognosis is not yet possible. Results: We apply a recently proposed feature selection method in an integrative analysis of three major microarray expression datasets to identify molecular subclasses and prognostic markers in ER-negative breast cancer. We find a subclass of basal tumors, characterized by over-expression of immune response genes, which has a better prognosis than the rest of ER-negative breast cancers. Moreover, we show that, in contrast to ER-positive tumours, the majority of prognostic markers in ER-negative breast cancer are over-expressed in the good prognosis group and are associated with activation of complement and immune response pathways. Specifically, we identify an immune response related seven-gene module and show that downregulation of this module confers greater risk for distant metastasis (hazard ratio 2.02, 95% confidence interval 1.2-3.4; P = 0.009), independent of lymph node status and lymphocytic infiltration. Furthermore, we validate the immune response module using two additional independent datasets. Conclusion: We show that ER-negative basal breast cancer is a heterogeneous disease with at least four main subtypes. Furthermore, we show that the heterogeneity in clinical outcome of ER- negative breast cancer is related to the variability in expression levels of complement and immune response pathway genes, independent of lymphocytic infiltration. information Genome Biology 2007, 8:R157 R157.2 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.2 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 The FDR is higher in ER- breast cancer Although cytokeratin markers have been shown to correlate with poor prognosis in breast cancer [11- 14], an attempt to correlate basal markers with survival within ER- disease has shown that these markers were not predictive of outcome [15]. Based on our work presented here, it appears that the prognostic 'signal' in ER- breast can- cer is much weaker than that in ER+ disease. This precludes the use of traditional supervised approaches, which assume a sufficiently low false discovery rate (FDR) for deriving gene expression based classifiers. A similar observation was reported by others [16]. Finding ER- subclasses using PACK g g If the aim is to identify subclasses within a tumor type, then it is natural that unsupervised methods be applied to sample sets that are composed entirely of this tumor type. In fact, given the hierarchical ER+/ER- subdivision for breast cancer, it is questionable whether ER- subgroups can be correctly defined based on clusters that were derived by using both ER+ and ER- samples, as was done in other studies (for example [21-23]). To see this, assume that all tumor types and genes are used in the clustering algorithm. It is very likely that the clusters within ER- tumors reflect not only the interesting var- iability of genes within ER- tumors but also the variability of genes that are important for classification of ER+ tumors. The variability of these genes in ER- tumors may represent unde- sired noise, which, if not removed, can affect the inferred clusters. Thus, in order to identify relevant subtypes of ER- tumors more robustly, we decided to use ER- tumors only. Moreover, in view of the relatively high FDR in ER- disease, we decided to apply the PACK methodology, which has already been shown to provide a more reliable identification of molecular classifiers [17]. Because PACK requires large Recently, we proposed a novel feature selection method (Pro- file Analysis using Clustering and Kurtosis [PACK]) [17], that selects genes using a pattern recognition method and that may significantly reduce the FDR. Using PACK in an inte- grated cohort of 186 ER- samples and 1,200 genes, we were able to identify distinct molecular subtypes, including a good prognosis subclass characterized by over-expression of immune response genes. However, these results were not val- idated in external cohorts. The purpose of this work is to extend our preliminary findings [17] by applying PACK to the same three breast cancer data- sets [5,9,18], but now using a much larger set of common genes (we rescued a significantly larger number of genes from our study [9] by imputing missing data, which led to a much larger number of overlapping genes, approximately 5,000, with the other two arrays.), and to further validate our find- ings using two external independent cohorts [7,19]. More generally, our goal is to elucidate the molecular taxonomy of Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. Finding ER- subclasses using PACK R157.3 http://genomebiology.com/2007/8/8/R157 FDR comparison in ER- and ER+ breast cancer Figure 1 FDR comparison in ER- and ER+ breast cancer. For various significance thresholds (sigth), we plot the fraction of observed genes with P values less than the significance threshold (black) as well as the corresponding fraction of false positives, as estimated using a q value analysis (red). (a) Overall survival for ER+ breast cancer. (b) Overall survival for ER- breast cancer. (c) Time to distant metastasis for ER+ breast cancer. (d) Time to distant metastasis for ER- breast cancer. P values were obtained from the log-rank test using Cox regression models. ER, estrogen receptor; FDR, false discovery rate. 0.00 0.04 0.08 0.0 0.1 0.2 0.3 0.4 Sigth OS (a) ER+ 0.00 0.04 0.08 0.0 0.1 0.2 0.3 0.4 Sigth OS (b) ER− 0.00 0.04 0.08 0.0 0.1 0.2 0.3 0.4 Sigth DM (c) ER+ 0.00 0.04 0.08 0.0 0.1 0.2 0.3 0.4 Sigth DM (d) ER− datasets used are summarized in Table 1 by platform type, number of ER- samples, and number of poor outcome events. 0.00 0.04 0.08 0.0 0.1 0.2 0.3 0.4 Sigth OS (a) ER+ 0.00 0.04 0.08 0.0 0.1 0.2 0.3 0.4 Sigth OS (b) ER− Briefly, we review the concepts that underpin PACK (see Materials and methods, below, and Figure 2). The hypothesis is that genes that play an important role as classifiers or biomarkers are more likely to have expression profiles that are mixtures of gaussian distributions. On the other hand, false positives, in spite of their spurious association with a phenotype, are less likely to be described by a mixture of dis- tributions. Thus, selecting genes based on whether they have structure in their expression profiles is likely to pick out the relevant markers from those that are just false positives. Next, we propose to focus on those genes that define the largest subgroups. Although genes that define small subgroups are also of interest, it is natural to identify first those genes that define the largest subclasses. While such features can be found from the inferred cluster sizes, it turns out that such features are generally also characterized by a negative (or close to zero) kurtosis profile (see Materials and methods, below) [17]. As shown previously, negative kurtosis expres- sion profiles are in effect a mixture of at least two (gaussian) distributions of approximately equal weights. Finding ER- subclasses using PACK Thus, by select- ing those genes that have the most negative kurtosis expres- sion profiles, we have identified the markers that define the largest subclasses within the sample set (Figure 2). It is clear that many of these features will be highly correlated because they define almost the same subclasses. It follows that further application of traditional clustering algorithms over these negative kurtosis profiles will enable reliable identification of the major subclasses within the sample set. We note that because we are interested in the most negative kurtosis pro- files and because the clusters in the individual gene profiles are only needed to study the cluster distribution of pheno- types, the cluster inference step on the individual gene pro- files (known as PAC) can be performed after computation of kurtosis (known as PAK) on the selected subset of negative kurtosis profiles (Figure 2). 0.00 0.04 0.08 0.0 0.1 0.2 0.3 0.4 Sigth DM (d) ER− 0.00 0.04 0.08 0.0 0.1 0.2 0.3 0.4 Sigth DM (c) ER+ (c) (d) FDR comp Figure 1 p g FDR comparison in ER- and ER+ breast cancer. For various significance thresholds (sigth), we plot the fraction of observed genes with P values less than the significance threshold (black) as well as the corresponding fraction of false positives, as estimated using a q value analysis (red). (a) Overall survival for ER+ breast cancer. (b) Overall survival for ER- breast cancer. (c) Time to distant metastasis for ER+ breast cancer. (d) Time to distant metastasis for ER- breast cancer. P values were obtained from the log-rank test using Cox regression models. ER, estrogen receptor; FDR, false discovery rate. p g FDR comparison in ER- and ER+ breast cancer. For various significance thresholds (sigth), we plot the fraction of observed genes with P values less than the significance threshold (black) as well as the corresponding fraction of false positives, as estimated using a q value analysis (red). (a) Overall survival for ER+ breast cancer. (b) Overall survival for ER- breast cancer. (c) Time to distant metastasis for ER+ breast cancer. (d) Time to distant metastasis for ER- breast cancer. P values were obtained from the log-rank test using Cox regression models. ER, estrogen receptor; FDR, false discovery rate. sample sizes (for small sample sizes, kurtosis estimates can have large variance and clustering algorithms that aim to pre- dict the optimal number of clusters have a high false negative rate), we applied it to the integrated data matrix derived pre- viously. Two additional independent ER- cohorts [7,19] were left out to serve as validation studies. The five microarray Table 1 Breast cancer datasets used Ref. Cohort name Oligo microarray platform ER- ER+ n Death/distant metastasis (n) n Death/distant metastasis (n) [18] NKI2 Agilent 69 34 226 45 [5] EMC Affymetrix 77 27 208 80 [9] NCH Agilent 40 14 93 21 [19] UPP Affymetrix 34 6 213 49 [7] JRH-2 Affymetrix 24 6 72 17 ER, estrogen receptor. PACK flow Figure 2 PACK flowchart Figure 2 PACK flowchart. (a) A schematic diagram of PACK, as used in this study. For each gene expression profile an unbiased estimate of its kurtosis, K, is computed. Genes with negative kurtosis are selected because only these define large subgroups (of sizes >22% of the total sample size). Further unsupervised clustering may then be performed on this subset of negative kurtosis profiles to find novel tumor subclasses. Alternatively, to find robust prognostic markers, negative kurtosis profiles are filtered further based on whether there is evidence of bimodality (C = 2). This step requires a cluster inference algorithm and a model selection criterion to discard those profiles that are best described by a single gaussian (C = 1; by random chance gaussian profiles may have negative kurtosis). Correlation to phenotypes (here phenotypes) is done with Fisher's test to evaluate whether the distribution of the categorical phenotype across the two clusters is significantly different from random. (b) Density curves of typical bimodal negative and positive kurtosis gene expression profiles. X-axis shows gene expression on a log2 scale. PACK, Profile Analysis using Clustering and Kurtosis. C owc a t gu e PACK flowchart. (a) A schematic diagram of PACK, as used in this study. For each gene expression profile an unbiased estimate of its kurtosis, K, is computed. Genes with negative kurtosis are selected because only these define large subgroups (of sizes >22% of the total sample size). Further unsupervised clustering may then be performed on this subset of negative kurtosis profiles to find novel tumor subclasses. Alternatively, to find robust prognostic markers, negative kurtosis profiles are filtered further based on whether there is evidence of bimodality (C = 2). This step requires a cluster inference algorithm and a model selection criterion to discard those profiles that are best described by a single gaussian (C = 1; by random chance gaussian profiles may have negative kurtosis). Correlation to phenotypes (here phenotypes) is done with Fisher's test to evaluate whether the distribution of the categorical phenotype across the two clusters is significantly different from random. (b) Density curves of typical bimodal negative and positive kurtosis gene expression profiles. X-axis shows gene expression on a log2 scale. PACK, Profile Analysis using Clustering and Kurtosis. ized by the expression patterns of four gene clusters that were found to be strongly enriched for specific gene ontologies (Figure 3a and Additional data file 3). Table 1 information Genome Biology 2007, 8:R157 R157.4 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 PACK flowchart Figure 2 PACK flowchart. (a) A schematic diagram of PACK, as used in this study. For each gene expression profile an unbiased estimate of its kurtosis, K, is computed. Genes with negative kurtosis are selected because only these define large subgroups (of sizes >22% of the total sample size). Further unsupervised clustering may then be performed on this subset of negative kurtosis profiles to find novel tumor subclasses. Alternatively, to find robust prognostic markers, negative kurtosis profiles are filtered further based on whether there is evidence of bimodality (C = 2). This step requires a cluster inference algorithm and a model selection criterion to discard those profiles that are best described by a single gaussian (C = 1; by random chance gaussian profiles may have negative kurtosis). Correlation to phenotypes (here phenotypes) is done with Fisher's test to evaluate whether the distribution of the categorical phenotype across the two clusters is significantly different from random. (b) Density curves of typical bimodal negative and positive kurtosis gene expression profiles. X-axis shows gene expression on a log2 scale. PACK, Profile Analysis using Clustering and Kurtosis. −3 −2 −1 0 1 2 3 0.0 0.1 0.2 0.3 0.4 Gene expression Density K < 0 Bi-modal: major subgroups −2 −1 0 1 2 0.0 0.2 0.4 0.6 Gene expression Density K > 0 Bi-modal: outlier subgroups Gene expression profile Compute kurtosis (PAK) K < 0 K > 0 Feature selection Estimate optimal number of clusters (PAC) C=2 C=1 Fisher’s test to correlate with phenotype (a) (b) Gene expression profile Compute kurtosis (PAK) K < 0 K > 0 Feature selection Estimate optimal number of clusters (PAC) C=2 C=1 Fisher’s test to correlate with phenotype (a) −3 −2 −1 0 1 2 3 0.0 0.1 0.2 0.3 0.4 Gene expression Density K < 0 Bi-modal: major subgroups −2 −1 0 1 2 0.0 0.2 0.4 0.6 Gene expression Density K > 0 Bi-modal: outlier subgroups (b) −3 −2 −1 0 1 2 3 0.0 0.1 0.2 0.3 0.4 Density K < 0 Bi-modal: major subgroups (b) (a) (b) Gene expression −2 −1 0 1 2 0.0 0.2 0.4 0.6 Gene expression Density K > 0 Bi-modal: outlier subgroups A subgroup of good prognosis in ER- breast cancer It further follows from these observations that ER- normal and luminal A samples were predominantly characterized by over-expression of ECM genes. ER- basal tumors, on the other hand, exhibited a more complex pattern and appeared to divide into at least four subgroups (CC+/IR+, CC+, ECM+, and IR+). To investigate further the relation of our five ER- subclasses with the intrinsic subtypes, we considered to which ER- sub- class ER+ samples of known intrinsic subtype were most sim- ilar. To this end we first constructed, for each of the five ER- subclasses, mean centroids over the 813 negative kurtosis genes (Additional data file 5). To validate the centroids, the same ER- samples were assigned a subclass using a nearest centroid criterion (samples for which the largest Pearson cor- relation coefficient was <0.25 were considered unclassified; see Materials and methods, below), which showed that 156 (84%) were classified, of which 143 (92%) were assigned the correct subclass. Next, using the SSP to classify the 527 ER+ samples into the intrinsic subtypes, we then assigned each of the 527 ER+ samples into an ER- subclass based on the same nearest centroid criterion (Table 3). As expected, only 4% of ER+ tumors were classified as basal, whereas the majority (82%) of them were luminal. Moreover, the analysis showed that ER+ luminal B samples were most similar to CC+ and CC+/IR+ ER- samples, which is consistent with the fact that all of these samples over-express cell cycle and cell proliferation genes. In contrast, ER+ luminal A samples were most similar to ECM+ (63%), IR+ (26%), and SR+ (8%) ER- samples. Not surprisingly, almost all (16/19 [84%]) 'normal' ER+ samples were most similar to ECM+ ER- samples. All basal ER+ sam- To further confirm our findings, we also generated Kaplan- Meier survival curves for the five identified subclasses using TTDM as the end-point (Figure 3b). This showed that the SR+ and CC+ subclasses had worst prognosis, whereas the IR+ sub- class was the group with best prognosis. Specifically, relative to the IR+ subclass the SR+ subgroup had a hazard ratio (HR) of 3.70 (95% confidence interval [CI] 1.49 to 9.24; P = 0.005), whereas the CC+ subgroup had an HR of 2.75 (95% CI 1.07 to 7.05; P = 0.035). A subgroup of good prognosis in ER- breast cancer A subgroup of good prognosis in ER- breast cancer We next considered whether the five identified clusters were associated with different prognostic groups. Because we had merged different cohorts, and it is questionable whether sur- vival data can be also merged together, we decided to test first the clusters for association with clinical outcome by using a dichotomized outcome variable. Specifically, poor outcome was defined as any death or distant metastasis event, whereas good outcome was defined as a patient alive or with no distant metastasis. By studying the distribution of good and poor out- come events in the respective clusters, significant associa- tions with prognosis could be found by means of Fisher's exact test (Table 2). Interestingly, this showed that the IR+ subgroup had better prognosis when compared with the ECM+ (P = 0.08), CC+ (P = 0.03), and SR+ (P = 0.005) subclasses. In order to relate the five identified molecular subtypes to the intrinsic breast cancer classification [21,26], we used the recently validated single sample predictor (SSP) [23] to clas- sify the 186 ER- samples into the various intrinsic subtypes (Figure 3a and Table 2). In addition, we studied the expres- sion profiles of recently validated basal markers [27] and genes in the ERBB2 amplicon across the five identified clus- ters (Figure 3a and Additional data file 4). Based on these fig- ures and Table 2, we could draw the following conclusions. First, the SR+ cluster was highly correlated with the usual HER2+ intrinsic subtype. Second, the CC+/IR+ and CC+ clus- ters defined distinct subtypes of basal tumors. Third, the ECM+ cluster was mostly basal, but it contained a relatively high proportion of normal-like and luminal-A-like ER- tumors; it also exhibited the most varied grade distribution, with most low-grade ER- tumors falling into this class. Finally, the main constituents of the IR+ cluster were basal and HER2+. Compared with the CC+/IR+ subgroup it also had better prog- nosis, although the difference was not statistically significant (P = 0.19). We thus combined the CC+/IR+ and IR+ subclasses together and evaluated the prognosis of this larger subclass relative to the rest of ER- samples. Consistent with our previous result [17] we found that the ER- tumors over- expressing immune response genes had better prognosis than ER- samples that did not (P = 0.02). A subgroup of good prognosis in ER- breast cancer Similarly, relative to the CC+/IR+ subclass, the SR+ subgroup had an HR of 2.35 (95% CI 1.13 to 4.88; P = 0.02), whereas for the CC+ subgroup it did not quite reach statistical significance (HR 1.80, 95% CI 0.83 to 3.89; P = 0.13). We verified the statistical significance of these sur- vival differences by 10,000 random permutations of the sam- ples, which showed that the theoretical P value estimates above were essentially identical to the empirically derived P values. PACK flow Figure 2 One group was charac- terized by over-expression of ERBB2, the steroid hormone receptor AR, and genes related to steroid estrogen response (such as GATA3, TFF1, and DNALI1). This subtype is there- fore similar to the apocrine subclass, recently proposed [24,25], which is characterized by over-expression of AR and genes that are either direct targets of ER or responsive to estrogen [24,25]. Thus, we decided to call this ER- subtype (over-expressing steroid response genes) 'SR+', although it is clear that it also defines the well known HER2+ subtype. Distinct molecular subgroups of ER breast cancer Applying PAK to the integrated ER- data matrix of 5,007 genes, we found 813 genes with a negative kurtosis profile (Additional data file 1). Interestingly, applying the same anal- ysis to ER+ breast cancer, we found only a much smaller number (193) of negative kurtosis profiles (Additional data file 2), despite there being roughly twice as many bimodal profiles in ER+ breast cancer (about 4500 in ER+ versus about 2,500 in ER-). We verified by explicit simulation that the sig- nificantly lower proportion of negative kurtosis profiles in ER+ disease could not be explained by the larger sample size in ER+ (527) compared with ER- disease (186; data not shown). The other four groups were characterized mainly by absent or lower expression of these steroid response genes. One of these four clusters was characterized by over-expression of genes related to cell cycle and cell proliferation pathways (CC+), and another cluster also had over-expression of immune response Having identified the relevant features, we next clustered the ER- tumors over these. Using hierarchical clustering with Pearson correlation metric and complete linkage, we found that samples clustered into five main groups, each character- Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.5 http://genomebiology.com/2007/8/8/R157 genes (CC+/IR+). For the remaining two clusters, one was characterized by over-expression of extracellular matrix genes (ECM+), and the other was characterized by over- expression of immune response genes (IR+) only. ples had expression profiles most similar to CC+/IR+ and CC+ subtypes. Interestingly, only 16 of the 42 (38%) ER+ HER2+ tumors exhibited significantly correlated expression profiles to any one of the five ER- subclasses, with most of these (11) mapping to the CC+/IR+ subtype. Prognostic markers in ER- tumors are associated with immune response functions The better prognosis of the IR+ subclass is likely due to spe- cific genes that are individually prognostic. In order to find these, we applied the PAC algorithm to the 813 genes with negative kurtosis expression profiles. Briefly, this procedure Genome Biology 2007, 8:R157 R157.6 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 (a) CC+/IR+ CC+ ECM+ SR+ IR+ FBN1 SPARC MMP11 ERBB2 AR C1QA HLA-F IGLC2 CDK2AP1 CDKN2A KRT17 CRYAB CDC25B (a) CC+/IR+ CC+ ECM+ SR+ IR+ FBN1 SPARC MMP11 ERBB2 AR C1QA HLA-F IGLC2 CDK2AP1 CDKN2A KRT17 CRYAB CDC25B Genome Biology 2007, 8:R157 Figure 3 (see legend on next page) SSP LYM.INF. GRADE BASAL.MARK. ERBB2.AMP. 0 2 4 6 8 10 12 0.0 0.2 0.4 0.6 0.8 1.0 (b) (c) HLA-F IGLC2 LY9 TNFRSF17 SPP1 XCL2 C1QA 0 2 4 6 8 10 12 0.0 0.2 0.4 0.6 0.8 1.0 HR=2.02 (1.2-3.4) p=0.009 (d) p = 0.003 SSP LYM.INF. GRADE BASAL.MARK. ERBB2.AMP. SSP LYM.INF. GRADE BASAL.MARK. ERBB2.AMP. (b) (c) (d) (c) F 2 9 7 2 A (c) 0 2 4 6 8 10 12 0.0 0.2 0.4 0.6 0.8 1.0 HR=2.02 (1.2-3.4) p=0.009 (d) (c) (b) (d) 0 2 4 6 8 10 12 0.0 0.2 0.4 0.6 0.8 1.0 p = 0.003 Figure 3 (see legend on next page) Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.7 http://genomebiology.com/2007/8/8/R157 Molecular subclasses in ER- breast cancer Figure 3 (see previous page) Molecular subclasses in ER- breast cancer. (a) Complete linkage hierarchical clustering of 186 ER- breast tumors over 813 genes with negative kurtosis profiles. Five sample clusters were identified and characterized in terms of the patterns of over-expression and under-expression of four gene clusters related to cell cycle (CC; blue), immune response (IR; red), extracellular matrix (ECM; green), and steroid hormone response (SR; pink) functions. Panels show the distribution of the SSP subtype [23], the lymphocytic infiltration score, histologic grade, basal marker [27], and ERBB2+ amplifier subtype. Panel color codes: SSP (pink = HER2, brown = basal, dark green = normal, sky blue = luminal A, and blue = luminal B); LYM.INF (black = high, gray = low, and white = missing); GRADE (black = high, blue = intermediate, sky blue = low, and white = missing), BASAL.MARK. (black = high and white = low), ERBB2- AMP (black = high and white = low). Prognostic markers in ER- tumors are associated with immune response functions The BASAL.MARK. profile represents an average over validated basal markers in [27], whereas the ERBB2-AMP profile was calculated as an average over three genes in the ERBB2 amplicon (ERBB2, STARD3, GRB7). (b) Kaplan-Meier curves for time to distant metastasis (years) and for the five subclasses identified in panel (a). (c) Partitioning around medoids clustering over the seven-gene prognostic immune response module. Panel color codes: purple = cluster over-expressing module, yellow = cluster under-expressing module, black = poor outcome samples, gray = good outcome samples, green = relative under-expression, and red = relative over-expression. (d) Kaplan-Meier curves for time to distant metastasis for the two groups identified in panel (c). Hazard ratio, 95% confidence interval, and log-rank test P values are shown. ER, estrogen receptor; SSP, single sample predictor. Machine [28] showed that immune/defense response was the most enriched GO, with seven genes falling into this category (C1QA, IGLC2, LY9, TNFRSF17, SPP1, XCL2, and HLA-F). The expression profiles for these seven genes confirmed the presence of distinct clusters with nonrandom distributions of good and poor outcome samples (Figure 4 provides detailed profiles of C1QA and IGLC2). selects features based on whether their expression profiles are best described as a mixture of gaussians or not, and then evaluates whether the distribution of good and poor outcome events among the inferred clusters is statistically different from random or not. Applying PAC, we found 22 genes with a Fisher test P < 0.05 (Additional data file 1). A Gene Ontology (GO) enrichment analysis of these 22 genes using the GOTree Table 2 Distribution of ER- samples among clusters, prognostic groups and intrinsic subtypes Cluster n Outcome LI ER- Good Poor High Low Luminal B Luminal A Normal Basal HER2 CC+/IR+ 39 25 14 7 2 0 0 0 38 1 CC+ 37 18 17 3 5 0 0 1 33 3 ECM+ 45 26 18 1 14 0 9 9 22 5 SR+ 36 16 20 2 4 1 1 0 2 32 IR+ 29 23 6 6 6 0 4 2 9 14 For the five clusters of Figure 2a, we give the number of samples per cluster (n) and their distributions over good/poor outcome, high/low lymphocytic infiltration (LI) score, and intrinsic subtypes as determined by the single sample predictor (SSP) classifier. Prognostic markers in ER- tumors are associated with immune response functions Clusters were labeled by the main Gene Ontology of genes over-expressed in the group: CC+ (cell cycle), CC+/IR+ (cell cycle and immune response), ECM+ (extracellular matrix), SR+ (steroid hormone response), and IR+ (immune response). ER, estrogen receptor. Table 2 Distribution of ER- samples among clusters, prognostic groups and intrinsic subtypes For the five clusters of Figure 2a, we give the number of samples per cluster (n) and their distributions over good/poor outcome, high/low lymphocytic infiltration (LI) score, and intrinsic subtypes as determined by the single sample predictor (SSP) classifier. Clusters were labeled by the main Gene Ontology of genes over-expressed in the group: CC+ (cell cycle), CC+/IR+ (cell cycle and immune response), ECM+ (extracellular matrix), SR+ (steroid hormone response), and IR+ (immune response). ER, estrogen receptor. Classification of ER+ intrinsic subtypes (527 samples from the integrated cohort NKI2 + EMC + NCH), 22 medullary breast cancers (MBCs) and 44 ductal breast cancers (DBCs) from [38], and 18 BRCA1 mutants from [3] into ER- subclasses, using the nearest centroid criterion with Pearson correlation as distance metric. Only samples with Pearson correlation coefficients larger than 0.25 were deemed classifiable. ER, estrogen receptor. Table 3 Classification of ER+ intrinsic subtypes, medullary breast cancer, and BRCA1 tumors into ER- subclasses ER+ MBC DBC BRCA1 Luminal B Luminal A Normal Basal HER2 n 97 337 32 19 42 22 44 18 n classifiable 37 113 19 17 16 20 33 16 CC+/IR+ 17 2 0 13 11 14 4 13 CC+ 20 2 0 4 1 3 3 2 ECM+ 0 71 16 0 0 1 3 1 SR+ 0 9 0 0 0 0 20 0 IR+ 0 29 3 0 4 2 3 0 Classification of ER+ intrinsic subtypes (527 samples from the integrated cohort NKI2 + EMC + NCH), 22 medullary breast cancers (MBCs) and 44 ductal breast cancers (DBCs) from [38], and 18 BRCA1 mutants from [3] into ER- subclasses, using the nearest centroid criterion with Pearson correlation as distance metric. Only samples with Pearson correlation coefficients larger than 0.25 were deemed classifiable. ER, estrogen receptor. Classification of ER+ intrinsic subtypes, medullary breast cancer, and BRCA1 tumors into ER- subclasses Classification of ER+ intrinsic subtypes (527 samples from the integrated cohort NKI2 + EMC + NCH), 22 medullary breast cancers (MBCs) and 44 ductal breast cancers (DBCs) from [38], and 18 BRCA1 mutants from [3] into ER- subclasses, using the nearest centroid criterion with Pearson correlation as distance metric. Only samples with Pearson correlation coefficients larger than 0.25 were deemed classifiable. ER, estrogen receptor. Genome Biology 2007, 8:R157 R157.8 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007 R157.8 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 Expression profiles of selected prognostic markers in ER- breast cancer Figure 4 Expression profiles of selected prognostic markers in ER- breast cancer. Expression profile (on a log2 scale) of selected prognostic markers (a) IGLC2 and (b) C1QA in the integrated cohort of 186 ER- tumours (NKI2 + EMC + NCH), and in the validation cohorts UPP and JRH-2. Good outcome samples are shown in green, and poor outcome samples in blue. Clusters were inferred using the variational Bayesian approach in NKI2 + EMC + NCH and the pam algorithm in the UPP and JRH-2 cohorts. Infered clusters are indicated by different shapes (triangles and diamonds). ER, estrogen receptor; pam, partitioning around medoids. Expression Figure 4 Expression profiles of selected prognostic markers in ER breast cancer Figure 4 Expression profiles of selected prognostic markers in ER- breast cancer. Expression profile (on a log2 scale) of selected prognostic markers (a) IGLC2 and (b) C1QA in the integrated cohort of 186 ER- tumours (NKI2 + EMC + NCH), and in the validation cohorts UPP and JRH-2. Good outcome samples are shown in green, and poor outcome samples in blue. Clusters were inferred using the variational Bayesian approach in NKI2 + EMC + NCH and the pam algorithm in the UPP and JRH-2 cohorts. Infered clusters are indicated by different shapes (triangles and diamonds). ER, estrogen receptor; pam, partitioning around medoids. In contrast, application of the same method to ER+ breast cancer yielded 29 genes (out of a possible 193) with P < 0.05 (Additional data file 2). In spite of there being only 29 genes in this list, there were many with mitotic cell cycle functions, notably UBE2C, MAD2L1, E2F1 and KIFC1, and GO enrich- ment analysis confirmed that the cell cycle GO was the most significantly enriched category followed by transcription regulatory activity. This result for ER+ breast cancer confirms findings reported elsewhere that poor prognosis in ER+ breast cancer is related mainly to over-expression of genes in cell cycle and cell proliferation pathways [3,5,7]. Notably, none of the identified prognostic genes were related to immune response functions. ters significantly associated with clinical outcome. Specifi- cally, the partitioning around medoids (pam) clustering algorithm [29] with two centers predicted one cluster with 52 good outcome and 56 poor outcome patients, and another cluster with 56 good outcome and only 19 poor outcome events, which was highly significant under Fisher's exact test (P = 0.0004; Figure 3c). Kaplan-Meier and Cox regression analyses further confirmed that the group not over-express- ing the seven-gene module (out of the seven genes the major- ity [six] are not over-expressed) had a greater risk for distant metastasis (HR 2.02, 95% CI 1.2 to 3.4; P = 0.009; Figure 3d). In contrast, application of the same method to ER+ breast cancer yielded 29 genes (out of a possible 193) with P < 0.05 (Additional data file 2). Expression Figure 4 In spite of there being only 29 genes in this list, there were many with mitotic cell cycle functions, notably UBE2C, MAD2L1, E2F1 and KIFC1, and GO enrich- ment analysis confirmed that the cell cycle GO was the most significantly enriched category followed by transcription regulatory activity. This result for ER+ breast cancer confirms findings reported elsewhere that poor prognosis in ER+ breast cancer is related mainly to over-expression of genes in cell cycle and cell proliferation pathways [3,5,7]. Notably, none of the identified prognostic genes were related to immune response functions. Table 3 0 50 100 150 −2 −1 0 1 2 3 NKI2+EMC+NCH (a) 0 5 10 20 30 −2 −1 0 1 2 3 UPP 5 10 15 20 −2 −1 0 1 2 3 JRH−2 0 50 100 150 −2 −1 0 1 2 3 NKI2+EMC+NCH (b) 0 5 10 20 30 −2 −1 0 1 2 3 UPP 5 10 15 20 −2 −1 0 1 2 3 JRH−2 0 50 100 150 −2 −1 0 1 2 3 NKI2+EMC+NCH (a) NKI2+EMC+NCH (b) 5 10 15 20 −2 −1 0 1 2 3 JRH−2 0 5 10 20 30 −2 −1 0 1 2 3 UPP 0 5 10 20 30 −2 −1 0 1 2 3 UPP (b) 5 10 15 20 −2 −1 0 1 2 3 JRH−2 0 50 100 150 −2 −1 0 1 2 3 Relation to STAT1 and IFN cluster Next, we investigated the relation of the good prognosis sub- group identified here with the novel IFN regulated cluster identified recently [23]. As shown previously [23], the IFN cluster, defined by over-expression of interferon regulated Having identified a prognostic module of seven immune response genes (henceforth called the IR module), we next confirmed that clustering over this module resulted in clus- Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.9 http://genomebiology.com/2007/8/8/R157 genes, including the transcriptional regulator STAT1, was most closely related to the basal subclass and had a prognos- tic performance similar to that of luminal B samples when compared with the luminal A and normal subtypes. Interest- ingly, when compared with the basal and HER2+ subclasses, the IFN group had better prognosis, although a formal com- parison was not conducted by Hu and coworkers [23]. measured for example by a higher degree of lymphocytic infiltration (LI). The association of high LI with good progno- sis is well known [31-34], and although a few conflicting results have also been reported [35-37], we thought it natural to consider whether upregulation of the identified immune response module conferred good prognosis independently of LI. To this end, we scored the samples in the NCH cohort for LI (see Materials and methods, below) and combined these with the available LI score information from the NKI2 cohort, yielding a total of 50 scored samples. We found that although there were proportionally more tumors with high LI scores in the group over-expressing the immune response genes (spe- cifically there were 11 high LI and 9 low LI samples versus 8 high LI and 22 low LI in the under-expressed group; Fisher test, P = 0.07), a multivariate Cox regression with TTDM as the outcome variable and the seven-gene IR module and LI score as predictors showed that the immune response module was still a strong predictor of clinical outcome, independent of LI (HR 2.05, 95% CI 0.71 to 5.97; P = 0.19; Table 4). (The P value is only marginally below statistical significance, which is most likely due to the relatively small sample size.) Supporting this result further, we did not find in ER- tumors any significant association between LI and clinical outcome (Table 4). Relation to medullary and BRCA1 ER- breast cancer Relation to medullary and BRCA1 ER- breast cancer To further confirm the independent prognostic power of the IR module from LI, we investigated the relationship of the identified good prognosis tumors with medullary breast cancers (MBCs), which are characterized by high LI scores and relatively good prognosis [38]. Thus, we considered to which ER- subclass the 22 MBC expression profiles from the report by Bertucci and coworkers [38] were most similar (Table 3). (For completeness and reference, we also per- formed the analysis for the 44 ductal breast cancers [DBCs], also profiled by Bertucci and coworkers [38].) This showed that of the 22 MBCs, 20 showed reasonably strong correlation to one of the ER- subclass centroids, 14 of which (70%) were most similar to the CC+/IR+ subtype, whereas only two (11%) were most similar to the IR+ subtype. In contrast, for the 33 DBC which could be classified, only four (12%) and three (9%) were most similar to the CC+/IR+ and IR+ subtypes. These results mirror the distribution of LI scores across the five ER- subclasses (Figure 3a and Table 2) and further confirms that the best prognostic group (IR+) is not related to MBC, whereas CC+/IR+ is. A similar analysis was performed for BRCA1 mutant tumors. Of the 16 BRCA1 mutants from the NKI2 cohort [3], which were also deemed classifiable based on a 0.25 correlation threshold, 13 (81%) had expression profiles most similar to the CC+/IR+ subtype (Table 3). None showed similarity to the IR+ subclass. Therefore, this suggests that ER- BRCA1 mutants, in common with MBCs, are most similar to the CC+/ IR+ subclass identified here. Relation to STAT1 and IFN cluster Among the 98 genes in the immune response gene cluster (Figure 3a and Additional data file 1), we identified a total of 14 with interferon related functions, including STAT1, SP110, NFKBI, IFI44, IFNGR1, ISGF3G, and IRF7. Interestingly, however, none of these genes showed association with prog- nosis except SP110. Thus, although it appears that our sub- class is related to the IFN class discovered by Hu and coworkers [23], it is also distinct in that the associated prog- nostic markers are not in the IFN cluster. Immune response module predicts outcome independently of lymph node status p y y p Because our IR gene cluster included STAT1 and interferon- induced genes, and these genes have been shown to be asso- ciated with lymph node (LN) metastasis [30], we considered whether the subgroup of ER- samples over-expressing the 98- gene IR cluster was significantly associated with LN status. Because all patients in the ECM cohort were LN negative, this analysis was only performed on the NKI2 and NCH cohorts (109 ER- patients, of whom 42 had LN involvement). Using pam clustering with two centers over these 98 genes and 109 samples, we found subgroups with similar proportions of LN metastases (43 LN negative and 28 LN positive versus 24 LN negative and 14 LN positive; Fisher's exact test P = 0.84). Moreover, clustering only over the 14 genes involved in the IFN subcluster still did not show a significantly nonrandom distribution of LN metastases among the clusters (P = 0.23), although in agreement with Huang and coworkers [30] the cluster over-expressing the IFN genes had proportionally more LN metastases. Similarly, the distribution of LN metas- tases among the two clusters predicted by the IR module was not significantly different from random (P = 0.48). While LN status itself was a significant predictor of distant metastasis both in univariate (HR 2.28, 95% CI 1.36 to 3.85; P = 0.002) and multivariate (HR 2.16, 95% CI 1.28 to 3.64; P = 0.004) Cox regression analysis (this result is for a multivariate model including LN status and the IR module as predictors.), impor- tantly, the IR module remained a prognostic predictor for TTDM (HR 1.93, 95% CI 1.14 to 3.26; P = 0.015) in the multi- variate model that included LN status (Table 4). This showed that the IR module identified here adds independent prog- nostic value over LN status in ER- breast cancer. External validation To confirm the robustness of our findings, we used the pam algorithm to classify patients in the two external cohorts into clusters over-expressing and under-expressing the IR module (Figure 5a,b). Remarkably, the predicted 20-sample cluster over-expressing the module was composed entirely of good outcome patients, whereas the remaining 35-sample cluster included 12 poor outcome events (Figure 5c), which was highly significant under Fisher's exact test (P = 0.002; the HR is singular because one cluster did not have any events). Having identified a prognostic module related to immune response, we next attempted to validate this finding using two independent breast cancer cohorts [7,19]. Specifically, the hypothesis to be tested was that over-expression of the iden- tified prognostic markers is associated with good prognosis, except for SPP1, for which good prognosis is hypothesized to be associated with under-expression. Because of the relatively small sample size of the two external cohorts, an algorithm that attempts to learn the optimal number of clusters (as implemented in PACK) is unlikely to capture structure because of a large false negative rate [39]. Hence, in order to define groups of over-expression and under-expression, we applied the pam algorithm with two centers to each of the seven genes in each of the two cohorts (Figure 4 and Addi- tional data files 6 and 7). Because the small number of events, six, in each of the two external cohorts implied a highly discrete P value distribution, Fisher test P values would be too conservative and poor approximations for type I errors [40]. To overcome this difficulty, we also considered the distribu- tion of good and poor outcome samples over the combined clusters of over-expression and under-expression (Table 5). This showed that four of the seven genes (C1QA, IGLC2, TNFRSF17, and LY9) were also highly prognostic in these two external cohorts, thus confirming the validity of our finding. Moreover, as in the three original cohorts, over-expression of these genes in the two external cohorts was associated with good prognosis (Figure 4 and Additional data files 6 and 7). For the other three genes (HLA-F, SPP1, and XCL2), P values did not reach statistical significance (P about 0.2), yet their expression profile trends were entirely consistent with those found in the integrated cohort, thus confirming their role as members of a robust prognostic module (Additional data files 6 and 7). Immune response module predicts outcome independently of lymphocytic infiltration To confirm the robustness of our findings, we used the pam algorithm to classify patients in the two external cohorts into clusters over-expressing and under-expressing the IR module (Figure 5a,b). Remarkably, the predicted 20-sample cluster over-expressing the module was composed entirely of good outcome patients, whereas the remaining 35-sample cluster included 12 poor outcome events (Figure 5c), which was highly significant under Fisher's exact test (P = 0.002; the HR is singular because one cluster did not have any events). Immune response module predicts outcome independently of lymphocytic infiltration The upregulation of immune response genes in good progno- sis tumors could be explained by the fact that these tumors elicit a stronger immune and inflammatory response, as Genome Biology 2007, 8:R157 R157.10 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 Table 4 Univariate and Multivariate Cox-regression model ER- (n = 186) ER+ (n = 527) HR (95% CI) P HR (95% CI) P LN 2.28 (1.36-3.85) 0.002 2.07 (1.47-2.90) <10-4 LI 1.06 (0.66-1.70) 0.9 1.50 (0.72-3.14) 0.58 IRM 2.02 (1.19-3.41) 0.009 1.25 (0.91-1.71) 0.19 LNa + IRM 2.16 (1.28-3.64) 0.004 2.10 (1.49-2.96) <10-4 LN + IRMa 1.93 (1.14-3.26) 0.015 1.29 (0.94-1.76) 0.11 LIa + IRM 0.86 (0.32-2.28) 0.76 1.75 (0.41-7.47) 0.45 LI + IRMa 2.05 (0.71-5.97) 0.19 0.57 (0.27-1.19) 0.13 LNa + LI + IRM 1.79 (0.70-4.62) 0.22 1.48 (0.68-3.19) 0.32 LN + LIa + IRM 0.84 (0.51-1.38) 0.72 1.65 (0.38-7.07) 0.5 LN + LI + IRMa 2.22 (0.76-6.50) 0.15 0.57 (0.27-1.20) 0.14 The table summarizes the hazard ratio (HR), 95% confidence interval (CI), and log-rank test P values of univariate Cox proportional hazards regression models, with lymph node status (LN = 1/0 for LN +/-), level of lymphocytic infiltration (LI = 1 for low infiltration score, and LI = 0 for high infiltration score) and the classification based on the seven-gene immune response related module (IRM; 2 = down-regulation of module, 1 = upregulation of module) as predictors. aCorresponding values in the multivariate Cox models including LN, LI, and IR module as predictors. The table compares the values for estrogen receptor (ER)- and ER+ breast cancer. Table 4 Univariate and Multivariate Cox-regression model The table summarizes the hazard ratio (HR), 95% confidence interval (CI), and log-rank test P values of univariate Cox proportional hazards regression models, with lymph node status (LN = 1/0 for LN +/-), level of lymphocytic infiltration (LI = 1 for low infiltration score, and LI = 0 for high infiltration score) and the classification based on the seven-gene immune response related module (IRM; 2 = down-regulation of module, 1 = upregulation of module) as predictors. aCorresponding values in the multivariate Cox models including LN, LI, and IR module as predictors. The table compares the values for estrogen receptor (ER)- and ER+ breast cancer. Table 5 In fact, GO analysis (using GOTree Machine) of the top 500 genes obtained from this rank sum test (all with q-values < 0.05) showed that cell cycle and transcription regulator activity related GOs were the only categories with highly significant P values (uncor- rected P < 10-6), and that the only enriched immune response related GO was that of humoral immune response, with 11 represented genes (including BLM, FADD, C3, C7, BCL2, NFKB1, and the IR module member TNFRSF17), and which was only marginally enriched (uncorrected P = 0.005). Although we verified that this humoral immune response module was associated with prognosis in the integrated ER+ cohort independent of LN status and LI (HR 2.26, 95% CI 0.97 to 5.26; P = 0.06) we were unable to validate this prog- nostic module in the external UPP and JRH-2 cohorts (Additional data file 8). Moreover, the co-regulation patterns for the genes in this module were less coherent than those for the IR module in ER- breast cancer (Figure 5 and Additional data file 8). Hence, independent of the methodology used, an IR related prognostic module in ER+ breast cancer could not be identified, which seems to suggest that a good prognosis subtype related to IR is specific to ER- disease. We believe that these differences between ER+ and ER- dis- ease are related to the different histopathologic characteris- Pam clustering over IR module in external ER- cohorts Figure 5 Pam clustering over IR module in external ER- cohorts. Heatmap of gene expression of seven-gene IR-module in ER- samples of the (a) UPP and (b) JRH-2 cohorts. Shown are the clusters over-expressing (purple) and under-expressing (yellow) the IR module, as predicted by the pam algorithm. Good outcome samples are shown in gray, and poor outcome samples in black. Green indicates relative under-expression, and red indicates relative over-expression. (c) Kaplan-Meier survival curves over combined external cohorts (for UPP end-point was disease-specific survival, and for JRH-2 it was recurrence-free survival), with the number of events and samples in each of the two predicted groups. ER, estrogen receptor; pam, partitioning around medoids. Table 5 We believe that these differences between ER+ and ER- dis- External validation of immune response prognostic module: distribution of poor and good outcome patients in over-and-under- expressed subgroups Gene UPP JRH-2 Combined Poor Good P Poor Good P Poor Good P IGLC2 High 0 12 0.04 0 7 0.09 0 19 0.003 Low 6 13 6 11 12 24 LY9 High 1 16 0.05 0 6 0.14 1 22 0.007 Low 5 9 6 12 11 21 TNFRSF17 High 1 16 0.05 0 10 0.02 1 26 0.001 Low 5 9 6 8 11 17 C1QA High 0 12 0.04 0 9 0.04 0 21 0.001 Low 6 13 6 9 12 22 mmune response prognostic module: distribution of poor and good outcome patients in over-and-under- External validation of immune response prognostic module: distribution of poor and good outcome patie expressed subgroups with clinical outcome [5,10,18,22], in ER- disease no such prognostic signatures have thus far been reported. Moreover, although in ER+ tumors subtypes of different prognostic risks, the luminal A and B subtypes, have been defined [21,22], no such subdivisions have been noted for ER- breast cancer. It is known that the two main subtypes of ER- breast cancer (ER-/HER2+ and basals) have worse prognosis com- pared with the luminal A subtype, but no outcome differences between the ER-/HER2+ and basal subtypes have been observed [15,21-23,26]. confirmed by application of PAC, which showed that, with the exception of XCL2, none of the other six genes were individu- ally prognostic. In this context, it is worth noting once again the absence of immune response related genes among the 29 PAC derived prognostic genes in ER+ disease, which would suggest that a good prognosis IR related subtype is absent in ER+ breast cancer. To investigate this further we checked, by performing Wilcoxon rank sum tests on the 5,007 genes, that the absence of immune response GOs was not just an artefact of the small number of genes picked out by PACK. Pam cluste Figure 5 g g Pam clustering over IR module in external ER- cohorts. Heatmap of gene expression of seven-gene IR-module in ER- samples of the (a) UPP and (b) JRH-2 cohorts. Shown are the clusters over-expressing (purple) and under-expressing (yellow) the IR module, as predicted by the pam algorithm. Good outcome samples are shown in gray, and poor outcome samples in black. Green indicates relative under-expression, and red indicates relative over-expression. (c) Kaplan-Meier survival curves over combined external cohorts (for UPP end-point was disease-specific survival, and for JRH-2 it was recurrence-free survival), with the number of events and samples in each of the two predicted groups. ER, estrogen receptor; pam, partitioning around medoids. information Table 5 (a) HLA−F IGLC2 LY9 TNFRSF17 SPP1 XCL2 C1QA (b) HLA−F IGLC2 LY9 TNFRSF17 SPP1 C1QA 0 2 4 6 8 10 0.0 0.2 0.4 0.6 0.8 1.0 (c) 0/20 12/35 (a) HLA−F IGLC2 LY9 TNFRSF17 SPP1 XCL2 C1QA (b) HLA−F IGLC2 LY9 TNFRSF17 SPP1 C1QA 0 2 4 6 8 10 0.0 0.2 0.4 0.6 0.8 1.0 (c) 0/20 12/35 The prognostic value of the IR module is specific to ER- tumours To confirm that the good prognosis conferred by activation of the IR module is specific to ER- breast cancer, we applied the same pam clustering algorithm over the seven genes to the integrated dataset of 527 ER+ breast tumors. This gave two clusters with unequal distributions of good and poor outcome samples (209 good and 99 poor for the cluster under-express- ing the genes versus 163 good and 47 poor for the cluster over- expressing the genes; P = 0.02). Although this suggested to us that over-expression of this seven-gene module also con- ferred better prognosis in ER+ samples, the association was much weaker than for ER- samples. Univariate Cox regression with TTDM as the outcome variable confirmed that under- expression of this seven-gene module conferred a much greater risk for distant metastasis in ER- tumors (HR 2.02, 95% CI 1.2 to 3.4; P = 0.009) than in ER+ tumors (HR 1.25, 95% CI 0.9 to 1.7; P = 0.16; Table 4). It is also noteworthy that, in contrast to the ER- case, in the multivariate model setting for ER+ tumors, a low LI score and LN involvement were stronger predictors of TTDM than the seven-gene module (HR 1.65, 95% CI 0.4 to 7.1 for LI score and HR 1.48, 95% CI 0.7 to 3.2 for LN involvement, versus HR <1; Table 4). The specificity of our prognostic module to ER- breast cancer was Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.11 http://genomebiology.com/2007/8/8/R157 Table 5 confirmed by application of PAC, which showed that, with the with clinical outcome [5,10,18,22], in ER- disease no such Table 5 External validation of immune response prognostic module: distribution of poor and good outcome patients in over-and-under- expressed subgroups Gene UPP JRH-2 Combined Poor Good P Poor Good P Poor Good P IGLC2 High 0 12 0.04 0 7 0.09 0 19 0.003 Low 6 13 6 11 12 24 LY9 High 1 16 0.05 0 6 0.14 1 22 0.007 Low 5 9 6 12 11 21 TNFRSF17 High 1 16 0.05 0 10 0.02 1 26 0.001 Low 5 9 6 8 11 17 C1QA High 0 12 0.04 0 9 0.04 0 21 0.001 Low 6 13 6 9 12 22 confirmed by application of PAC, which showed that, with the exception of XCL2, none of the other six genes were individu- ally prognostic. In this context, it is worth noting once again the absence of immune response related genes among the 29 PAC derived prognostic genes in ER+ disease, which would suggest that a good prognosis IR related subtype is absent in ER+ breast cancer. To investigate this further we checked, by performing Wilcoxon rank sum tests on the 5,007 genes, that the absence of immune response GOs was not just an artefact of the small number of genes picked out by PACK. In fact, GO analysis with clinical outcome [5,10,18,22], in ER- disease no such prognostic signatures have thus far been reported. Moreover, although in ER+ tumors subtypes of different prognostic risks, the luminal A and B subtypes, have been defined [21,22], no such subdivisions have been noted for ER- breast cancer. It is known that the two main subtypes of ER- breast cancer (ER-/HER2+ and basals) have worse prognosis com- pared with the luminal A subtype, but no outcome differences between the ER-/HER2+ and basal subtypes have been observed [15,21-23,26]. Discussion A striking difference between ER+ and ER- disease is emerg- ing at the level of mRNA expression. Although in ER+ disease a significant number of genes have been found that correlate Genome Biology 2007, 8:R157 R157.12 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 tics of the tumors. The prognostic signatures derived for ER+ breast cancer are characterized by genes related to cell cycle and cell proliferation pathways, and are also highly correlated with the histologic grade of the tumors [7,22]. It is not a coincidence that most luminal B tumours are of high grade, whereas the great majority of luminal A tumours are of low grade [7,22]. It appears that there may be a whole plethora of diverse oncogenic pathways that drive the over-activation of cell cycle and cell growth pathways in poor prognosis tumors. This would explain the larger number of prognostic genes found in ER+ disease (the great majority of which are related to cell cycle ontologies) as well as the stronger prognostic sig- nals (relatively large differences in log2 expression between poor and good prognosis tumours), an effect that is probably driven by oncogenic amplifications. This interpretation would also fit in well with our finding that most bimodal pro- files in ER+ breast cancer have positive kurtosis values, because this could be a reflection of a more diverse range of small amplifier subgroups in ER+ breast cancer. number of genes in the 98-gene IR cluster show expression variability that is not explained by LI. This is confirmed fur- ther by two recent studies that profiled breast cancer cell lines [27,38], which showed that a considerable number of immune response related genes do exhibit significant variable expression across the basal cell subtype. Moreover, we found that two (SPP1 and HLA-F) of the three IR module genes that we could map to good quality probes in [27,38] showed twofold changes across the eight basal cell lines. Thus, these findings together suggest that a significant pro- portion of the expression of the IR module genes in the good prognosis tumors is tumor-intrinsic in origin. Discussion That tumor- intrinsic expression of IR genes can have an impact on prog- nosis of breast cancer patients is plausible in view of recent studies that show, for example, how amplification of kinase oncogenes can activate the nuclear factor-κB pathway, and hence immune response pathways, in both breast cancer cell lines and patient derived breast tumors [41]. Similarly, another recent study [42] used breast cancer cell lines to show how BRCA1/IFN-γ pathways may regulate target genes involved in innate immune response, providing another pos- sible mechanism for tumor intrinsic IR gene expression variability. In contrast, most ER- tumours are of high grade, which would explain why any differences in clinical outcome within ER- disease are not related to differential activation of cell cycle pathways. Instead, the work presented here shows that differ- ences in clinical outcome within ER- disease are mainly related to differentially expressed genes in the complement and immune response pathways, and that the association with prognosis can be independent of lymphocytic infiltration (LI) and LN status. In fact, for ER- tumors we observed that even though there were proportionally more high LI samples in the group over-expressing the IR module, these did not necessarily have better prognosis. The fact that LI could not explain the observed association of the IR module with out- come was supported further by our finding that medullary breast cancers, which are characterized by high LI scores, had expression profiles most similar to the CC+/IR+ subtype rather than the IR+ subtype, which had the best prognosis overall. The better prognosis of the CC+/IR+ subtype relative to CC+ and SR+ ER- breast cancer is therefore entirely consistent with the CC+/IR+ subclass being medullary breast cancers (MBCs), as MBC is known to have marginally better prognosis than other basal tumors [38]. On the other hand, the IR+ subclass, which had the best prognosis among the five ER- subclasses, was only marginally associated with high LI and was unrelated to MBC. Also consistent with these obser- vations, it is important to note again the distinction between the identified seven-gene prognostic IR module and the 98- gene IR cluster that was derived from unsupervised hierarchi- cal clustering. Clearly, we found a strong statistical associa- tion between high LI and over-expression of the 98-gene IR cluster. Discussion Specifically, there were 13 high LI and eight low LI samples in the combined IR+ and CC+/IR+ clusters relative to six high LI and 23 low LI samples in the rest of the cohort (Fisher test P = 0.007). In contrast, the association between high LI and over-expression of the IR module was much weaker (P = 0.07). Again, this suggests that a significant In spite of identifying only a relatively small module of prog- nostic genes, we were nevertheless able to validate their prog- nostic potential in two external cohorts. It is likely that an integrative analysis similar to the one used here but applied to multiple cohorts that were all profiled on exactly the same genome-wide platform would allow further expansion of this module to include other members of the complement and immune response pathways. Interestingly, from the seven prognostic markers that composed the IR module, two have already been associated with clinical outcome in breast can- cer. Specifically, C1QA, which is a gene involved in the classi- cal complement pathway, was recently shown to harbor a single nucleotide polymorphism that correlated with distant metastasis in breast cancer [43]. Two recent studies also implicated SPP1 (osteopontin) in metastatic breast cancer [44,45]. It is important also to note that the robustness of the identi- fied prognostic markers is a consequence of the PACK meth- odology. Despite being a conservative procedure that filters out many true positives, PACK allows, by efficient removal of false positives, a more reliable identification of prognostic markers. We tested this further by applying two popular sta- tistical tools, singular value decomposition (SVD) [46] and the shrunken centroids classifier (PAMR) [47], to the inte- grated ER- dataset to determine whether we could derive a similar if not identical prognostic IR module. Using SVD we found that none of the inferred SVD components showed a correlation with prognosis (Wilcoxon rank sum test P > 0.05), whereas at a FDR threshold of 0.3 PAMR yielded 21 prognos- tic genes, of which only two (the IR module member Genome Biology 2007, 8:R157 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. R157.13 http://genomebiology.com/2007/8/8/R157 TNFRSF17 and KLRD1) had immune response related func- tions. PACK: profile analysis using clustering and kurtosis PACK: profile analysis using clustering and kurtosis The hypothesis underlying PACK [17] is that genes that are true biologic or clinical markers have expression profiles that are generated by a mixture of two or more underlying distri- butions, whereas spurious features are more likely to have profiles generated by a single distribution. The biologic valid- ity of this assumption was proved through a FDR analysis [17]. PACK can be viewed as a semi-supervised algorithm, consist- ing of two main steps: a feature selection criterion and a supervised step, in which the selected features are correlated to a phenotype (Figure 2). It is important to note that PACK is a flexible modular algorithm in that the feature selection step can be applied on its own. In this case, there are two possible versions of the algorithm: PAC and PAK. The precise way in which these two algorithms are used in PACK will depend on the purpose of the exercise. Below, we describe the PACK strategy implemented in this paper, which is slightly different from that applied previously [17]. Besides identifying a module of genes that is prognostic in over 240 ER- breast tumors, PACK also provided us with a novel subclassification of ER- breast cancer. Specifically, clus- tering over PACK selected genes identified five different sub- types (CC+, CC+/IR+, IR+, ECM+, and SR+) characterized by the over-expression patterns of four distinct gene clusters, each enriched for IR, ECM, CC, and SR genes, respectively. Moreover, we related these subtypes to the gene expression based intrinsic subclasses. This showed that the basal sub- group was a heterogeneous group with at least four distinct subtypes (CC+, CC+/IR+, ECM+, and IR+), whereas the ER-/ HER2+ subgroup showed strong overlap with the SR+ and IR+ subtypes. Conclusion hil i b While in ER+ breast cancer prognostic markers are associated mainly with cell cycle pathways, in ER- disease prognostic markers are associated with immune response pathways. In particular, we have identified a subclass of ER- tumors that over-express immune response genes and that has a good prognosis compared with the rest of ER- breast tumors, inde- pendently of LN status or LI. Furthermore, we have identified an associated module of complement and immune response genes that define prognostic markers valid in over 240 ER- samples. where X is any random variable and E denotes the expecta- tion. For a gaussian , so that K(X) = 0. Most nongaussian distributions necessarily have either K > 0, in which case they are called supergaussian or leptokurtic, or K < 0, in which case they are called subgaus- sian or platykurtic. Specifically, a mixture of two approxi- mately equal mass gaussians must have negative kurtosis because the two modes on either side of the center of mass effectively flatten out the distribution. To see this, consider a gene whose expression profile is described by a mixture of two gaussians. Then, the kurtosis, K, is a function of two parameters (we assume for simplicity that the gaussians are of equal variance σ2, although this assumption is not needed for the result below); the effect size of the gene, as defined by the effective separation e between the two gaussians (e = μ/σ, where μ is the separation), and the ratio of cluster weights (π1, E X X E X X [( ) ] [( ) ] − = − 4 2 2 3 where X is any random variable and E denotes the expecta- where X is any random variable and E denotes the expecta- tion. For a gaussian , so that K(X) = 0. Most nongaussian distributions necessarily have either K > 0, in which case they are called supergaussian or leptokurtic, or K < 0, in which case they are called subgaus- sian or platykurtic. Specifically, a mixture of two approxi- mately equal mass gaussians must have negative kurtosis because the two modes on either side of the center of mass effectively flatten out the distribution. To see this, consider a gene whose expression profile is described by a mixture of two gaussians. Feature selection with PAK: using negative kurtosis to find genes defining major subclasses Kurtosis is related to the fourth central moment and can con- veniently be defined as follows [49]: K X ( ) [( ) ] [( ) ] ≡ − − − E X X E X X 4 2 2 3 (1) (1) Conclusion hil i b Then, the kurtosis, K, is a function of two parameters (we assume for simplicity that the gaussians are of equal variance σ2, although this assumption is not needed for the result below); the effect size of the gene, as defined by the effective separation e between the two gaussians (e = μ/σ, where μ is the separation), and the ratio of cluster weights (π1, E X X E X X [( ) ] [( ) ] − = − 4 2 2 3 Discussion Thus, in agreement with findings presented previously [17], this reinforces the advantage of PACK over other pattern recognition tools and supervised methods that do not use pattern recognition steps, such as for example those based on t-tests. TNFRSF17 and KLRD1) had immune response related func- tions. Thus, in agreement with findings presented previously [17], this reinforces the advantage of PACK over other pattern recognition tools and supervised methods that do not use pattern recognition steps, such as for example those based on t-tests. ther normalized, if necessary, by transforming them onto a common log2 scale and shifting the median of each array to zero. We also created an automated computational pipeline (Perl scripts on a Linux platform) to crosslink the annotation provided for each dataset with UniGene. For some datasets, the linkage relied on Ensembl [48] external database identifi- ers. Thus each probe was associated with a universal gene name. This procedure generated a nonredundant set of gene identifiers for the subsequent integrative analysis. The absence of a prognostic IR module in ER+ breast cancer is intriguing. The seven-gene IR module was only marginally associated with prognosis in ER+ disease, and importantly this association was not independent of LI or LN status. Repeating the same unsupervised analysis (PAK) and semi- supervised analysis (PACK) in ER+ breast cancer also did not find a prognostic immune response module. By using a tradi- tional supervised method, a prognostic IR module was iden- tifiable but failed to validate in the two external cohorts. Thus, to determine fully whether such a robust prognostic IR mod- ule exists for ER+ breast cancer, it may be necessary to con- duct larger integrative studies that use the same microarray platform so that the analysis can be performed over a larger set of common genes. Software packages used where and σ are the mean and standard deviation esti- mates of the profile. A standard error estimate of K was obtained by performing 10,000 random simulations, with n = 186 (number of ER- samples), which showed that the stand- ard error estimate, 0.36, was essentially identical to the theo- retical estimate, √(24/n) [50]. x All analyses were performed using the R statistical program- ming language [55]. The following add-on packages were used: vabayelMix for the PACK implementation, survival for the Cox regression models, qvalue for FDR estimation, and cluster for the partitioning around medoids (pam) clustering algorithm. Two notes with the feature selection step are in order. First, the kurtosis threshold used to select features depends on how large the smallest subgroup must be. Generally, given the effective separation values that are typical for differential gene expression, we find that a zero kurtosis threshold (as used in this report) generally picks out subgroups within the individual gene expression profiles that are at least as large as 30% of the total sample size [17]. Second, in principle, genes defining major subclasses could be found using a clustering step to infer two clusters (PAC) and setting a lower bound threshold (for instance, 30%) on the size of the smallest clus- ter. However, this approach is computationally more expen- sive, because PAC attempts to estimate the optimal number of clusters in the profile. However, this model selection step is a necessary one to ensure that profiles for which there is no objective evidence of bimodality are excluded (see below). Datasets and gene annotation One possibility is to use the EM algorithm to learn the parameters for the two different models C = 1 and C = 2, and perform model selection using the Bayesian Infor- mation Criterion (BIC) score [51,52]. Alternatively, the opti- mal number of clusters, C, can be inferred using a lower bound on the model evidence, as provided by a variational Bayesian (VB) approach [39,53,54]. The results we report here were obtained using the VB algorithm for model selec- tion. Thus, genes for which C = 1 were excluded from further analysis. Finally, association with the phenotype (here prog- nosis) was determined using Fisher's exact test to test whether poor outcome events were unevenly distributed across the two clusters. (2) where a and b are the quadratic roots 2 ± √3. Thus, for e ≠ 0, the kurtosis is negative if and only if (2 - √3) < R < (2 + √3). This in turn requires the smallest cluster weight, πmin, to be in the range (approximately) of 0.22 <πmin < 0.5. It follows that for the case of approximately equal weights, where R ≅ 1 (πmin ≅ 0.5), the kurtosis is always negative and in the limit of large cluster separations (when e >> 1) the kurtosis decreases monotonically, asymptotically approaching the lower bound - 2. Thus, kurtosis provides a useful measure for ranking genes based on how platykurtic their profiles are. Given a gene's expression profile x = (x1, ..., xn), an unbiased estimate for the kurtosis [50] is as follows: K x n n x x n n n n n n i i n ( ) ( ) ( ) ( )( )( ) ( ) ( )( )  + − − − − − − − − = ∑ 1 1 2 3 3 1 2 3 4 1 4 2 σ (3) (3) The SSP classifier The classification of the samples in the NKI2, EMC, and NCH cohorts into the intrinsic subtypes was performed using the single sample predictor (SSP) [23] and was done for each cohort separately because this guaranteed a larger number of overlapping genes. In the SSP, samples were assigned the intrinsic subtype for which the corresponding Spearman rank correlation between the sample and SSP centroid was maxi- mal [23]. The ER- subclass centroids From the hierarchical clustering with Pearson correlation metric and complete linkage diagram (Figure 3a) we con- structed mean centroids for each of the five subclasses. Clas- sification of external samples to these centroids was performed using the nearest centroid criterion. Because these centroids were defined over ER- samples only, external sam- ples (which may not be ER-) may not show strong correlation to any of these centroids. We thus validated, through 10,000 Monte Carlo (MC) randomisations, that samples with a max- imal pearson coefficient larger than 0.25 were significantly correlated with the corresponding centroid (P < 0.0001). Samples with maximal correlation coefficients smaller than 0.25 were deemed to be unclassifiable. Datasets and gene annotation The microarray breast cancer datasets considered in this work are described elsewhere [5,7,9,18,19]. For these cohorts we used the normalized data, which are available in the public domain (see [5,7,9,18,19]). The retrieved datasets were fur- Genome Biology 2007, 8:R157 sue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 R157.14 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. http://genomebiology.com/2007/8/8/R157 π2), that is R = π1/(1 - π1). Specifically, a short computation reveals that R = π1/(1 - π1). Specifically, a short computation p x G x i k i k k k CM ( | ) ( | , ) θ π μ σ = =∑ 1 (4) (4) K e R e R R a R b R R R e ( , ) ( )( ) ( ) ( ( ) ) = − − + + + 4 4 2 2 2 1 1 1 (2) Where πk are the weights of the components, (μk, σk) are the mean and standard deviation of the univariate gaussian k, and θ denotes the set of all parameters. In the above, CM denotes the maximum number of clusters that can be inferred, which in our application we set to 2. The optimal number of clusters, C, can be inferred using one of various approaches. One possibility is to use the EM algorithm to learn the parameters for the two different models C = 1 and C = 2, and perform model selection using the Bayesian Infor- mation Criterion (BIC) score [51,52]. Alternatively, the opti- mal number of clusters, C, can be inferred using a lower bound on the model evidence, as provided by a variational Bayesian (VB) approach [39,53,54]. The results we report here were obtained using the VB algorithm for model selec- tion. Thus, genes for which C = 1 were excluded from further analysis. Finally, association with the phenotype (here prog- nosis) was determined using Fisher's exact test to test whether poor outcome events were unevenly distributed across the two clusters. Where πk are the weights of the components, (μk, σk) are the mean and standard deviation of the univariate gaussian k, and θ denotes the set of all parameters. In the above, CM denotes the maximum number of clusters that can be inferred, which in our application we set to 2. The optimal number of clusters, C, can be inferred using one of various approaches. Additional data files The following additional data are available with the online version of this manuscript. Additional data file 1 is a table showing the 813 genes with negative kurtosis expression profiles over 186 ER- tumors, together with the predicted number of clusters and Fisher's test P value with outcome as binary phenotype. Additional data file 2 is a table showing the 193 genes with negative kurtosis expression profiles over 527 ER+ samples, together with the predicted number of clusters and Fisher's test P value with outcome as binary phenotype. Additional data file 3 is a figure showing hierarchical cluster- ing over 186 ER- breast cancers (gene annotated version). Additional data file 4 is a figure showing the distribution of basal and ERBB2 markers among ER- subtypes. Additional data file 5 is a table showing the centroids of gene expression for each of the five identified ER- subtypes. Additional data file 6 is a figure showing expression profiles of immune response module genes in ER- samples of the external UPP cohort. Additional data file 7 is a figure showing expression profiles of immune response module genes in ER- samples of the external JRH-2 cohort. Additional data file 8 is a figure showing the clustering of ER+ samples over the humoral immune response gene module in the two external UPP and JRH-2 cohorts. Additional data files Additi l d t fil G ith ti k t i i fil i ER b t C l l b l th th ti k t i f it i fil 86 ER l th b f l t di t d b PAC d Fi h ' t t P l t ti f i ti b t t d th t l t Cli k h f fil Additi l d t fil G ith ti k t i i fil i ER b t C l l b l th th ti k t i f it i fil ER l th b f l t di t d b PAC d Fi h ' t t P l t ti f i ti b t t d th t l t Cli k h f fil Additi l d t fil Hi hi l l t i 86 ER b t t t d i Hi hi l l t i 86 ER b t d 8 ti k t i fil l t d i th PAK l ith l i d i th t t Fi i l t id tifi d d h t i d i t f i f l t d t ll l (CC) i (IR) t ll l t i (ECM) d t id h (SR) f ti R d d t l ti i d l ti d i Cli k h f fil Additi l d t fil Di t ib ti f b l d ERBB k ER bt (A) Hi hi l l t i d d ith th diff t ER b t d fi d b th l t i i Fi (B) Th di t ib ti f l h ti i filt ti (LI) d hi t l i d C l d bl k hi h LI d hi h d l LI bl i t di t d d k bl l d (C) E i fil f lid t d b l k f [ ] ER bt (D) E i fil f i th ERBB li C l d l ti d i d l ti i Cli k h f fil Additi l d t fil G i t id f ER b l T bl i th i t id th fi id tifi d ER b l C t id d fi d th 8 ith ti k t i i fil Cli k h f fil Additi l d t fil 6 E i fil f i d l i ER l f t l UPP h t E i fil ( l l ) f i d l i th lid ti ER h t UPP Bl k i di t d t l d d t l Cl t i f d i th l ith I f d l t i di t d b diff t h (t i l d di d ) Cli k h f fil Additi l d t fil E i fil f i d l i ER l f t l JRH h t E i fil ( l l ) f i d l i th lid ti ER h t UPP Bl k i di t d t l d d t l Cl t i f d i th l ith I f d l t i di t d b diff t h (t i l d di d ) Cli k h f fil Additi l d t fil 8 H l i d l i t l ER+ h t H t f i f th h l IR d l i th ER+ l f th (A) UPP d (B) JRH h t Sh th l t i ( l ) d d i ( ll ) th h l IR d l di t d b th l ith G d t l t d i d t l i bl k G i di t l ti d i d d l ti i (C) K l M i i l bi d t l h t (f UPP th d i t di ifi i l d f JRH it f i l) ith th b f t d l i h f th t di t d Cli k h f fil 10. Additional data files 10. Teschendorff AE, Naderi A, Barbosa-Morais NL, Pinder SE, Ellis IO, Aparicio S, Brenton JD, Caldas C: A consensus prognostic gene expression classifier for ER positive breast cancer. Genome Biol 2006, 7:R101. 11. van de Rijn M, Perou CM, Tibshirani R, Haas P, Kallioniemi O, Kononen J, Torhorst J, Sauter G, Zuber M, Kochli OR, et al.: Expres- sion of cytokeratins 17 and 5 identifies a group of breast car- cinomas with poor clinical outcome. Am J Pathol 2002, 161:1991-1996. 12. Malzahn K, Mitze M, Thoenes M, Moll R: Biological and prognostic significance of stratified epithelial cytokeratins in infiltrating ductal breast carcinomas. Virchows Arch 1998, 433:119-129. 13. Rakha EA, El-Rehim DA, Paish C, Green AR, Lee AH, Robertson JF, Blamey RW, Macmillan D, Ellis IO: Basal phenotype identifies a poor prognostic subgroup of breast cancer of clinical importance. Eur J Cancer 2006, 42:3149-3156. p J 14. Rakha EA, El-Sayed ME, Green AR, Lee AH, Robertson JF, Ellis IO: Prognostic markers in triple-negative breast cancer. Cancer 2007, 109:25-32. 15. Jumppanen M, Gruvberger-Saal S, Kauraniemi P, Tanner M, Bendahl PO, Lundin M, Krogh M, Kataja P, Borg A, Ferno M, et al.: Basal-like phenotype is not associated with patient survival in estro- gen-receptor-negative breast cancers. Breast Cancer Res 2007, 9:R16. 16. Eden P, Ritz C, Rose C, Ferno M, Peterson C: 'Good Old' clinical markers have similar power in breast cancer prognosis as microarray gene expression profilers. Eur J Cancer 2004, 40:1837-1841. 17. Teschendorff AE, Naderi A, Barbosa-Morais NL, Caldas C: PACK: Profile Analysis using Clustering and Kurtosis to find molec- ular classifiers in cancer. Bioinformatics 2006, 22:2269-2275. 18. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, et al.: A gene- expression signature as a predictor of survival in breast cancer. N Engl J Med 2002, 347:1999-2009. Lymphocyte infiltration scores g p y 6. Pawitan Y, Bjohle J, Amler L, Borg AL, Egyhazi S, Hall P, Han X, Hol- mberg L, Huang F, Klaar S, et al.: Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res 2005, 7:R953-R964. For the samples from our NCH cohort [9] we used the follow- ing scoring method. Lymphocytic infiltration (LI) was assessed in whole tumour sections from frozen sections stained with hematoxylin and eosin. The intensity of lym- phocytic infiltrate was first graded semi-quantitatively as minimal or mild (1), moderate (2), and marked (3). The LI scores were then dichotomized (we considered mild and moderate as low LI and marked as high LI) to make them comparable with the binary LI scores used by van 't Veer and coworkers [3]. 7. Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, et al.: Gene expression profiling in breast cancer: understanding the molecular basis of histo- logic grade to improve prognosis. J Natl Cancer Inst 2006, 98:262-272. 8. Foekens JA, Atkins D, Zhang Y, Sweep FC, Harbeck N, Paradiso A, Cufer T, Sieuwerts AM, Talantov D, Span PN, et al.: Multicenter val- idation of a gene expression-based prognostic signature in lymph node-negative primary breast cancer. J Clin Oncol 2006, 24:1665-1671. 9. Naderi A, Teschendorff AE, Barbosa-Morais NL, Pinder SE, Green AR, Powe DG, Robertson JF, Aparicio S, Ellis IO, Brenton JD, et al.: A gene-expression signature to predict survival in breast can- cer across independent data sets. Oncogene 2007, 26:1507-1516. 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Racila E, Racila DM, Ritchie JM, Taylor C, Dahle C, Weiner GJ: The pattern of clinical breast cancer metastasis correlates with a single nucleotide polymorphism in the C1qA component of complement. Immunogenetics 2006, 58:1-8. y 23. Hu Z, Fan C, Oh DS, Marron JS, He X, Qaqish BF, Livasy C, Carey LA, Reynolds E, Dressler L, et al.: The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 2006, 7:96. 44. Allan AL, George R, Vantyghem SA, Lee MW, Hodgson NC, Engel CJ, Holliday RL, Girvan DP, Scott LA, Postenka CO, et al.: Role of the integrin-binding protein osteopontin in lymphatic metastasis of breast cancer. Am J Pathol 2006, 169:233-246. 24. Farmer P, Bonnefoi H, Becette V, Tubiana-Hulin M, Fumoleau P, Lar- simont D, Macgrogan G, Bergh J, Cameron D, Goldstein D, et al.: Identification of molecular apocrine breast tumours by microarray analysis. Oncogene 2005, 24:4660-4671. J 45. 21:3025-3033. de Silva Rudland S, Martin L, Roshanlall C, Winstanley J, Leinster S, Platt-Higgins A, Carroll J, West C, Barraclough R, Rudland P: Asso- ciation of S100A4 and osteopontin with specific prognostic factors and survival of patients with minimally invasive breast cancer. Clin Cancer Res 2006, 12:1192-1200. 25. Doane AS, Danso M, Lal P, Donaton M, Zhang L, Hudis C, Gerald WL: An estrogen receptor-negative breast cancer subset charac- terized by a hormonally regulated transcriptional program and response to androgen. Oncogene 2006, 25:3994-4008. 46. Alter O, Brown PO, Botstein D: Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc Natl Acad Sci USA 2003, 100:3351-3356. p g g 26. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pol- lack JR, Ross DT, Johnsen H, Akslen LA, et al.: Molecular portraits of human breast tumours. Nature 2000, 406:747-752. 47. Tibshirani R, Hastie T, Narasimhan B, Chu G: Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 2002, 99:6567-6572. 27. Charafe-Jauffret E, Ginestier C, Monville F, Finetti P, Adelaide J, Cer- vera N, Fekairi S, Xerri L, Jacquemier J, Birnbaum D, Bertucci F: Gene expression profiling of breast cell lines identifies potential new basal markers. Oncogene 2006, 25:2273-2284. 48. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, et al.: The Ensembl genome database project. Nucleic Acids Res 2002, 30:38-41. 28. Zhang B, Schmoyer D, Kirov S, Snoddy J: GOTree Machine (GOTM): a web-based platform for interpreting sets of inter- esting genes using Gene Ontology hierarchies. BMC Bioinformatics 2004, 5:1-8. p j 49. Balanda KP, MacGillivray HL: Kurtosis: a critical review. Am Stat 1988, 42:111-119. 29. Kaufman L, Rousseeuw PJ: Finding Groups in Data: An Introduction to Cluster Analysis New York: Wiley; 1990. 50. Snedecor GW, Cochran WG: Statistical Methods 6th edition. Ames, IA: Iowa State University Press; 1967. 51. Schwarz G: Estimating the dimension of a model. Annls Stat 1978, 6:461-464. 30. Huang E, Cheng SH, Dressman H, Pittman J, Tsou MH, Horng CF, Bild A, Iversen ES, Liao M, Chen CM, et al.: Gene expression predic- tors of breast cancer outcomes. Lancet 2003, 361:1590-1596. 52. Yeung KY, Fraley C, Murua A, Raftery AE, Ruzzo WL: Model-based clustering and data transformations for gene expression data. Bioinformatics 2001, 17:977-987. 31. Acknowledgements g This research was supported by grants from Cancer Research UK. We thank Ali Naderi for useful discussions. g This research was supported by grants from Cancer Research UK. We thank Ali Naderi for useful discussions. 19. g J 19. Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, Bergh J: An expression signature for p53 Genome Biology 2007, 8:R157 http://genomebiology.com/2007/8/8/R157 R157.16 Genome Biology 2007, Volume 8, Issue 8, Article R157 Teschendorff et al. 21:3025-3033. Bertucci F, Finetti P, Cervera N, Charafe-Jauffret E, Mamessier E, Adelaide J, Debono S, Houvenaeghel G, Maraninchi D, Viens P, et al.: Gene expression profiling shows medullary breast cancer is a subgroup of basal breast cancers. Cancer Res 2006, 66:4636-4644. 39. Teschendorff AE, Wang Y, Barbosa-Morais NL, Brenton JD, Caldas C: A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data. Bioinformatics 2005, Genome Biology 2007, 8:R157
https://openalex.org/W3153210820
https://ir.lib.hiroshima-u.ac.jp/52804/files/4185
Japanese
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Carnosic Acid and Carnosol Activate AMPK, Suppress Expressions of Gluconeogenic and Lipogenic Genes, and Inhibit Proliferation of HepG2 Cells
International journal of molecular sciences
2,021
cc-by
210
【背景】 【背景】 ローズマリーは古くから香辛料や薬草として使用されており、解毒作用や抗酸化作用、血行改 善作用、炎症抑制作用など多くの効能を有し、糖尿病や脂肪肝などを含む様々な代謝疾患に対す る治療的側面を有している可能性があり注目されている。 ローズマリーは古くから香辛料や薬草として使用されており、解毒作用や抗酸化作用、血行改 善作用、炎症抑制作用など多くの効能を有し、糖尿病や脂肪肝などを含む様々な代謝疾患に対す る治療的側面を有している可能性があり注目されている。 これまでにローズマリー抽出物の成分であるcarnosic acid (CA)、carnosol (CL)、rosmarinic acid (RA) の代謝改善作用に関して、特に骨格筋でAMPK を介して問う取り込みを亢進させる ことが報告されている (Clin Exp Pharmacol Physiol. 2016, Int J Mol Sci. 2018, Molecules. 2017)。一方で、その肝臓における作用に関しては、マウスを用いた実験で脂肪肝改善作用が複 数報告されているものの、その機序についてはCA がPPARγ発現低下を介して肝脂肪蓄積を抑 制するがAMPK に依らずEGFR/MAPK 依存的である (J Gastroenterol. 2012) という報告も あり、AMPK の寄与については不明な点が多い。 また、ローズマリー抽出物の抗腫瘍効果については多くの報告があるが、CL がAMPK 活性化 を介して前立腺癌細胞株の増殖抑制効果を示すという報告 (Pharm Res. 2008) 以外には AMPK を介する機序についての報告はほとんどない。 また、ローズマリー抽出物の抗腫瘍効果については多くの報告があるが、CL がAMPK 活性化 を介して前立腺癌細胞株の増殖抑制効果を示すという報告 (Pharm Res. 2008) 以外には AMPK を介する機序についての報告はほとんどない。 また、ローズマリー抽出物の抗腫瘍効果については多くの報告があるが、CL がAMPK 活性化 を介して前立腺癌細胞株の増殖抑制効果を示すという報告 (Pharm Res. 2008) 以外には AMPK を介する機序についての報告はほとんどない。 これらのことから私はHepG2 細胞を用いてCA、CL のAMPK を介した培養肝細胞での糖代 謝や脂質代謝、細胞増殖に対する影響について検討を行った。 これらのことから私はHepG2 細胞を用いてCA、CL のAMPK を介した培養肝細胞での糖代 謝や脂質代謝、細胞増殖に対する影響について検討を行った。 【方法 結果】 はじめにローズマリー抽出物 (RM-21B base) のAMPK 活性化をC2C12 細胞 (myotube) で 確認したところ、濃度依存的にAMPK の活性化がみられた。またローズマリー抽出物に含まれ る主要な構成成分であるCA、CL、RA についてAMPK の活性化を評価したところ、CA、CL でのみ濃度依存的にAMPK の活性化がみられた。そこで以降の実験では、CA、CL 共にAMPK が活性化した最低濃度 (10 µM) を用いて実験を行った。 我々は以前にAMPK 活性化が糖新生抑制に働くことを報告している (Horike N, et al. J Biol Chem. 2008) が、CA、CL 添加によりForskolin 刺激時の糖新生律速酵素遺伝子 (Pck1、G6pc) の誘導が抑制され、ルシフェラーゼアッセイでの検討においてもPck1 promoter 活性の抑制が 認められ、CA、CL は糖新生を抑制することが示唆された。 我々は以前にAMPK 活性化が糖新生抑制に働くことを報告している (Horike N, et al. J Biol Chem. 2008) が、CA、CL 添加によりForskolin 刺激時の糖新生律速酵素遺伝子 (Pck1、G6pc) の誘導が抑制され、ルシフェラーゼアッセイでの検討においてもPck1 promoter 活性の抑制が 認められ、CA、CL は糖新生を抑制することが示唆された。 次に脂肪酸合成や脂肪酸酸化に及ぼす影響について評価を行った。肝がん細胞株HepG2 をCA、 CL とともに24h incubation し脂肪酸合成及び脂肪酸酸化に関わる遺伝子発現量を検討したと ころ、CA、CL の添加によって脂肪酸合成に働くFAS、ACC1、SREBP-1c の発現量は減少し、 一方で脂肪酸酸化に働くCPT1a の発現量は増加傾向を示し、AMPK 阻害剤Compound C の添 加によってcancel された。以上からCA、CL は脂肪酸酸化を亢進し脂肪酸合成を抑制するので はないかと示唆された。 次に脂肪酸合成や脂肪酸酸化に及ぼす影響について評価を行った。肝がん細胞株HepG2 をCA、 CL とともに24h incubation し脂肪酸合成及び脂肪酸酸化に関わる遺伝子発現量を検討したと ころ、CA、CL の添加によって脂肪酸合成に働くFAS、ACC1、SREBP-1c の発現量は減少し、 一方で脂肪酸酸化に働くCPT1a の発現量は増加傾向を示し、AMPK 阻害剤Compound C の添 加によってcancel された。以上からCA、CL は脂肪酸酸化を亢進し脂肪酸合成を抑制するので はないかと示唆された。 さらにCA、CL の細胞増殖への影響についてHepG2 を用いて検討した。MTT assay での添加 24h 後の細胞の生存率は、CA、CL 投与群では低下し、Compound C の添加により回復した。 またCA、CL 添加によりAMPK 依存的なp53 リン酸化の亢進及びmTORC1 活性の低下が認め られ、CA ではcleaved caspase-3 の発現増加も見られapoptosis 亢進も示唆された。以上から CA、CL はAMPK 依存的にp53 を活性化、mTORC1 活性を抑制することで、細胞増殖抑制に 働く可能性が示唆された。 働く可能性が示唆された。 【結論】 ローズマリー抽出物の成分であるcarnosic acid、carnosol は糖新生抑制、脂肪酸合成抑制、脂 肪酸酸化亢進作用ならびに細胞増殖抑制作用を呈し、少なくともその機序の一部はAMPK 依存 的であると示唆された。
https://openalex.org/W3172015668
https://www.mdpi.com/2076-2615/11/6/1645/pdf?version=1623207553
English
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Lorenz Plot Analysis in Dogs with Sinus Rhythm and Tachyarrhythmias
Animals
2,021
cc-by
11,731
Citation: Romito, G.; Guglielmini, C.; Poser, H.; Baron Toaldo, M. Lorenz Plot Analysis in Dogs with Sinus Rhythm and Tachyarrhythmias. Animals 2021, 11, 1645. https:// doi.org/10.3390/ani11061645 animals animals animals Keywords: electrocardiography; Holter; Poincaré plot; heart rate variability; canine Lorenz Plot Analysis in Dogs with Sinus Rhythm and Tachyarrhythmias   Citation: Romito, G.; Guglielmini, C.; Poser, H.; Baron Toaldo, M. Lorenz Plot Analysis in Dogs with Sinus Rhythm and Tachyarrhythmias. Animals 2021, 11, 1645. https:// doi.org/10.3390/ani11061645 Academic Editors: Paola Giuseppina Brambilla and Chiara Locatelli Received: 28 April 2021 Accepted: 28 May 2021 Published: 1 June 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- animals animals Lorenz Plot Analysis in Dogs with Sinus Rhythm and Tachyarrhythmias Giovanni Romito 1 , Carlo Guglielmini 2,* , Helen Poser 2 and Marco Baron Toaldo 1,† Giovanni Romito 1 , Carlo Guglielmini 2,* , Helen Poser 2 and Marco Baron Toaldo 1,† Giovanni Romito 1 1 Department of Veterinary Medical Sciences, Alma Mater Studiorum—University of Bologna, 40064 Bologna, Italy; giovanni.romito2@unibo.it (G.R.); marco.barontoaldo@unibo.it (M.B.T.) 1 Department of Veterinary Medical Sciences, Alma Mater Studiorum—University of Bologna, 40064 Bologna, Italy; giovanni.romito2@unibo.it (G.R.); marco.barontoaldo@unibo.it (M.B.T.) 2 Department of Animal Medicine, Production and Health, University of Padova, 35020 Padua, Italy; helen.poser@unipd.it 1 Department of Veterinary Medical Sciences, Alma Mater Studiorum—University of Bologna, 40064 Bologna, Italy; giovanni.romito2@unibo.it (G.R.); marco.barontoaldo@unibo.it (M.B.T.) 2 Department of Animal Medicine, Production and Health, University of Padova, 35020 Padua, Italy; helen.poser@unipd.it g y g 2 Department of Animal Medicine, Production and Health, University of Padova, 35020 Padua, It helen.poser@unipd.it * Correspondence: carlo.guglielmini@unipd.it; Tel.: +39-04-9827-2505 * Correspondence: carlo.guglielmini@unipd.it; Tel.: +39-04-9827-2505 † Current address: Department for Small Animals, Division of Cardiology, Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland. Correspondence: carlo.guglielmini@unipd.it; Tel.: +39-04-9827-2505 † Current address: Department for Small Animals, Division of Cardiology, Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland. Simple Summary: The Lorenz plot (LP) is a geometrical method to assess the dynamics of heart rate variability. It consists of a two-dimensional Cartesian coordinate system derived from electrocar- diographic monitoring, in which each recorded R-R interval is plotted as a function of the previous R-R interval, and the values of each pair of successive R-R interval define a dot in the plot. The resultant clusters of dots can be evaluated quantitatively and qualitatively, and categorized into distinct geometrical patterns. In humans, several studies have demonstrated that the analysis of LP patterns (LPPs) has the potential to speed-up and improve the accuracy of arrhythmia detection and differentiation, especially in patients with tachyarrhythmias. As data on LP analysis are limited in dogs, this study describes the graphic features of LP derived from Holter recordings obtained in dogs with sinus rhythm and tachyarrhythmias, and analyzes the usefulness of LPP recognition in this species. We sought to evaluate if distinct cardiac rhythms imprint distinct and reproducible LPPs in dogs, as previously described in humans, and if each LLP can be used as a sensitive and specific indicator of a particular cardiac rhythm in this species. 1. Introduction A variety of Holter software algorithms have emerged in the last decades to speed- up rhythm analysis and simplify the interpretation of complex cardiac rhythms. Lorenz plots (LP), also known as Poincaré plots or scatterplots, provide visual representation of oscillations in the period between consecutive heartbeats, by plotting each R-R interval against the next one in a two-dimensional Cartesian coordinate system and depicting it as a dot. In this way, recorded beats are organized into clusters of dots with particular shapes, sizes, and positions according to the R-R interval fluctuations and the underlying cardiac rhythm [1,2]. In humans, analysis of such clusters in patients with sinus rhythm (SR) and tachyarrhythmias has allowed for the identification of 10 distinct LP patterns, each one having its own specific graphic characteristics, nomenclature, and excellent diagnostic accuracy for rhythm diagnosis [2]. Therefore, LPs could represent an attractive diagnostic tool in veterinary cardiology as well. Regrettably, only a few studies have described the graphic features of LP in dogs with and without arrhythmias [3–7], and the only study aimed at characterizing the LP patterns in arrhythmic dogs evaluated LPs generated from 1-h Holter recordings [6]. Therefore, the purposes of this study are threefold: (1) to evaluate the graphic charac- teristics of LPs derived from long-term Holter analysis obtained from dogs with SR and tachyarrhythmias; (2) to assess the reproducibility of LP pattern classification; and (3) to de- termine the diagnostic performance of LP patterns in identifying different cardiac rhythms. We hypothesized that distinct cardiac rhythms would imprint distinct and recognizable LP patterns in dogs. 2. Materials and Methods 2.1. Study Population Holter recordings from all dogs that underwent a Holter analysis as part of the di- agnostic evaluation at the veterinary teaching hospitals of the University of Bologna and Padova between June 2006 and January 2019 were retrospectively reviewed. Holter record- ings belonged to dogs with cardiac and/or extra-cardiac disorders associated with rhythm irregularities detected during cardiac auscultation and/or surface electrocardiogram, or to clinically healthy dogs of predisposed canine breeds (e.g., Doberman Pinschers) screened for dilated cardiomyopathy. Inclusion was restricted to good quality Holter recordings with ≥20 h of valid data and a Holter diagnosis of SR or tachyarrhythmias, either supraven- tricular or ventricular. For the purpose of this study, Holter recordings obtained from dogs with atrial fibrillation (AF) were included only if this tachyarrhythmia was observed for the entire duration of the monitoring. Recordings showing advanced or complete atrioven- tricular blocks, and those consistent with sick sinus syndrome, were excluded. Information regarding signalment, underlying cardiac or extracardiac disorders, and ongoing cardiac treatment at the time of Holter recording were obtained from medical records.   Abstract: The Lorenz plot (LP), a graphical representation of heart rate variability, has been poorly studied in dogs to date. The present study aimed to describe the graphic features of LP in dogs with sinus rhythm (SR) and tachyarrhythmias, and to analyze the usefulness of its pattern recognition. One hundred and nineteen canine Holter recordings were retrospectively evaluated. Cardiac rhythms were classified as: SR; SR with frequent (>100) premature ectopies (atrial, SR-APCs; ventricular, SR-VPCs; atrial and ventricular, SR-APCs-VPCs); atrial fibrillation (AF); and AF with frequent VPCs (AF-VPCs). Lorenz plots were studied qualitatively and quantitatively, and classified by distinct LP patterns (LPPs). Repeatability and reproducibility of LPP classification and diagnostic value were determined. Recordings included: 48 SR, 9 SR-APCs, 35 SR-VPCs, 5 SR-APCs-VPCs, 4 AF, and 18 AF- VPCs. Ten LPPs were identified: comet (n = 12), torpedo (n = 3), Y-shaped (n = 6), diamond (n = 10), diamond with a central silent zone (n = 17), double side-lobe (DSL) (n = 47), triple side-lobe (n = 1), quadruple side-lobe (n = 2), fan (n = 18), and fan with DSL (n = 3). Repeatability and reproducibility of LPP classification were excellent. The DSL pattern was both highly sensitive (91.3%) and specific (94.5%) for SR with frequent premature ectopies, either APCs, or VPCs, or both. The remaining LPPs had lower diagnostic value (high specificity but low sensitivity). Distinct rhythms imprint distinct and reproducible LPPs in dogs. The majority of canine LPPs are specific but insensitive indicators of SR and tachyarrhythmias. Academic Editors: Paola Giuseppina Brambilla and Chiara Locatelli Received: 28 April 2021 Accepted: 28 May 2021 Published: 1 June 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. 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:// Keywords: electrocardiography; Holter; Poincaré plot; heart rate variability; canine creativecommons.org/licenses/by/ Animals 2021, 11, 1645. https://doi.org/10.3390/ani11061645 https://www.mdpi.com/journal/animals 2 of 13 Animals 2021, 11, 1645 2.2. Holter Monitoring and Rhythm Analysis Holter recordings were obtained at the two centers using the same standardized technique [8] and analyzed using a commercially available software program designed for humans (Cube Holter software, Cardioline S.p.A.). The monitoring was conducted in the dog’s home environment during their daily routines, and the owners were instructed to note all activities in a diary. Holter data were acquired with a resolution of 10-bit and at a sampling frequency of 250 Hz and were then transferred to a computer for analysis. A standard protocol for semiautomatic arrhythmia analysis was performed as previously described [9–11]. Initially, a single board-certified cardiologist (GR) manually checked the entire recording to assess its quality, ensure that the software triggered correctly on every complex, and label possible unidentified complexes. Based on R-R intervals, the software automatically calculated minimum, mean, and maximal heart rates. Subsequently, events marked by the software were manually checked by the same operator to confirm correct classification. The software distinguished QRS complex of sinus and supraventric- Animals 2021, 11, 1645 3 of 13 3 of 13 ular origin (N) from wide QRS complexes (‘atypical’). The software defined more than 3 successive N at a heart rate <60 beats per minute as bradycardia, and N-N intervals >2 s as sinus pauses. The software also noted events with an NN interval at least 80% shorter than the previous N-N interval. These events were manually differentiated into atrial premature complexes ([APCs], i.e., abnormal P waves conducting normal-appearing QRS complexes [12,13]) and premature normal complexes (i.e., premature sinus complexes during sinus arrhythmia; the latter was defined as a regularly irregular SR, which is charac- terized by cyclic variations of the R-R intervals and is associated with a rate appropriate for temperament and level of activity of the dog [9–11]). Atypical complexes were manually checked to confirm if they were ectopic complexes of ventricular origin (i.e., wide and abnormal looking QRS not associated with sinus P waves [12,13]). The software defined atypical complexes with a coupling interval at least 5% shorter than the previous N-N interval as ventricular premature complexes (VPCs). For the purposes of this study, only the number of APCs and VPCs, and not their organization into atrial and ventricular allorhythmias, was considered. 2.2. Holter Monitoring and Rhythm Analysis Presence of AF entirely relied on manual analysis and was based on standard criteria (i.e., replacement of isoelectric baseline and sinus P waves by sequential less-defined deflections varying in amplitude, morphology and cycle length, as- sociated with normal-appearing QRS complexes, and irregular ventricular rhythm [12,13]). In light of arrhythmias analysis, the same operator made a final rhythm diagnosis for each recording. g For statistical analysis, given the wide range of electrocardiographic abnormali- ties identified on Holter recordings, cardiac rhythms were arbitrarily divided into the following classes: (1) SR: SR (with/without phases of SR arrhythmia) as dominant rhythm throughout the recording, including both pure SR and SR associated with in- frequent (<100/Holter [14,15]) APCs or VPCs; (2) SR-APCs: SR associated with frequent (>100/Holter) APCs, both isolated and organized into atrial allorhythmias; (3) SR-VPCs: SR associated with frequent VPCs (>100/Holter), both isolated and organized into ven- tricular allorhythmias; (4) SR-APCs-VPCs: SR associated with frequent APCs and VPCs (in both cases, >100/Holter), both isolated and organized into atrial and/or ventricular allorhythmias; (5) AF: AF as dominant rhythm throughout the recording, including both pure AF and AF associated with infrequent VPCs (<100/Holter); and (6) AF-VPCs: AF associated with frequent VPCs (>100/Holter), both isolated and organized into ventricular allorhythmias. In Holter recordings from the last class, particular attention was paid to manually differentiate true VPCs from QRS-complex changes related to rate-dependent aberrancy due to the Ashman phenomenon. Such differentiation was primarily based on the following electrocardiographic criteria: (1) the coupling interval of the wide QRS complex with the previous beat (true VPCs typically have a fixed coupling interval, while the Ashman phenomenon systematically results from a long R-R/short R-R sequence); (2) the presence or absence of a pause after the wide QRS complex (true VPCs are typically followed by a post-extrasystolic pause, whereas such pause is not expected in the case of the Ashman phenomenon); (3) the morphology of the wide QRS complex (the morphology of true VPCs can vary over the same recording due to the occurrence of VPCs arising from different ectopic foci, whereas the QRS-configuration tends to be stable in the case of Ashman phenomenon); and (4) the tendency of the wide QRS complex beats to form groups (VPCs tend to organize in couplets, triplets, or bigeminy, whereas such type of organization is atypical for the Ashman phenomenon) [16]. 2.4. Lorenz Plot Analysis 2.4. Lorenz Plot Analysis O th f ti Once the aforementioned steps were completed, the arrhythmia filter was disabled, and the complete population of recorded complexes was used to create LPs from the entire time of recording. On LPs, each R-R interval (R-Rn, dots depicted on the X-axis) was plotted against the following one (R-Rn + 1, dots depicted on the Y-axis), so that the coordinates of each dot were: R-R, R-R + 1 (Figure 1). Once the aforementioned steps were completed, the arrhythmia filter was disabled, and the complete population of recorded complexes was used to create LPs from the entire time of recording. On LPs, each R-R interval (R-Rn, dots depicted on the X-axis) was plot- ted against the following one (R-Rn + 1, dots depicted on the Y-axis), so that the coordi- nates of each dot were: R-R, R-R + 1 (Figure 1). Figure 1. Example figure showing the basic principles of Lorenz plot generation. On the figure bot- tom, a selected portion of a Holter recording from this study shows a sinus rhythm with regular R- R intervals transiently interrupted by a ventricular premature complex with a post-ectopic pause (PP). Above the tracing, a two-dimensional Cartesian coordinates map of R-R intervals is illustrated. The X-axis is the R-Rn interval and the Y-axis is the R-Rn + 1 interval. In this example, the first two R-R intervals are regular (a), creating a dot on the diagonal line (identity line) (A). The third R-R interval is premature (b); therefore, the correspondent dot moves below the line to point B. The fourth R-R interval is longer due to the PP; thus, the correspondent dot moves above the line to point C. The fifth R-R interval returns to the initial value (a); consequently, the correspondent dot moves to point D. Since the last R-R interval is identical to the preceding one (a), the last dot returns to point A. Repetition of this process using the entire population of R-R intervals recorded during a Holter monitoring creates the final Lorenz plot. Figure 1. Example figure showing the basic principles of Lorenz plot generation. On the figure bottom, a selected portion of a Holter recording from this study shows a sinus rhythm with regular R-R intervals transiently interrupted by a ventricular premature complex with a post-ectopic pause (PP). Above the tracing, a two-dimensional Cartesian coordinates map of R-R intervals is illustrated. 2.4. Lorenz Plot Analysis 2.4. Lorenz Plot Analysis O th f ti The X-axis is the R-Rn interval and the Y-axis is the R-Rn + 1 interval. In this example, the first two R-R intervals are regular (a), creating a dot on the diagonal line (identity line) (A). The third R-R interval is premature (b); therefore, the correspondent dot moves below the line to point B. The fourth R-R interval is longer due to the PP; thus, the correspondent dot moves above the line to point C. The fifth R-R interval returns to the initial value (a); consequently, the correspondent dot moves to point D. Since the last R-R interval is identical to the preceding one (a), the last dot returns to point A. Repetition of this process using the entire population of R-R intervals recorded during a Holter monitoring creates the final Lorenz plot. Figure 1. Example figure showing the basic principles of Lorenz plot generation. On the figure bot- tom, a selected portion of a Holter recording from this study shows a sinus rhythm with regular R- R intervals transiently interrupted by a ventricular premature complex with a post-ectopic pause (PP). Above the tracing, a two-dimensional Cartesian coordinates map of R-R intervals is illustrated. The X-axis is the R-Rn interval and the Y-axis is the R-Rn + 1 interval. In this example, the first two R-R intervals are regular (a), creating a dot on the diagonal line (identity line) (A). The third R-R interval is premature (b); therefore, the correspondent dot moves below the line to point B. The fourth R-R interval is longer due to the PP; thus, the correspondent dot moves above the line to point C. The fifth R-R interval returns to the initial value (a); consequently, the correspondent dot moves to point D. Since the last R-R interval is identical to the preceding one (a), the last dot returns to point A. Repetition of this process using the entire population of R-R intervals recorded during a Holter monitoring creates the final Lorenz plot. Figure 1. Example figure showing the basic principles of Lorenz plot generation. On the figure bottom, a selected portion of a Holter recording from this study shows a sinus rhythm with regular R-R intervals transiently interrupted by a ventricular premature complex with a post-ectopic pause (PP). Above the tracing, a two-dimensional Cartesian coordinates map of R-R intervals is illustrated. 2.3. Heart Rate Variability Analysis The software allowed analysis of heart rate variability (HRV), including both time- and frequency-domain analysis. Complexes of ventricular origin were automatically excluded from HRV analysis. Consequently, NN intervals included in the HRV analysis comprised sinus complexes and APCs [9–11]. For the purposes of this study, only time-domain variables were considered, including: the standard deviation of all the N-N intervals; the standard deviation of the means of the N-N intervals for all 5 min segments; the mean of Animals 2021, 11, 1645 4 of 13 time- N N the standard deviations of all the N-N intervals for all 5 min segments; the percentage of interval differences of successive N-N intervals more than 50 ms; and the square root of the mean squared differences of successive N-N intervals [1,9–11]. The HRV of dogs from the SR class was categorized as ‘normal’ or ‘reduced’ based on data previously reported in the canine literature [17]. the mean of the standard deviations of all the N N intervals for all 5 min segments; the percentage of interval differences of successive N-N intervals more than 50 ms; and the square root of the mean squared differences of successive N-N intervals [1,9–11]. The HRV of dogs from the SR class was categorized as ‘normal’ or ‘reduced’ based on data previ- ously reported in the canine literature [17]. the standard deviations of all the N-N intervals for all 5 min segments; the percentage of interval differences of successive N-N intervals more than 50 ms; and the square root of the mean squared differences of successive N-N intervals [1,9–11]. The HRV of dogs from the SR class was categorized as ‘normal’ or ‘reduced’ based on data previously reported in the canine literature [17]. the mean of the standard deviations of all the N N intervals for all 5 min segments; the percentage of interval differences of successive N-N intervals more than 50 ms; and the square root of the mean squared differences of successive N-N intervals [1,9–11]. The HRV of dogs from the SR class was categorized as ‘normal’ or ‘reduced’ based on data previ- ously reported in the canine literature [17]. 2.4. Lorenz Plot Analysis 2.4. Lorenz Plot Analysis O th f ti Note that both arms are clearly attached to the CC, acting as its direct continuation and not as distinct ECs. Table 1 Quantitative and qualitative features of Lorenz plot patterns Figure 2. Graphic criteria used for classification of Lorenz plot patterns. (A): Example Lorenz plot generated from a Holter recording obtained from a dog with atrial fibrillation. Maximal length (Lmax) and maximal width (Wmax) of the cluster of dots are illustrated by blue and red lines, respectively. (B): Example Lorenz plot generated from a Holter recording obtained from a dog with sinus rhythm associated with a normal heart rate variability and frequent ventricular premature complexes. The central cluster (CC) and eccentric cluster (EC) are illustrated by red and blue dotted lines, respectively. Note that both CCs are located along the line of identity and that the main CC is placed at the lower left corner of the graph. Note also that both ECs arise from the lower left corner of the graph close to the body of the main CC and then extend outside the line of identity, one approximately parallel to the X-axis and the other approximately parallel to the Y-axis of the plot. (C): Example Lorenz plot from a Holter recording obtained from a dog with a diagnosis of sinus rhythm associated with a normal heart rate variability. Red dotted lines outline the margin of the CC and its diverging arms. Note that both arms are clearly attached to the CC, acting as its direct continuation and not as distinct ECs. 2.4. Lorenz Plot Analysis 2.4. Lorenz Plot Analysis O th f ti Table 1 reports the criteria of classification of LP patterns. The nomenclature already proposed in humans [2] and dogs [5–7] was used when the characteristics of patterns obtained from dogs included in the study were similar to those previously described; otherwise, a new nomenclature was proposed. identity were defined as ‘central’ and ‘eccentric’, respectively [2]. When more than one CC was present, the term ‘main’ was used to define the cluster of dots located at the left lower corner of the graph. Table 1 reports the criteria of classification of LP patterns. The no- menclature already proposed in humans [2] and dogs [5–7] was used when the character- istics of patterns obtained from dogs included in the study were similar to those previ- ously described; otherwise, a new nomenclature was proposed. Figure 2. Graphic criteria used for classification of Lorenz plot patterns. (A): Example Lorenz plot generated from a Holter recording obtained from a dog with atrial fibrillation. Maximal length (Lmax) and maximal width (Wmax) of the cluster of dots are illustrated by blue and red lines, respectively. (B): Example Lorenz plot generated from a Holter recording obtained from a dog with sinus rhythm associated with a normal heart rate variability and frequent ventricular premature complexes. The central cluster (CC) and eccentric cluster (EC) are illustrated by red and blue dotted lines, respectively. Note that both CCs are located along the line of identity and that the main CC is placed at the lower left corner of the graph. Note also that both ECs arise from the lower left corner of the graph close to the body of the main CC and then extend outside the line of identity, one approximately parallel to the X-axis and the other approximately parallel to the Y- axis of the plot. (C): Example Lorenz plot from a Holter recording obtained from a dog with a diagnosis of sinus rhythm associated with a normal heart rate variability. Red dotted lines outline the margin of the CC and its diverging arms. Note that both arms are clearly attached to the CC, acting as its direct continuation and not as distinct ECs. Table 1 Quantitative and qualitative features of Lorenz plot patterns Figure 2. Graphic criteria used for classification of Lorenz plot patterns. (A): Example Lorenz plot generated from a Holter recording obtained from a dog with atrial fibrillation. 2.4. Lorenz Plot Analysis 2.4. Lorenz Plot Analysis O th f ti The X-axis is the R-Rn interval and the Y-axis is the R-Rn + 1 interval. In this example, the first two R-R intervals are regular (a), creating a dot on the diagonal line (identity line) (A). The third R-R interval is premature (b); therefore, the correspondent dot moves below the line to point B. The fourth R-R interval is longer due to the PP; thus, the correspondent dot moves above the line to point C. The fifth R-R interval returns to the initial value (a); consequently, the correspondent dot moves to point D. Since the last R-R interval is identical to the preceding one (a), the last dot returns to point A. Repetition of this process using the entire population of R-R intervals recorded during a Holter monitoring creates the final Lorenz plot. The resulting cloud of dots was characterized by: (1) a shape, fitted to the plot with the mean R-R interval as its center; (2) a length, the major axis passing through the mean R-R interval along the bisector (line of identity); and (3) a width, the minor axis passing through the mean R-R interval perpendicular to the major axis [1,2,5]. Then, as previously described in humans [2], each LP was studied qualitatively by assessing the specific shape The resulting cloud of dots was characterized by: (1) a shape, fitted to the plot with the mean R-R interval as its center; (2) a length, the major axis passing through the mean R-R interval along the bisector (line of identity); and (3) a width, the minor axis passing through the mean R-R interval perpendicular to the major axis [1,2,5]. Then, as previously described in humans [2], each LP was studied qualitatively by assessing the specific shape of the contour of the main central cluster (CC) of dots, and also quantitatively by assessing three geometrical indexes: (1) the ratio of the maximal length to the maximal width; (2) the number of CCs and eccentric clusters (ECs) of dots; and (3) the number of branches arising from the main CC (Figure 2). Clusters of dots located along and outside the line Animals 2021, 11, 1645 5 of 13 essing th; (2) of identity were defined as ‘central’ and ‘eccentric’, respectively [2]. When more than one CC was present, the term ‘main’ was used to define the cluster of dots located at the left lower corner of the graph. 2.4. Lorenz Plot Analysis 2.4. Lorenz Plot Analysis O th f ti Maximal length (Lmax) and maximal width (Wmax) of the cluster of dots are illustrated by blue and red lines, respectively. (B): Example Lorenz plot generated from a Holter recording obtained from a dog with sinus rhythm associated with a normal heart rate variability and frequent ventricular premature complexes. The central cluster (CC) and eccentric cluster (EC) are illustrated by red and blue dotted lines, respectively. Note that both CCs are located along the line of identity and that the main CC is placed at the lower left corner of the graph. Note also that both ECs arise from the lower left corner of the graph close to the body of the main CC and then extend outside the line of identity, one approximately parallel to the X-axis and the other approximately parallel to the Y-axis of the plot. (C): Example Lorenz plot from a Holter recording obtained from a dog with a diagnosis of sinus rhythm associated with a normal heart rate variability. Red dotted lines outline the margin of the CC and its diverging arms. Note that both arms are clearly attached to the CC, acting as its direct continuation and not as distinct ECs. Figure 2. Graphic criteria used for classification of Lorenz plot patterns. (A): Example Lorenz plot generated from a Holter recording obtained from a dog with atrial fibrillation. Maximal length (Lmax) and maximal width (Wmax) of the cluster of dots are illustrated by blue and red lines, respectively. (B): Example Lorenz plot generated from a Holter recording obtained from a dog with sinus rhythm associated with a normal heart rate variability and frequent ventricular premature complexes. The central cluster (CC) and eccentric cluster (EC) are illustrated by red and blue dotted lines, respectively. Note that both CCs are located along the line of identity and that the main CC is placed at the lower left corner of the graph. Note also that both ECs arise from the lower left corner of the graph close to the body of the main CC and then extend outside the line of identity, one approximately parallel to the X-axis and the other approximately parallel to the Y- axis of the plot. (C): Example Lorenz plot from a Holter recording obtained from a dog with a diagnosis of sinus rhythm associated with a normal heart rate variability. Red dotted lines outline the margin of the CC and its diverging arms. CC: central cluster; CSZ: central silent zone; DSL: double side lobe; EC: eccentric cluster; Lmax/Wmax: ratio of the maximal length to the maximal width; LP: Loren plot; NA: not applicable; QSL: quadruple side lobe; TSL: triple side lobe. 2.4. Lorenz Plot Analysis 2.4. Lorenz Plot Analysis O th f ti Animals 2021, 11, 1645 6 of 13 2.5. Statistical Analysis 2.5. Statistical Analysis Statistical analysis was performed with dedicated software (Microsoft Excel, version 2016, Microsoft Corporation; R, version 3.5.2, R Foundation for Statistical Computing, Vienna, Austria). The Shapiro–Wilk test was used to verify data distribution. Normally and non-normally distributed data were expressed as mean, standard deviation, and median (interquartile range), respectively. Repeatability and reproducibility of the classification of LP patterns were determined through intraobserver and interobserver agreement, re- spectively. The intraobserver agreement was determined from data generated by the same observer (GR) who evaluated blindly, four months apart, 20 randomly selected LPs. The in- terobserver agreement was determined from data generated by a second blinded observer (MBT) who analyzed the same 20 LPs used for intraobserver agreement. Intra and interob- server agreement were measured using the kappa statistics, as previously described [18]. The diagnostic value of LP analysis in identifying different rhythm classes was quantified in terms of sensitivity and specificity using standard formulas [19]. 2.4. Lorenz Plot Analysis 2.4. Lorenz Plot Analysis O th f ti q p p LP Pattern Lmax/Wmax CC (No.) EC (No.) Branches from CC (No.) LP Morphology Comet >1 1 0 0 Comet/club Torpedo >1 1 0 0 Cigarette Y-shaped NA 1 0 2 Y Diamond 1 or >1 1 0 0 Diamond/rhombus Diamond with CSZ 1 or >1 2 0 0 Diamond/rhombus with a central rarefaction area DSL NA, <1, 1 or >1 1 or 2 2 0 or 2 One of the first five morphologies with two lateral fusiform ECs (one left-sided and one right-sided) TSL NA, <1, 1 or >1 1 or 2 3 0 or 2 One of the first five morphologies with three lateral small and fusiform ECs (two left-sided and one right-sided) QSL NA, <1, 1 or >1 1 or 2 4 0 or 2 One of the first five morphologies with four lateral small and fusiform ECs (two left-sided and two right-sided) Fan 1 or <1 1 0 0 Triangular Table 1. Quantitative and qualitative features of Lorenz plot patterns. LP Pattern Lmax/Wmax CC (No.) EC (No.) Branches from CC (No.) LP Morphology Comet >1 1 0 0 Comet/club Torpedo >1 1 0 0 Cigarette Y-shaped NA 1 0 2 Y Diamond 1 or >1 1 0 0 Diamond/rhombus Diamond with CSZ 1 or >1 2 0 0 Diamond/rhombus with a central rarefaction area DSL NA, <1, 1 or >1 1 or 2 2 0 or 2 One of the first five morphologies with two lateral fusiform ECs (one left-sided and one right-sided) TSL NA, <1, 1 or >1 1 or 2 3 0 or 2 One of the first five morphologies with three lateral small and fusiform ECs (two left-sided and one right-sided) QSL NA, <1, 1 or >1 1 or 2 4 0 or 2 One of the first five morphologies with four lateral small and fusiform ECs (two left-sided and two right-sided) Fan 1 or <1 1 0 0 Triangular Fan with DSL 1 or <1 1 2 0 Triangular with two lateral small and fusiform ECs (one left-sided and one right-sided) CC: central cluster; CSZ: central silent zone; DSL: double side lobe; EC: eccentric cluster; Lmax/Wmax: ratio of the maximal length to the maximal width; LP: Loren plot; NA: not applicable; QSL: quadruple side lobe; TSL: triple side lobe. Lmax/Wmax CC EC Branches from CC LP Table 1. Quantitative and qualitative features of Lorenz plot patterns. No. of dogs Age (years) Body weight (kg) Sex (M/NM/F/NF) 3.1. Study Population and Holter Analysis The study population included 119 Holter recordings from 102 client-owned dogs, with 11 animals undergoing more than one Holter monitoring. Sixteen (15.7%) and eighty- four (82.3%) dogs were clinically healthy and affected by cardiac or systemic diseases, respectively, whereas clinical diagnosis was not available in the remaining two (2%) dogs. Of the 119 Holter recordings, 62 (52.1%) were obtained from dogs without any cardiac treatment, 56 (47.1%) from dogs receiving at least one cardiac drug at the time of monitoring, whereas no data were available for one dog (0.8%) (Table 2). Table 2. Demographic data from dogs used in this study. Variable No. of dogs 102 Age (years) 10.0 (6.5–12) Body weight (kg) 25.8 (13.8–35.0) Sex (M/NM/F/NF) 49/8/22/23 Breed (No. of dogs) Mixed breed (24) Doberman Pinscher (10) Boxer (9) German Shepherd, Labrador Retriever (5) English Bulldog, Golden Retriever (4) Cocker Spaniel, Corso (3) American Staffordshire Terrier, Cavalier King Charles Spaniel, English Pointer, Italian Hound, Pug (2) Basset Hound, Bolognese, Bouvier des Flandres, Briard, Czechoslovak Wolfdog, Dogo Argentino, English Setter, French Bulldog, Great Danes, Irish Setter, Irish Terrier, Jack Russell Terrier, Leonberger, Miniature Pinscher, Neapolitan Mastiff, Newfoundland, Nova Scotia Duck Tolling Retriever, Parson Russell Terrier, Poodle, Rottweiler, Shih Tzu, Vizsla, Weimaraner, West Highland White Terrier, Yorkshire Terrier (1) Clinical status (H/D/NA) 16/84/2 D: systemic and/or cardiac disease; F: female; H: healthy; M: male; NA: not available; NF: neutered female; NM: neutered male. Table 2. Demographic data from dogs used in this study. No. of dogs Age (years) Body weight (kg) Sex (M/NM/F/NF) Breed (No. of dogs) Clinical status (H/D/NA) c and/or cardiac disease; F: female; H: healthy; M: male; NA: not available; NF: neutered female; NM: neutered male. The mean duration of Holter monitoring was 23.3 ± 1 h and all recordings had good quality ECGs that included the whole night. The SR was the most numerous class, followed by the SR-VPCs, and the AF-VPCs classes, whereas the SR-APCs, the SR-APCs-VPCs, and the AF classes were less frequent. Table 3 presents detailed information on rhythm classes and clinical diagnosis. 7 of 13 Animals 2021, 11, 1645 Table 3. Electrocardiographic, clinical, and treatment data related to Holter recordings used in this study. Holter Diagnosis (No.) Clinical Diagnosis (No.) Ongoing Cardiac Treatment (No.) SR (48) (No. 3.2. Classification, Repeatability and Reproducibility of Lorenz Plot Patterns Lorenz plot analysis allowed for the identification of 10 distinct patterns (Figure 3 and Table 4). Features of six patterns were similar to those previously described in both humans and dogs, including comet, torpedo, Y-shaped, double side lobe (DSL), triple side lobe (TSL), and fan. The following nomenclature was proposed for the remaining four LP patterns: diamond, diamond with a central silent zone (CSZ) (i.e., a well-defined region of low density of dots within a PP pattern), quadruple side-lobe (QSL), and fan with DSL. The terms DSL, TSL, and QSL were used when one among the comet, torpedo, Y-shaped, diamond, or diamond with CSZ configuration was associated with two, three, and four ECs, respectively. Table 4. Frequency of Lorenz plot patterns and related rhythm classes from Holter recordings used in this study. Lorenz Plot Pattern (No.) Rhythm Classes (No.) Comet (12) SR with normal HRV (12) Torpedo (3) SR with reduced HRV (3) Y-shaped (6) SR with normal HRV (6) Diamond (10) SR with normal HRV (8); SR-APCs (1); SR-VPCs (1) Diamond with CSZ (17) SR with normal HRV (15); SR-APCs (1); AF (1) Double side lobe (47) SR-VPCs (31); SR-APCs (7); SR-APCs-VPCs (5); SR with normal HRV (4) Triple side lobe (1) SR-VPCs (1) Quadruple side lobe (2) SR-VPCs (2) Fan (18) AF-VPCs (16); AF (2) Fan with double side lobe (3) AF-VPCs (2); AF (1) AF: atrial fibrillation; APC: atrial premature complex; CSZ: central silent zone; HRV: heart rate variability; SR: sinus rhythm; VPC: ventricular premature complex. Table 4. Frequency of Lorenz plot patterns and related rhythm classes from Holter recordings used in this study. Table 4. Frequency of Lorenz plot patterns and related rhythm classes from Holter recordings used in this study. 3.1. Study Population and Holter Analysis of VPCs: 2 (0–9)) cMMVD (16); AH (13); cardiac tumor, CHD (3); DCM, dMMVD, NA, suspected myocarditis, NM-TLoC, PH (2); Pheochromocytoma (1) pimobendan (5); benazepril, furosemide (4); sotalol (3); amiodarone, atenolol, mexiletine (2); spironolactone (1) SR-APCs (9) (No. of APCs: 2444 (1578–3502)) cMMVD (4); dMMVD (3); AH, non-specific LV cardiomyopathy (1) benazepril, pimobendan (3); furosemide (2); amiodarone, amlodipine, hydrochlorothiazide, sildenafil, spironolactone, torasemide (1) SR-VPCs (35) (No. of VPCs: 1589 (389–11,751)) cMMVD (8); DCM (6); suspected myocarditis (5); AC, CHD (4); cardiac tumor (3); AH, dMMVD (2); non-specific BV cardiomyopathy (1) amiodarone (6); pimobendan (5); furosemide, sotalol (4); benazepril (3); atenolol, mexiletine (1) SR-APCs-VPCs (5) (No. of APCs: 953 (332–3992)) (No. of VPCs: 1049 (175–2822)) dMMVD (2); cardiac tumor, DCM, suspected myocarditis (1) benazepril, furosemide, pimobendan (4); amlodipine (2); atenolol, mexiletine (1) AF (4) (No. of VPCs: (33 (8–65) DCM (2); dMMVD, suspected myocarditis (1) benazepril, furosemide, pimobendan (3); digoxin (2); diltiazem (1) AF-VPCs (18) (No. of VPCs: 982 (366–2369)) dMMVD (9); cMMVD (4); DCM (3); HWD, CHD (1) pimobendan (14); benazepril, furosemide (10); diltiazem (8); digoxin (7); torasemide (3); amlodipine, hydrochlorothiazide, spironolactone (1) AC: arrhythmogenic cardiomyopathy; AF: atrial fibrillation; AH: apparently healthy; APC: atrial premature complex; BV: bi-ventricular; CHD: congenital heart disease; cMMVD: compensated myxomatous mitral valve disease (American College of Veterinary Internal Medicine stage B1 + B2); DCM: dilated cardiomyopathy; dMMVD: decompensated myxomatous mitral valve disease (American College of Veterinary Internal Medicine stage C + D); HWD: heartworm disease; LV: left ventricular; NA: not available; NM-TLoC: suspected neurally-mediated transient loss of consciousness; PH: pulmonary hypertension; SR: sinus rhythm; VPC: ventricular premature complex. Table 3. Electrocardiographic, clinical, and treatment data related to Holter recordings used in this study. Holter Diagnosis (No.) Clinical Diagnosis (No.) Ongoing Cardiac Treatment (No.) SR (48) (No. of VPCs: 2 (0–9)) cMMVD (16); AH (13); cardiac tumor, CHD (3); DCM, dMMVD, NA, suspected myocarditis, NM-TLoC, PH (2); Pheochromocytoma (1) pimobendan (5); benazepril, furosemide (4); sotalol (3); amiodarone, atenolol, mexiletine (2); spironolactone (1) SR-APCs (9) (No. of APCs: 2444 (1578–3502)) cMMVD (4); dMMVD (3); AH, non-specific LV cardiomyopathy (1) benazepril, pimobendan (3); furosemide (2); amiodarone, amlodipine, hydrochlorothiazide, sildenafil, spironolactone, torasemide (1) SR-VPCs (35) (No. of VPCs: 1589 (389–11,751)) cMMVD (8); DCM (6); suspected myocarditis (5); AC, CHD (4); cardiac tumor (3); AH, dMMVD (2); non-specific BV cardiomyopathy (1) amiodarone (6); pimobendan (5); furosemide, sotalol (4); benazepril (3); atenolol, mexiletine (1) SR-APCs-VPCs (5) (No. 3.1. Study Population and Holter Analysis of APCs: 953 (332–3992)) (No. of VPCs: 1049 (175–2822)) dMMVD (2); cardiac tumor, DCM, suspected myocarditis (1) benazepril, furosemide, pimobendan (4); amlodipine (2); atenolol, mexiletine (1) AF (4) (No. of VPCs: (33 (8–65) DCM (2); dMMVD, suspected myocarditis (1) benazepril, furosemide, pimobendan (3); digoxin (2); diltiazem (1) AF-VPCs (18) (No. of VPCs: 982 (366–2369)) dMMVD (9); cMMVD (4); DCM (3); HWD, CHD (1) pimobendan (14); benazepril, furosemide (10); diltiazem (8); digoxin (7); torasemide (3); amlodipine, hydrochlorothiazide, spironolactone (1) AC: arrhythmogenic cardiomyopathy; AF: atrial fibrillation; AH: apparently healthy; APC: atrial premature complex; BV: bi-ventricular; CHD: congenital heart disease; cMMVD: compensated myxomatous mitral valve disease (American College of Veterinary Internal Medicine stage B1 + B2); DCM: dilated cardiomyopathy; dMMVD: decompensated myxomatous mitral valve disease (American College of Veterinary Internal Medicine stage C + D); HWD: heartworm disease; LV: left ventricular; NA: not available; NM-TLoC: suspected neurally-mediated Table 3. Electrocardiographic, clinical, and treatment data related to Holter recordings used in this study. SR-VPCs (35) (No. of VPCs: 1589 (389–11,751)) SR-APCs-VPCs (5) (No. of APCs: 953 (332–3992)) (No. of VPCs: 1049 (175–2822)) AF (4) (No. of VPCs: (33 (8–65) AF-VPCs (18) (No. of VPCs: 982 (366–2369)) AC: arrhythmogenic cardiomyopathy; AF: atrial fibrillation; AH: apparently healthy; APC: atrial premature complex; BV: bi-ventricular; CHD: congenital heart disease; cMMVD: compensated myxomatous mitral valve disease (American College of Veterinary Internal Medicine stage B1 + B2); DCM: dilated cardiomyopathy; dMMVD: decompensated myxomatous mitral valve disease (American College of Veterinary Internal Medicine stage C + D); HWD: heartworm disease; LV: left ventricular; NA: not available; NM-TLoC: suspected neurally-mediated transient loss of consciousness; PH: pulmonary hypertension; SR: sinus rhythm; VPC: ventricular premature complex. 3.2. Classification, Repeatability and Reproducibility of Lorenz Plot Patterns 3.2. Classification, Repeatability and Reproducibility of Lorenz Plot Patterns Lorenz Plot Pattern (No.) Rhythm Classes (No.) Comet (12) SR with normal HRV (12) Torpedo (3) SR with reduced HRV (3) Y-shaped (6) SR with normal HRV (6) Diamond (10) SR with normal HRV (8); SR-APCs (1); SR-VPCs (1) Diamond with CSZ (17) SR with normal HRV (15); SR-APCs (1); AF (1) Double side lobe (47) SR-VPCs (31); SR-APCs (7); SR-APCs-VPCs (5); SR with normal HRV (4) Triple side lobe (1) SR-VPCs (1) Quadruple side lobe (2) SR-VPCs (2) Fan (18) AF-VPCs (16); AF (2) Fan with double side lobe (3) AF-VPCs (2); AF (1) AF: atrial fibrillation; APC: atrial premature complex; CSZ: central silent zone; HRV: heart rate variability; SR: sinus rhythm; VPC: ventricular premature complex. Table 4. Frequency of Lorenz plot patterns and related rhythm classes from Holter recordings used in this study. 8 of 13 Animals 2021, 11, 1645 Fig- ure 3. Lorenz plot patterns identified in the study population. (A): comet; (B): torpedo; (C): Y-shaped; (D): diamond; (E): diamond with a central silent zone; (F): double side-lobe (DSL); (G): triple side-lobe (TSL); (H): quadruple side-lobe (QSL); (I): fan; (L): fan with DSL. Red asterisks and blue arrowheads indicate the central silent zone and the eccentric clusters, respectively. Note that, in this figure, the DSL, TSL, and the QSL patterns are created by the association of the diamond with a central silent zone configuration with two eccentric clusters, the association of the diamond with a central silent zone configuration with three eccentric clusters, and the association of the diamond configuration with four eccentric clusters, respectively. Figure 3. Lorenz plot patterns identified in the study population. (A): comet; (B): torpedo; (C): Y-shaped; (D): diamond; (E): diamond with a central silent zone; (F): double side-lobe (DSL); (G): triple side-lobe (TSL); (H): quadruple side-lobe (QSL); (I): fan; (L): fan with DSL. Red asterisks and blue arrowheads indicate the central silent zone and the eccentric clusters, respectively. Note that, in this figure, the DSL, TSL, and the QSL patterns are created by the association of the diamond with a central silent zone configuration with two eccentric clusters, the association of the diamond with a central silent zone configuration with three eccentric clusters, and the association of the diamond configuration with four eccentric clusters, respectively. ure 3. Lorenz plot patterns identified in the study population. 3.2. Classification, Repeatability and Reproducibility of Lorenz Plot Patterns (A): comet; (B): torpedo; (C): Y-shaped; (D): diamond; (E): diamond with a central silent zone; (F): double side-lobe (DSL); (G): triple side-lobe (TSL); (H): quadruple side-lobe (QSL); (I): fan; (L): fan with DSL. Red asterisks and blue arrowheads indicate the central silent zone and the eccentric clusters, respectively. Note that, in this figure, the DSL, TSL, and the QSL patterns are created by the association of the diamond with a central silent zone configuration with two eccentric clusters, the association of the diamond with a central silent zone configuration with three eccentric clusters, and the association of the diamond configuration with four eccentric clusters, respectively. Figure 3. Lorenz plot patterns identified in the study population. (A): comet; (B): torpedo; (C): Y-shaped; (D): diamond; (E): diamond with a central silent zone; (F): double side-lobe (DSL); (G): triple side-lobe (TSL); (H): quadruple side-lobe (QSL); (I): fan; (L): fan with DSL. Red asterisks and blue arrowheads indicate the central silent zone and the eccentric clusters, respectively. Note that, in this figure, the DSL, TSL, and the QSL patterns are created by the association of the diamond with a central silent zone configuration with two eccentric clusters, the association of the diamond with a central silent zone configuration with three eccentric clusters, and the association of the diamond configuration with four eccentric clusters, respectively. Table 4. Frequency of Lorenz plot patterns and related rhythm classes from Holter recordings used in this study. Lorenz Plot Pattern (No.) Rhythm Classes (No.) The intra- and interobserver agreement was high: K = 0.94 (standard error = 0.06; 95% confidence interval = 0.81–1.0) and K = 0.87 (standard error = 0.09; 95% confidence interval = 0.7–1.0), respectively. Comet (12) Torpedo (3) 3.3. Diagnostic Value of Lorenz Plot Patterns Y-shaped (6) SR with normal HRV (6) Diamond (10) SR with normal HRV (8); SR-APCs (1); SR-VPCs (1) Diamond with CSZ (17) SR with normal HRV (15); SR-APCs (1); AF (1) Double side lobe (47) SR-VPCs (31); SR-APCs (7); SR-APCs-VPCs (5); Comet, torpedo, Y-shaped, diamond, and diamond with CSZ patterns were predomi- nantly associated with SR (Table 4). Specifically, the torpedo pattern was associated with SR with reduced HRV, while comet, Y-shaped, diamond, and diamond with CSZ patterns were associated with SR and normal HRV (Table 5). The remaining patterns were mainly associated with tachyarrhythmias. Specifically, the DSL was predominantly associated with SR with frequent ectopic complexes, either APCs, VPCs, or both; the TSL and the QSL exclusively with SR with frequent VPCs; and the fan and the fan with DSL exclusively with AF, either with or without frequent VPCs (Table 4). Table 5. Time-domain heart rate variability parameters obtained from dogs of the sinus rhythm class, divided based on their Lorenz plot patterns. HRV Variable Lorenz Plot Pattern (No.) Comparis. Intervals * Comet (12) Torpedo (3) Y-Shaped (6) Diamond (10) Diamond with CSZ (17) PNN50 (%) 43.7 ± 17.2 9.3 ± 4.2 34.0 51.0 48.0 56 ± 10 (25.7–46.7) (41.5–58.5) (32.2–61.5) (18–75) RMSSD (ms) 148.8 ± 85.6 32.3 ± 6.1 130.5 174.0 204.0 325 ± 118 (85.2–307.7) (131.0–182.0) (122.2-289.5) (112-610) SDANN (ms) 124.9 ± 64.5 72.0 (69.0–93.0) 145.5 120 131.0 195 ± 52 (133.5–196.5) (91.0–174.5) (111.5–163.5) (112–322) SDNN (ms) 188.2 ± 95.3 84.0 ± 26.1 215.7 ± 111.0 204.0 208.0 331 ± 87 (179.0–224.0) (165.2–248.2) (148–521) SDNNIDX (ms) 155.0 ± 88.0 53.7 ± 15.3 143.0 164.6 ± 58.7 180.5 260 ± 76 (111.7–238) (122.2–215.5) (88–415) CSZ: central silent zone; HRV: heart rate variability; PNN50: percentage of interval differences of successive NN intervals more than 50 ms; RMSSD: square root of the mean squared differences of successive NN intervals; SDANN: standard deviation of the means of the NN intervals for all 5 min segments; SDNN: standard deviation of all the NN intervals; SDNNIDX: mean of the standard deviations of all the NN intervals for all 5 min segments. * Calvert, C.A.; Wall, M. Effect of severity of myocardial failure on heart rate variability in Doberman Pinschers with and without echocardiographic evidence of dilated cardiomyopathy [17]. ain heart rate variability parameters obtained from dogs of the sinus rhythm class, divided based on Table 5. CSZ: central silent zone; HRV: heart rate variability; PNN50: percentage of interval differences of successive NN intervals more than 50 ms; RMSSD: square root of the mean squared differences of successive NN intervals; SDANN: standard deviation of the means of the NN intervals for all 5 min segments; SDNN: standard deviation of all the NN intervals; SDNNIDX: mean of the standard deviations of all the NN intervals for all 5 min segments. * Calvert, C.A.; Wall, M. Effect of severity of myocardial failure on heart rate variability in Doberman Pinschers with and without echocardiographic evidence of dilated cardiomyopathy [17]. Comet (12) Torpedo (3) 3.3. Diagnostic Value of Lorenz Plot Patterns Time-domain heart rate variability parameters obtained from dogs of the sinus rhythm class, d their Lorenz plot patterns. CSZ: central silent zone; HRV: heart rate variability; PNN50: percentage of interval differences of successive NN intervals more than 50 ms; RMSSD: square root of the mean squared differences of successive NN intervals; SDANN: standard deviation of the means of the NN intervals for all 5 min segments; SDNN: standard deviation of all the NN intervals; SDNNIDX: mean of the standard deviations of all the NN intervals for all 5 min segments. * Calvert, C.A.; Wall, M. Effect of severity of myocardial failure on heart rate variability in Doberman Pinschers with and without echocardiographic evidence of dilated cardiomyopathy [17]. 9 of 13 Animals 2021, 11, 1645 9 of 13 Comet, torpedo, Y-shaped, diamond, and diamond with CSZ patterns were poorly sensitive but highly specific in diagnosing the SR class. The DSL pattern appeared more sensitive than specific in diagnosing individually the SR-APCs, SR-VPCs, and SR-APCs- VPCs classes. However, when used to diagnose SR with frequent premature complexes irrespective of their origin (i.e., considering together the APCs, VPCs, and SR-APCs-VPCs classes), both sensitivity and specificity were high. The low number of TSL and QLS patterns limited individual statistical analysis, but when they were grouped together, low sensitivity and high specificity in diagnosing the SR-VPCs class were found. The fan pattern was more specific than sensitive in diagnosing both the AF and AF-VPCs classes. Similarly, the fan with DSL pattern was highly specific but poorly sensitive in diagnosing both the AF and AF-VPCs classes (Table 6). Table 6. Diagnostic value of Lorenz plot patterns for the diagnosis of cardiac rhythms. Comet (12) Torpedo (3) 3.3. Diagnostic Value of Lorenz Plot Patterns Lorenz Plot Pattern Cardiac Rhythm Se (%) Sp (%) (95% CI) (95% CI) Comet SR 25.0 (13.6–39.6) 100 (94.9–100) Torpedo SR 6.2 (1.3–17.2) 100 (94.9–100) Y-shaped SR 12.5 (4.7–25.3) 100 (94.9–100) Diamond SR 16.7 (7.5–30.2) 97.2 (90.2–99.7) Diamond with CSZ SR 31.2 (18.7–46.3) 97.2 (90.2–99.7) DSL SR-APCs 77.8 (39.9–97.2) 63.6 (53.9–72.6) SR-VPCs 88.6 (73.3–96.8) 81.0 (70.9–88.7) SR-APCs-VPCs 100 (47.8–100) 63.2 (53.6–72) SR with frequent ECs of any origin (APCs, VPCs or both) 91.3 (79.2–97.6) 94.5 (86.6–98.5) TSL + QSL SR-VPCs 8.8 (1.9–23.7) 100 (95.8–100) Fan AF 50.0 (6.8–93.2) 86.1 (78.4–91.8) AF-VPCs 88.9 (65.3–98.6) 98.0 (93–99.8) Fan with DSL AF 25.0 (0.6–80.6) 98.3 (93–99.8) AF-VPCs 11.1 (1.4–34.7) 99.0 (94.6–99.9) AF: atrial fibrillation; APC: atrial premature complex; CI: confidence interval; CSZ: central silent zone; DSL: double side lode; EC: ectopic complex; QSL: quadruple side lobe; Se: sensitivity; Sp: specificity; SR: sinus rhythm; TSL: triple side lobe; VPC: ventricular premature complex. Table 6. Diagnostic value of Lorenz plot patterns for the diagnosis of cardiac rhythms. AF: atrial fibrillation; APC: atrial premature complex; CI: confidence interval; CSZ: central silent zone; DSL: double side lode; EC: ectopic complex; QSL: quadruple side lobe; Se: sensitivity; Sp: specificity; SR: sinus rhythm; TSL: triple side lobe; VPC: ventricular premature complex. 4. Discussion The main findings of the present study revealed that: (1) SR and tachyarrhythmias imprint peculiar signatures on canine LPs that can be categorized into 10 patterns; (2) the intra and interobserver agreement of LP patterns classification was excellent; and (3) the majority of LP patterns were highly specific but less sensitive indicators of canine SR and tachyarrhythmias. y y Similar to humans [2,20–23], the comet and torpedo pattern were exclusively observed in dogs from the SR class, in particular in those with normal and reduced HRV, respectively. Graphically, comet and torpedo patterns had one CC characterized by a length bigger than the width. However, the former is narrow at the bottom and gradually gets wider towards the top along the line of identity showing a certain degree of asymmetry, and the latter maintains a relatively symmetric shape with a limited width. Human studies have demonstrated that an enhanced vagal cardiac activity leads to increased cluster width and asymmetry [2,20–23]. This can explain why dogs with SR and severely reduced HRV had a torpedo rather than a comet pattern. As previously observed in healthy dogs [5–7], three other LP patterns predominantly occurred in the SR class with normal HRV, namely the Y-shaped, diamond, and diamond with CSZ. The Y-shaped pattern showed the most intense distribution of dots at the lower left corner of the graph, forming a stalk that extended from the X-axis at an angle of approximately 45◦and splitting into two diverging arms approximately parallel to the X-axis and Y-axis of the plot. The stalk represents consecutive R-R intervals of a similar Animals 2021, 11, 1645 10 of 13 10 of 13 length (i.e., phases of regular SR), while the diverging arms are created by long-short and short-long R-R intervals (i.e., premature sinus complexes and sinus pauses during phases of sinus arrhythmia, respectively). Other LPs had a diamond configuration due to an additional cluster of dots filling the gap between the aforementioned arms. These dots represent consecutive R-R intervals with a longer length (e.g., phases of sinus bradycardia). Lastly, many LPs with a diamond configuration had a CSZ. 4. Discussion This area represents a range of R-R intervals occurring infrequently when compared to others, and is likely due to the initiation of beats from different sinus node areas characterized by a fixed range of discharge rates or variation in the exit block from the sinus node under the physiologic control of the autonomic nervous system [7]. The reasons for these different LP patterns found in dogs from the SR class with normal HRV may depend on differences in breeds, age, sex, clinical status, and treatments [9–11,17,24–26]. Similar to human [2,27] and previous canine [6] studies, the DSL pattern was predom- inant in dogs with frequent ectopic complexes of any origin. Graphically, the human DSL pattern is composed by a central comet or torpedo configuration and two ECs [2]. Given the wide range of patterns associated with canine SR, we classified a DSL pattern when either a comet, torpedo, Y-shaped, diamond, and diamond with CSZ configuration was associated with two ECs. Eccentric clusters arose from the lower left corner of the graph, close to the body of the main CC, and then diverged distally, approximately parallel to the X-axis and Y-axis of the plot. The long-short R-R intervals produced by VPCs following sinus complexes, and the short-long R-R intervals produced by post-ectopic pauses following VPCs, created the right-sided and the left-sided ECs, respectively. Variable EC length, thickness, and density were observed in this study, as already reported in humans [2]. This finding likely reflects the variable number of premature ectopic complexes observed and the variable duration of their coupling intervals and post-ectopic pauses. In addition to the DSL pattern, an additional left-sided EC, creating a TSL pattern, was observed in a dog with SR + VPC. This pattern has been already described in humans and dogs with frequent VPCs and compensatory post-ectopic pauses [2,6,27]. Two dogs from this study, both from the SR-VPCs class, showed two left-sided and two right-sided ECs, creating a QSL pattern. This previously unreported pattern may derive from the coexistence of two ventricular foci, each one generating frequent VPCs with peculiar coupling intervals and stable duration of the relative post-ectopic pauses. p p p As in previous human [2,28] and canine [6] reports, the fan pattern was identified exclusively in dogs showing AF as the dominant cardiac rhythm. Graphically, this pattern shows widely scattered data dots organized into a single CC located along the line of identity. 4. Discussion The shape of the most concentrated cluster resembles a triangle where the width is often bigger than the length, and the triangular apex is at the left lower corner of the graphs. Two dogs from the AF-VPCs class and one dog from the AF showed also two ECs, creating a fan with DSL pattern. Interestingly, the dog from the AF class had a number of VPCs (93 VPCs/Holter) close to the threshold beyond which the shift from the AF to the AF-VPCs class was set. Therefore, the VPCs of this dog were frequent enough to generate visible ECs. Intriguingly, 16/18 dogs from the AF-VPCs class had a fan rather a fan with DSL pattern. This can be explained by the relationship between the refractory period of the atrioventricular node during AF, and the prematurity of VPCs as well as the duration of their post-ectopic pauses. When coupling intervals of VPCs and duration of relative post-ectopic pauses significantly differ from R-R intervals recorded during AF, the resultant ECs should be clearly separated from the fan pattern envelope; conversely the fan pattern and ECs can overlap [29]. Regarding the reproducibility of LP patter classification, this study found an excellent intra and interobserver agreement. This finding is in line with the human literature, where good to excellent intra and interobserver agreement of LP pattern classification has been reported [2]. The majority of observed LP patterns were highly specific but less sensitive in identify- ing distinct rhythm classes; this was different from human LP patterns, which demonstrated Animals 2021, 11, 1645 11 of 13 11 of 13 both high sensitivity and specificity [2]. The reasons for this discrepancy are not immedi- ately clear. Differences in study population size, rhythm classes analyzed, and software employed for LPs analysis can be a source of discrepancy [2]. Additionally, species-related peculiarities should be considered. For example, the discharge regularity of the human sinus node explains why human SR imprints only two patterns on LP (comet and tor- pedo) [2]. In contrast, the widely variable canine HRV led to five LP patterns in dogs from the SR class (comet, torpedo, Y-shaped, diamond, and diamond with CSZ), which inevitably reduce the sensitivity of each of them. Interestingly, the DSL pattern was both highly sensitive and specific in diagnosing SR with frequent premature ectopic complexes irrespective of their origin (i.e., considering together the APCs, VPCs, and SR-APCs-VPCs classes). 4. Discussion This finding could bear relevance in small animal practice, especially in busy hospitals. Indeed, veterinary cardiologists often deal, over the same workday, not only with Holter analysis, but also with clinical and echocardiographic examinations, manage- ment of hospitalized patients, and interventional procedures. This can delay the Holter analysis completion, and, therefore, the start of antiarrhythmic treatment in some dogs with tachyarrhythmias. Therefore, one possible clinical implication of this result could be the strong justification to give priority to thorough Holter analysis when a DSL pattern is present, with the aim to start rapidly an antiarrhythmic treatment, if necessary. p p y y y This study has some limitations. First, the low frequency of some specific rhythm classes limited the statistical analysis of the relative LP patterns. Additionally, we did not include dogs with incessant tachyarrhythmias other than AF, which theoretically could generate a torpedo pattern. Moreover, only the number of ectopies, but not their organization into allorhythmias, was considered. This choice was purposefully taken, primarily to fill the information gap regarding the effect of ectopies on canine LP. We preferred to exclude from this initial study the analysis of the effect of the different types of organization of ectopies (e.g., bigeminy, trigeminy, or tachycardia) on LP in order to simplify this preliminary analysis, already rich in numerical and graphic data. However, it is among our future goals to perform such an analysis to expand further our comprehension on the effect of canine rhythm disturbances on LP. A second limitation relies on the variable duration of Holter recordings, ranging from 20–24 h. However, our recordings fulfilled the recommendations for HRV assessment in humans (i.e., at least 18 h of analyzable ECG data that includes the whole night) [1]. Third, we focused on examining the effects of frequent tachyarrhythmias on the LP shape, which implies that the effects of arrhythmic episodes with a low incidence could have been obscured by the more numerous sinus complexes. A fourth limitation could be related to our definition of ‘frequent’ ectopic complexes, which was based on previously reported canine cut-offs [14,15]. Moreover, it is important to note that an identical cut-off has been used in studies analyzing LPs in humans [2,27]. Author Contributions: Conceptualization, G.R. and M.B.T.; investigation, G.R.; resources, G.R., C.G., H.P., and M.B.T.; data curation, G.R.; writing—original draft preparation, G.R.; writing—review 4. Discussion Lastly, given the lack of standardized and universally accepted thresholds for classifying canine HRV as ‘normal’ and ‘reduced’, classification of time-domain HRV variables of dogs from this study was arbitrary and based on comparison with a previous study [17]. Although that study only included dogs of a single breed (i.e., Doberman Pinschers), we anyway deemed appropriate to use it for comparison because it was the study analyzing the HRV parameters of our interest in the larger group of healthy dogs [17]. 5. Conclusions For the first time in dogs, we showed that SR and tachyarrhythmias imprint peculiar configurations on LPs that could be classified into a set of 10 patterns. Additionally, this study demonstrated an excellent reproducibility of LP pattern classification in dogs. The majority of LP patterns were highly specific but less sensitive in identifying SR and tachyarrhythmias in this species. Further studies are warranted to analyze LP patterns in dogs with different cardiac rhythms. Animals 2021, 11, 1645 12 of 13 12 of 13 and editing, C.G., H.P., and M.B.T. All authors have read and agreed to the published version of the manuscript. and editing, C.G., H.P., and M.B.T. All authors have read and agreed to the published version of the manuscript. Funding: This research received no external funding. Funding: This research received no external funding. Institutional Review Board Statement: Ethical approval for this study was waived by the Organism in charge of Animal Welfare (Organismo Preposto al Benessere degli Animali, OPBA) of the University of Padova. Data Availability Statement: The data presented in this study are available on request from the corresponding author. Data Availability Statement: The data presented in this study are available on request from the corresponding author. Conflicts of Interest: The authors declare no conflict of interest. Conflicts of Interest: The authors declare no conflict of interest. References Holter monitoring in clinically healthy Cavalier King Charles Spaniels, Wire-Haired Dachshunds, and Cairn Terriers. J. Vet. Intern. Med. 2011, 25, 460–468. [CrossRef] 10. Rasmussen, C.E.; Falk, T.; Zois, N.E.; Moesgaard, S.G.; Häggström, J.; Pedersen, H.D.; Ablad, B.; Nilsen, H.Y.; Olsen, L.H. Heart rate, heart rate variability, and arrhythmias in dogs with myxomatous mitral valve disease. J. Vet. Intern. 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Prevalence of intestinal nematodes infection in school children of urban areas of district Lower Dir, Pakistan
Brazilian Journal of Biology
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Abstract Intestinal parasitism is the main cause of disease all over the world and described as a significant community health problem. The current study intended to find out the occurrence and identification of hazard factors linked with IPIs among 4-12 years aged shool-age children residing in Lower Dir district, Pakistan during 2019 - 2020. A cross-sectional school-based study was conducted using a pre-arranged pre-tested survey. Anthropometric data and stool collection were done to obtain the findings. The direct wet mount preparation in saline/iodine/methods was used for stool examination. Data were investigated using the GraphPad Prism 5. A total of 400 children studied (mean age of 8.6±3.6 years) the total incidence rate for the intestinal parasitic disease was established to be 71.75%. Of the 400 children studied, the overall prevalence rate for intestinal parasitic infections was found to 71.75% Ascaris lumbricoides (33.1%), Trichuris trichiura (1.04%), E. vermicularis (1.39%), Hookworm (19.86%) were identified in children living in the study area. We concluded that there is a mass scale campaigns were required to generate alertness about health and sanitation in children and the need for the development of effective poverty control programs because deworming (killing of worm with drugs) alone is not adequate to control parasitic infections. Keywords: nematodes infection, poly-parasitism, urban life, unhygienic, poor nutrition. Prevalência de infecção por nematoides intestinais em escolares de áreas urbanas do distrito de Lower Dir, Paquistão H. Ur. Rahmana* , N.Khatoonb, S.Arshadb, Z.Masoodc, B.Ahmadd, W. Khand , N. Rafiqa, M. I. Khana, M. Kabire,, Z. Ul Haqf , I. Kamalf, E. Khang, M. Rashidh, A. ul Haqi, Y. Garedaghij aAbdul Wali Khan University Mardan, Department of Zoology, Mardan, Pakistan bUniversity of Karachi, Karachi-Pakistan cSardar Bahadur Khan women University, Quetta, Pakistan dUniversity of Malakand, Department of Zoology, Lower Dir, Pakistan eUniversity of Sargodha, Department of Biological Sciences, Sub Campus Bhakkar, Bhakkar, Punjab, Pakistan fHazara University Mansehra, Department of Zoology, Mansehra, Pakistan gGovernment Degree College, Department of Zoology, Thana, Malakand, Pakistan hFederal Urdu University, Department of Zoology, Gulshan Iqbal Campus, Karachi, Pakistan iShaheed Benazir Bhutto University, Department of Zoology, Dir Upper, Pakistan jIslamic Azad University, Tabriz Medical Sciences, Faculty of Veterinary Medicine, Department of Parasitology, Tabriz, Iran H. Ur. Rahmana* , N.Khatoonb, S.Arshadb, Z.Masoodc, B.Ahmadd, W. Khand , N. Rafiqa, M. I. Khana, M. Kabire,, Z. Ul Haqf , I. Kamalf, E. Khang, M. Rashidh, A. ul Haqi, Y. Garedaghij 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 work is properly cited. Prevalence of intestinal nematodes infection in school children of urban areas of district Lower Dir, Pakistan Prevalência de infecção por nematoides intestinais em escolares de áreas urbanas do distrito de Lower Dir, Paquistão *e-mail: hafeezzoologest@gmail.com Received: October 21, 2020 – Accepted: February 21, 2021 THE INTERNATIONAL JOURNAL ON NEOTROPICAL BIOLOGY THE INTERNATIONAL JOURNAL ON NEOTROPICAL BIOLOGY ISSN 1519-6984 (Print) ISSN 1678-4375 (Online) ISSN 1519-6984 (Print) ISSN 1678-4375 (Online) Original Article Brazilian Journal of Biology, 2022, vol. 82, e244158  |  https://doi.org/10.1590/1519-6984.244158 Resumo O parasitismo intestinal é a principal causa de doença em todo o mundo e descrito como um importante problema de saúde comunitária. O presente estudo buscou descobrir a ocorrência e identificação de fatores de risco relacionados a infecções parasitárias intestinais (IPIs) entre crianças em idade escolar de 4 a 12 anos residentes no distrito de Lower Dir, Paquistão durante 2019-2020. Um estudo transversal baseado em escola foi realizado usando uma pesquisa preestabelecida e pré-testada. Dados antropométricos e coleta de fezes foram feitos para obtenção dos achados. A preparação de montagem úmida direta em solução salina/iodo/métodos foi usada para exame de fezes. Os dados foram investigados usando o GraphPad Prism 5. Em um total de 400 crianças estudadas (idade média de 8,6±3,6 anos), a taxa de incidência total da parasitose intestinal foi estabelecida em 71,75%. Das 400 crianças estudadas, a taxa de prevalência global de infecções parasitárias intestinais foi de 71,75%. Ascaris lumbricoides (33,1%), Trichuris trichiura (1,04%), E. vermicularis (1,39%), Ancilostomíase (19,86%) foram identificados em crianças morando na área de estudo. Concluímos que há necessidade de campanhas em massa para gerar alerta sobre saúde e saneamento nas crianças, e a necessidade do desenvolvimento de programas efetivos de controle da pobreza, pois a desparasitação por si só não é adequada para controlar as infecções parasitárias. Palavras-chave: infecção por nematoides, poliparasitismo, vida rural, anti-higiênico, má nutrição. 1/7 Rahman, H.Ur. et al. 3. Data Collection The questionnaire was organized on the demographic data (age and gender) as well as socioeconomic profile of the inhabitants. 2.1.1. Location and boundary Lower Dir is the is a part of old district Dir of Malakand division. It is located in Hindu Kush range and the area occupied is 5,284 km2. These days it forms two districts of Pakistan - Upper Dir and Lower Dir (1,585km2). In the Northside of Dir Lower the rocky mountainous peaks raise from 1100 to 3119 meters. About every of it connects in the basin of the Panjkora which rise in the Hindu Kush at Lat. 35.45 and connect the River Swat close to Chakdara, where the district is naturally penetrated, at Lat. 34.40 (Figure 1). 2.1. Study sites 2.1. Study sites 2.1. Study sites 1. Introduction amid egg yield and the figure of fully developed worms is composite. In Pakistan Ascaris lumbricoides illness is broadly common, with changeable division in all regions of the country. Therefore, accurate analysis of soil transmitted helminthiasis play a key role in human being patient organization, drug efficiency assessment, organization of contaminated human being, detecting manage programs and removal (McCarthy et al., 2012; Speich et al., 2014). Intestinal Helminths are prevalent in those parts of the world where high temperature, poor cleanness, impure water, and imperfect and crowded accommodation exist. The disease rate is maximum in family existing in Sub- Saharan parts of Africa, after that Asia and next Caribbean and Latin America (Silva et al., 2003; Brooker et al., 2006). There is large number of nematode worms, but a small number for human infection. Among them, some are the soil-transmitted helminths Ancylostoma duodenale, Necator americanus, Ascaris lumbricoides and Trichuris trichiura are most prevalent organisms on the earth, estimated to infect almost one-sixth of the global population. Ascaris lumbricoides, Trichuris trichiura and hookworm of human origin are a group of nematode parasites infecting human alimentary canal when ingested eggs or larva (Khan et al., 2019b). In recent past decade various studies have been published on intestinal parasites infecting different sectors of human population in the region as Khan et al. (2011, 2012, 2014, 2016, 2017c,b, 2018a, b, 2019a, b), Arshad et al. (2019), Khan and Khan (2015), Noor un Nisa et al. (2011), Khan et al. (2020, 2021a,b, 2022), Iqbal et al. (2021), Rahman et al. (2022), Ulhaq et al. (2022). Brazilian Journal of Biology, 2022, vol. 82, e244158 2. Materials and Methods The overall weight of STHs infection shown about 70% of infection happened in Asia (Pullan et al., 2014) as well as 26.4% of Asian study inhabitants hosted as a minimum one STP species. In Pakistan, Ascaris lumbricoides infection is broadly common, with changeable division in all regions of the country. Different species of human intestinal worms have been recorded previous workers in different parts of the Malakand region and Pakistan as well (Arshad et al., 2019). Three and 3.5 Billion individuals are approximately contaminated through intestinal parasites including 1.47 Billion with A.lumbricoides, 13 million with A.duodenale/N.americanus and 1.05 billion with T.trichura. More than 40 million school-going children are expected to be contaminated with STHs. Children range from 5 to 15 years in age are commonly polluted, though the occurrence of A.duodenale/N.americanus disease tends to increase by growing time. Therefore, young girls and women during delivery are mainly infected with A.duodenale/N. americanus (Luong, 2003). A. lumbricoides go after extremely equivalent lines with a stable increase initial childhood to mean youth, and then turn down into the mature period program. This is dissimilar as of the hookworms when they able to initiate in near the beginning childhood and childhood but after that go up during fully developed life moreover attainment to upland or merely go down from 40 years or so. There were no information on age- correlated frequency or power designed for human Strongyloides stercoralis in the writing, and all STHs existed confront of understanding worm mass as of the investigative tests used (Olsen et al., 2009). 4. Laboratory Examination The stool sample was examined by naked eyes to find out of mature or some immature stage of parasites. Then stool samples were faced to microscopic examination, with the help of wet-mount procedure (Lugol’s iodine solutions and Salt solution). The formol-ether concentration was also planned for the verification of negative cases selected to positive. Three 3 g of stool were emulsified in 3 drops of salt solution (0.9%) or Lugol’siodine solution (WHO, 1991). Only one drop of the suspension was placed on the centre of the slide with the help of wooden stirrer and after that, a cover-slip was sited. The slides with sample suspension were studied with help of the sample microscope first below low 10× power and after that high 40× power objectives. Salines direct smear was used for the identification of tapeworm eggs. At the top of direct stool microscopic assessment, one 1 gram 125 of each stool sample was emulsified in 10% formol-ether and formalin solution concentration technique was carry out as to elevate the opportunity of scrutinized parasites (WHO, 1991). One characteristic of nematodes are calculated known their predictable global occurrence was the relationship aimed at the incidence and power of illness. Whereas occurrence stand for the population exaggerated by something as of one to thousands (huge infection) of worms, the quantity of fake negatives depends on the investigative method used. However, the disease is disadvantaged on illness intensity and the greater part of worm load is greatly over-dispersed by a hypothetical quantity of 80% of every worm below 20% of those contaminated. The majority exploratory procedure suggests not direct actions of illness, depending on the existence of eggs within the faces, and by greatest are merely semi-quantitative, because the affiliation Brazilian Journal of Biology, 2022, vol. 82, e244158 2/7 Nematode infection among school children of urban areas Figure 1. Location Sites of the study area in lower Dir region (Khyber, Pakhtunkhwa). Figure 1. Location Sites of the study area in lower Dir region (Khyber, Pakhtunkhwa). Figure 2. A. lumbricoides unfertile egg. 5. Parasite Identification Intestinal parasites were examined under the microscope and recognized based on morphological characteristics of eggs, larvae and adult stages through valid and standard keys. 6. Statistical Analysis SPSS, Graph Pad Prism and Minitab were use to calculate the results. If P-value is less than 0.05, it will be considered as statistically important. Brazilian Journal of Biology, 2022, vol. 82, e244158 7. Result lumbricoides, H.dimanuta, hookworm 5 (2.5) H.nana, T.saginata, A.lumbricoides 7 (3.57) 27 (13.77) 4 species (n=12) A.lumbricoides, hookworm, T.saginata, H. dimunuta 2 (1.02) A.lumbricoides, E.vermicularis, H. nana, hookworm 3 (1.53) H.nana, T. saginata, hookworm, E.vermicularis 7 (3.57) 12 (6.12) Total poly parasitism 92 (46.93) Total of infected individuals 196 (49) Total No. Examined 400 Table 2. Frequency distribution of intestinal parasites identified from school children stools. Group Parasite species Population infected Prevalence (%) Helminth Ascaris lumbricoides 95 33.1 Taenia saginata 65 22.64 Hook worms 57 19.86 Hymenolepis nana 54 18.81 Enterobius vermiculari 4 1.39 Hymenolepis.diminuta 4 1.39 Trichuris trichura 3 1.04 Taxocara spp 2 0.69 Total helminth infection 284 99.3 Total number of infection 287 71.75 Total number of individual infected 400 Rahman, H.Ur. et al. Rahman, H.Ur. et al. Table 1. Proportion of mono-parasitism and poly parasitism of intestinal parasitic infections in school children of Lower Dir, Pakistan. Type of infection No. of species Species associated Cases (%) Mono-parasitism 1species (n=121) hookworm 27 (13.77) Ascaris lumbricoides 70 (35.71) Enterobius vermicularis 15 (7.65) Trichuris trichiura 9 (4.59) Total mono -parasitism 121 (61.73) poly-parasitism 2 species (n=36) A. lumbricoides, hookworm 11 (5.61) A. lumbricoides, H. nana 10 (5.10) T. saginata, hookworm , 12 (6.12) H. nana, T. trichura 1 (0.5) A. lumbricoides, Taxocara spp 2 (1.02) 36 (18.36) 3 species (n=27) T. saginata, A. lumbricoides, hookworm 5 (2.5) H. nana, E.vermicularis,T. saginata 4 (2.04) A.lumbricoides, H. nana, E. vermicularis 4 (0.04) H. nana, T. saginata, hookworm 2 (1.02) A. lumbricoides, H.dimanuta, hookworm 5 (2.5) H.nana, T.saginata, A.lumbricoides 7 (3.57) 27 (13.77) 4 species (n=12) A.lumbricoides, hookworm, T.saginata, H. dimunuta 2 (1.02) A.lumbricoides, E.vermicularis, H. nana, hookworm 3 (1.53) H.nana, T. saginata, hookworm, E.vermicularis 7 (3.57) 12 (6.12) Total poly parasitism 92 (46.93) Total of infected individuals 196 (49) Total No. Examined 400 Table 2. Frequency distribution of intestinal parasites identified from school children stools. Group Parasite species Population infected Prevalence (%) Helminth Ascaris lumbricoides 95 33.1 Taenia saginata 65 22.64 Hook worms 57 19.86 Hymenolepis nana 54 18.81 Enterobius vermiculari 4 1.39 Hymenolepis.diminuta 4 1.39 Trichuris trichura 3 1.04 Taxocara spp 2 0.69 Total helminth infection 284 99.3 Total number of infection 287 71.75 Total number of individual infected 400 Table 3. Prevalence of intestinal tapeworms and nematodes parasitic infections among school children in Lower Dir KP, Pakistan. 7. Result The prevalence of intestinal parasites is at least a single infection was 195 (61.73%). Mixed infection was observed in 92 (46.93%) among school children who had an intestinal parasitic infection. Of these proportion, 36 (18.36%) are double, 27 (13.77%) triple and 12 (6.12%) quadruple infections were observed (Table 1). Figure 2. A. lumbricoides unfertile egg. Figure 3. A. lumbricoides fertile egg. The overall prevalence of intestinal parasite was 71.75% (n=287/400). Multiple parasitic infections were identified in 32.05% (n=92/400) individuals (Table 1). The most common prevalent parasite is A. lumbricoides (34.49%) hookworm (19.86%), E. vermicularis (1.39%), T. trichiura (1.04%) (Table 2). Table 3 demonstrated over all infection if A.lumbriciodes, A.duodenale, E.vermicularis, T.saginata, H.nana and H.diminuta as 33.1%, 19.8%, 1.39%, 1.04%, 22.6% 18.8% and 1.39%. of the children below age 8 years were more infected than above 8 years, however males were highly infected than females. Regarding the prevalence of Toxocara spp which showed same percent prevalence in both the genders and ages as well. 7.1. Plaetes Figure 2 to 7. Figure 3. A. lumbricoides fertile egg. Brazilian Journal of Biology, 2022, vol. 82, e244158 3/7 Rahman, H.Ur. et al. Table 3. Prevalence of intestinal tapeworms and nematodes parasitic infections among school children in Lower Dir KP, Pakistan. Parasite Ages Sex Over all % <8 >8 Male Female Nematodes Ascaris lumbricoides 57 38 77 18 95 33.1 Ancylostoma duodenale 30 27 41 16 57 19.86 Enterobius vermicularis 3 1 3 1 4 1.39 Trichuris trichura 3 - 3 - 3 1.04 Taxocara spp 1 1 1 1 2 0.69 Cestodes Taenia saginata 45 20 48 17 65 22.64 Hymenolepis nana 36 18 45 9 54 18.81 Hymenolepis diminuta 3 1 2 2 4 1.39 Table 1. Proportion of mono-parasitism and poly parasitism of intestinal parasitic infections in school children of Lower Dir, Pakistan. Type of infection No. of species Species associated Cases (%) Mono-parasitism 1species (n=121) hookworm 27 (13.77) Ascaris lumbricoides 70 (35.71) Enterobius vermicularis 15 (7.65) Trichuris trichiura 9 (4.59) Total mono -parasitism 121 (61.73) poly-parasitism 2 species (n=36) A. lumbricoides, hookworm 11 (5.61) A. lumbricoides, H. nana 10 (5.10) T. saginata, hookworm , 12 (6.12) H. nana, T. trichura 1 (0.5) A. lumbricoides, Taxocara spp 2 (1.02) 36 (18.36) 3 species (n=27) T. saginata, A. lumbricoides, hookworm 5 (2.5) H. nana, E.vermicularis,T. saginata 4 (2.04) A.lumbricoides, H. nana, E. vermicularis 4 (0.04) H. nana, T. saginata, hookworm 2 (1.02) A. Brazilian Journal of Biology, 2022, vol. 82, e244158 7. Result Parasite Ages Sex Over all % <8 >8 Male Female Nematodes Ascaris lumbricoides 57 38 77 18 95 33.1 Ancylostoma duodenale 30 27 41 16 57 19.86 Enterobius vermicularis 3 1 3 1 4 1.39 Trichuris trichura 3 - 3 - 3 1.04 Taxocara spp 1 1 1 1 2 0.69 Cestodes Taenia saginata 45 20 48 17 65 22.64 Hymenolepis nana 36 18 45 9 54 18.81 Hymenolepis diminuta 3 1 2 2 4 1.39 Total No. of infection 287 71.75 Total No. of samples 400 alence of intestinal tapeworms and nematodes parasitic infections among school children in Lower Dir KP, Pakistan. 4/7 Nematode infection among school children of urban areas Figure 4. Hookworm egg. Figure 6. Trichuris trichiura. Figure 6. Trichuris trichiura. Figure 4. Hookworm egg. Figure 7. E. vermicularis egg. Figure 5. Trichuris trichiura. Figure 5. Trichuris trichiura. Figure 5. Trichuris trichiura. Figure 7. E. vermicularis egg. The eggs are getting out in the faces and expose in the surroundings, afterwards establish in water, soil, impure fruit and vegetables. Leave the eggshell out and infective embryonated eggs swallowed, and exceed through the liver to the blood stream, lungs, and then returned to small intestine departure the respiratory tract and after that swallowed. In the current study A. lumbricoides was the most prevalent parasite 33.1% (n=95) in urban locality of Lower Dir, which is comparable with 30.1% in District Swat (Noor-un-Nisa et al., 2011), 39.8% in district Swat (Khan et al., 2011), 39.8%in District Swat (Khan and Khan, 2015), 31.7% in district Swat (Khan et al., 2019b) and 33.3% in Panjab (Dar et al., 2013). But the present prevalence rate is high when compared with, 15% in Banu (Khan and Khan, 2015), 17%,20.3% in Swat (Khan et al., 2018a), 1.4% in Peshawar (Ilyas et al., 2018), 7.76% in Swat (Khan et al., 2019a), 4.0% in Quetta % (Arshad et al., 2019), 17.5% in Punjab (Kosar et al., 2017), 1.1% in Larkana, 5.5%in Karachi (Arshad et al., 2019), 12% in AJK (Khan et al., 2017a).The present prevalence rate is low when compared, 55.8% in Swat (Khan et al., 2017c), 53.0% in Swat (Khan et al., Brazilian Journal of Biology, 2022, vol. 82, e244158 8. Discussion Albendazole and mebendazole in the treatment of ancylostomiasis in school children between the ages of 6-15 in Swat, Pakistan. Journal of the Pakistan Medical Association, vol. 71, no. 8, pp. 2058-2060. KHAN, M.M., AWAN, A.K., KHAN, R.M.A., AHMED, N., HUSSAIN, W. and KHAN, M.A., 2017a. Prevalence of worm infestation and malnutrition in school going children and risk factors responsible for worm infestation. International Journal of Pathology, vol. 15, no. 1, pp. 9-14. KHAN, W. and KHAN, A., 2015. Diversity of intestinal parasites in male and female students and workers of Education Department of Swat, Pakistan. Pakistan Journal of Zoology, vol. 47, no. 2, pp. 565-568. KHAN, W., ARSHAD, S., KHATOON, N., KHAN, I., AHMAD, N., KAMAL, M., ULHASSAN, H., KHAN, N., HAQ, A.U., ILYAS, M. and ULLAH, S., 2021a. Food handlers: an important reservoir of protozoans and helminth parasites of public health importance. Brazilian Journal of Biology, vol. 82. Enterobius vermicularis (pinworm) is an intestinal nematode parasite that infection is the main agent for contact-borne infectious helminth. The present survey established the prevalence of E.vermicularis (1.39%), in children of district Dir is greater than previous studies .E. vermicularis infection among children are lower than studies conducted 22.75% in Islamabad, 10.7% Swat (Khan et al., 2011), 10.3% in district Swat (Noor-un-Nisa et al., 2011), 10% in AJK (Khan et al., 2017a), 9.52% in Swat (Khan et al., 2018a), 8.25% Swat (Noor-un-Nisa et al., 2011), 8.25% Swat (Khan and Khan, 2015), 5.05% in Swat (Khan et al., 2019b), and 14.4% Swat (Khan et al., 2017b). The prevalence rate of E. vermicularis in children of the district Lower Dir is high and not negligible due to highly transmittable infection. KHAN, W., IMRAN. and WAHAB, A., 2016. Intestinal obstruction by Ascaris lumbricoides in a 12 year old boy: a case report in Pakistan. Journal of Bacteriology & Parasitology, vol. 7, no. 1, p. 1000262. http://dx.doi.org/10.4172/2155-9597.1000262. KHAN, W., IQBAL, M. and OMER, D.A.D., 2020. Have we forgotten the threat posed by fascioliasis? A potential threat to public health. Iranian Journal of Public Health, vol. 49, no. 4, pp. 814. KHAN, W., KHAN, J., KHAN, N., IQBAL, R., ULLAH, A., GHAFFAR, R., MEHMOOD, S.A., AHMAD, S., KHAN, S. and ULLAH, F., 2019a. Soil-transmitted helminth infections in school children of three districts of Malakand region, Khyber Pakhtunkhwa, Pakistan. Pakistan Journal of Pharmaceutical Sciences, vol. 32, no. 2, suppl., pp. 799-803. PMid:31103975. 8. Discussion Parasitic infection of helminths is generally prevalent all over the world. These parasites were changeable according to the environmental conditions, customs climatic, local behaviour, in the urban and rural region the globe. Therefore, we planned to throw some light on parasitic infections in schoolchildren. Parasitism is one of the greatest problems in developing and underdeveloped countries including Pakistan where population increase day by day, low per capita income, smallest health facilities, reduced nutrition in the joint family system particularly in rural localities with maximum chances of contact, provide ideal conditions for intestinal helminthic infections. In the current study overall prevalence of intestinal parasites infection among school children of urban areas of Lower Dir, Pakistan was 49% (n=196/400). The highest prevalence was recorded in Islamabad 94.4%, while the lowest in other studies. Ascaris lumbricoides (roundworm) is the most common parasite, infecting over 1/5 of the world population. 5/7 Rahman, H.Ur. et al. 2017b), 66.4 in district Swat, Upper Dir and Lower Dir (Khan et al., 2019b). DAR, U.F., IQBAL, M.S., LATIF, M.Z., JAVAID, M.S., NAYYAR, U. and NIZAMI, R., 2013. Worm infestation among children of rural area of central Punjab. PJMHS, vol. 7, no. 3, pp. 713-715. Ancylostoma duodenale (hookworm) incidence rate is 19.86% in the present study. This nematode infection is nearly comparable with 20% in Azad Jammu and Kasmir (Khan et al., 2018b), 7.58% in Islamabad, 6.70%in district Swat (Noor-un-Nisa et al., 2011), 6.91% in district Swat, Lower and Upper Dir (Khan et al., 2019a), 6.45% in district Swat (Khan et al., 2017b) and 5.99% in district Swat (Khan et al., 2017c). The infection rate was high then other studies, 3.64% in Swat (Noor-un-Nisa et al., 2011), 3.64% in district Swat (Khan and Khan, 2015), 2.90% in Swat (Khan et al., 2018b), 3.96% (Khan et al., 2018a), 1.08% in district Swat (Khan et al., 2019b), 0.85% in Peshawar (Ilyas et al., 2018);m0.4% in Karachi (Arshad et al., 2019); 33.4% was found in school children of Lower district Lower Dir, Pakistan (Khan et al., 2022) and 41.9% of prevalence was noted by Ulhaq et al. (2022). The infection rate was low 41.7% study conducted in Punjab (Dar et al., 2013). ILYAS, M., KHAN, I., UR REHMAN, F. and SHAHID, M., 2018. Frequency of gastrointestinal parasites among children in clinical practices Peshawar, KPK, Pakistan. KJMS, vol. 11, no. 1, pp. 31-36. IQBAL, M., KHAN, W., KHAN, F. and KHAN, I., 2021. 8. Discussion The current prevalence rate of Trichuris trichiura is 1.04% in district Lower Dir. This is comparable, with 1.3% in Punjab (Kosar et al., 2017), 1.3% in Quetta (Arshad et al., 2019) and 0.42% in Lahore (Anwar et al., 2018). The prevalence rate of the present study is low when compared with, 26.2% Swat (Khan et al., 2017b), 19.1% Swat (Khan and Khan, 2015), 19.1% Swat (Khan et al., 2012), 19.0% in Swat (Khan et al., 2011), 15.9% in Swat (Noor-un-Nisa et al., 2011), 14.9% Swat (Khan and Khan, 2015), 14.3% Swat (Khan et al., 2018a), 11% in AJK (Khan et al., 2017b), 8.73% Swat (Khan et al., 2019a) and 8.30% in Swat (Khan et al., 2019b). The above nematodes were found share with cestodes infection in 19.7% of the study population (Rahman et al., 2022). KHAN, W., KHAN, N.I., BUKHARI, S.N.F. and BEGUM, N., 2019b. Prevalence of Intestinal Parasitic Infection among Drug Addicts in District Swat, Khyber Pakhtunkhwa, Pakistan. Iranian Journal of Parasitology, vol. 14, no. 2, pp. 359-361. PMid:31543928. KHAN, W., NISA, N. and KHAN, A., 2017b. Soil transmitted helminthiasis in different occupational groups in Swat, Khyber Pakhtunkhwa, Pakistan. Pakistan Journal of Pharmaceutical Sciences, vol. 30, no. 4, pp. 1345-1350. PMid:29039336. KHAN, W., NOOR-UN-NISA and KHAN, A., 2011. An investigation of incidence of intestinal parasites in under and above 15 years age in farmers of Swat, Pakistan. Proceedings of Parasitology, vol. 52, pp. 43-53. References KHAN, W., NOOR-UN-NISA and KHAN, A., 2012. Endemicity of intestinal parasites with special reference to nematodes in individuals related to education (students, staff and teachers) in Swat, K.P.K, Pakistan. Pakistan Journal of Nematology, vol. 30, no. 1, pp. 77. ANWAR, M., REHAN, M.W. and AHSEN, W., 2018. Frequency and determinants of intestinal parasitic infections in patients attending tertiary care hospitals. Pakistan Journal of Medical & Health Sciences, vol. 12, no. 2, pp. 659-661. KHAN, W., NOOR-UN-NISA and KHAN, A., 2014. A case of Fasciola hepatica infection in Swat, Pakistan. Pakistan Journal of Zoology, vol. 46, no. 6, pp. 1789-1790. ARSHAD, S., KHATOON, N., WARIND, J.A., KHAN, A., WAHEED, S. and KHAN, W., 2019. The prevalence of human intestinal protozoal and helminthic infection in Karachi. International Journal of Biology and Biotechnology, vol. 16, no. 2, pp. 319-323. KHAN, W., NOOR-UN-NISA and NAWAZ, M.A., 2018a. Prevalence of potentially important intestinal pathogenic protozoan parasitic infections in different occupational groups of Swat, Pakistan. Pakistan Journal of Zoology, vol. 50, no. 1, pp. 1-400. http:// dx.doi.org/10.17582/journal.pjz/2018.50.1.123.129. BROOKER, S., CLEMENTS, A.C. and BUNDY, D.A., 2006. Global epidemiology, ecology and control of soil-transmitted helminth infections. Advances in Parasitology, vol. 62, pp. 221-261. http:// dx.doi.org/10.1016/S0065-308X(05)62007-6. PMid:16647972. Brazilian Journal of Biology, 2022, vol. 82, e244158 6/7 Nematode infection among school children of urban areas OLSEN, A., VAN LIESHOUT, L., MARTI, H., POLDERMAN, T., POLMAN, K., STEINMANN, P., STOTHARD, R., THYBO, S., VERWEIJ, J.J. and MAGNUSSEN, P., 2009. Strongyloidiasis–the most neglected of the neglected tropical diseases? Transactions of the Royal Society of Tropical Medicine and Hygiene, vol. 103, no. 10, pp. 967-972. http://dx.doi.org/10.1016/j.trstmh.2009.02.013. PMid:19328508. KHAN, W., NOOR-UN-NISA. and KHAN, A., 2017c. Prevalence and risk factors associated with intestinal parasitic infections among food handlers of Swat, Khyber Pakhtunkhwa, Pakistan. Journal of Food and Nutrition Research, vol. 5, no. 5, pp. 331-336. http:// dx.doi.org/10.12691/jfnr-5-5-7. KHAN, W., NOOR-UN-NISA. and NAWAZ, M.A., 2018b. Incidence of tapeworm infection in human population of Swat, Pakistan: an occupation based study. Pakistan Journal of Zoology, vol. 50, no. 2, pp. 639-639. http://dx.doi.org/10.17582/journal. pjz/2018.50.2.639.645. PULLAN, R.L., SMITH, J.L., JASRASARIA, R. and BROOKER, S.J., 2014. Global numbers of infection and disease burden of soil transmitted helminth infections in 2010. Parasites & Vectors, vol. 7, no. 1, pp. 37. http://dx.doi.org/10.1186/1756-3305-7-37. PMid:24447578. KHAN, W., PANHWAR, W.A., MEHMOOD, S.A., AHMED, S., AHMED, M.S., KHAN, N., KHAN, M.M., AKRAM, W. and ULLAH, S., 2021b. References Pinworm infection in school children of four districts of Malakand region, Khyber Pakhtunkhwa, Pakistan. Brazilian Journal of Biology, vol. 82. RAHMAN, H., KHAN, W., MEHMOOD, S.A., AHMED, S., YASMIN, S., AHMAD, W., HAQ, Z.U., SHAH, M.I.A., KHAN, R., AHMAD, U., KHAN, A.A. and DE LOS RÍOS ESCALANTE, P., 2022. Prevalence of cestodes infection among school children of urban parts of Lower Dir district, Pakistan. Brazilian Journal of Biology = Revista Brasileira de Biologia, vol. 82, pp. e242205. http://dx.doi. org/10.1590/1519-6984.242205. KHAN, W., RAHMAN, H., RAFIQ, N., KABIR, M., AHMED, M.S. and ESCALANTE, P.D.L.R., 2022. Risk factors associated with intestinal pathogenic parasites in schoolchildren. Saudi Journal of Biological Sciences, vol. 29, no. 4, pp. 2782-2786. SILVA, N.R., BROOKER, S., HOTEZ, P.J., MONTRESOR, A., ENGELS, D. and SAVIOLI, L., 2003. Soil-transmitted helminth infections: updating the global picture. Trends in Parasitology, vol. 19, no. 12, pp. 547-551. http://dx.doi.org/10.1016/j.pt.2003.10.002. PMid:14642761. KOSAR, S., AFSHAN, K., SALMAN, M., RIZVI, S., NASEEM, A.A., FIRASAT, S., JAHAN, S., MILLER, J.E. and QAYYUM, M., 2017. Prevalence and risk factors associated with intestinal parasitic infections among schoolchildren in Punjab, Pakistan. Tropical Biomedicine, vol. 34, no. 4, pp. 770-780. PMid:33592946. SPEICH, B., UTZINGER, J., MARTI, H., AME, S.M., ALI, S.M., ALBONICO, M. and KEISER, J., 2014. Comparison of the Kato-Katz method and ether-concentration technique for the diagnosis of soil-transmitted helminth infections in the framework of a randomised controlled trial. European Journal of Clinical Microbiology & Infectious Diseases, vol. 33, no. 5, pp. 815-822. http://dx.doi.org/10.1007/s10096-013-2019-1. PMid:24272064. LUONG, T.V., 2003. De-worming school children and hygiene intervention. International Journal of Environmental Health Research, vol. 13, suppl. 1., pp. S153-S159. http://dx.doi.org/1 0.1080/0960312031000102912. PMid:12775391. MCCARTHY, J.S., LUSTIGMAN, S., YANG, G.J., BARAKAT, R.M., GARCÍA, H.H., SRIPA, B., WILLINGHAM, A.L., PRICHARD, R.K. and BASÁÑEZ, M.G., 2012. A research agenda for helminth diseases of humans: diagnostics for control and elimination programmes. PLoS Neglected Tropical Diseases, vol. 6, no. 4, pp. e1601. http://dx.doi.org/10.1371/journal.pntd.0001601. PMid:22545166. ULHAQ, Z., KHAN, W., KHAN, M.F., KABIR, M., UJJAN, A.A., ULLAH, W., MASOOD, Z., KHAN, S. and DE LOS RÍOS ESCALANTE, P., 2022. Prevalence of intestinal parasitic diseases in school children of rural areas of district Lower Dir, Pakistan. Brazilian Journal of Biology = Revista Brasileira de Biologia, vol. 82, e243150. http://dx.doi.org/10.1590/1519-6984.243150. PMid:34644727. NOOR-UN-NISA, KHAN, W. and KHAN, A., 2011. A prevalence of intestinal parasites in male and female shepherds of Swat, Pakistan. International Journal of Biology and Biotechnology, vol. 8, no. 4, pp. 597-603. Brazilian Journal of Biology, 2022, vol. 82, e244158 References WORLD HEALTH ORGANIZATION – WHO, 1991. Basic laboratory methods in medical parasitology. Geneva: WHO. 7/7 Brazilian Journal of Biology, 2022, vol. 82, e244158
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Knowledge Representation in a Proof Checker for Logic Programs
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7 Knowledge Representation in a Proof Checker for Logic Programs Emmanouil Marakakis, Haridimos Kondylakis and Nikos Papadakis Department of Sciences, Technological Educational Institute of Crete, Greece 7 Emmanouil Marakakis, Haridimos Kondylakis and Nikos Papadakis Department of Sciences, Technological Educational Institute of Crete, Greece www.intechopen.com 1. Introduction Lately the need for systems that ensure the correctness of software is increasing rapidly. Software failures can cause significant economic loss, endanger human life or environmental damage. Therefore, the development of systems that verify the correctness of software under all circumstances is crucial. Formal methods are techniques based on mathematics which aim to make software production an engineering subject as well as to increase the quality of software. Formal verification, in the context of software systems, is the act of proving or disproving the correctness of a system with respect to a certain formal specification or property, using formal methods of mathematics. Formal program verification is the process of formally proving that a computer program does exactly what is stated in the program specification it was written to realize. Automated techniques for producing proofs of correctness of software systems fall into two general categories: 1) Automated theorem proving (Loveland, 1986), in which a system attempts to produce a formal proof given a description of the system, a set of logical axioms, and a set of inference rules. 2) Model checking, in which a system verifies certain properties by means of an exhaustive search of all possible states that a system could enter during its execution. Neither of these techniques works without human assistance. Automated theorem provers usually require guidance as to which properties are "interesting" enough to pursue. Model checkers can quickly get bogged down in checking millions of uninteresting states if not given a sufficiently abstract model. Interactive verifiers or proof checkers are programs which are used to help a user in building a proof and/or find parts of proofs. These systems provide information to the user regarding the proof in hand, and then the user can make decisions on the next proof step that he will follow. Interactive theorem provers are generally considered to support the user, acting as clerical assistants in the task of proof construction. The interactive systems have been more suitable for the systematic formal development of mathematics and in mechanizing formal methods (Clarke & Wing, 1996). Proof editors are interactive language editing systems which ensure that some degree of “semantic correctness” is maintained as the user develops the proof. The proof checkers are placed between the two extremes, which are the automatic theorem provers and the proof editors (Lindsay, 1988). 2. An Overview of the main components of the proof checker This verifier of logic programs requires a lot of interaction with the user. That is why emphasis is placed on the design of its interface. The design of the interface aims to facilitate the proof task of the user. A screenshot of the main window of our system is shown in Fig. 1. Fig. 1. The main window of the proof-checker. Initially, all proof decisions are taken by the programmer. The design of the interface aims to facilitate the proof task of the user. This interactive verifier of logic programs consists of three distinct parts the interface, the prover or transformer and the knowledge base (KB). The interface offers an environment where the user can think and decide about the proof steps that have to be applied. The user specifies each proof step and the prover performs it. A high-level design of our system is depicted in Fig. 2. The main components of the proof checker with their functions are shown in this figure. The prover of the system consists of the following two components. 1) The component “Spec Transformer” transforms a Fig. 1. The main window of the proof-checker. Fig. 1. The main window of the proof-checker. Initially, all proof decisions are taken by the programmer. The design of the interface aims to facilitate the proof task of the user. This interactive verifier of logic programs consists of three distinct parts the interface, the prover or transformer and the knowledge base (KB). The interface offers an environment where the user can think and decide about the proof steps that have to be applied. The user specifies each proof step and the prover performs it. A high-level design of our system is depicted in Fig. 2. The main components of the proof checker with their functions are shown in this figure. The prover of the system consists of the following two components. 1) The component “Spec Transformer” transforms a Initially, all proof decisions are taken by the programmer. The design of the interface aims to facilitate the proof task of the user. This interactive verifier of logic programs consists of three distinct parts the interface, the prover or transformer and the knowledge base (KB). The interface offers an environment where the user can think and decide about the proof steps that have to be applied. The user specifies each proof step and the prover performs it. 1. Introduction www.intechopen.com 162 Advances in Knowledge Representation In this chapter we will present a proof checker or an interactive verifier for logic programs which are constructed by a schema-based method (Marakakis, 1997), (Marakakis & Gallagher, 1994) and we will focus on the knowledge representation and on its use by the core components of the system. A meta-program is any program which uses another program, the object program, as data. Our proof checker is a meta-program which reasons about object programs. The logic programs and the other elements of the theory represented in the Knowledge Base (KB) of our system are the object programs. The KB is the data of the proof checker. The proof checker accesses and changes the KB. The representation of the underlying theory (object program) in the proof checker (meta-program) is a key issue in the development of the proof checker. Our System has been implemented in Sicstus Prolog and its interface has been implemented in Visual Basic (Marakakis, 2005), (Marakakis & Papadakis, 2009) www.intechopen.com 2. An Overview of the main components of the proof checker A high-level design of our system is depicted in Fig. 2. The main components of the proof checker with their functions are shown in this figure. The prover of the system consists of the following two components. 1) The component “Spec Transformer” transforms a www.intechopen.com 163 Knowledge Representation in a Proof Checker for Logic Programs specification expressed in typed FOL into structured form which is required by our correctness method (Marakakis, 1997), (Marakakis, 2005). 2) The component “Theorem Proof Checker supports the proof task of the selected correctness theorem. specification expressed in typed FOL into structured form which is required by our correctness method (Marakakis, 1997), (Marakakis, 2005). 2) The component “Theorem Proof Checker supports the proof task of the selected correctness theorem. The “KB Update” subsystem allows the user to update the KB of the system through a user- friendly interface. The knowledge base (KB) and its contents are also shown in Fig. 2. The KB contains the representation of specifications, theorems, axioms, lemmas, and programs complements. It also has the representation of FOL laws in order to facilitate their selection for application. These entities are represented in ground representation (Hill & Gallagher, 1998). The main benefit of this representation is the distinct semantics of the object program variables from the meta-variables. It should be noted that the user would like to see theorems, axioms, lemmas and programs in a comprehensible form which is independent of their representation. However, the ground representation cannot be easily understood by users. Moreover, the editing of elements in ground representation is error-prone. Part of the interface of the system is the “Ground-Nonground Representation Transformer” component which transforms an expression in ground representation into a corresponding one in the standard formalism of FOL and vice-versa. The standard form of expressions helps users in the proof task and for the update of the KB. Fig. 2. Main components of the proof-checker. Fig. 2. Main components of the proof-checker. 3. Knowledge representation Knowledge and representation are two distinct concepts. They play a central role in the development of intelligent systems. Knowledge is a description of the world, i.e. the problem domain. Representation is how knowledge is encoded. Reasoning is how to extract more information from what is explicitly represented. www.intechopen.com 164 Advances in Knowledge Representation Different types of knowledge require different types of representation. Different types of knowledge representation require different types of reasoning. The most popular knowledge representation methods are based on logic, rules, frames and semantic nets. Our discussion will be focused on knowledge representation based on logic. Different types of knowledge require different types of representation. Different types of knowledge representation require different types of reasoning. The most popular knowledge representation methods are based on logic, rules, frames and semantic nets. Our discussion will be focused on knowledge representation based on logic. Logic is a language for reasoning. It is concerned with the truth of statements about the world. Each statement is either “true” or “false”. Logic includes the following: a) syntax which specifies the symbols in the language and how they can be combined to form sentences, b) semantics which specify how to assign a truth to a sentence based on its meaning in the world and c) inference rules which specify methods for computing new sentences from existing sentences. There are different types of logic, i.e. propositional logic, first-order predicate logic, fuzzy logic, modal logic, description logic, temporal logic, etc. We are concerned on knowledge representation and reasoning based on typed first-order predicate logic because our correctness method is based on typed FOL. Another classification of knowledge representation is procedural and declarative knowledge representation. Declarative knowledge concerns representation of the problem domain (world) as a set of truth sentences. This representation expresses “what something is”. On the other hand, the procedural knowledge concerns tasks which must be performed to reach a particular goal. In procedural representation, the control information which is necessary to use the knowledge is embedded in the knowledge itself. It focuses on “how something is done”. In the same way, declarative programming is concerned with writing down “what” should be computed and much less with “how” it should be computed (Hill & Lloyd, 1994). Declarative programming separates the control component of an algorithm (the “how”) from the logic component (the “what”). 3. Knowledge representation The key idea of declarative programming is that a program is a theory (in some suitable logic) and computation is deduction from the theory (Lloyd, 1994). The advantages of declarative programming are: a) teaching, b) semantics, c) programmer productivity, c) meta-programming and e) parallelism. Declarative programming in Logic Programming means that programs are theories. The programmer has to supply the intended interpretation of the theory. Control is usually supplied automatically by the system, i.e. the logic programming language. We have followed the declarative knowledge representation for the representation of the knowledge base of our system. www.intechopen.com 3.1 Meta-programming, ground and non-ground representation A language which is used to reason about another language (or possibly itself) is called meta-language and the language reasoned about is called the object language. A meta-program is a program whose data is another program, i.e. the object program. Our proof-checker is a meta-program which manipulates other logic programs. It has been implemented in Prolog and the underlying theory, i.e. the logic programs being verified and the other elements of the KB, is the object program. An important decision is how to represent programs of the object language (i.e. the KB elements in our case) in the programs of the meta-language, i.e. in the meta-programs. Ground representation and non-ground representation are the two main approaches to the representation of object programs in meta-programs. We have followed the ground representation approach for the representation of the elements of the KB of our system. Initially, ground and non-ground representation will be discussed. Then, we will see the advantages and the drawbacks of the two representations. www.intechopen.com 165 Knowledge Representation in a Proof Checker for Logic Programs In logic programming there is not clear distinction between programs and data because data can be represented as program clauses. The semantics of a meta-program depend on the way the object program is represented in the meta-program. Normally, a distinct representation is given to each symbol of the object language in the meta-language. This is called naming relation (Hill & Gallagher, 1998). Rules of construction can be used to define the representation of the constructed terms and formulas. Each expression in the language of the object program should have at least one representation as an expression in the language of the meta-program. The naming relation for constants, functions, propositions, predicates and connectives is straightforward. That is, constants and propositions of the object language can be represented as constants in the meta-language. Functions and predicates of the object language can be represented as functions in the language of meta- program. A connective of the object language can be represented either as a connective or as a predicate or as a function in the meta-language. The main problem is the representation of the variables of the object language in the language of the meta-program. There are two approaches. One approach is to represent the variables of the object program as ground terms in the meta-program. This representation is called ground representation. www.intechopen.com 3.1 Meta-programming, ground and non-ground representation The object program in our proof checker is represented as clauses. The underlying theory is fixed for each proof task. programming. The object program in our proof checker is represented as clauses. The underlying theory is fixed for each proof task. 3.2 Ground representation of object programs in the proof-checker The KB shown in Fig. 2 contains the representation of specifications, theorems, axioms, lemmas and programs complements. It also has the representation of FOL laws in order to facilitate their selection for application. These KB elements are represented in ground representation (Hill & Gallagher, 1998).. The representation of the main symbols of the object language which are used in this chapter is shown below. Object language symbol Representation constant constant object program variable term v(i), i is natural function term g(i), i is natural proposition, formulas of FOL term f(i), i is natural predicate term p(i), i is natural connectives (,,~,↔) \/, /\, ~, -> , <-> exist () ex for all ( ) all length of sequence x1(#x1) len(v(1):Type):nat operation plus (+) plus operation minus (-) minus type variable term tv(i), i is natural type sequence seq empty sequence (<>) nil_seq sequence constructor seq_cons(Head, Tail) where Head and Tail are (Head :: Tail) defined in ground representation accordingly. operator / (Object/Type) (Object : Type) x1i /Type (e.g. x1/α1) v(1, i:nat):Type (e.g. v(1, 1:nat):tv(1) ) equality (=) eq inequality (≠) ~eq less-equal (≤) le greater-equal (≥) ge type natural (N) nat type integer (Z) int nonzero naturals (N1) posInt Object language symbol Representation constant constant object program variable term v(i), i is natural function term g(i), i is natural proposition, formulas of FOL term f(i), i is natural predicate term p(i), i is natural connectives (,,~,↔) \/, /\, ~, -> , <-> exist () ex for all ( ) all length of sequence x1(#x1) len(v(1):Type):nat operation plus (+) plus operation minus (-) minus type variable term tv(i), i is natural type sequence seq empty sequence (<>) nil_seq sequence constructor seq_cons(Head, Tail) where Head and Tail are (Head :: Tail) defined in ground representation accordingly. operator / (Object/Type) (Object : Type) x1i /Type (e.g. x1/α1) v(1, i:nat):Type (e.g. v(1, 1:nat):tv(1) ) equality (=) eq inequality (≠) ~eq less-equal (≤) le greater-equal (≥) ge type natural (N) nat type integer (Z) int nonzero naturals (N1) posInt Predicates are represented by their names assuming that each predicate has a unique name. In case of name conflicts, we use the ground term p(i) where i is natural. Sum of n elements, i.e. 1 n i i x  is represented as the following ground term: sum(1:nat, v(2):nat, v(3, i.e. 3.1 Meta-programming, ground and non-ground representation The other approach is to represent the variables of the object program as variables (or non-ground terms) in the meta-program. This representation is called non-ground representation. Using non-ground representation of the object program is much easier to make an efficient implementation of the meta-program than using ground representation. In non-ground representation, there is no need to provide definitions for renaming, unification and application of substitutions of object language formulas. These operations which are time consuming do not require special treatment for the object language terms. The inefficiency in ground representation is mainly due to the representation of the variables of the object program as constants in the meta-program. Because of this representation complicated definitions for renaming, unification and application of substitutions to terms are required. On the other hand, there are semantic problems with non-ground representation. The meta- program will not have clear declarative semantics. There is not distinction of variables of the object program from the ones of the meta-program which range over different domains. This problem can be solved by using a typed logic language instead of the standard first- order predicate logic. The ground representation is more clear and expressive than the non- ground one and it can be used for many meta-programming tasks. Ground representation is suitable for meta-programs which have to reason about the computational behavior of the object program. The ground representation is required in order to perform any complex meta-programming task in a sound way. Its inherent complexity can be reduced by specialization. That is, such meta-programs can be specialized with respect to the representation of the object program (Gallagher 1993). Another issue is how the theory of the object program is represented in the meta-program. There are again two approaches. One approach is the object program to be represented in the meta-program as program statements (i.e. clauses). In this case, the components of the object program are fixed and the meta-program is specialized for just those programs that can be constructed from these components. The other approach is the object program to be represented as a term in a goal that is executed in the meta-program. In this case the object program can be either fixed or it can be constructed dynamically. In this case the meta- program can reason about arbitrary object programs. This is called dynamic meta- www.intechopen.com 166 Advances in Knowledge Representation programming. 3.3.2 Object program variables Object program variables and variables in specifications are expressed using the lower case English letter x followed by a positive integer which is the unique identifier of the variables e.g. x1, x2, x3, x4 etc. Each object variable is represented in ground form by a term of the form v(N) where N stands for the unique identifier of the variable. For example, the ground representation of the object variables x1, x2, x3 is v(1) ,v(2) and v(3) respectively. Note that, the quantifier of each variable comes before the variable in the formula. Subscripted variables of the form x1i represent elements from constructed objects. They are represented by a term of the form v(Id, i:nat):ElementType where the first argument “Id” represents its unique identifier and the second one represents its subscript. “Id” is a natural number. This type of variables occurs mainly in specifications. A term like v(Id, i:nat):ElementType can be assumed as representing either a regular compound term or an element of a structured object like a sequence. The distinction is performed by checking the types of the elements x and x(i). For example, for i=1 by checking x1:seq(α1) and x1(1:nat):α1, it can be inferred that x1(1:nat):α1 is an element of x1:seq(α1). 3.3.1 Type variables The type variables are specified by the lower case Greek letter a followed by a positive integer which is the unique identifier of the variables e.g. a1, a2, a3, a4 etc. Each type variable is represented in ground form by a term of the form tv(N) or in simplified form tvN where N stands for the unique identifier of the variable. For example, the ground representation of type variables a1, a2, a3 could be tv(1) or tv1, tv(2) or tv2, tv(3) or tv3 respectively. 3.4 Representation of axioms and lemmas A set of axioms is applied to each DT including the “domain closure” and the “uniqueness” axioms which will be also presented later on Section 3.7. Each axiom is specified by a FOL formula. Axioms are represented by the predicates “axiom_def_ID/1” and “axiom_def/4” as follows. The predicate 3.2 Ground representation of object programs in the proof-checker 1 n i i x  is represented as the following ground term: sum(1:nat, v(2):nat, v(3, v(4):nat):Type):Type where “Type” is the type of xi. v(4):nat):Type):Type where “Type” is the type of xi. www.intechopen.com 167 Knowledge Representation in a Proof Checker for Logic Programs “axiom_def_ID(Axiom_Ids)” represents the identifiers of all axioms in the KB. Its argument “Axiom_Ids” is a list with the identifiers of the axioms. For example, the representation “axiom_def_ID([1,2,3,4])” says that the KB has four axioms with identifiers 1,2,3 and 4. The specification of each axiom is represented by a predicate of the following form “axiom_def(Axiom_Id, DT_name, Axiom_name, Axiom_specification)”. Representation: fol_law(2,’  distribution’, [f1 /\ (f2 \/ f3) <-> (f1 /\ f2) \/ (f1 /\ f3)]). fol_law(2,’  distribution’, [f1 /\ (f2 \/ f3) <-> (f1 /\ f2) \/ (f1 /\ f3)]). Representation: Similarly, lemmas are represented by the predicates “lemma_sp_ID/1” and “lemma_sp/4”. Specification: P  (Q  R) ↔ (P Q)  (P  R) Representation: fol_law(2,’  distribution’, [f1 /\ (f2 \/ f3) <-> (f1 /\ f2) \/ (f1 /\ f3)]). “axiom_def(Axiom_Id, DT_name, Axiom_name, Axiom_specification)”. “axiom_def(Axiom_Id, DT_name, Axiom_name, Axiom_specification)”. The argument “Axiom_Id” is the unique identifier of the axiom, i.e. a positive integer. “DT_name” is the name of the DT which the axiom is applied to. “Axiom_name” is the name of axiom. “Axiom_specification” is a list which has the representation of the specification of the axiom. Example: Domain closure axiom for sequences. Informally, this axiom says that a sequence can be either empty or it will consist from head and tail. www.intechopen.com 168 Advances in Knowledge Representation Specification: [ x1/seq(a2),[x1= < >  ( x3/a2, x4/seq(a2),[x1=x3::x4])]] Representation: axiom_def (1, sequences, ’domain closure’, [all v(1):seq(tv(1)), (eq(v(1):seq(tv(1)),nil_seq) \/ [ex v(2):tv(1), ex v(3):seq(tv(1)), eq(v(1):seq(tv(1)),seq_cons(v(2):tv(1), v(3):seq(tv(1))):seq(tv(1))) ])]). [ x1/seq(a2),[x1= < >  ( x3/a2, x4/seq(a2),[x1=x3::x4])]] [ x1/seq(a2),[x1= < >  ( x3/a2, x4/seq(a2),[x1=x3::x4])]] “fol_law(FOL_law_Id, FOL_law_description, FOL_law_specification).”. The argument “FOL_law_Id” is the unique identifier of the FOL law, i.e. a positive integer. “FOL_law_description” is the name of a FOL law. “FOL_law_specification” is a list which has the ground representation of the specification of FOL law. The argument “FOL_law_Id” is the unique identifier of the FOL law, i.e. a positive integer. “FOL_law_description” is the name of a FOL law. “FOL_law_specification” is a list which has the ground representation of the specification of FOL law. 3.5 Representation of first-order logic laws The FOL laws are equivalence preserving transformation rules. Each FOL law is specified by a FOL formula. They are represented by predicates fol_law_ID/1 and fol_law/3 as follows. The predicate The FOL laws are equivalence preserving transformation rules. Each FOL law is specified by a FOL formula. They are represented by predicates fol_law_ID/1 and fol_law/3 as follows. The predicate “fol_law_ID(FOL_laws_Ids)” represents the identifiers of all FOL laws in the KB. Its argument “FOL_laws_Ids” is a list with the identifiers of all FOL laws. The specification of each FOL law is represented by a predicate of the form represents the identifiers of all FOL laws in the KB. Its argument “FOL_laws_Ids” is a list with the identifiers of all FOL laws. The specification of each FOL law is represented by a predicate of the form “fol_law(FOL_law_Id, FOL_law_description, FOL_law_specification).”. Representation: theorem(1, progr1, spec_struct1, [all v(1):seq(int),all v(2):int, (sum(v(1):seq(int), v(2):int):int <-> sum_s(v(1):seq(int), v(2):int))]). x1/seq(Z),  x2/Z (sum(x1,x2) ↔ sums(x1,x2)) x1/seq(Z),  x2/Z (sum(x1,x2) ↔ sums(x1,x2)) Comp(Pr)  Spec  A |=  x1/seq(Z), x2/Z (sum(x1,x2) ↔ sumS(x1, x2)) Pr is the logic program for predicate sum/2, excluding the DT definitions. Comp(Pr) is the complement of the program Pr. Spec is the specification of predicate sum/2, i.e. sumS(x1,x2). A is the theory for sequences, i.e. the underlying DTs for predicate sum/2, including the specifications of the DT operations. 3.6.1 Initial theorem The theorems that have to be proved must also be represented in the KB. Each theorem is specified by a FOL formula. They are represented by the predicates “theorem_ID/1” and “theorem/4” as follows. The predicate “theorem/4” as follows. The predicate “theorem_ID(Theorems_Ids)” “theorem_ID(Theorems_Ids)” “theorem_ID(Theorems_Ids)” www.intechopen.com 169 Knowledge Representation in a Proof Checker for Logic Programs represents the identifiers of all theorems that are available in the KB. Its argument “Theorems_Ids” is a list with the identifiers of all theorems. The specification of each theorem is represented by a predicate of the form represents the identifiers of all theorems that are available in the KB. Its argument “Theorems_Ids” is a list with the identifiers of all theorems. The specification of each theorem is represented by a predicate of the form “theorem(Theorem_Id, Program_Id, Spec_struct_Id, Theorem_specification).” “theorem(Theorem_Id, Program_Id, Spec_struct_Id, Theorem_specification).” “theorem(Theorem_Id, Program_Id, Spec_struct_Id, Theorem_specification).” The argument “Theorem_Id” is the unique identifier of the theorem, i.e. a positive integer. The arguments “Program_Id” and “Spec_struct_Id” are the unique identifiers of the program and the structured specifications respectively. “Theorem_specification” is a list which has the representation of the specification of theorem. Example: The predicate sum(x1, x2) where Type(sum) = seq(Z)  Z is true iff x2 is the sum of the sequence of integers x1. The correctness theorem for predicate sum/2 and the theory which is used to prove it is as follows. 3.6.2 Theorems in structured form The specification of a theorem may need to be transformed into structured form in order to proceed to the proof. The structure form of theorems facilitates the proof task. Each theorem in structured form is specified by a FOL formula. They are represented by the predicates “theorem_struct_ID/1” and “theorem_struct/4” as follows. The predicate “theorem_struct_ID(Theorems_Ids)” “theorem_struct_ID(Theorems_Ids)” represents the identifiers of all theorems available in the KB with the specification part in structured form. Its argument “Theorems_Ids” is a list with the identifiers of all theorems in structured form. The specification of each theorem is represented by a predicate of the form Representation: 3.7 An example theory and theorem Throughout this Chapter we use the correctness theorem and theory for predicate sum/2. That is, Comp(Pr)  Spec  A |=  x1/seq(Z), x2/Z (sum(x1,x2) ↔ sumS(x1, x2)) The ground representation of theory is also illustrated. Theory The logic program completion Comp(Pr) of Pr is as follows. Representation:  progr_clause(progr1, 1,[all v(1):seq(int), all v(2):int, [sum(v(1):seq(int),v(2):int) <-> ((p1(v(1):seq(int)) /\p2(v(1):seq(int), v(2):int)) \/ [ex v(3):int, ex v(4):seq(int), ex v(5):int, x1/seq(Z),x2/Z,[sum(x1,x2)↔ (p1(x1)p2(x1,x2) [x3/Z, x4/seq(Z),  x5/Z,[~p1(x1)p3(x1,x3,x4)p4(x1,x3,x5,x2)sum(x4,x5)]])] x1/seq(Z),[p1(x1)↔empty_seq(x1)]  x1/seq(Z),x2/Z,[p2(x1,x2) ↔neutral_add_subtr_int(x2)]  x1/seq(Z),x2/Z,x3/seq(Z),[p3(x1,x2,x3)↔p5(x1,x2,x3)p6(x1,x2,x3)]  x1/seq(Z),x2/Z,x3/seq(Z),[p5(x1,x2,x3)↔head(x1,x2)]  x1/seq(Z),x2/Z,x3/seq(Z),[p6(x1,x2,x3)↔tail(x1,x3)]  x1/seq(Z),x2/Z,x3/Z,x4/Z,[p4(x1,x2,x3,x4)↔plus_int(x3,x2,x4)] theorem_struct(1, progr1, spec_struct1, [all v(1):seq(int), all v(2):int, (sum(v(1):seq(int), v(2):int) <-> ((eq(v(1):seq(int),nil_seq:seq(tv(1))) /\eq(v(2):int,0:int)) \/ [ex v(3):int, ex v(4):int, ex v(5):seq(int), (eq(v(1):seq(int), seq_cons(v(4):int, v(5):seq(int)):seq(int) ) /\ eq(v(2):int,plus(v(4):int, v(3):int)) /\ sum_s(v(5):seq(int), v(3):int) )]) )]). x1/seq(Z),  x2/Z (sums(x1,x2) ↔ [x1=<>x2=0 [x4/Z, x5/Z, x6/seq(Z),[x1=x5::x6 x2=x5+x4 sums(x6,x4)]]]) x1/seq(Z),  x2/Z (sums(x1,x2) ↔ [x1=<>x2=0 [x4/Z, x5/Z, x6/seq(Z),[x1=x5::x6 x2=x5+x4 sums(x6,x4)]]]) “theorem_struct(Theorem_struct_Id,Program_Id,Spec_struct_Id, Theorem_specification).”. “theorem_struct(Theorem_struct_Id,Program_Id,Spec_struct_Id, Theorem_specification) The argument “Theorem_struct_Id” is the unique identifier, i.e. a positive integer, of the theorem whose specification part is in structured form. The arguments “Program_Id” and “Spec_struct_Id” are the unique identifiers of the program and the structured specifications respectively. “Theorem_specification” is a list which has the representation of the specification of theorem. www.intechopen.com 170 Advances in Knowledge Representation Theory The logic program completion Comp(Pr) of Pr is as follows. Representation: x1/seq(Z),x2/Z,[sum(x1,x2)↔ (p1(x1)p2(x1,x2) [x3/Z, x4/seq(Z),  x5/Z,[~p1(x1)p3(x1,x3,x4)p4(x1,x3,x5,x2)sum(x4,x5)]])] x1/seq(Z),[p1(x1)↔empty_seq(x1)]  x1/seq(Z),x2/Z,[p2(x1,x2) ↔neutral_add_subtr_int(x2)]  x1/seq(Z),x2/Z,x3/seq(Z),[p3(x1,x2,x3)↔p5(x1,x2,x3)p6(x1,x2,x3)]  x1/seq(Z),x2/Z,x3/seq(Z),[p5(x1,x2,x3)↔head(x1,x2)]  x1/seq(Z),x2/Z,x3/seq(Z),[p6(x1,x2,x3)↔tail(x1,x3)]  x1/seq(Z),x2/Z,x3/Z,x4/Z,[p4(x1,x2,x3,x4)↔plus_int(x3,x2,x4)] Example In order to construct the theorem in structured form the predicate specification must be transformed into structured form. The initial logic specification for predicate sum/2 is the following.  x1/seq(Z), x2/Z (sumS(x1,x2) ↔ x2 =  1 # 1 1 x i i x ) The logic specification of sumS(x1,x2) in structured form and its representation are following. Theorem Specification: Representation: theorem_struct(1, progr1, spec_struct1, [all v(1):seq(int), all v(2):int, (sum(v(1):seq(int), v(2):int) <-> ((eq(v(1):seq(int),nil_seq:seq(tv(1))) /\eq(v(2):int,0:int)) \/ [ex v(3):int, ex v(4):int, ex v(5):seq(int), (eq(v(1):seq(int), seq_cons(v(4):int, v(5):seq(int)):seq(int) ) /\ eq(v(2):int,plus(v(4):int, v(3):int)) /\ sum_s(v(5):seq(int), v(3):int) )]) )]). 3.7 An example theory and theorem Throughout this Chapter we use the correctness theorem and theory for predicate sum/2 That is, Comp(Pr)  Spec  A |=  x1/seq(Z), x2/Z (sum(x1,x2) ↔ sumS(x1, x2)) The ground representation of theory is also illustrated. Representation:  progr_clause(progr1, 1,[all v(1):seq(int), all v(2):int, [sum(v(1):seq(int),v(2):int) <-> ((p1(v(1):seq(int)) /\p2(v(1):seq(int), v(2):int)) \/ [ex v(3):int, ex v(4):seq(int), ex v(5):int, www.intechopen.com 171 Knowledge Representation in a Proof Checker for Logic Programs [~p1(v(1):seq(int)) /\ p3(v(1):seq(int), v(3):int,v(4):seq(int)) /\ p4(v(1):seq(int),v(3):int, v(5):int, v(2):int) /\ sum(v(4):seq(int),v(5):int)]])]]). [~p1(v(1):seq(int)) /\ p3(v(1):seq(int), v(3):int,v(4):seq(int)) /\ p4(v(1):seq(int),v(3):int, v(5):int, v(2):int) /\ sum(v(4):seq(int),v(5):int)]])]]). q  progr_clause(progr1, 2, [all v(6):seq(int),[p1(v(6):seq(int)) <-> empty_seq(v(6):seq(int))]]).  progr_clause(progr1, 3, [all v(7):seq(int), all v(8):int,[p2(v(7):seq(int), v(8):int) <-> neutral_add_subtr_int(v(8):int)]]).  progr_clause(progr1, 3, [all v(7):seq(int), all v(8):int,[p2(v(7):seq(int), v(8):int) <-> neutral_add_subtr_int(v(8):int)]]).  progr_clause(progr1, 4, [all v(9):seq(int), all v(10):int, all v(11):seq(int), [p3(v(9):seq(int), v(10):int, v(11):seq(int))<-> p5(v(9):seq(int), v(10):int, v(11):seq(int)) /\ p6(v(9):seq(int), v(10):int, v(11):seq(int))]]).  progr_clause(progr1, 4, [all v(9):seq(int), all v(10):int, all v(11):seq(int), [p3(v(9):seq(int), v(10):int, v(11):seq(int))<-> p5(v(9):seq(int), v(10):int, v(11):seq(int)) /\ p6(v(9):seq(int), v(10):int, v(11):seq(int))]]). q  progr_clause(progr1, 5, [all v(12):seq(int), all v(13):int, all v(14):seq(int),[p5(v(12):seq(int), v(13):int, v(14):seq(int)) <-> head(v(12):seq(int), v(13):int)]]).  progr_clause(progr1, 5, [all v(12):seq(int), all v(13):int, all v(14):seq(int),[p5(v(12):seq(int), v(13):int, v(14):seq(int)) <-> head(v(12):seq(int), v(13):int)]]).  progr_clause(progr1, 6, [all v(15):seq(int), all v(17):int, all v(16):seq(int),[p6(v(15):seq(int), v(17):int, v(16):seq(int))<-> tail(v(15):seq(int), v(16):seq(int))]]).  progr_clause(progr1, 6, [all v(15):seq(int), all v(17):int, all v(16):seq(int),[p6(v(15):seq(int), v(17):int, v(16):seq(int))<-> tail(v(15):seq(int), v(16):seq(int))]]).  progr_clause(progr1, 7, [all v(18):seq(int), all v(19):int, all v(20):int, all v(21):int,[p4(v(18):seq(int), v(19):int, v(20):int, v(21):int) <-> plus_int(v(20):int, v(19):int, v(21):int)]]). The logic specification (Spec) is shown in Section 3.6 and its representation in ground form. The theory A of the DT operations including the specification of the DT operations is as follows. The theory A of the DT operations including the specification of the DT operations is as follows. Axioms Domain closure axiom for sequences Domain closure axiom for sequences  x1/seq(a2),[x1= < >  ( x3/a2,x4/seq(a2),[x1=x3::x4])] Its ground representation is shown in section 3.4. Its ground representation is shown in section 3.4. Uniqueness axioms for sequences Uniqueness axioms for sequences i x1/a2,x3/seq(a2),[~[x1::x3/a2= < > ]] ii x1/a2,x3/a2,x4/seq(a2),x5/seq(a2),[x1::x4=x3::x5 x1=x3 x4=x5] Representation:  axiom_def(2, sequences, "uniqueness i", [all v(1):tv(1), all v(2):seq(tv(1)), [~[eq(seq_cons (v(1):tv(1), v(2):seq(tv(1))):tv(1),nil_seq:seq(tv(1)))]]]). q q q  axiom_def(3, sequences, "uniqueness ii", [all v(1):tv(1), all v(2):tv(1), all v(3):seq(tv(1)), all v(4):seq(tv(1)),[eq(seq_cons(v(1):tv(1), v(3):seq(tv(1))):seq(tv(1)), seq_cons(v(2):tv(1), v(4):seq(tv(1))):seq(tv(1))) -> (eq(v(1):tv(1), v(2):tv(1)) /\ eq(v(3):seq(tv(1)), v(4):seq(tv(1))))]]). Definition of summation operation over 0 entities Definition of summation operation over 0 entities x1/seq(Z),[x1= < > Σ((i=1 to #x1 ) x1i )=0] Representation:  axiom_def(4, sequences, "summation over 0 entities", [all v(1):seq(int), [eq(v(1):seq(int),nil_seq) -> eq(sum(1:int,len(v(1):seq(int)):int, v(1,v(3):nat):int), 0:int)]]).  axiom_def(4, sequences, "summation over 0 entities", [all v(1):seq(int), [eq(v(1):seq(int),nil_seq) -> eq(sum(1:int,len(v(1):seq(int)):int, v(1,v(3):nat):int), 0:int)]]). Representation:  dtOp_sp(empty_seq, 1, "seq: empty", [all v(1):seq(tv(1)), [empty_seq(v(1):seq(tv(1))) <-> eq(v(1):seq(tv(1)),nil_seq:seq(tv(1)))]]). q q q q  dtOp_sp(head, 2, "seq: head", [all v(1):seq(tv(1)), all v(2):tv(1),[head(v(1):seq(tv(1)), v(2):tv(1)) <-> [~eq(v(1):seq(tv(1)),nil_seq:seq(tv(1))) /\ [ex v(3):seq(tv(1)), [eq(v(1):seq (tv(1)),seq_cons(v(2):tv(1), v(3):seq(tv(1))):tv(1))]]]]]). q q  dtOp_sp(tail, 3, "seq: tail", [all v(1):seq(tv(1)), all v(2):seq(tv(1)), [tail(v(1):seq(tv(1)), v(2):seq(tv(1))) <-> [ex v(3):tv(1),[~eq(v(1):seq(tv(1)), nil_seq:seq (tv(1))) /\ eq(v(1), seq_cons(v(3):tv(1),v(2):seq(tv(1))):tv(1))]]]]). q ( ( ) ( ) ( ) q( ( ))) ( )) )  dtOp_sp(neutral_add_subtr_int, 8, "int: neutral_add_subtr_int", [all v(1):int, [neutral_add_subtr_int(v(1):int) <-> eq(v(1):int,0:int)]]).  dtOp_sp(plus_int, 9,"int: plus_int", [all v(1):int, all v(2):int, all v(3):int, [plus_int(v(1):int,v(2):int,v(3):int) <-> eq(v(3):int,plus(v(2):int,v(1):int))]]). Lemmas www.intechopen.com 172 Advances in Knowledge Representation x1/seq(a2),[x1 ≠ < > ↔ [x3/a2,x4/seq(a2),[x1=x3::x4/a2]]] x1/a2,x3/seq(a2),x4/seq(a2),[x3=x1::x4(x5/N,[2≤x5≤#x3x3(x5)=x4(x5-1)])] x1/seq(a2),x3/seq(a2),x4/a2,[x1=x4::x3#x1=#x3+1] x1/a2,x3/seq(a2),x4/seq(a2),[x3=x1::x4/a2x1=x31/a2] Representation:  lemma_sp(1, sequences, "Non-empty sequences have at least one element",[all v(1):seq(tv(1)), [~eq(v(1):seq(tv(1)),nil_seq:seq(tv(1))) <-> [ex v(2):tv(1), ex v(3):seq(tv(1)), [eq(v(1):seq(tv(1)), seq_cons(v(2):tv(1), v(3):seq(tv(1))):tv(1))]]]]).  lemma_sp(1, sequences, "Non-empty sequences have at least one element",[all v(1):seq(tv(1)), [~eq(v(1):seq(tv(1)),nil_seq:seq(tv(1))) <-> [ex v(2):tv(1), ex v(3):seq(tv(1)), [eq(v(1):seq(tv(1)), seq_cons(v(2):tv(1), v(3):seq(tv(1))):tv(1))]]]]). q q  lemma_sp(2,sequences,"if sequence s has tail t then the element si is identical to the element ti- 1",[all v(1):tv(1), all v(2):seq(tv(1)), all v(3):seq(tv(1)),[eq(v(2):seq(tv(1)), seq_cons(v(1):tv(1), v(3):seq(tv(1))):seq(tv(1))) -> (all v(4):nat, [le(2:nat, v(4):nat) /\ le(v(4):nat, len(v(2):seq (tv(1))):nat) -> eq(v(2, v(4):nat):tv(1), v(3, minus(v(4): nat,1:nat) ))])]]). q  lemma_sp(3, sequences, "If sequence s has tail t then the length of s is equal to the length of t plus 1", [all v(1):seq(tv(1)), all v(2):seq(tv(1)), all v(3):tv(1), [eq(v(1):seq(tv(1)), seq_cons(v(3):tv(1), v(2):seq(tv(1))):seq(tv(1))) -> eq(len(v(1):seq(tv(1))): nat,plus(len(v(2): seq(tv(1))):nat,1:nat))]]). q  lemma_sp(4, sequences, "If sequence s is non-empty then its head h is identical to its first element", [all v(1):tv(1), all v(2):seq(tv(1)), all v(3):seq(tv(1)),[eq(v(2):seq(tv(1)), seq_cons(v(1):tv(1), v(3):seq(tv(1))):tv(1)) -> eq(v(1):tv(1), v(2, 1:int):tv(1))]]). Logic specifications of DT operations Logic specifications of DT operations  x1/seq(a2),[empty_seq(x1)↔ x1= < > ]  x1/Z,[neutral_add_subtr_int(x1) ↔x1=0]  x1/seq(a2),x3/a2,[head(x1,x3) ↔ [x1≠ < >  [ x4/seq(a2),[x1=x3::x4/a2]]]]  x1/seq(a2),x3/seq(a2),[tail(x1,x3)↔ [x4/a2,[x1≠< > x1=x4::x3/a2]]]  x1/Z,x2/Z,x3/Z,[plus_int(x1,x2,x3)x3=x2+x1]  x1/seq(a2),[empty_seq(x1)↔ x1= < > ]  x1/seq(a2),[empty_seq(x1)↔ x1= < > ]  x1/Z,[neutral_add_subtr_int(x1) ↔x1=0]  x1/Z,[neutral_add_subtr_int(x1) ↔x1=0]  x1/seq(a2),x3/a2,[head(x1,x3) ↔ [x1≠ < >  [ x4/seq(a2),[x1=x3::x4/a2]]]]  x1/seq(a2),x3/seq(a2),[tail(x1,x3)↔ [x4/a2,[x1≠< > x1=x4::x3/a2]]]  x1/Z,x2/Z,x3/Z,[plus_int(x1,x2,x3)x3=x2+x1] 4. Schematic view of the Interaction of the main components In this section, a schematic view of the proof checker and the interaction of its main components will be shown. In addition, the functions of its components will be discussed. An example of a proof step will illustrate the use of the KB representation in the proof task. www.intechopen.com 173 Knowledge Representation in a Proof Checker for Logic Programs user Make necessary  selections Knowledge  Base ‐specifications ‐axioms ‐lemmas ‐specs DT  operations ‐logic programs Perform Proof Step • Select Theory • Select Proof Scheme • Specify Theorem 1 2 3 Fig. 3. Schematic View of the Theorem Proof Checker. o edge Base ‐specifications ‐axioms ‐lemmas ‐specs DT  operations ‐logic programs p ‐axioms ‐lemmas ‐specs DT  operations ‐logic programs Make necessary  selections Perform Proof Step Fig. 3. Schematic View of the Theorem Proof Checker. 4.2 Schematic view of specification transformer Fig. 4 depicts the procedure for transforming a specification in the required structured form, which is similar to the previous case. In this case however, the underlying theory consists of Spec U Axioms U Lemmas. Initially, the user selects a specification, then the rest elements of the theory are automatically selected by the system. Next, in step 2, the user has to select specific theory elements and transformation rules. In step 3, the selected transformation rule is performed. Step 2 and step 3 are performed iteratively until the specification is transformed in the required structured form. user Make necessary  selections Knowledge Base -specifications -axioms -lemmas -specs DT operations Transformation Step Select Logic Specification and  rest elements of the theory 1 2 3 Fig. 4. Schematic View of Specification Transformer. 4.3 Illustration of a proof step The “Transformation Step” procedure is actually a sub-procedure of the “Perform Proof Step” procedure and that is why we will not present it. The schematic view of the main algorithm for the procedure which performs a proof step, i.e. “performProofStep”, is shown in Fig. 5. It is assumed that the user has selected some theory elements, and a transformation rule that should be applied to the current proof step. Select Logic Specification and  rest elements of the theory Knowledge Base -specifications -axioms -lemmas -specs DT operations Make necessary  selections Transformation Step Fig. 4. Schematic View of Specification Transformer. 4.1 Schematic view of the theorem proof checker The process of proving a theorem is shown in Fig. 3 and consists of three steps.  Step 1: In order to prove the correctness of a theorem the user initially has to specify the theorem that is going to be proved and to select the theory and the proof scheme that will be used for the proof. The theory is retrieved from the KB and it is presented to the user for selection. It consists of a program complement, a logic specification, axioms and lemmas. The corresponding window of the interface which allows the user to make these selections is shown in Fig. 6. g  Step 2: After the selection the user proceeds to the actual proof of the specific theorem. In order to do that he has to select specific parts from the theorem, the theory and the transformation rules that will be applied. The transformation rules that can be applied are first order logic (FOL) laws, folding and unfolding.  Step 3: In this step the selected transformation is applied and the equivalent form of the theorem is presented to the user. The user can validate the result. He is allowed to approve or cancel the specific proof step. The last two steps are performed iteratively until the theorem is proved. The last two steps are performed iteratively until the theorem is proved. www.intechopen.com 174 Advances in Knowledge Representation 4.3 Illustration of a proof step The “Transformation Step” procedure is actually a sub-procedure of the “Perform Proof Step” procedure and that is why we will not present it. The schematic view of the main algorithm for the procedure which performs a proof step, i.e. “performProofStep”, is shown in Fig. 5. It is assumed that the user has selected some theory elements, and a transformation rule that should be applied to the current proof step. The “Transformation Step” procedure is actually a sub-procedure of the “Perform Proof Step” procedure and that is why we will not present it. The schematic view of the main algorithm for the procedure which performs a proof step, i.e. “performProofStep”, is shown in Fig. 5. It is assumed that the user has selected some theory elements, and a transformation rule that should be applied to the current proof step. www.intechopen.com Knowledge Representation in a Proof Checker for Logic Programs 175 Fig. 5. Schematic view of the “performProofStep” procedure. Fig. 5. Schematic view of the “performProofStep” procedure. Fig. 5. Schematic view of the “performProofStep” procedure. The function block diagram of the algorithm “performProofStep” shown in Fig. 5 will be discussed through an example. Consider that our theorem has been transformed and its current form is the following: x1/seq(Z),x2/Z (sums(x1,x2) ↔ (x1= <> x2=0  [x3/Z,[x4/seq(Z),false x2=x4+x3 sums(x4,x3)]])) (x1= <> x2=0  [x3/Z,[x4/seq(Z),false x2=x4+x3 sums(x4,x3)]])) The user has selected the following FOL law to be applied to the above theorem: P false ↔false P false ↔false Initially, the current theorem is converted to the corresponding ground representation by the procedure “ConvertGr” and we get: Initially, the current theorem is converted to the corresponding ground representation by the procedure “ConvertGr” and we get: [all v(1):seq(int),[all v(2):int,sum_s(v(1):seq(int),v(2):int)<-> (eq(v(1):seq(int),nil_seq:seq(int))/\eq(v(2):int,0:int) \/ [ex v(3):int,[ex v(4):int,[ex v(5):seq(int), false/\eq(v(2):int,plus(v(4):int,v(3):int):int)/\sum_s(v(5):seq(int),v(3):int)]]])]] Then, the procedure “applyProofStep” applies the transformation rule to the current theorem and derives the new theorem. In order to do that, this procedure constructs and asserts a set of clauses which implement the selected transformation rule. Then, it applies this set of clauses and derives the new theorem in ground representation. That is, [all v(1):seq(int),[all v(2):int,sum_s(v(1):seq(int),v(2):int)<-> (eq(v(1):seq(int),nil_seq:seq(int))/\eq(v(2):int,0:int) \/ [ex v(3):int,[ex v(4):int,[ex v(5):seq(int), false /\ sum_s(v(5):seq(int),v(3):int)]]])]] [all v(1):seq(int),[all v(2):int,sum_s(v(1):seq(int),v(2):int)<-> (eq(v(1):seq(int),nil_seq:seq(int))/\eq(v(2):int,0:int) \/ [ex v(3):int,[ex v(4):int,[ex v(5):seq(int), false /\ sum_s(v(5):seq(int),v(3):int)]]])]] The new theorem is then converted to the corresponding non-ground form in order to be presented to the user. That is, [x1/seq(Z),[x2/Z,sums(x1,x2) ↔ (x1=<> x2=0  [x3/Z,[x4/seq(Z), falsesums(x4,x3)]])]] www.intechopen.com 176 Advances in Knowledge Representation 5.1 Interface illustration of the “Prove Program Correctness” task If the user selects the button “Prove Program Correctness” from the main window, the window shown in Fig. 6 will be displayed. The aim of this window is to allow the user to select the appropriate theory and proof scheme that he will use in his proof. In addition, the user can either select a theorem or define a new one. After the appropriate selections, the user can proceed to the actual proof of the theorem by selecting the button “Prove Correctness Theorem”. The window that appears next is shown in Fig. 7. The aim of this window is to assist the user in the proof task. The theorem to be proved and its logic specification are displayed in the corresponding position on the top-left side of the window. This window has many functions. The user is able to choose theory elements from the KB that will be used for the current proof step. After selection by the user of the appropriate components for the current proof step the proper inference rule is selected and it is applied automatically. The result of the proof step is shown to the user. Moreover, the user is able to cancel the last proof step, or to create a report with all the details of the proof steps that have been applied so far. 5. System interface To enable users to guide this proof checker it is necessary to provide a well-designed user interface. The design of the interface of an interactive verifier depends on the intended user. In our verifier we distinguish two kinds of users, the “basic users” and the “advanced or experienced users”. We call “basic user” a user who is interested in proving a theorem. We call an “advanced user” a user who in addition to proving a theorem he/she may want to enhance the KB of the system in order to be able to deal with additional theorems. Such a user is expected to be able to update the KB of axioms, lemmas, predicate specifications, specifications of DT operations and programs. We will use the word “user” to mean both the “basic user” and the “advanced user”. Both kinds of users are expected to know very well the correctness method which is supported by our system (Marakakis, 2005). Initially, the system displays the main, top-level window as shown in Fig. 1. This window has a button for each of its main functions. The name of each button defines its function as well, that is, “Transform Logic Specification into Structured Form”, “Prove Program Correctness” and “Update Knowledge Base”. The selection of each button opens a new window which has a detailed description of the required functions for the corresponding operation. Now we will illustrate the “Prove Program Correctness” function to better understand the whole interaction with the user. 5.1.1 Illustration of a proof step Let’s assume that the user has selected a theorem to be proved, its corresponding theory and a proof scheme. Therefore, he has proceeded to the verification task. For example, he likes to prove the following theorem: Comp(Pr)  Spec  A |=  x1/seq(Z), x2/Z (sum(x1,x2) ↔ sumS(x1,x2)) 6. Results The results of this research work involve the development of a proof checker that can be used efficiently by its users for the proof of correctness theorems for logic programs constructed by our schema-based method (Marakakis, 1997). The system has been tested and allows the verification of non-trivial logic programs. Our proof checker is highly modular, and allows the user to focus on proof decisions rather than on the details of how to apply each proof step, since this is done automatically by the system. The update of the KB is supported by the proof-checker as well. The overall interface of our system is user– friendly and facilitates the proof task. The main features of our system which make it to be an effective and useful tool for the interactive verification of logic programs constructed by the method (Marakakis, 1997) are the following.  The proof of the correctness theorem is guided by the logic-program construction method (Marakakis, 1997). That is, the user has to select a proof scheme based on the applied program schema for the construction of the top-level predicate of the logic program whose correctness will be shown.  Proof steps can be cancelled at any stage of the proof. Therefore, a proof can move to any previous state. any previous state.  The system supports the proof of a new theorem as part of the proof of the initial theorem.  The system supports the proof of a new theorem as part of the proof of the initial theorem.  The update of the theories stored in the KB of the system is supported as well.  The overall verification task including the update of the KB is performed through a user-friendly interface.  At any stage during the verification task the user can get a detailed report of all proof steps performed up to that point. So, he can get an overall view of the proof performed so far. Comp(Pr)  Spec  A |=  x1/seq(Z), x2/Z (sum(x1,x2) ↔ sumS(x1,x2)) The user has selected the “Incremental” proof scheme which requires proof by induction on an inductive DT. Let assume that the correctness theorem has been transformed to the following form: www.intechopen.com www.intechopen.com 177 Knowledge Representation in a Proof Checker for Logic Programs x1/seq(Z),x2/Z, sum(x1,x2) ↔ [x3/Z,x4/Z,x5/seq(Z), x1<>  x1=x4::x5  x1 <>  x1=x4::x5  x2=x4+x3  sum(x5,x3)] Fig. 6. The window for selecting Theory, Theorem and Proof Scheme Fig. 7. The window for proving a correctness theorem x1/seq(Z),x2/Z, sum(x1,x2) ↔ [x3/Z,x4/Z,x5/seq(Z), x1<>  x1=x4::x5  x1 <>  x1=x4::x5  x2=x4+x3  sum(x5,x3)]  sum(x5,x3)] Fig. 6. The window for selecting Theory, Theorem and Proof Scheme g g y Fig. 7. The window for proving a correctness theorem Fig. 7. The window for proving a correctness theorem Fig. 7. The window for proving a correctness theorem Fig. 7. The window for proving a correctness theorem www.intechopen.com 178 Advances in Knowledge Representation In order to proceed to the next proof step the following steps should be performed:  First, the user selects “Logic Spec. of DT_Op” and then he selects the “Head” DT operation:  First, the user selects “Logic Spec. of DT_Op” and then he selects the “Head” DT operation: x1/seq(a2),x3/a2,[head(x1,x3) ↔ [x1 < >  [x4/seq(a2),[x1=x3::x4/a2]]]] x1/seq(a2),x3/a2,[head(x1,x3) ↔ [x1 < >  [x4/seq(a2),[x1=x3::x4/a2]]]] x1/seq(a2),x3/a2,[head(x1,x3) ↔ [x1 < >  [x4/seq(a2),[x1=x3::x4/a2]]]]  Then he selects the button “Apply Proof Step” and the result is shown in the next line of the “Induction Step” area:  Then he selects the button “Apply Proof Step” and the result is shown in the next line of the “Induction Step” area: x1/seq(Z),x2/Z, sum(x1,x2) ↔ [x3/Z,x4/Z,x5/seq(Z), x1<> x1=x4::x5  head(x1, x4) x2=x4+x3 sum(x5,x3)] x1/seq(Z),x2/Z, sum(x1,x2) ↔ [x3/Z,x4/Z,x5/seq(Z), x1<> x1=x4::x5  head(x1, x4) x2=x4+x3 sum(x5,x3)] The user continues applying proof steps until to complete the proof of the theorem. 7. Conclusions This chapter has presented our proof checker. It has been focused on the knowledge representation layer and on its use by the main reasoning algorithms. Special importance on www.intechopen.com 179 Knowledge Representation in a Proof Checker for Logic Programs the implementation of the proof checker has been given on flexibility so the system being developed could be enhanced with additional proof tasks. Finally, the main implementation criteria for the knowledge representation are the support for an efficient and modular implementation of the verifier. the implementation of the proof checker has been given on flexibility so the system being developed could be enhanced with additional proof tasks. Finally, the main implementation criteria for the knowledge representation are the support for an efficient and modular implementation of the verifier. In our proof checker, a proof is guided by the selected proof scheme. The selection of a proof scheme is related with the construction of the top-level predicate of the program that will be verified. The user-friendly interface of our system facilitates the proof task in all stages and the update of the KB. Its modular implementation makes our proof checker extensible and amenable to improvements. The natural progression of our proof checker is the addition of automation. That is, we intend to move proof decisions from the user to the system. The verifier should have the capacity to suggest proof steps to the user. Once they are accepted by the user they will be performed automatically. Future improvements aim to minimize the interaction with the user and to maximize the automation of the verification task. 8. References Clarke, E. & Wing, J. (1996). Formal Methods: State of the Art and Future Directions, ACM Computing Surveys, Vol. 28, No. 4, pp. 626-643, December, 1996. Gallagher, J. (1993). Tutorial on Specialization of Logic Programs, Proceedings of PERM’93, the ACM Sigplan Symposium on Partial Evaluation and Semantics-Based Program Manipulation, pp. 88-98, ACM Press, 1993. Hill, P. M. & Gallagher, J. (1998). Meta-programming in Logic Programming, Handbook of Logic in Artificial Intelligence and Logic Programming, vol. 5, edited by D. Gabbay, C. Hogger, J. Robinson, pp. 421-497, Clarendon Press, Oxford, 1998. Hill, P. M. & Lloyd, J. W. (1994). The Gödel Programming Language, The MIT Press, 1994. Lindsay, P. (1988). A Survey of Mechanical Support for Formal Reasoning, Software Engineering Journal, vol. 3, no. 1, pp.3-27, 1988. Lloyd, J.W. (1994). Practical Advantages of Declarative Programming. In Proceedings of the Joint Conference on Declarative Programming, GULP-PRODE’94, 1994. Loveland, D. W. (1986). Automated Theorem Proving: Mapping Logic in AI, Proceedings of the ACM SIGART International Symposium on Methodologies for Intelligent Systems, pp. 214-229, Knoxville, Tennessee, United States, October 22-24, 1986. Marakakis, E. (1997). Logic Program Development Based on Typed, Moded Schemata and Data Types, PhD thesis, University of Bristol, February, 1997. Marakakis, E. (2005). Guided Correctness Proofs of Logic Programs, Proc. the 23th IASTED International Multi-Conference on Applied Informatics, edited by M.H. Hamza, pp. 668- 673, Innsbruck, Austria, 2005. Marakakis, E. & Gallagher. J.P. (1994). Schema-Based Top-Down Design of Logic Programs Using Abstract Data Types, LNCS 883, Proc. of 4th Int. Workshops on Logic Program Synthesis and Transformation - Meta-Programming in Logic, pp.138-153, Pisa, Italy, 1994. www.intechopen.com 180 Advances in Knowledge Representation Advances in Knowledge Representation 180 Marakakis, E. & Papadakis, N. (2009). An Interactive Verifier for Logic Programs, Proc. Of 13th IASTED International Conference on Artificial Intelligence and Soft Computing , pp. 130-137, 2009. Marakakis, E. & Papadakis, N. (2009). An Interactive Verifier for Logic Programs, Proc. Of 13th IASTED International Conference on Artificial Intelligence and Soft Computing , pp. 130-137, 2009. www.intechopen.com Advances in Knowledge Representation Edited by Dr. Carlos Ramirez Advances in Knowledge Representation Edited by Dr. Carlos Ramirez ISBN 978-953-51-0597-8 Hard cover, 272 pages Publisher InTech Published online 09, May, 2012 Published in print edition May, 2012 Advances in Knowledge Representation offers a compilation of state of the art research works on topics such as concept theory, positive relational algebra and k-relations, structured, visual and ontological models of knowledge representation, as well as detailed descriptions of applications to various domains, such as semantic representation and extraction, intelligent information retrieval, program proof checking, complex planning, and data preparation for knowledge modelling, and a extensive bibliography. It is a valuable contribution to the advancement of the field. The expected readers are advanced students and researchers on the knowledge representation field and related areas; it may also help to computer oriented practitioners of diverse fields looking for ideas on how to develop a knowledge-based application. How to reference In order to correctly reference this scholarly work, feel free to copy and paste the following: Emmanouil Marakakis, Haridimos Kondylakis and Nikos Papadakis (2012). Knowledge Representation in a Proof Checker for Logic Programs, Advances in Knowledge Representation, Dr. Carlos Ramirez (Ed.), ISBN: 978-953-51-0597-8, InTech, Available from: http://www.intechopen.com/books/advances-in-knowledge- representation/knowledge-representation-in-a-proof-checker-for-logic-programs www.intechopen.com www.intechopen.com InTech China Unit 405, Office Block, Hotel Equatorial Shanghai No.65, Yan An Road (West), Shanghai, 200040, China Phone: +86-21-62489820 Fax: +86-21-62489821 InTech China Unit 405, Office Block, Hotel Equatorial Shanghai No.65, Yan An Road (West), Shanghai, 200040, China Phone: +86-21-62489820 Fax: +86-21-62489821 InTech Europe University Campus STeP Ri Slavka Krautzeka 83/A 51000 Rijeka, Croatia Phone: +385 (51) 770 447 Fax: +385 (51) 686 166 www.intechopen.com © 2012 The Author(s). Licensee IntechOpen. This is an open access artic stributed under the terms of the Creative Commons Attribution 3.0 cense, which permits unrestricted use, distribution, and reproduction in ny medium, provided the original work is properly cited. © 2012 The Author(s). Licensee IntechOpen. This is an open access article distributed under the terms of the Creative Commons Attribution 3.0 License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Reference range of complete blood count, Ret-He, immature reticulocyte fraction, reticulocyte production index in healthy babies aged 1–4 months
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Reference range of complete blood count, Ret‑He, immature reticulocyte fraction, reticulocyte production index in healthy babies aged 1–4 months OPEN Harapan Parlindungan Ringoringo 1*, Lina Purnamasari 2, Ari Yunanto 3, Meitria Syahadatina 4 & Nurul Hidayah 5 Harapan Parlindungan Ringoringo 1*, Lina Purnamasari 2, Ari Yunanto 3, Meitria Syahadatina 4 & Nurul Hidayah 5 Establishing reference ranges of the complete blood count (CBC), reticulocyte hemoglobin content (Ret-He), immature reticulocyte fraction (IRF), and reticulocyte production index (RPI) helps diagnose a disease related to the changes in erythrocyte indices, white blood count, platelets, and reticulocytes, especially in babies. Therefore, the study aims to establish a reference range for CBC and reticulocyte parameters in healthy babies aged 1–4 months. The study design was a cross-sectional study with descriptive analysis of CBC and reticulocyte in babies aged 1–4 months. Three hundred forty-eight babies met the inclusion criteria. This study recruited 89 babies aged 1 month, 87 babies aged 2 months, 86 babies aged 3 months, and 86 babies aged 4 months. The P5-P95 reference range of healthy babies for hemoglobin (Hb) aged 1 month, 2 months, 3 months, and 4 months was 9.95 to 15.45 g/dL, 9.74 to 13.42 g/dL, 9.51 to 12.40 g/dL, and 10.04 to 13.10 g/dL respectively. The P3-P97 reference range of healthy babies for Hb aged 1 month, 2 months, 3 months, and 4 months was 9.60 to 15.90 g/dL, 9.46 to 13.97 g/dL, 9.26 to 12.82 g/dL, and 10.00 to 13.33 g/dL respectively. This study also defined reference ranges for CBC, Ret-He, IRF, and RPI. The reference range of CBC, Ret-He, IRF, and RPI for healthy babies aged 1–4 months in this study can be used as a benchmark. All ages anemia prevalence was 22.8% globally in 2019. The prevalence was highest among children under five years, 39.7%, with the most contributing cause being dietary iron deficiency (ID)1. Anemia is still a major global health problem. Thereby, the early detection of anemia is crucial considering its long-term effects that can interfere with a baby’s growth and development. Several studies have shown the impact of iron deficiency anemia (IDA) on cognitive and behavioral ­deteriorations2–4. Then, early diagnosis and treatment of impending brain dysfunction in the pre-anemic stage are necessary to prevent neurological deficits. Iron deficiency and IDA are caused by not giving oral iron supplementation and low iron stores at birth; the baby’s growth rate is swift, and inadequate iron intake. www.nature.com/scientificreports www.nature.com/scientificreports Discussion Establishing the lower limit of P3-P97 and P5-P95 on examining specific parameters is commonly used statisti- cally. For example, the WHO (World Health Organization) and CDC (Centers Of Disease Control and Preven- tion) growth charts set the lower limit of Weight-for-age, Length/height-for-age, Head circumference-for-age, and Arm circumference-for-age at ­P310. Determination of the lower limit of Hb with P3-P97 and P5-P95, of course, by considering race, ethnicity, age, gender, and altitude above sea ­level11. This study accommodates all reference range limits to be used flexibly.h gl y The results of this study showed the reference range of CBC, reticulocyte count, Ret-He, IRF, and RPI at P3-P97 and P5-P95. Values below the lower limit of the reference range of Hb according to age can be used as a limit to determine if a baby has anemia. In addition, the value below the lower limit of the reference range of Ret- He according to age can be used as a limit to determine whether a baby has ID. The baby is suffered from IDA; if the value of Hb and Ret-He is below the lower limit of the reference range. Thus, for example, this study indicates that the lower limit of Hb for healthy babies aged 4 months (see Tables 1 and 2) can be taken at P3 and P5, i.e., 10.00 g/dL and 10.04 g/dL, respectively. In addition, this study indicates that the lower limit of Ret-He for healthy babies aged 4 months (see Tables 1 and 2) can be taken at P3, and P5, i.e., 17.40 pg and 19.22 pg, respectively.hf g g g y Therefore, to determine whether a baby aged 4 months is suffering from IDA if the value of Hb and Ret- He is below the lower limit of the reference range. Combining several parameters, Hb, MCV, MCH, RDW, reticulocyte count, and Ret He, in conjunction with the peripheral blood smear examination, will make an IDA diagnosis undoubtedly. The examples above can also be used for babies aged 1 month, 2 months, and 3 months (see Tables 1 and 2).i One study showed that IDA, iron depletion and iron deficiency incidence in babies aged 0–6 months were 40.8, 28.0 and 27.0%, respectively. The incidence of IDA in babies aged 0 months, 1 month, and 2 months were 11.8, 10.9 and 11.3%, respectively. Resultsh Three hundred forty-eight healthy babies (boys 53.4%, girls 46.6%) met the inclusion criteria. Therefore, this study recruited 89 babies aged 1 month (boys 59.6%, girls 40.4%), 87 babies aged 2 months (boys 49.4%, girls 50.6%), 86 babies aged 3 months (boys 52.3%, girls 47.7%), and 86 babies aged 4 months (52.3% boys, 47.7% girls). P5-P95 and P3-P97 of the complete blood count, reticulocyte count, Ret-He, immature reticulocyte frac- tion, and reticulocyte production index for healthy babies aged 1–4 months can be seen in Tables 1 and 2.h The P5-P95 reference range of healthy babies for hemoglobin (Hb) aged 1 month, 2 months, 3 months, and 4 months was 9.95 to 15.45 g/dL, 9.74 to 13.42 g/dL, 9.51 to 12.40 g/dL, and 10.04 to 13.10 g/dL respectively. The P3-P97 reference range of healthy babies for Hb aged 1 month, 2 months, 3 months, and 4 months was 9.60 to 15.90 g/dL, 9.46 to 13.97 g/dL, 9.26 to 12.82 g/dL, and 10.00 to 13.33 g/dL respectively. www.nature.com/scientificreports/ addition, to monitor oral iron therapy, these combining parameters can be used too. For example, a lower value than the lower limit of the Hb reference range according to age indicates a baby is anemic. addition, to monitor oral iron therapy, these combining parameters can be used too. For example, a lower value than the lower limit of the Hb reference range according to age indicates a baby is anemic. On the other hand, other erythrocyte indices reference ranges are needed to diagnose anemia, especially suspected IDA. The main problem is determining if a baby has IDA with a simple, cheap, and fast laboratory test; a small amount of blood is drawn and can be done in almost any health facility. It is even better if the ID can be detected before IDA occurs. Conventionally, ID diagnosis is based on determining biochemical parameters, such as ferritin, transferrin saturation, and soluble transferrin receptor. Nevertheless, these biomarkers are strongly influenced by the diurnal phase, inflammation, infection, and malignancy, and of course, they are expensive, and not every health facility can check them. In addition, many studies have shown that Ret-He can show iron deficiency without ­anemia5–7. Therefore, a lower value than the lower limit of the Ret-He reference range according to age indicates that an infant is iron deficient.h i The clinical utility of IRF applied in various circumstances, such as monitoring anemia treatment and neonatal transfusion needs, can be a prognostic factor in prematurity anemia and diagnosing and monitoring aplastic anemias. Furthermore, RPI monitors bone marrow response to iron-treated ­anemia8. In addition, RPI can be used as a diagnostic guide to the etiology of ­anemia9. Uniquely, all erythrocyte indices and reticulocyte parameters can be seen automatically on the Sysmex XN-450 Hematology Analyzer (Sysmex Corporation, Japan).h The purpose of this study was to obtain the lower limit of the baby’s hemoglobin value related to the age so that it can be used to declare an anemic baby or not. Moreover, establishing reference ranges of the CBC, Ret-He, IRF, and RPI helps diagnose a disease related to the changes in erythrocyte indices, white blood count, platelets, and reticulocytes, especially in healthy babies aged 1–4 months. Reference range of complete blood count, Ret‑He, immature reticulocyte fraction, reticulocyte production index in healthy babies aged 1–4 months OPEN t q Reference range data for complete blood count (CBC), reticulocyte hemoglobin content (Ret-He), immature reticulocyte fraction (IRF), and reticulocyte production index (RPI) for babies 1–4 months old are limited. Therefore, determination of the reference range of CBC, Ret He, IRF, and RPI in babies 1–4 months is essential to determine whether a baby is anemic or not. Combining several parameters, Hb (hemoglobin), MCV (mean corpuscular volume), MCH (mean corpuscular hemoglobin), RDW (red cell distribution with), reticulocyte count, Ret He, IRF, and RPI will undoubtedly make it easier to determine if a baby has ID before IDA occurs. In 1Division of Hematology‑Oncology, Department of Child Health, Faculty of Medicine, Lambung Mangkurat University – RSD Idaman Banjarbaru, Banjarbaru, South Kalimantan, Indonesia. 2Pediatric Resident, Department of Child Health, Faculty of Medicine, Lambung Mangkurat University- Ulin General Hospital, Banjarmasin, South Kalimantan, Indonesia. 3Division of Nenonatology, Department of Child Health, Faculty of Medicine, Lambung Mangkurat University- Ulin General Hospital, Banjarmasin, South Kalimantan, Indonesia. 4Faculty of Medicine, Reproductive Health-Maternal and Child Health-Family Planning, Lambung Mangkurat University, Banjarmasin, South Kalimantan, Indonesia. 5Division of Neurology, Department of Child Health, Faculty of Medicine, Lambung Mangkurat University- Ulin General Hospital, Banjarmasin, South Kalimantan, Indonesia. *email: parlinringoringo@ulm.ac.id | https://doi.org/10.1038/s41598-023-27579-3 Scientific Reports | (2023) 13:423 www.nature.com/scientificreports/ Discussion P5-P95 of the white blood count, red blood cell count, hemoglobin, hematocrit, mean corpuscular volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, platelet, red cell distribution with standard deviation, red cell distribution with coefficient of variation, platelet distribution with, mean platelets volume, plateletcrit, neutrophils, lymphocyte, monocyte, eosinophils, eosinophils absolute, basophils, basophils absolute, reticulocyte count, Ret-He, immature reticulocyte fraction, reticulocyte production index, immature platelet fraction, and immature granulocyte for healthy babies aged 1–4 months. The results of this study for reference range of other erythrocyte indices, leukocyte, diff count, and platelets can be considered a guide in diagnosing a disease relating to the changes in erythrocyte indices, white blood count, platelets, especially in babies.l The results of this study for reference range of other erythrocyte indices, leukocyte, diff count, and platelets can be considered a guide in diagnosing a disease relating to the changes in erythrocyte indices, white blood count, platelets, especially in babies.l p p y Immature reticulocyte fraction indicates the younger fraction of reticulocytes, reflecting erythropoietic activ- ity. Several studies have demonstrated the clinical utility of IRF. For example, an increase in IRF within a few days indicates recovery of bone marrow following bone marrow transplantation, erythropoiesis-stimulating agent therapy, or ­chemotherapy17–19. Molina et al. consider an IRF value greater than 10% to indicate early marrow ­recovery20. Chang et al. stated that increased IRF (IRF ≥ 0.23) and increased absolute reticulocyte count (ARC) generally indicated an adequate erythroid response to anemia. Meanwhile, an IRF of 0.23 or less in patients with anemia reflects bone marrow that is nonresponsive or under-responsive to the ­anemia21. Immature reticulocyte fraction may be the first sign of hematologic recovery. It is a powerful indicator of post-chemotherapy aplasia in children with cancer, serving as an additional parameter of impaired bone marrow ­function22. A low total count with a relatively high IRF indicates a regenerating marrow, whereas reticulocytopenia with low IRF is typical of severe aplastic anemia or renal failure. A high total count with high IRF occurs in acute hemolysis and blood loss. In contrast, a low to average total count with a high IRF occurs in dyserythropoietic and during the early response to haematinics. It may also help decide whether macrocytic anemia is megaloblastic or ­nonmegaloblastic23. Mullier et al. Discussion CBC 1 Month (N = 89) 2 Months (N = 87) 3 Months (N = 86) 4 Months (N = 86) WBC (10ˆ3/uL) 6.24–12.76 5.73–12.84 6.88–13.66 6.06–14.32 RBC (10ˆ6/uL) 3.03–4.89 3.21–4.55 3.38–4.70 3.71–5.09 HGB (g/dL) 9.95 – 15.45 9.74–13.42 9.51–12.40 10.04–13.10 HCT (%) 28.20–43.95 28.00–38.14 28.14–35.80 29.14–38.36 MCV (fL) 86.35–101.85 78.54–95.42 71.91–88.33 70.25–84.85 MCH (pg) 29.75–35.20 27.48–32.72 24.70–30.27 23.64–28.97 MCHC (g/dL) 32.25–36.90 32.78–37.00 32.84–36.27 32.07–35.50 PLT (10ˆ3/ul) 0.13–0.57 0.07–0.63 0.10 – 0.62 0.16–0.59 RDW SD (fL) 43.25–64.50 35.54–52.36 33.00–44.94 30.90–39.69 RDW CV (%) 13.05–18.30 11.94–15.54 11.54–14.93 11.50–13.96 PDW(fL) 9.50–16.97 8.43–19.12 8.62–15.94 9.23–16.42 MPV(fL) 9.30–12.47 8.90–12.67 8.80–12.06 9.09–12.31 PCT (%) 0.19–0.60 0.16–0.63 0.29–0.62 0.19–0.60 Neutrophils (Gpt/L) 0.81–3.55 0.77–4.62 1.07–3.95 0.85–4.54 Lymphocyte (Gpt/L) 3.80–7.68 3.88–8.48 4.33–9.50 4.13–10.16 Monocyte Gpt/L) 0.61–1.86 0.41–1.37 0.42–1.42 0.33–1.19 Eosinophils (Gpt/L) 0.22–1.31 0.14–0.79 0.14–1.11 0.16–1.26 Eosinophils absolut (Gpt/L) 1.45–13.64 0.93–8.96 1.13–13.05 1.12–17.47 Basophils (Gpt/L) 0.02–0.13 0.01–0.11 0.02–0.16 0.01–0.15 Basophils absolut (Gpt/L) 0.15–1.34 0.10–1.05 0.14–1.73 0.09–1.82 Reticulocyte (Tpt/L) 5.95–22.35 4.38–21.64 3.00–16.91 2.94–12.87 Reticulocyte (%) 0.47–2.06 0.92–3.11 0.63–2.90 0.56–1.78 Ret_He (pg) 21.95–28.30 20.74–26.60 17.96–29.70 19.22–29.70 IRF(%) 5.95–22.35 4.38–21.64 3.00–16.91 2.94–12.87 RPI 0.30–1.10 0.34–1.42 0.24–1.30 0.20–0.90 IPF (%) 0.60–15.80 0.54–16.58 0.60–12.56 0.74–13.20 IG (Gpt/L) 0.01–0.12 0.00–0.09 0.00–0.04 0.00–0.03 CBC 1 Month (N = 89) 2 Months (N = 87) 3 Months (N = 86) 4 Months (N = 86) WBC (10ˆ3/uL) 6.24–12.76 5.73–12.84 6.88–13.66 6.06–14.32 RBC (10ˆ6/uL) 3.03–4.89 3.21–4.55 3.38–4.70 3.71–5.09 HGB (g/dL) 9.95 – 15.45 9.74–13.42 9.51–12.40 10.04–13.10 HCT (%) 28.20–43.95 28.00–38.14 28.14–35.80 29.14–38.36 MCV (fL) 86.35–101.85 78.54–95.42 71.91–88.33 70.25–84.85 MCH (pg) 29.75–35.20 27.48–32.72 24.70–30.27 23.64–28.97 MCHC (g/dL) 32.25–36.90 32.78–37.00 32.84–36.27 32.07–35.50 PLT (10ˆ3/ul) 0.13–0.57 0.07–0.63 0.10 – 0.62 0.16–0.59 RDW SD (fL) 43.25–64.50 35.54–52.36 33.00–44.94 30.90–39.69 RDW CV (%) 13.05–18.30 11.94–15.54 11.54–14.93 11.50–13.96 PDW(fL) 9.50–16.97 8.43–19.12 8.62–15.94 9.23–16.42 MPV(fL) 9.30–12.47 8.90–12.67 8.80–12.06 9.09–12.31 PCT (%) 0.19–0.60 0.16–0.63 0.29–0.62 0.19–0.60 Neutrophils (Gpt/L) 0.81–3.55 0.77–4.62 1.07–3.95 0.85–4.54 Lymphocyte (Gpt/L) 3.80–7.68 3.88–8.48 4.33–9.50 4.13–10.16 Monocyte Gpt/L) 0.61–1.86 0.41–1.37 0.42–1.42 0.33–1.19 Eosinophils (Gpt/L) 0.22–1.31 0.14–0.79 0.14–1.11 0.16–1.26 Eosinophils absolut (Gpt/L) 1.45–13.64 0.93–8.96 1.13–13.05 1.12–17.47 Basophils (Gpt/L) 0.02–0.13 0.01–0.11 0.02–0.16 0.01–0.15 Basophils absolut (Gpt/L) 0.15–1.34 0.10–1.05 0.14–1.73 0.09–1.82 Reticulocyte (Tpt/L) 5.95–22.35 4.38–21.64 3.00–16.91 2.94–12.87 Reticulocyte (%) 0.47–2.06 0.92–3.11 0.63–2.90 0.56–1.78 Ret_He (pg) 21.95–28.30 20.74–26.60 17.96–29.70 19.22–29.70 IRF(%) 5.95–22.35 4.38–21.64 3.00–16.91 2.94–12.87 RPI 0.30–1.10 0.34–1.42 0.24–1.30 0.20–0.90 IPF (%) 0.60–15.80 0.54–16.58 0.60–12.56 0.74–13.20 IG (Gpt/L) 0.01–0.12 0.00–0.09 0.00–0.04 0.00–0.03 Table 1. Discussion This means that the age of 0–6 months, especially 0–2 months, is critical for a baby to suffer from an iron deficiency with or without anemia. Nevertheless, the impact will also affect the incidence of iron deficiency at a later age. Li et al. showed that of 1,127 6-months-old infants in Beijing, the prevalence of anemia was ~ 11.8%12. Chen et al. showed that from 509 infants aged 1–12 months, The prevalence of ID and IDA were 3.7 and 2.7%, respectively, in babies under 6 months of age, but increased to 20.4 and 6.6%, respectively, in babies above 6 months of ­age13. Salah et al. show that from 654 infants aged 9–12 months, the prevalence of anemia and IDA was 34.6 and 32.6%, ­respectively14. Nazari et al. found that the prevalence of ID and IDA in children under six years of age was 27.7 and 18.2%, respectively. Considering the high prevalence of ID and IDA in infancy, especially at 0–6 months, iron supplementation in the form of elemental iron at a dose of 1 mg/kg/day should be given to all babies born at term from ­birth15. Another study showed that Daily iron supplementation from early life 36 h at a dose of 2 mg/kg is efficacious for improving iron status and motor development at 6 months in babies at ­risk16. https://doi.org/10.1038/s41598-023-27579-3 Scientific Reports | (2023) 13:423 | www.nature.com/scientificreports/ Table 1. P5-P95 of the white blood count, red blood cell count, hemoglobin, hematocrit, mean corpuscular volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, platelet, red cell distribution with standard deviation, red cell distribution with coefficient of variation, platelet distribution with, mean platelets volume, plateletcrit, neutrophils, lymphocyte, monocyte, eosinophils, eosinophils absolute, basophils, basophils absolute, reticulocyte count, Ret-He, immature reticulocyte fraction, reticulocyte production index, immature platelet fraction, and immature granulocyte for healthy babies aged 1–4 months. Discussion P3-P97 of the white blood count, red blood cell count, hemoglobin, hematocrit, mean corpuscular volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, platelet, red cell distribution with standard deviation, red cell distribution with coefficient of variation, platelet distribution with, mean platelets volume, plateletcrit, neutrophils, lymphocyte, monocyte, eosinophils, eosinophils absolute, basophils, basophils absolute, reticulocyte count, Ret-He, immature reticulocyte fraction, reticulocyte production index, immature platelet fraction, and immature granulocyte for healthy babies aged 1–4 months. different pediatric ages, especially in babies. Therefore, the reference value of the RPI range in this study can be considered to assess the responsiveness of the anemia therapy given. However, according to Bracho et al., the RPI is an inadequate tool for evaluating the bone marrow response in the presence of anemia due to differences in hematologic values between children and adults. In addition, the absence of information on the maturation time of reticulocytes in ­children25.h y The power of this study is that it parades all reference ranges of CBC, Ret He, IRF, and RPI at P3-P97 and P5-P95 for healthy babies aged 1–4 months. The weakness of this study is that the altitude above sea level, race, genetics, ethnicity, and population of this study is different from other areas. Hence, it certainly affects the refer- ence range of CBC and reticulocyte parameters. In this study, 96.5% reside at altitudes less than 100 m. Again, however, race, genetics, and ethnicity differed from other countries. Therefore, this reference range for CBC and reticulocyte parameters in healthy babies aged 9–11 months can be used in countries with demographic, socioeconomic, and population structures, such as Southeast Asia, especially Indonesia. Table 2.   P3-P97 of the white blood count, red blood cell count, hemoglobin, hematocrit, mean corpuscular volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, platelet, red cell distribution with standard deviation, red cell distribution with coefficient of variation, platelet distribution with, mean platelets volume, plateletcrit, neutrophils, lymphocyte, monocyte, eosinophils, eosinophils absolute, basophils, basophils absolute, reticulocyte count, Ret-He, immature reticulocyte fraction, reticulocyte production index, immature platelet fraction, and immature granulocyte for healthy babies aged 1–4 months. Discussion showed that IRF, combined with reticulocyte count, may be helpful in hereditary spherocytosis (HS) diagnosis as a high reticulocyte count characterizes HS without an equally elevated IRF. Therefore, a reticulocytes/IRF ratio higher than 7.7 is a precondition for screening HS ­cases24. The IRF increases earlier than the reticulocyte number. It helps monitor the efficacy of therapy in nutritional anemias such as megaloblastic or IDA. Therefore, the reference value of the IRF range in this study can be considered to assess the responsiveness of the anemia therapy given.hl y g The reticulocyte count reflects the erythropoietic activity of bone marrow. In addition, it is valuable in diag- nosing anemias and monitoring bone marrow response to therapy. RPI is currently used in pediatrics to assess bone marrow responsiveness to anemia therapy given. However, considering that “conventional” RPI was devel- oped from a study conducted in adults, it is necessary to have an RPI based on standard values adjusted for Scientific Reports | (2023) 13:423 | https://doi.org/10.1038/s41598-023-27579-3 www.nature.com/scientificreports/ CBC 1 Month (N = 89) 2 Months (N = 87) 3 Months (N = 86) 4 Months (N = 86) WBC (10ˆ3/uL) 5.88–13.43 5.46–13.85 6.55–16.14 5.86–15.16 RBC (10ˆ6/uL) 2.92–5.09 3.08–4.62 3.08–4.78 3.54–5.15 HGB (g/dL) 9.60–15.90 9.46–13.97 9.26–12.82 10.00–13.33 HCT (%) 27.13–48.32 26.95–39.71 27.57–36.69 28.62–39.04 MCV (fL) 84.28–103.63 77.73–96.82 70.35–90.94 65.25–86.62 MCH (pg) 29.17–35.65 26.86–33.02 24.03–30.99 22.48–29.10 MCHC (g/dL) 31.67–37.29 32.49–37.50 32.02–36.38 31.92–36.04 PLT (10ˆ3/ul) 0.09–0.64 0.05–0.65 0.10–0.66 0.15–0.61 RDW SD (fL) 42.44–67.15 35.12–55.56 32.56–48.59 30.70–40.60 RDW CV (%) 12.97–18.96 11.60–16.10 11.20–17.35 11.42–14.41 PDW(fL) 8.82–17.84 8.20–22.81 8.45–16.10 8.93–17.50 MPV(fL) 8.90–12.58 8.70–13.20 8.70–12.50 8.77–12.64 PCT (%) 0.16–0.67 0.15–0.66 0.12–0.65 0.18–0.65 Neutrophils (Gpt/L) 0.74–4.08 0.66–5.34 1.00–4.97 0.77–5.08 Lymphocyte (Gpt/L) 3.30–8.12 3.46–8.95 4.11–10.42 3.48–10.73 Monocyte Gpt/L) 0.60–2.06 0.35–1.43 0.41–1.50 0.31–1.41 Eosinophils (Gpt/L) 0.19–1.50 0.12–0.84 0.11–1.17 0.15–2.17 Eosinophils absolut (Gpt/L) 1.00–14.61 0.85–9.54 1.03–15.00 0.78–27.34 Basophils (Gpt/L) 0.02–0.13 0.01–0.14 0.02–0.23 0.01–0.17 Basophils absolut (Gpt/L) 0.14–1.48 0.05–1.16 0.12–3.02 0.07–2.35 Reticulocyte (Tpt/L) 5.61–25.58 3.70–23.12 2.67–25.66 2.33–13.38 Reticulocyte (%) 0.38–2.53 0.58–3.49 0.57–3.32 0.52–1.98 Ret_He (pg) 21.74–28.56 19.85–27.24 16.78–30.24 17.40–30.22 IRF(%) 5.61–25.58 3.70–23.12 2.67–25.66 2.33–13.38 RPI 0.20–1.48 0.26–1.60 0.20–1.40 0.20–1.00 IPF (%) 0.57–18.48 0.50–20.79 0.50–17.04 0.70–14.38 IG ( Gpt/L ) 0.01–0.14 0.00–0.14 0.00–0.04 0.00–0.03 Table 2. Material and methodsh Study population. The study design was a cross-sectional study with descriptive analysis of CBC and retic- ulocyte in babies aged 1–4 months. The study was conducted at 10 Community Health Centers in Banjarbaru, South Kalimantan, from August 2020 to August 2021. Inclusion criteria are babies born at term (gestational age 37–42 weeks) with birth weight ≥ 2500 g, babies are not twins, not taking a hematinic drug, and normal nutri- tional status. Exclusion criteria were hematological diseases and congenital anomalies. In addition, gestational age and birth weight had obtained from the mother’s medical record (Maternal and Child Health Book). The doctor in charge declared the baby healthy. At the time of recruitment, the baby’s weight, length, and head cir- cumference were measured by health personnel. Nutritional status is assessed based on body weight and length, divided into good nutrition and undernutrition. Good nutrition if the z-score is − 2 SD to + 3 SD in this study. In contrast, undernutrition if the z-score is < − 2 ­SD26. All of the baby’s parents had signed the informed con- sent. This study obtained ethical clearance from the Research Ethics Commission of the Medical Faculty of the https://doi.org/10.1038/s41598-023-27579-3 Scientific Reports | (2023) 13:423 | www.nature.com/scientificreports/ University of Lambung Mangkurat No. 272/KEPK-FK ULM/EC/VIII/2020. All methods have been performed under the relevant guidelines and regulations of the Declaration of Helsinki. Blood sampling. Every baby who meets the inclusion and exclusion criteria will be taken a blood sample of 1 ml from the median cubital vein. First, the blood sample was put in a tube with EDTA anticoagulant, homog- enized by turning it over, and stored in a storage box. Then the blood sample was sent to the Banjarbaru Idaman Hospital Laboratory. The Sysmex XN-450 Hematology Analyzer (Sysmex Corporation, Japan) was doing com- plete blood count and reticulocyte examinations. Statistical analysis. All baby anthropometry measurements were analyzed by SPSS ver.25 for P3-P97 and P5-P95. Moreover, the CBC and reticulocyte laboratory findings were analyzed by SPSS ver.25 for P3-P97 and P5-P95. All data are presented in narrative and table. Reference range P3-P97 means that 94% of normal indi- viduals have normal laboratory results, while the other 6% may not be sick outside the normal limits. Reference range P5-P95 means that 90% of normal individuals have normal laboratory results, while 10% may not be sick outside the normal limits. Data availability Research data can be provided by the Corresponding Author if needed. Received: 16 February 2022; Accepted: 4 January 2023 Received: 16 February 2022; Accepted: 4 January 2023 References 1. Gardner, W. & Kassebaum, N. Global, regional, and national prevalence of anemia and its causes in 204 countries and territories, 1990–2019. Curr. Dev. Nutr. 4, 830 (2020).i 1. Gardner, W. & Kassebaum, N. Global, regional, and national prevalence of anemia and its causes in 204 countries and territories, 1990–2019. Curr. Dev. Nutr. 4, 830 (2020).i 2. East, P. et al. Iron deficiency in infancy and neurocognitive and educational outcomes in young adulthood. Dev. Psychol. 57 962–975 (2021).ii 3. Lukowski, A. F. et al. Iron deficiency in infancy and neurocognitive functioning at 19 years: Evidence of long-term deficits in executive function and recognition memory. Nutr. Neurosci. 13, 54–70 (2010).i 3. Lukowski, A. F. et al. Iron deficiency in infancy and neurocognitive functioning at 19 years: Evidence of long-term deficits in executive function and recognition memory. Nutr. Neurosci. 13, 54–70 (2010).i 4. McCarthy, E. K. et al. Behavioral consequences at 5 y of neonatal iron deficiency in a low-risk maternal–infant cohort. Am. J. Clin Nutr. 113, 1032–1041 (2021).f 4. McCarthy, E. K. et al. Behavioral consequences at 5 y of neonatal iron deficiency in a low-risk maternal–infant cohort. Am. J. Clin. Nutr. 113, 1032–1041 (2021).f 5. Ennis, K. M., Dahl, L. V., Rao, R. B. & Georgieff, M. K. Reticulocyte hemoglobin content as an early predictive biomarker of brain iron deficiency. Pediatr. Res. 84, 765–769 (2018).i i y ( ) 6. Pomrop, M. et al. Reticulocyte hemoglobin concentration for screening iron deficiency in very low birth weight preterm neon l l d h //d / / ( ) i y 6. Pomrop, M. et al. Reticulocyte hemoglobin concentration for screening iron deficiency in very low birth weight preterm neonates. J Matern-Fetal Neonatal Med https://doi org/10 1080/14767058 2020 1818216 (2020) i 6. Pomrop, M. et al. Reticulocyte hemoglobin concentration for screening iron deficiency in very low birth weight preterm neonates. J. Matern-Fetal Neonatal Med. https://​doi.​org/​10.​1080/​14767​058.​2020.​18182​16 (2020). p, y g gi y y g p J. Matern-Fetal Neonatal Med. https://​doi.​org/​10.​1080/​14767​058.​2020.​18182​16 (2020).fii J. Matern-Fetal Neonatal Med. https://​doi.​org/​10.​1080/​14767​05 7. Düzenli Kar, Y. & Altınkaynak, K. Reticulocyte hemoglobin equivalent in differential diagnosis of iron deficiency, iron defic anemia and β thalassemia trait in children. Turk. J. Biochem. 46, 45–51 (2021). 8. Adane, T. & Asrie, F. G. Z. Clinical utility of immature reticulocyte fraction. J. Clin. Chem. Lab. Med. 4, 172 (2021). 9. Riley, R. S., Ben-Ezra, J. M., Goel, R. & Tidwell, A. References Reticulocytes and reticulocyte enumeration. J. Clin. Lab. Anal. 15, (2001). ( ) 10. WHO. Child growth standards. https://​www.​who.​int/​tools/​child-​growth-​stand​ards/​stand​ards.hi 1. Beutler, E. W. J. The definition of anemia: What is the lower limit of normal of the blood hemoglobin concentration?. Blood 107 1747–1750 (2006). 12. Li, Q., Liang, F., Liang, W., Shi, W. & Han, Y. Prevalence of anemia and its associated risk factors among 6-months-old infants in Beijing. Front. Pediatr. https://​doi.​org/​10.​3389/​fped.​2019.​00286 (2019).i j g p g p 13. Chen, C.-M. et al. Iron status of infants in the first year of life in northern Taiwan. Nutrients 12, 139 (2020).hi i y 14. Salah, R. W., Hasab, A. A. H., El-Nimr, N. A. & Tayel, D. I. The prevalence and predictors of iron deficiency anemia among rur infants in nablus governorate. J. Res. Health Sci. 18, e00417 (2018). g 15. Ringoringo, H. P. Disertasi. Pendekatan diagnostik status besi bayi berusia 0 bulan sampai 6 bulan di Banjarbaru: saat terbaik pemberian suplementasi zat besi (Universitas Indonesia, 2008).f pemberian suplementasi zat besi (Universitas Indonesia, 2008f 16. Bora, R., Ramasamy, S., Brown, B., Wolfson, J. & Rao, R. Effect of iron supplementation from neonatal period on the iron status of6-month-old infants at-risk for early iron deficiency: A randomized interventional trial. J. Matern. Fetal Neonatal Med. 34, 1421–1429 (2021).ht ( ) 7. d’Onofrio, G., Tichelli, A., Foures, C. & Theodorsen, L. Indicators of haematopoietic recovery after bone marrow transplantation The role of reticulocyte measurements. Clin. Lab. Haematol. 18(Suppl 1), 45–53 (1996).l h y pp 18. Testa, U. et al. Autologous stem cell transplantation: evaluation of erythropoietic reconstitution by highly fluorescent reticulocyte counts, erythropoietin, soluble transferrin receptors, ferritin, TIBC and iron dosages. Br. J. Haematol. 96, 762–775 (1997).t 9. Noronha, J. F. A. et al. Immature reticulocytes as an early predictor of engraftment in autologous and allogeneic bone marrow transplantation. Clin. Lab. Haematol. 25, 47–54 (2003).tt p 0. Molina, J. R. et al. Reticulocyte maturation parameters are reliable early predictors of hematopoietic engraftment after allogeneic stem cell transplantation. Biol. Blood Marrow Transplant. 13, 172–182 (2007).i p p 21. Chang, C.-C. & Kass, L. Clinical significance of immature reticulocyte fraction determined by automated reticulocyte counting. Am. J. Clin. Pathol. 108, 69–73 (1997). ( ) 22. Luczyński, W., Ratomski, K., Wysocka, J., Krawczuk-Rybak, M. & Jankiewicz, P. Immature reticulocyte fraction (IRF)–an universal marker of hemopoiesis in children with cancer?. Adv. Med. Sci. 51, 188–190 (2006).f p 23. Acknowledgements Th h h k g The authors thank Estiani for helping input the research data to SPSS ver.25. The authors did not receive any funds or grants. Author contributions H.P.R. makes Study Design, Data Collection, Statistical Analysis, Data Interpretation, Manuscript Preparation. L.P. makes Study Design, Data Collection, Statistical Analysis, Data Interpretation, Manuscript Preparation. A.Y. makes Study Design, Data Interpretation, Manuscript Preparation MS makes Study Design, Statistical Analy- sis, Data Interpretation, Manuscript Preparation. N.H. makes Study Design, Data Interpretation, Manuscript Preparation. H.P.R. prepared Supplementary Tables 1–7. H.P.R. and L.P. wrote the main manuscript text. All authors reviewed the manuscript. References Bain, B. J., Bates, I. & Laffan, M. A. Dacie and Lewis Practical Haematology (Elsevier Ltd, 2017). 24. Mullier, F. et al. Additional erythrocytic and reticulocytic parameters helpful for diagnosis of hereditary spherocytosis: Results of a multicentre study. Ann. Hematol. 90, 759–768 (2011). a multicentre study. Ann. Hematol. 90, 759–768 (2011). y 5. Bracho, F. J. & Osorio, I. A. Evaluation of the reticulocyte production index in the pediatric population. Am. J. Clin. Pathol. 154 70–77 (2020). 26. Ariati, N. N., Wiardani, N. K., Kusumajaya, A. A. N., Supariasa, I. D. N. & Sidiartha, L. Buku saku antropometri gizi Anak PAUD [Internet] (Inteligensia Media (Kelompok Penerbit Intrans Publishing), 2020). Scientific Reports | (2023) 13:423 | https://doi.org/10.1038/s41598-023-27579-3 www.nature.com/scientificreports/ Competing interests h p g The authors declare no competing interests. © The Author(s) 2023 Additional informationh Supplementary Information The online version contains supplementary material available at https://​doi.​org/​ 10.​1038/​s41598-​023-​27579-3. Correspondence and requests for materials should be addressed to H.P.R. 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) 2023 https://doi.org/10.1038/s41598-023-27579-3 Scientific Reports | (2023) 13:423 |
https://openalex.org/W2134872935
https://centaur.reading.ac.uk/15707/1/2010_Dunwell_et_al_Palm.pdf
English
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Production of haploids and doubled haploids in oil palm
BMC plant biology
2,010
cc-by
15,641
Production of haploids and doubled haploids in oil palm Published Version Dunwell, J. M. ORCID: https://orcid.org/0000-0003-2147-665X, Wilkinson, M. J., Nelson, S., Wening, S., Sitorus, A. C., Mienanti, D., Alfiko, Y., Croxford, A. E., Ford, C. S., Forster, B. P. and Caligari, P. D. S. (2010) Production of haploids and doubled haploids in oil palm. BMC Plant Biology, 10. 218. ISSN 1471-2229 doi: https://doi.org/10.1186/1471-2229-10- 218 Available at https://centaur.reading.ac.uk/15707/ It is advisable to refer to the publisher’s version if you intend to cite from the work. See Guidance on citing . To link to this article DOI: http://dx.doi.org/10.1186/1471-2229-10-218 Publisher: BioMed Central All outputs in CentAUR are protected by Intellectual Property Rights law, including copyright law. Copyright and IPR is retained by the creators or other copyright holders. Terms and conditions for use of this material are defined in the End User Agreement . www.reading.ac.uk/centaur * Correspondence: j.m.dunwell@reading.ac.uk; jjw@aber.ac.uk † Contributed equally 1School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK 2Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK Full list of author information is available at the end of the article Abstract Background: Oil palm is the world’s most productive oil-food crop despite yielding well below its theoretical maximum. This maximum could be approached with the introduction of elite F1 varieties. The development of such elite lines has thus far been prevented by difficulties in generating homozygous parental types for F1 generation. Results: Here we present the first high-throughput screen to identify spontaneously-formed haploid (H) and doubled haploid (DH) palms. We secured over 1,000 Hs and one DH from genetically diverse material and derived further DH/mixoploid palms from Hs using colchicine. We demonstrated viability of pollen from H plants and expect to generate 100% homogeneous F1 seed from intercrosses between DH/mixoploids once they develop female inflorescences. Conclusions: This study has generated genetically diverse H/DH palms from which parental clones can be selected in sufficient numbers to enable the commercial-scale breeding of F1 varieties. The anticipated step increase in productivity may help to relieve pressure to extend palm cultivation, and limit further expansion into biodiverse rainforest. Desire for a more generic H/DH production system to improve agricultural yields is increasing as population growth, climate change, biofuel demand and other land- use pressures intensify. Clearly, in any species the production of F1 varieties depends not only on the pro- duction of homozygous lines to act as parents, but also it requires an efficient method to intercross the parents. This latter procedure is relatively simple in species with an outcrossing breeding system, like maize or oil palm, compared with those with an inbreeding system like rice or wheat. Production of F1 hybrids has been achieved successfully in this category of crops (for example hybrid rice in China) but often requires a male sterility system. Production of haploids and doubled haploids in oil palm Jim M Dunwell1*†, Mike J Wilkinson2*†, Stephen Nelson3, Sri Wening4, Andrew C Sitorus4, Devi Mienanti4, Yuzer Alfiko4, Adam E Croxford2, Caroline S Ford2, Brian P Forster5, Peter DS Caligari3,5,6 © 2010 Dunwell 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. Central Archive at the University of Reading Reading’s research outputs online Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Dunwell et al. BMC Plant Biology 2010, 10:218 Open Access Background Success of early F1 hybrid maize varieties exemplifies the advantages of heterosis [1]. The use of doubled haploids as parents for F1 variety production fully exploits this phenomenon and has enabled substantial yield improve- ments in several crops [2,3]. This strategy was outlined with the first DH crop variety [4] and has led to H/DH production systems being described for >250 species [5]. However, few of these protocols generate the large num- bers of Hs/DHs needed for commercial breeding, with just three methods (androgenesis, wide crossing, gyno- genesis [6]) routinely adopted for H/DH production in only 30 species [5]. The most important of these meth- ods in widespread use in commercial breeding is the generation of haploids in maize via pollination with a haploid inducing line such as a ‘Stock 6’ derivative. Annually, oil palm (Elaeis guineensis) yields eight to ten times more oil per hectare than rapeseed or soybean [7,8] and in 2008 generated 38.9 million tonnes of oil worldwide [9]. The area assigned to the crop expanded ~1.7 fold between 1997 (8.7 M ha) and 2007 (14.6 M ha) [9] with further increases forecast. Over this same period global production of palm oil increased ~2.2 fold from 18 to 38.9 Mt y-1. Thus, yield increases have been Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 2 of 25 characteristics of H/DH (slow growth, altered flowering phenology, smaller stomata and smaller organs [5]) could be used for diagnosis but are difficult to score qualitatively on a large scale and require plants of a rea- sonable size. An alternative strategy is to seek undefined atypical phenotypic features that may arise from reduced cell size and/or the hemizygous state of haploid indivi- duals (homozygous for DHs) and that are manifest at the seedling stage when high-throughput visual assess- ment is more plausible. A more directed approach is also possible. Spontaneous H/DH seedlings are often associated with aberrant germination features, such as twin embryos from the same carpel [20], providing a defined feature for phenotypic selection. Here, we com- bined a large-scale visual survey for undefined atypical palm seedling phenotypes coupled with active selection for seeds with twin embryos to assemble a sub-popula- tion of seedlings enriched for H/DHs. achieved predominantly by expansion of cultivated area and not through yield enhancement. Background This trend raises concerns over the ecological impact of felling rainforest to accommodate oil palm cultivation [10,11] and has sti- mulated debate over strategies to limit further agricul- tural expansion [12-14]. One option explored here is to use market forces to help address the problem. If F1 varieties could increase yields sufficiently to exceed demand, commodity prices would fall. This would dis- courage clear felling and simultaneously incentivise early replacement of existing plantations with high-yielding varieties. Feasibility of the approach clearly relies on the ability to gain marked improvements in yield. Current yields of oil palm (generally 4-10.5 t ha-1) [15,16] are much lower than the most conservative estimates of the crop’s potential (17 t ha-1 [14] to 60 t ha-1 [16]). Indeed, yields per hectare in the two largest producer countries (Indonesia and Malaysia) have remained static for 30 years [9]. It should be noted, however, that in both these countries there are examples of selected varieties with much higher yields, with the highest yields from commercial breeding trials already exceeding 10 t ha-1. Results markers used Ploidy 50-Mix5-7 11260406301 9 x 50-03060367C 07280501801 15 x 50-03060260C-2 07280501901 15 x 53-03080954C-2 09270500101 10 x 53-03090761C-5 09280504501 10 x BATCH 51;03060318C;1 060728_0010_01_a 15 x BATCH 53;03090761C;5 060728_0018_01_a 15 x 0623/172;05095508C;1 060728_0021_01_a 15 x BATCH 50;03060260C;2 060728_0027_01_a 15 x 0611/32;05050248C;1 060728_0032_01_a 15 x 0611/16;05050228C;1 060728_0034_01_a 15 x BATCH 53;03080954C;2 060728_0035_01_a 15 x 06 412;04059061B;3 060728_0050_01_a 14 2x 0628/152;05100720C;1 060729_0021_01_a 15 x 0628/185;05100351C;1 060729_0063_01_a 15 x BATCH 51;03060626C;1 060729_0127_02_a 15 x BATCH 67;0409034MC;2 060729_0130_02_a 14 2x BATCH 67;0409034MC;4 060729_0131_02_a 15 2x BATCH 67;0409034MC;15 060729_0132_02_a 15 2x BATCH 65;0409034MC;7 060729_0134_02_a 15 2x BATCH 65;0409034MC;35 060729_0138_02_a 15 2x BATCH 65;0409034MC;56 060729_0139_02_a 15 2x BATCH 65;0409034MC;50 060729_0141_02_a 15 2x BATCH 65;0409034MC;47 060729_0142_02_a 15 2x 0628/53;05090595C;1 060731_0043_01_a 15 x 0627/125;05090717C;2 060731_0065_01_a 15 x 0627/12;05080220C;1 060731_0080_01_a 15 x 0627/6;05080095C;1 060731_0086_01_a 14 x 0631/ Normal;05039033B;31 060731_0265_01_a 14 x 64-0409021MC-34 02130604301 15 2x 64-0410040MC-1 02130604801 15 2x 51-03060626C 02130605301 15 x 64-0410040MC-20 02140600401 15 2x 64-0410040MC-16 02140600801 15 2x 65-0409021MC-2 02140601001 15 2x 06 412B-04059061B-3 02170605501 15 2x 06 412B-04129091B 02170605801 15 2x 0550-15/05010827C 02200602401 15 x 0550-17/05010442C-1 02200602601 15 x 0550-23/05020059C 02200603101 15 x 0550-33/05020568C 02200603401 15 x 0550-36/05020420C-2 02200603701 15 x 0550-40/05010880C 02200607501 14 x had twin embryos. More than 2,000 of these seedlings (including all those with twin embryos) were trans- ferred to the nursery prior to further screening. Although Hs could be identified relatively easily on the basis of their reduced genome size, we initially wished to target the more difficult, but more valuable DHs to circumvent the need for chromosome doubling. For the second level screen, we exploited the fact that Hs and DHs would be either hemi- or homozygous across all loci; thus individuals exhibiting heterozygosity at any locus could be discarded. Applying this logic, we performed a sequential screen using 9-15 microsatellite markers (Table 1) on all individuals and found 117 seedlings that exhibited a single allele across all loci (Table 2). These individuals were retained as candidate H/DH, and subsequent flow cytometry of leaf samples identified 83 as H, and 34 as diploid (Table 2). The haploid status of six palms was further confirmed by cytological examination of intact cells from root squashes. Each contained the expected 16 chromo- somes (Figure 2). A larger-scale survey for heterozygosity was then per- formed using 97 additional microsatellites (Table 3) to confirm absolute hemizygosity of Hs and identify ‘false’ candidate DHs showing any heterozygosity. Results Over two years, we performed two large-scale screens for morphological ‘off-types’ among oil palm seedlings generated by the Bah Lias Research Station, Indonesia. The first screen utilised 10,900,000 seedlings from a wide range of crosses and identified 3,854 morphologi- cal ‘off-types’ (H/DH candidates), of which 53 had twin embryos and 3,801 were phenotypically abnormal (Fig- ure 1). The second screen of approximately 10,000,000 seedlings from commercial seed production activities and approximately 1,000,000 seedlings from breeding experiments generated 5,704 H/DH candidates, of which 5,601 were phenotypically abnormal and 103 To date, a H/DH-derived F1 breeding approach has been precluded by the repeated failure to secure H/DHs via anther or microspore culture [17] and successful generation of H/DHs in oil palm is unreported in the literature. The report of a spontaneous H in the related coconut palm [18] and in other species [19] nevertheless gave hope that spontaneous Hs may also occur in oil palm. However, the characteristically rare occurrence of spontaneous H/DHs necessitates development of an effective high-throughput screening system. Phenotypic Figure 1 Seed germination morphology for H/DH identification. a: normal; b: abnormal; c: twin embryo. Figure 1 Seed germination morphology for H/DH identification. a: normal; b: abnormal; c: twin embryo. Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 3 of 25 Table 2 Results of ploidy analysis by flow cytometry of 117 candidate H/DH palms identified as both morphologically atypical and homozygous for the markers listed in Table 1 Candidate DNA sample code No. Results markers used Ploidy 50-Mix5-7 11260406301 9 x 50-03060367C 07280501801 15 x 50-03060260C-2 07280501901 15 x 53-03080954C-2 09270500101 10 x 53-03090761C-5 09280504501 10 x BATCH 51;03060318C;1 060728_0010_01_a 15 x BATCH 53;03090761C;5 060728_0018_01_a 15 x 0623/172;05095508C;1 060728_0021_01_a 15 x BATCH 50;03060260C;2 060728_0027_01_a 15 x 0611/32;05050248C;1 060728_0032_01_a 15 x 0611/16;05050228C;1 060728_0034_01_a 15 x BATCH 53;03080954C;2 060728_0035_01_a 15 x 06 412;04059061B;3 060728_0050_01_a 14 2x 0628/152;05100720C;1 060729_0021_01_a 15 x 0628/185;05100351C;1 060729_0063_01_a 15 x BATCH 51;03060626C;1 060729_0127_02_a 15 x BATCH 67;0409034MC;2 060729_0130_02_a 14 2x BATCH 67;0409034MC;4 060729_0131_02_a 15 2x BATCH 67;0409034MC;15 060729_0132_02_a 15 2x BATCH 65;0409034MC;7 060729_0134_02_a 15 2x BATCH 65;0409034MC;35 060729_0138_02_a 15 2x BATCH 65;0409034MC;56 060729_0139_02_a 15 2x BATCH 65;0409034MC;50 060729_0141_02_a 15 2x BATCH 65;0409034MC;47 060729_0142_02_a 15 2x 0628/53;05090595C;1 060731_0043_01_a 15 x 0627/125;05090717C;2 060731_0065_01_a 15 x 0627/12;05080220C;1 060731_0080_01_a 15 x 0627/6;05080095C;1 060731_0086_01_a 14 x 0631/ Normal;05039033B;31 060731_0265_01_a 14 x 64-0409021MC-34 02130604301 15 2x 64-0410040MC-1 02130604801 15 2x 51-03060626C 02130605301 15 x 64-0410040MC-20 02140600401 15 2x 64-0410040MC-16 02140600801 15 2x 65-0409021MC-2 02140601001 15 2x 06 412B-04059061B-3 02170605501 15 2x 06 412B-04129091B 02170605801 15 2x 0550-15/05010827C 02200602401 15 x 0550-17/05010442C-1 02200602601 15 x 0550-23/05020059C 02200603101 15 x 0550-33/05020568C 02200603401 15 x 0550-36/05020420C-2 02200603701 15 x n 2,000 of these seedlings in embryos) were trans- r to further screening. ed relatively easily on the e size, we initially wished ut more valuable DHs to omosome doubling. For xploited the fact that Hs mi- or homozygous across ibiting heterozygosity at . Applying this logic, we using 9-15 microsatellite dividuals and found 117 ngle allele across all loci were retained as candidate cytometry of leaf samples s diploid (Table 2). The was further confirmed by intact cells from root he expected 16 chromo- erozygosity was then per- icrosatellites (Table 3) to y of Hs and identify ‘false’ eterozygosity. All Hs pro- les across all microsatel- d heterozygosity via locus ed. All diploids were het- d so discarded. However, 9582C) identified from a homozygous across all 36 airs used to identify s H candidates in the Reverse primer (5’-3’) TCAAAATTAAGAAAGTATGC CGCGTGAAAGATATGAATCAAC GGATGTATGCTTTACCTCCGAAT CTCCTTTTCCCCATCACAGA ATTCTGAAAGGAGGGGGAAA TGCCTCTGGTTGTTAGTCTGG T TGGCAATCAGCACACATTCT TGTGGTCTCCTGAGGAAGATG CCCCTTTTGCTTCCCTATTT CCAGAATCATCAGACTCGGACAG TTCAACATACCGTCTGTA GGCACCAAACACAGTAA AGAACCACCGGAGTTAC TTTTCTCCATAGTCCGTTAC TGGCTGGCTTCGGTCTTAG [27]. Table 2 Results of ploidy analysis by flow cytometry of 117 candidate H/DH palms identified as both morphologically atypical and homozygous for the markers listed in Table 1 Candidate DNA sample code No. Markers 10-15 obtained from Billotte et al. [27]. Results All Hs pro- duced single-allele peak profiles across all microsatel- lites, thereby discounting fixed heterozygosity via locus duplication for all markers used. All diploids were het- erozygous at several loci and so discarded. However, one diploid (0644-219/05049582C) identified from a later screen (see below) was homozygous across all 36 Table 1 Microsatellite primer pairs used to identify homozygous DH or hemizygous H candidates in the initial molecular screen No. Forward primer (5’-3’) Reverse primer (5’-3’) 1 GAGATTACAAAGTCCAAACC TCAAAATTAAGAAAGTATGC 2 ACGCATGCAGCTAGCTTTTC CGCGTGAAAGATATGAATCAAC 3 CACGCACGCAGTTTATTCTT GGATGTATGCTTTACCTCCGAAT 4 CCCCTTTTGCTTCCCTATTT CTCCTTTTCCCCATCACAGA 5 GACACAAGCAAAAACAAAAGCA ATTCTGAAAGGAGGGGGAAA 6 ATATGTGTGGGTGTGCGTGT TGCCTCTGGTTGTTAGTCTGG 7 TCTCTCTCTCTCTCTCTATGTGTGTGT TGGCAATCAGCACACATTCT 8 GCAGCTCTTTCCACACCTCT TGTGGTCTCCTGAGGAAGATG 9 TTTTCCCCATCACAGAATTG CCCCTTTTGCTTCCCTATTT 10 TAGCCGCACTCCCACGAAGC CCAGAATCATCAGACTCGGACAG 11 AGCTCTCATGCAAGTAAC TTCAACATACCGTCTGTA 12 CCTTCAAGCAAAGATACC GGCACCAAACACAGTAA 13 GTAGCTTGAACCTGAAA AGAACCACCGGAGTTAC 14 GCTCGTTTTTGTTTAGGTGA TTTTCTCCATAGTCCGTTAC 15 CCTCGGGTTATCCTTTTTACC TGGCTGGCTTCGGTCTTAG Markers 10-15 obtained from Billotte et al. [27]. Table 1 Microsatellite primer pairs used to identify homozygous DH or hemizygous H candidates in the initial molecular screen Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 4 of 25 Table 2: Results of ploidy analysis by flow cytometry of 117 candidate H/DH palms identified as both morpholo- gically atypical and homozygous for the markers listed in Table 1 (Continued) 0551-36/05020511C 02200607601 15 x 0551-32/05020361C-1 02210600401 15 x 0552-4/05010836C-2 02210600901 15 x 0552-38/05020501C 02210603101 14 x 0552-39/05020415C 02210603201 15 x 0552-31/05020858C 02210603701 15 x 0552-91/05020375C 02210603901 15 x 0552-111/05020626C 02210607201 15 x 0552-128/05020558C-1 02210607701 15 x 0601-35/05020946C 02210608201 15 x 0601-42/05030201C-6 02210609501 15 x 0601-51/05030224C-2 02220600201 15 x 0607-21/05040317C-3 02220601801 14 x 0606-32/05040240C 02220606201 13 x 0601-77/05020961C 02230600701 15 x 0601-62/05030147C 02230601401 15 x 0601-54/05030462C 02230601901 15 x 0551-21/05020271C-1 02200605801 14 x 0601-9/05020843C-2 02230603101 15 x 0602-17/05020631C-1 02230605501 15 x 0607-111/05040970C-1 03010600201 15 x 0607-81/05040578C-1 03010600501 15 x 0607-73/05040573C-1 03010605101 15 x 0607-89/05040748C-3 03010605501 15 x 0607-102/05050016C-2 03010606601 15 x 0608-15/05040519C-3 03010606901 15 x 0608-45/05041003C-1 03150603401 15 x 0610-60/05041024C-2 03150604401 15 x 0610-124/05055039C-1 03150604601 15 x 0609-54/05050089C-2 03150604701 15 x 0610-41/05050352C-1 03150606701 15 x 0609-58/05050255C-1 03220600201 15 x 0610-82/05050099C-2 03220601401 15 x 0610-77/05050353C-1 03220602701 15 x 0610-121/05055090C-1 03220603301 15 x 0610-81/05050099C-1 03220605901 15 x 0609-100/05055311C-1 03290600301 15 x 0610-11/05040938C-1 03290601101 15 x 0610-68/05050376C-3 03290602001 15 x 0610-58/05050344C-1 03290602201 15 x 0610-73/05050594C-3 03290603301 15 x 0611-84/05050714C-4 03290605001 15 x 0611-70/05050223C-1 03290606701 15 x 0611-73/05050351C-1 03290608001 15 x 0610-67/05050376C-2 04050600501 15 x 0610-40/05050102C-2 04050600901 15 x 0611-99/05050544C-1 04050602601 15 x 0611-110/05055011C-1 04050603601 15 x 0612-2/05050017C-1 04050609101 15 x mapped loci found to be heterozygous in the maternal parent (palm number BL013/12-06). Results Taking account of linkage between mapped markers, the probability of such an individual occurring by chance following selfing Figure 2 Chromosome spread of a haploid root cell from oil palm containing 16 C-metaphase chromosomes Table 2: Results of ploidy analysis by flow cytometry of 117 candidate H/DH palms identified as both morpholo- gically atypical and homozygous for the markers listed in Table 1 (Continued) 0551-36/05020511C 02200607601 15 x 0551-32/05020361C-1 02210600401 15 x 0552-4/05010836C-2 02210600901 15 x 0552-38/05020501C 02210603101 14 x 0552-39/05020415C 02210603201 15 x 0552-31/05020858C 02210603701 15 x 0552-91/05020375C 02210603901 15 x 0552-111/05020626C 02210607201 15 x 0552-128/05020558C-1 02210607701 15 x 0601-35/05020946C 02210608201 15 x 0601-42/05030201C-6 02210609501 15 x 0601-51/05030224C-2 02220600201 15 x 0607-21/05040317C-3 02220601801 14 x 0606-32/05040240C 02220606201 13 x 0601-77/05020961C 02230600701 15 x 0601-62/05030147C 02230601401 15 x 0601-54/05030462C 02230601901 15 x 0551-21/05020271C-1 02200605801 14 x 0601-9/05020843C-2 02230603101 15 x 0602-17/05020631C-1 02230605501 15 x 0607-111/05040970C-1 03010600201 15 x 0607-81/05040578C-1 03010600501 15 x 0607-73/05040573C-1 03010605101 15 x 0607-89/05040748C-3 03010605501 15 x 0607-102/05050016C-2 03010606601 15 x 0608-15/05040519C-3 03010606901 15 x 0608-45/05041003C-1 03150603401 15 x 0610-60/05041024C-2 03150604401 15 x 0610-124/05055039C-1 03150604601 15 x 0609-54/05050089C-2 03150604701 15 x 0610-41/05050352C-1 03150606701 15 x 0609-58/05050255C-1 03220600201 15 x 0610-82/05050099C-2 03220601401 15 x 0610-77/05050353C-1 03220602701 15 x 0610-121/05055090C-1 03220603301 15 x 0610-81/05050099C-1 03220605901 15 x 0609-100/05055311C-1 03290600301 15 x 0610-11/05040938C-1 03290601101 15 x 0610-68/05050376C-3 03290602001 15 x 0610-58/05050344C-1 03290602201 15 x 0610-73/05050594C-3 03290603301 15 x 0611-84/05050714C-4 03290605001 15 x 0611-70/05050223C-1 03290606701 15 x 0611-73/05050351C-1 03290608001 15 x 0610-67/05050376C-2 04050600501 15 x 0610-40/05050102C-2 04050600901 15 x 0611-99/05050544C-1 04050602601 15 x 0611-110/05055011C-1 04050603601 15 x 0612-2/05050017C-1 04050609101 15 x Table 2: Results of ploidy analysis by flow cytometry of 117 candidate H/DH palms identified as both morpholo- gically atypical and homozygous for the markers listed in Table 1 (Continued) 0612-70/05050530C-1 04050609201 15 x 0612-76/05050512C-1 04050610301 15 x 0611-109/05055144C-1 04120600101 15 x 0611-31/05050220C-1 04120600601 15 x 0611-38/05050284C-4 04120600901 15 x 0611-40/05050171C-1 04120601101 14 x 0612-80/05050713C-1 04120603101 15 x 65-0409034 MC-66 060829_0001_02_a 15 2x 65-0409034 MC-68 060829_0002_02_a 15 2x 65-0409034 MC-72 060829_0003_02_a 14 2x 65-0409034 MC-111 060829_0005_02_a 15 2x 65-0409034 MC-94 060829_0011_02_a 14 2x 65-0409034 MC-120 060829_0012_02_a 15 2x 65-0409034 MC-144 060829_0013_02_a 15 2x 65-0409034 MC-133 060829_0015_02_a 15 2x 65-0409034 MC-187 060829_0020_02_a 15 2x 65-0409034 MC-193 060829_0021_02_a 14 2x 65-0409034 MC-199 060829_0023_02_a 15 2x 65-0409034 MC-135 060829_0025_02_a 15 2x 65-0409034 MC-114 060829_0026_02_a 13 2x 65-0409034 MC-147 060829_0027_02_a 15 2x 65-0409034 MC-36 B 060829_0030_02_a 15 2x 65-0409034 MC-39 A 060829_0031_02_a 15 2x 65-0409034 MC-73 A 060829_0034_02_a 15 2x 65-0409034 MC-71 A 060829_0035_02_a 14 2x Note: in this initial round, no DH was found. Results The DH (0644-219/05049582C) was detected in a subsequent batch. Table 2: Results of ploidy analysis by flow cytometry of 117 candidate H/DH palms identified as both morpholo- gically atypical and homozygous for the markers listed in Table 1 (Continued) Note: in this initial round, no DH was found. The DH (0644-219/05049582C) was detected in a subsequent batch. Note: in this initial round, no DH was found. The DH (0644-219/05049582C) was detected in a subsequent batch. mapped loci found to be heterozygous in the maternal parent (palm number BL013/12-06). Taking account of linkage between mapped markers, the probability of such an individual occurring by chance following selfing mapped loci found to be heterozygous in the maternal parent (palm number BL013/12-06). Taking account of linkage between mapped markers, the probability of such an individual occurring by chance following selfing Figure 2 Chromosome spread of a haploid root cell from oil palm containing 16 C-metaphase chromosomes. Figure 2 Chromosome spread of a haploid root cell from oil palm containing 16 C-metaphase chromosomes. Page 5 of 25 Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Table 3 Microsatellite markers (described by Billotte et al. [27]) used for a larger- and homozygosity of DH candidates previously identified by the morphological s markers) and flow cytometry screen No. Forward primer (5’-3’) Reverse pr 16 GACCTTTGTCAGCATACTTGGTGTG GCAGGCCT 17 ATGCATGTGATTTTATTAGGTGAGA CGACCCTCA 18 AAGCTAGCGACCTATGATTTTAGA AAACAAGT 19 CCCACCACCCCTAGCTTCTC ACCCCGGT 20 AGAGAGAGAGAGTGCGTATG GTCCCTGTG 21 GGGTAGCAAACCTTGTATTA ACTTCCATT 22 CGAGGCCCAAAAACATTCAC GGTCCCGA 23 TTGCGGCCCATCGTAATC TCCCTGCAG 24 AGGGAATTGGAAGAAAAGAAAG TCCTGAGCT 25 AGCAAGAGCAAGAGCAGAACT CTTGGGGG 26 TAGCCATGCCGCCACCACTT CAATCCATT 27 CTTACCCCGCCTCCTCTCCT CGAAATGC 28 CCTTATATCGCACGGGTTCC TTCTTGGGG 29 GCAAGATGCAATGGAGTTCA CAAACCGC 30 GCAAAATTCAAAGAAAACTTA CTGACAGTG 31 CGTTCATCCCACCACCTTTC GCTGCGAG 32 GAATGTGGCTGTAAATGCTGAGTG AAGCCGCA 33 ACATTCCCTCTATTATTCTCAC GTTTTGTTTG 34 AAGCCAACTTCACAGATATGTTGAT ATGAGCCTA 35 AGTGAGGTATGGTTGATTAGGA TATTGATAG 36 CTCCGATGGTCAAGTCAGA AAATGGGG 37 GCCGTTCAAGTCAATTAGAC TTTGGGAGC 38 TGCTTCTTGTCCTTGATACA CCACGTCTA 39 CACCACATGAAGCAAGCAGT CCTACCACA 40 TTTTATTTTCCCTCTCTTTTGA ATTGCGTCT 41 CATATGGCGCACAGGCAC GCAATACA 42 AGTTGGTTTGCTGATTTG TGTTGCTTC 43 GCTGAAGATGAAATTGATGTA TTCAGGTCC 44 ATGACCTAAAAATAAAATCTCAT ACAGATCA 45 GGTGCAAGAGAGGAGGAATG TTTGGTAGT 46 GTTTGGCTTTGGACATG TCCATCACA 47 TGTTTTGTTTCGTGCATGTG GGCTGACA 48 CGGTTTTGTCGCATCTATG GTCGTCAGG 49 CAATCATTGGCGAGAGA CGTCACCTT 50 GAGCATGACGCAAACAAAGG GCAACATG 51 TCCAAGTAGCAAATGATGAC TGCCCTGAA 52 GAAGGGGCATTGGATTT TACCTATTA 53 AACACTCCAGAAGCCAGGTC GGTTTAGGT 54 GATCCCAATGGTAAAGACT AAGCCTCA 55 TGTGGTTTGAGGCATCTTCT GCCCACCA 56 TAGCCGCACTCCCACGAAGC CCAGAATC 57 TCAAAGAGCCGCACAACAAG ACTTTGCTG 58 GGGGATGAGTTTGTTTGTTC CCTGCTTGG 59 TCTAATGCTCCCAAGGTACA GGCTTGGTC 60 AGCTCTCATGCAAGTAAC TTCAACATA 61 TCCTCACTGCTCCTCTAATC ACTCCCTAT 62 AGGGAGGCGAACGAGAAACA CGACTGCTG 63 CTACGGACTCACACCTATAT ATGGTTCAT 64 GTGAGCGATTGAGGGGTGTG GGGGCTTG Table 3 Microsatellite markers (described by Billotte et al. Results [27]) used for a larger-scale survey for hemizygosity of Hs and homozygosity of DH candidates previously identified by the morphological screen, microsatellite pre-screen (15 markers) and flow cytometry screen No. Forward primer (5’-3’) Reverse primer (5’-3’) 16 GACCTTTGTCAGCATACTTGGTGTG GCAGGCCTGAAATCCCAAAT 17 ATGCATGTGATTTTATTAGGTGAGA CGACCCTCAGTCAATCAGTAAG 18 AAGCTAGCGACCTATGATTTTAGA AAACAAGTAATGTGCATAACCTTTC 19 CCCACCACCCCTAGCTTCTC ACCCCGGTCCAAATAAAATC 20 AGAGAGAGAGAGTGCGTATG GTCCCTGTGGCTGCTGTTTC 21 GGGTAGCAAACCTTGTATTA ACTTCCATTGTCTCATTATTCT 22 CGAGGCCCAAAAACATTCAC GGTCCCGATCCCGTCTACTG 23 TTGCGGCCCATCGTAATC TCCCTGCAGTGTCCCTCTTT 24 AGGGAATTGGAAGAAAAGAAAG TCCTGAGCTGGGGTGGTC 25 AGCAAGAGCAAGAGCAGAACT CTTGGGGGCTTCGCTATC 26 TAGCCATGCCGCCACCACTT CAATCCATTAGCGTGCCCTTCT 27 CTTACCCCGCCTCCTCTCCT CGAAATGCCCTTCCTTTACACTA 28 CCTTATATCGCACGGGTTCC TTCTTGGGGTCTCGCTACGG 29 GCAAGATGCAATGGAGTTCA CAAACCGCAGCAAGTCAGA 30 GCAAAATTCAAAGAAAACTTA CTGACAGTGCAGAAAATGTTATAGT 31 CGTTCATCCCACCACCTTTC GCTGCGAGGCCACTGATAC 32 GAATGTGGCTGTAAATGCTGAGTG AAGCCGCATGGACAACTCTAGTAA 33 ACATTCCCTCTATTATTCTCAC GTTTTGTTTGGTATGCTTGT 34 AAGCCAACTTCACAGATATGTTGAT ATGAGCCTAACAAAGCACATTCTAA 35 AGTGAGGTATGGTTGATTAGGA TATTGATAGCATTTGGGATTAG 36 CTCCGATGGTCAAGTCAGA AAATGGGGAAGGCAATAGTG 37 GCCGTTCAAGTCAATTAGAC TTTGGGAGCAAGCATTATCA 38 TGCTTCTTGTCCTTGATACA CCACGTCTACGAAATGATAA 39 CACCACATGAAGCAAGCAGT CCTACCACAACCCCAGTCTC 40 TTTTATTTTCCCTCTCTTTTGA ATTGCGTCTCTTTCCATTGA 41 CATATGGCGCACAGGCAC GCAATACAAGAGCACCCAAAT 42 AGTTGGTTTGCTGATTTG TGTTGCTTCTTTGATTTTC 43 GCTGAAGATGAAATTGATGTA TTCAGGTCCACTTTCATTTA 44 ATGACCTAAAAATAAAATCTCAT ACAGATCATGCTTGCTCACA 45 GGTGCAAGAGAGGAGGAATG TTTGGTAGTCGGGCGTTTTA 46 GTTTGGCTTTGGACATG TCCATCACAGGAGGTATAG 47 TGTTTTGTTTCGTGCATGTG GGCTGACATGCAACACTAAC 48 CGGTTTTGTCGCATCTATG GTCGTCAGGGAACAACAGT 49 CAATCATTGGCGAGAGA CGTCACCTTTCAGGATATG 50 GAGCATGACGCAAACAAAGG GCAACATGTTTGATGCATTAATAGTC 51 TCCAAGTAGCAAATGATGAC TGCCCTGAAACCCTTGA 52 GAAGGGGCATTGGATTT TACCTATTACAGCGAGAGTG 53 AACACTCCAGAAGCCAGGTC GGTTTAGGTATTGGAACTGATAGAC 54 GATCCCAATGGTAAAGACT AAGCCTCAAAAGAAGACC 55 TGTGGTTTGAGGCATCTTCT GCCCACCAAAAGAAAGTAGT 56 TAGCCGCACTCCCACGAAGC CCAGAATCATCAGACTCGGACAG 57 TCAAAGAGCCGCACAACAAG ACTTTGCTGCTTGGTGACTTA 58 GGGGATGAGTTTGTTTGTTC CCTGCTTGGCGAGATGA 59 TCTAATGCTCCCAAGGTACA GGCTTGGTCCACGATCTT 60 AGCTCTCATGCAAGTAAC TTCAACATACCGTCTGTA 61 TCCTCACTGCTCCTCTAATC ACTCCCTATGGACCTTAGTC Table 3 Microsatellite markers (described by Billotte et al. [27]) used for a larger-scale survey for hemizygosity of Hs and homozygosity of DH candidates previously identified by the morphological screen, microsatellite pre-screen (15 k ) d fl t t Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 6 of 25 Table 3: Microsatellite markers (described by Billotte et al. Results [27]) used for a larger-scale survey for hemizygosity of Hs and homozygosity of DH candidates previously identified by the morphological screen, microsatellite pre-screen (15 markers) and flow cytometry screen (Continued) 65 AGGGCAAGTCATGTTTC TATAAGGGCGAGGTATT 66 GAAGCCTGAGACCGCATAGA TTCGGTGATGAAGATTGAAG 67 TTTCTTATGGCAATCACACG GGAGGGCAGGAACAAAAAGT 68 GTTTATCATTTTGGGGTCAG CGGTGTCCCTCAGGATGTA 69 CATGCACGTAAAGAAAGTGT CCAAATGCACCCTAAGA 70 AATCCAAGTGGCCTACAG CATGGCTTTGCTCAGTCA 71 TGTAGGTGGTGGTTAGG TGTCAGACCCACCATTA 72 AGCAAGACACCATGTAGTC GACACGTGGGATCTAGAC 73 AAAAGCCGATAGTGGGAACA ATGCTGAGAGGTGGAAAATAGAG 74 GTCCATGTGCATAAGAGAG CTCTTGGCATTTCAGATAC 75 AGCCAATGAAGGATAAAGG CAAGCTAAAACCCCTAATC 76 CAATTCCAGCGTCACTATAG AGTGGCAGTGGAAAAACAGT 77 GGGCTTTCATTTTCCACTAT GCTCAACCTCATCCACAC 78 GACAGCTCGTGATGTAGA GTTCTTGGCCGCTATAT 79 ACTTGTAAACCCTCTTCTCA GTTTCATTACTTGGCTTCTG 80 CCTTCAAGCAAAGATACC GGCACCAAACACAGTAA 81 CCACTGCTTCAAATTTACTAG GCGTCCAAAACATAAATCAC 82 GGGAGAGGAAAAAATAGAG CCTCCCTGAGACTGAGAAG 83 AGCAGGGCAAGAGCAATACT TTCAGCAGCAGGAAACATC 84 GCCTATCCCCTGAACTATCT TGCACATACCAGCAACAGAG 85 CATCAGAGCCTTCAAACTAC AGCCTGAATTGCCTCTC 86 ATTCATTGCCATTCCCTTCA TTGTCCCCTCTGTTCACTCA 87 ATTGCAGAGATGATGAGAAG GAGATGCTGACAATGGTAGA 88 TCTCCCAAATCACTAGAC ATCTGCAAGGCATATTC 89 ACGTTTTGGCAACTCTC ACTCCCCTCTTTGACAT 90 TCCACTCTGGCAACTCC AAGGATGGGCTTTGTAGT 91 TTTAGAGGACAAGGAGATAAG CGACCGTGTCAAGAGTG 92 AGCAAAATGGCAAAGGAGAG GGTGTGTGCTATGGAAGATCATAGT 93 GTAGCTTGAACCTGAAA AGAACCACCGGAGTTAC 94 AAGCCACCAGGATCATC GTCATTGCCACCTCTAACT 95 TTACTTGCTAAGCTCTCTAGC TGGCTGTTTAATCTGTCTG 96 TCTATATTTGGTTGGCTTGA ACTCATTTCAATCTCAGTGTC 97 TGCTACGTGCTGAAATA ATTTCAGGTTCGCTTCA 98 CCTCCACTTCTCTTCATCTT CTTCCTCAAGCTCAAACAAT 99 GATGTTGCCGCTGTTTG CATCCCATTTCCCTCTT 100 ATGCTCCACCAAGTTTA CACATCCTAGCATCATTG 101 AAGCAATATAGGTTCAGTTC TCATTTTCTAATTCCAAACAAG 102 GCTCGTTTTTGTTTAGGTGA TTTTCTCCATAGTCCGTTAC 103 CAGCACACAAATGACAT CACCTTTCCTTTTTGTC 104 CCTATTCCTTACCTTTCTGT GACTTACTATCTTGGCTCAC 105 CCTTGCATTCCACTATT AGTTCTCAAGCCTCACA 106 CCTCCTTTGGAATTATG GTGTTTGATGGGACATACA 107 ATTGGAGAGCACTTGGATAG TTCTCTTCCTTCTCACTTGT Table 3: Microsatellite markers (described by Billotte et al. [27]) used for a larger-scale survey for hemizygosity of Hs and homozygosity of DH candidates previously identified by the morphological screen, microsatellite pre-screen (15 markers) and flow cytometry screen (Continued) Table 3: Microsatellite markers (described by Billotte et al. [27]) used for a larger-scale survey for hemizygosity of Hs and homozygosity of DH candidates previously identified by the morphological screen, microsatellite pre-screen (15 markers) and flow cytometry screen (Continued) Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Dunwell et al. BMC Plant Biology 2010, 10:218 Page 7 of 25 Figure 3 Principal Coordinates Analysis Plot of 95 diploid and 27 haploid palms based on 28 microsatellites. Red diamonds: haploids; green squares: commercial pisiferas; blue triangles: commercial teneras; yellow diamonds: commercial duras; purple diamonds: Ghanaian wild material. Microsatellite data in Table 7. Figure 3 Principal Coordinates Analysis Plot of 95 diploid and 27 haploid palms based on 28 microsatellites. Red diamonds: haploids; green squares: commercial pisiferas; blue triangles: commercial teneras; yellow diamonds: commercial duras; purple diamonds: Ghanaian wild material. Microsatellite data in Table 7. Figure 3 Principal Coordinates Analysis Plot of 95 diploid and 27 haploid palms based on 28 microsatellites. Red diamonds: haploids; green squares: commercial pisiferas; blue triangles: commercial teneras; yellow diamonds: commercial duras; purple diamonds: Ghanaian wild material. Microsatellite data in Table 7. was 8.72 × 10-8 (see Methods). This palm was therefore deemed a spontaneous DH. Results selection proving substantially more effective than screening for twin embryos. This result suggests that our method could be used to secure large numbers of Hs but is less able to isolate DHs at useful frequencies. This finding, when coupled with the routine nature of H These initial screens collectively revealed 83 sponta- neous Hs but no DHs (although one DH was discovered subsequently), with the undirected phenotypic ‘off-type’ Figure 4 Selection of haploid oil palm plants growing in a nursery. Figure 4 Selection of haploid oil palm plants growing in a nursery. Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 8 of 25 chromosome doubling in other crops [21], suggested the most promising route for commercial DH production lay in the isolation of Hs followed by somatic doubling. In subsequent screening of abnormal seedlings, high- throughput flow cytometry therefore replaced molecular analysis for candidate H identification. Haploid identity was then supported using at least 15 microsatellite mar- kers. Plants identified as diploid by flow cytometry con- tinued to be screened for DHs as above. Using this amended screening procedure, we have identified over 1,100 H palms from approximately 60 million seedlings (to July 2009). Figure 5 Doubled haploid palm. To have maximum utility this H/DH material should encompass as much genetic diversity from within the breeding germplasm as possible. A Principal Coordi- nates Analysis performed on H profiles using 28 micro- satellite loci showed the first two axes accounted for 58% of the detected variation. While most Hs had a strong affinity to commercial duras, Hs have also been generated from pisifera types and overall variability amongst Hs encompassed that seen for the entire com- mercial palm material (Figure 3). Effort then focussed on the creation of DHs from this rich germplasm of H genotypes (Figure 4). The most direct route to obtain DHs is to use chemical applica- tion to induce chromosome doubling. We applied a range of treatments to 50 H seedlings and screened leaves of the recovered material for evidence of chromo- some doubling. Flow cytometry revealed that 48 seed- lings contained substantial diploid sectors in their leaves; one palm was 100% doubled after exposure to10 mM colchicine (Figure 5) and 100 ppm GA3. To date, 16 H genotypes have produced pollen. This finding demonstrates scope for securing fertile gametes from diploid inflorescences or inflorescence sectors for DH or F1 production. Results Indeed, seed set using pollen from DH material has now been achieved (data not shown). Whilst further optimization work is required, our results when combined with experience in other crops [21] sug- gest routine production of fertile DH oil palm lines will be a relatively simple task. Figure 5 Doubled haploid palm. Figure 5 Doubled haploid palm. In the case of oil palm, the efficacy of our H screening combined with the demonstrated ability to create DH palms, opens the way for the development of 100% true- breeding parental clones for F1 variety breeding. There- after, it is hoped that the potential genetic gain available from oil palm F1 hybrids will match that in other crops. If such a gain is achieved it could be beneficial in several ways. First, high-yielding F1 palms are likely to acceler- ate replacement of palms in existing plantations and cause a step-increase in production. Secondly, this breeding strategy provides greater flexibility for breeders to respond rapidly to emergent threats (e.g. climate change). Thirdly, using palm oil and its associated wastes for energy generation [7] could substantially reduce carbon-based emissions currently associated with the palm oil lifecycle [23]. Fourthly, DH oil palms could be exploited in combination with transgenic techniques that are now available for this crop [24]. Looking for- ward, the clear challenge is to maintain and improve oil palm productivity in the face of a changing climate Discussion and Conclusions The simple high-throughput phenotypic-genotypic seed- ling selection system used here provides a fourth practi- cal approach to supplement androgenesis, wide crossing and gynogenesis [6] and has potential for many crops where H/DH production remains elusive. The prospect of adopting a similar untargeted approach more widely seems both plausible and attractive, and may be possible without experienced operators, especially as sophisti- cated phenomic screening systems [22] become more accessible. Page 9 of 25 Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Dunwell et al. BMC Plant Biology 2010, 10:218 Abnormal seedlings 124,094 1st molecular screening 111,320 Flow cytometry 25,235 Haploid 1,123 Diploid 24,027 Doubled haploid 4 2nd molecular screening 11,897 Alive 858 Dead 265 Germinated seeds 95,265,687 Morphological screening Molecular screening Flow Cytometry 50 haploids produced per month Figure 6 Summary of stages for identification of haploid and doubled haploid palm. Germinated seeds 95,265,687 Flow cytometry 25,235 Haploid 1,123 ure 6 Summary of stages for identification of haploid and doubled haploid palm. crops recalcitrant to in vitro based H/DH systems. This methodology, in particular the application of high- throughput flow cytometry, has recently been applied successfully to two other tropical crops, namely rubber (Hevea brasiliensis L.) and cocoa (Theobroma cacao L.) (Nasution et al. unpublished). crops recalcitrant to in vitro based H/DH systems. This methodology, in particular the application of high- throughput flow cytometry, has recently been applied successfully to two other tropical crops, namely rubber (Hevea brasiliensis L.) and cocoa (Theobroma cacao L.) (Nasution et al. unpublished). sufficient to keep pace with growing demand [25]. How- ever, it is important to point out that breeding is simply one stage in a long process from plantation to the even- tual processed product and the economic realities of this international industry will finally determine the impact of any novel technology on the global agricul- tural system for this crop. Methods The provision here of a system for haploid-based F1 hybrid breeding in oil palm represents the first techno- logical breakthrough likely to lead to step improvements in yield for this crop, and can also be applied to other Hs and DHs were identified using three methods: a mor- phological screen; homozygosity/hemizygosity assessment; and ploidy level measurement. Initial screens emphasized Figure 7 PCR amplicons generated by microsatellite marker 10 fractionated in 2% w/v agarose. Lanes 1-11 & 12-20: candidate H/DH palm plants; lane L: HyperladderI (Bioline, UK); lane 21: heterozygote control; lane 22: homozygote control. Candidates in lanes 1, 3, 4, 7, 8, 10, 11, 13, 16, 17, 19, 20 were deemed heterozygous and discarded. Figure 7 PCR amplicons generated by microsatellite marker 10 fractionated in 2% w/v agarose. Lanes 1-11 & 12-20: candidate H/DH palm plants; lane L: HyperladderI (Bioline, UK); lane 21: heterozygote control; lane 22: homozygote control. Candidates in lanes 1, 3, 4, 7, 8, 10, 11, 13, 16, 17, 19, 20 were deemed heterozygous and discarded. Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 10 of 25 Table 4 Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) No Marker Forward Primer (5’-3’) Reverse Primer (5’-3’) 1 VS1 GAGATTACAAAGTCCAAACC TCAAAATTAAGAAAGTATGC 2 OPSSR 3 ACGCATGCAGCTAGCTTTTC CGCGTGAAAGATATGAATCAAC 3 OPSSR 7 CACGCACGCAGTTTATTCTT GGATGTATGCTTTACCTCCGAAT 4 OPSSR 8 CCCCTTTTGCTTCCCTATTT CTCCTTTTCCCCATCACAGA 5 OPSSR 9 GACACAAGCAAAAACAAAAGCA ATTCTGAAAGGAGGGGGAAA 6 OPSSR 14 ATATGTGTGGGTGTGCGTGT TGCCTCTGGTTGTTAGTCTGG 7 OPSSR 19 TCTCTCTCTCTCTCTCTATGTGTGTGT TGGCAATCAGCACACATTCT 8 OPSSR 29 GCAGCTCTTTCCACACCTCT TGTGGTCTCCTGAGGAAGATG 9 OPSSR 30 TTTTCCCCATCACAGAATTG CCCCTTTTGCTTCCCTATTT 10 OPSSR32 GAACAAAACGGGAAGAAGCA CCTCAAATGGGAGAAACCAG 11 mEgUWA07 CGGATAGAGGCAGCAAGACT CTCGGGTTGTTTAACCCATT 12 mEgUWA44 TTGAGACGTCGTTCCTTTCC AGCGGAGACCCAATAATCCT 13 mEgUWA50 CCTGCAACTGCAAATGAGAC TCCAGACACAAACTACACACACC 14 mEgCIR0037 Published by Billotte et al. [27] 15 mEgCIR0055 Published by Billotte et al. [27] 16 mEgCIR0059 Published by Billotte et al. [27] 17 mEgCIR0067 Published by Billotte et al. [28] 18 mEgCIR0074 Published by Billotte et al. [27] 19 mEgCIR0146 Published by Billotte et al. [27] 20 mEgCIR0163 Published by Billotte et al. [27] 21 mEgCIR0173 Published by Billotte et al. [27] 22 mEgCIR0177 Published by Billotte et al. [27] 23 mEgCIR0192 Published by Billotte et al. [27] 24 mEgCIR0195 Published by Billotte et al. [27] 25 mEgCIR0243 Published by Billotte et al. [27] 26 mEgCIR0246 Published by Billotte et al. [27] 27 mEgCIR0257 Published by Billotte et al. [27] 28 mEgCIR0268 Published by Billotte et al. [27] 29 mEgCIR0328 Published by Billotte et al. Methods [27] 30 mEgCIR0359 Published by Billotte et al. [27] 31 mEgCIR0366 Published by Billotte et al. [27] 32 mEgCIR0369 Published by Billotte et al. [27] 33 mEgCIR0380 Published by Billotte et al. [27] 34 mEgCIR0399 Published by Billotte et al. [27] 35 mEgCIR0408 Published by Billotte et al. [27] 36 mEgCIR0409 Published by Billotte et al. [27] 37 mEgCIR0425 Published by Billotte et al. [27] 38 mEgCIR0433 Published by Billotte et al. [27] 39 mEgCIR0439 Published by Billotte et al. [27] 40 mEgCIR0445 Published by Billotte et al. [27] 41 mEgCIR0446 Published by Billotte et al. [27] 42 mEgCIR0465 Published by Billotte et al. [27] 43 mEgCIR0521 Published by Billotte et al. [27] 44 mEgCIR0551 Published by Billotte et al. [27] 45 mEgCIR0555 Published by Billotte et al. [27] 46 mEgCIR0588 Published by Billotte et al. [27] 47 mEgCIR0772 Published by Billotte et al. [27] 48 mEgCIR0773 Published by Billotte et al. [27] 49 mEgCIR0774 Published by Billotte et al. [27] 50 mEgCIR0775 Published by Billotte et al. [27] Table 4 Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) Table 4 Microsatellite markers used to screen for heterozygosity on the maternal parent (palm candidate palm (0644-219/05049582C) Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 11 of 25 Table 4: Microsatellite markers used to screen for heterozygosity on the maternal paren candidate palm (0644-219/05049582C) (Continued) 51 mEgCIR0778 Published by Billotte et al. [27 52 mEgCIR0779 Published by Billotte et al. [27 53 mEgCIR0781 Published by Billotte et al. [27 54 mEgCIR0786 Published by Billotte et al. [27 55 mEgCIR0787 Published by Billotte et al. [27 56 mEgCIR0788 Published by Billotte et al. [27 57 mEgCIR0790 Published by Billotte et al. [27 58 mEgCIR0793 Published by Billotte et al. [27 59 mEgCIR0800 Published by Billotte et al. [27 60 mEgCIR0801 Published by Billotte et al. [27 61 mEgCIR0802 Published by Billotte et al. [27 62 mEgCIR0803 Published by Billotte et al. [27 63 mEgCIR0804 Published by Billotte et al. [27 64 mEgCIR0825 Published by Billotte et al. Methods [27 65 mEgCIR0827 Published by Billotte et al. [27 66 mEgCIR0844 Published by Billotte et al. [27 67 mEgCIR0874 Published by Billotte et al. [27 68 mEgCIR0878 Published by Billotte et al. [27 69 mEgCIR0882 Published by Billotte et al. [27 70 mEgCIR0886 Published by Billotte et al. [27 71 mEgCIR0894 Published by Billotte et al. [27 72 mEgCIR0905 Published by Billotte et al. [27 73 mEgCIR0906 Published by Billotte et al. [27 74 mEgCIR0910 Published by Billotte et al. [27 75 mEgCIR0912 Published by Billotte et al. [27 76 mEgCIR1729 Published by Billotte et al. [27 77 mEgCIR1740 Published by Billotte et al. [27 78 mEgCIR1753 Published by Billotte et al. [27 79 mEgCIR1773 Published by Billotte et al. [27 80 mEgCIR1917 Published by Billotte et al. [27 81 mEgCIR1977 Published by Billotte et al. [27 82 mEgCIR1996 Published by Billotte et al. [27 83 mEgCIR2110 Published by Billotte et al. [27 84 mEgCIR2144 Published by Billotte et al. [27 85 mEgCIR2149 Published by Billotte et al. [27 86 mEgCIR2188 Published by Billotte et al. [27 87 mEgCIR2212 Published by Billotte et al. [27 88 mEgCIR2215 Published by Billotte et al. [27 89 mEgCIR2380 Published by Billotte et al. [27 90 mEgCIR2387 Published by Billotte et al. [27 91 mEgCIR2414 Published by Billotte et al. [27 92 mEgCIR2417 Published by Billotte et al. [27 93 mEgCIR2422 Published by Billotte et al. [27 94 mEgCIR2423 Published by Billotte et al. [27 95 mEgCIR2427 Published by Billotte et al. [27 96 mEgCIR2436 Published by Billotte et al. [27 97 mEgCIR2440 Published by Billotte et al. [27 98 mEgCIR2492 Published by Billotte et al. [27 99 mEgCIR2518 Published by Billotte et al. [27 100 mEgCIR2525 Published by Billotte et al. [27 101 mEgCIR2569 Published by Billotte et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) e markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH -219/05049582C) (Continued) Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. Methods [27 Table 4: Microsatellite markers used to screen for heterozygosity candidate palm (0644-219/05049582C) (Continued) 51 mEgCIR0778 52 mEgCIR0779 53 mEgCIR0781 54 mEgCIR0786 55 mEgCIR0787 56 mEgCIR0788 57 mEgCIR0790 58 mEgCIR0793 59 mEgCIR0800 60 mEgCIR0801 61 mEgCIR0802 62 mEgCIR0803 63 mEgCIR0804 64 mEgCIR0825 65 mEgCIR0827 66 mEgCIR0844 67 mEgCIR0874 68 mEgCIR0878 69 mEgCIR0882 70 mEgCIR0886 71 mEgCIR0894 72 mEgCIR0905 73 mEgCIR0906 74 mEgCIR0910 75 mEgCIR0912 76 mEgCIR1729 77 mEgCIR1740 78 mEgCIR1753 79 mEgCIR1773 80 mEgCIR1917 81 mEgCIR1977 82 mEgCIR1996 83 mEgCIR2110 84 mEgCIR2144 85 mEgCIR2149 86 mEgCIR2188 87 mEgCIR2212 88 mEgCIR2215 89 mEgCIR2380 90 mEgCIR2387 91 mEgCIR2414 92 mEgCIR2417 93 mEgCIR2422 94 mEgCIR2423 95 mEgCIR2427 96 mEgCIR2436 97 mEgCIR2440 98 mEgCIR2492 99 mEgCIR2518 100 mEgCIR2525 Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) [27] 51 mEgCIR0778 52 mEgCIR0779 53 mEgCIR0781 54 mEgCIR0786 55 mEgCIR0787 56 mEgCIR0788 57 mEgCIR0790 58 mEgCIR0793 59 mEgCIR0800 60 mEgCIR0801 61 mEgCIR0802 62 mEgCIR0803 63 mEgCIR0804 64 mEgCIR0825 65 mEgCIR0827 66 mEgCIR0844 67 mEgCIR0874 68 mEgCIR0878 69 mEgCIR0882 70 mEgCIR0886 71 mEgCIR0894 72 mEgCIR0905 73 mEgCIR0906 74 mEgCIR0910 75 mEgCIR0912 76 mEgCIR1729 77 mEgCIR1740 78 mEgCIR1753 79 mEgCIR1773 80 mEgCIR1917 81 mEgCIR1977 82 mEgCIR1996 83 mEgCIR2110 84 mEgCIR2144 85 mEgCIR2149 86 mEgCIR2188 87 mEgCIR2212 88 mEgCIR2215 89 mEgCIR2380 90 mEgCIR2387 91 mEgCIR2414 92 mEgCIR2417 93 mEgCIR2422 94 mEgCIR2423 95 mEgCIR2427 96 mEgCIR2436 97 mEgCIR2440 98 mEgCIR2492 99 mEgCIR2518 100 mEgCIR2525 101 mEgCIR2569 Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Dunwell et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) e markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH -219/05049582C) (Continued) Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 12 of 25 Table 4: Microsatellite markers used to screen for heterozygosity candidate palm (0644-219/05049582C) (Continued) 102 mEgCIR2575 103 mEgCIR2577 104 mEgCIR2590 105 mEgCIR2595 106 mEgCIR2600 107 mEgCIR2621 108 mEgCIR2628 109 mEgCIR2763 110 mEgCIR2813 111 mEgCIR2860 112 mEgCIR2887 113 mEgCIR2893 114 mEgCIR3040 115 mEgCIR3111 116 mEgCIR3160 117 mEgCIR3194 118 mEgCIR3213 119 mEgCIR3232 120 mEgCIR3295 121 mEgCIR3296 122 mEgCIR3297 123 mEgCIR3298 124 mEgCIR3300 125 mEgCIR3301 126 mEgCIR3305 127 mEgCIR3307 128 mEgCIR3310 129 mEgCIR3311 130 mEgCIR3316 131 mEgCIR3321 132 mEgCIR3328 133 mEgCIR3350 134 mEgCIR3384 135 mEgCIR3389 136 mEgCIR3399 137 mEgCIR3400 138 mEgCIR3402 139 mEgCIR3427 140 mEgCIR3428 141 mEgCIR3433 142 mEgCIR3439 143 mEgCIR3477 144 mEgCIR3519 145 mEgCIR3526 146 mEgCIR3533 147 mEgCIR3534 148 mEgCIR3535 149 mEgCIR3538 150 mEgCIR3543 151 mEgCIR3544 152 mEgCIR3546 Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) [27] 102 mEgCIR2575 103 mEgCIR2577 104 mEgCIR2590 105 mEgCIR2595 106 mEgCIR2600 107 mEgCIR2621 108 mEgCIR2628 109 mEgCIR2763 110 mEgCIR2813 111 mEgCIR2860 112 mEgCIR2887 113 mEgCIR2893 114 mEgCIR3040 115 mEgCIR3111 116 mEgCIR3160 117 mEgCIR3194 118 mEgCIR3213 119 mEgCIR3232 120 mEgCIR3295 121 mEgCIR3296 122 mEgCIR3297 123 mEgCIR3298 124 mEgCIR3300 125 mEgCIR3301 126 mEgCIR3305 127 mEgCIR3307 128 mEgCIR3310 129 mEgCIR3311 130 mEgCIR3316 131 mEgCIR3321 132 mEgCIR3328 133 mEgCIR3350 134 mEgCIR3384 135 mEgCIR3389 136 mEgCIR3399 137 mEgCIR3400 138 mEgCIR3402 139 mEgCIR3427 140 mEgCIR3428 141 mEgCIR3433 142 mEgCIR3439 143 mEgCIR3477 144 mEgCIR3519 145 mEgCIR3526 146 mEgCIR3533 147 mEgCIR3534 148 mEgCIR3535 149 mEgCIR3538 150 mEgCIR3543 151 mEgCIR3544 152 mEgCIR3546 Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) e markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH -219/05049582C) (Continued) ndidate palm (0644 219/05049582C) (Continued) 153 mEgCIR3555 Published by Billotte et al. [27 154 mEgCIR3557 Published by Billotte et al. [27 155 mEgCIR3563 Published by Billotte et al. [27 156 mEgCIR3567 Published by Billotte et al. [27 157 mEgCIR3569 Published by Billotte et al. [27 158 mEgCIR3574 Published by Billotte et al. [27 159 mEgCIR3587 Published by Billotte et al. [27 160 mEgCIR3590 Published by Billotte et al. [27 161 mEgCIR3592 Published by Billotte et al. [27 162 mEgCIR3593 Published by Billotte et al. [27 163 mEgCIR3607 Published by Billotte et al. [27 164 mEgCIR3622 Published by Billotte et al. [27 165 mEgCIR3633 Published by Billotte et al. [27 166 mEgCIR3639 Published by Billotte et al. [27 167 mEgCIR3643 Published by Billotte et al. [27 168 mEgCIR3649 Published by Billotte et al. [27 169 mEgCIR3653 Published by Billotte et al. [27 170 mEgCIR3655 Published by Billotte et al. [27 171 mEgCIR3663 Published by Billotte et al. [27 172 mEgCIR3668 Published by Billotte et al. [27 173 mEgCIR3672 Published by Billotte et al. [27 174 mEgCIR3683 Published by Billotte et al. [27 175 mEgCIR3684 Published by Billotte et al. [27 176 mEgCIR3691 Published by Billotte et al. [27 177 mEgCIR3693 Published by Billotte et al. [27 178 mEgCIR3696 Published by Billotte et al. [27 179 mEgCIR3698 Published by Billotte et al. [27 180 mEgCIR3705 Published by Billotte et al. [27 181 mEgCIR3711 Published by Billotte et al. [27 182 mEgCIR3716 Published by Billotte et al. [27 183 mEgCIR3718 Published by Billotte et al. [27 184 mEgCIR3722 Published by Billotte et al. [27 185 mEgCIR3727 Published by Billotte et al. [27 186 mEgCIR3728 Published by Billotte et al. [27 187 mEgCIR3732 Published by Billotte et al. [27 188 mEgCIR3737 Published by Billotte et al. [27 189 mEgCIR3739 Published by Billotte et al. [27 190 mEgCIR3745 Published by Billotte et al. [27 191 mEgCIR3747 Published by Billotte et al. [27 192 mEgCIR3750 Published by Billotte et al. [27 193 mEgCIR3755 Published by Billotte et al. [27 194 mEgCIR3766 Published by Billotte et al. [27 195 mEgCIR3769 Published by Billotte et al. [27 196 mEgCIR3775 Published by Billotte et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) [27 197 mEgCIR3782 Published by Billotte et al. [27 198 mEgCIR3785 Published by Billotte et al. [27 199 mEgCIR3787 Published by Billotte et al. [27 200 mEgCIR3788 Published by Billotte et al. [27 201 mEgCIR3792 Published by Billotte et al. [27 202 mEgCIR3807 Published by Billotte et al. [27 203 mEgCIR3808 Published by Billotte et al. [27 Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 13 of 25 Table 4: Microsatellite markers used to screen for heterozygosity candidate palm (0644-219/05049582C) (Continued) 153 mEgCIR3555 154 mEgCIR3557 155 mEgCIR3563 156 mEgCIR3567 157 mEgCIR3569 158 mEgCIR3574 159 mEgCIR3587 160 mEgCIR3590 161 mEgCIR3592 162 mEgCIR3593 163 mEgCIR3607 164 mEgCIR3622 165 mEgCIR3633 166 mEgCIR3639 167 mEgCIR3643 168 mEgCIR3649 169 mEgCIR3653 170 mEgCIR3655 171 mEgCIR3663 172 mEgCIR3668 173 mEgCIR3672 174 mEgCIR3683 175 mEgCIR3684 176 mEgCIR3691 177 mEgCIR3693 178 mEgCIR3696 179 mEgCIR3698 180 mEgCIR3705 181 mEgCIR3711 182 mEgCIR3716 183 mEgCIR3718 184 mEgCIR3722 185 mEgCIR3727 186 mEgCIR3728 187 mEgCIR3732 188 mEgCIR3737 189 mEgCIR3739 190 mEgCIR3745 191 mEgCIR3747 192 mEgCIR3750 193 mEgCIR3755 194 mEgCIR3766 195 mEgCIR3769 196 mEgCIR3775 197 mEgCIR3782 198 mEgCIR3785 199 mEgCIR3787 200 mEgCIR3788 201 mEgCIR3792 202 mEgCIR3807 203 mEgCIR3808 Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) [27] 153 mEgCIR3555 154 mEgCIR3557 155 mEgCIR3563 156 mEgCIR3567 157 mEgCIR3569 158 mEgCIR3574 159 mEgCIR3587 160 mEgCIR3590 161 mEgCIR3592 162 mEgCIR3593 163 mEgCIR3607 164 mEgCIR3622 165 mEgCIR3633 166 mEgCIR3639 167 mEgCIR3643 168 mEgCIR3649 169 mEgCIR3653 170 mEgCIR3655 171 mEgCIR3663 172 mEgCIR3668 173 mEgCIR3672 174 mEgCIR3683 175 mEgCIR3684 176 mEgCIR3691 177 mEgCIR3693 178 mEgCIR3696 179 mEgCIR3698 180 mEgCIR3705 181 mEgCIR3711 182 mEgCIR3716 183 mEgCIR3718 184 mEgCIR3722 185 mEgCIR3727 186 mEgCIR3728 187 mEgCIR3732 188 mEgCIR3737 189 mEgCIR3739 190 mEgCIR3745 191 mEgCIR3747 192 mEgCIR3750 193 mEgCIR3755 194 mEgCIR3766 195 mEgCIR3769 196 mEgCIR3775 197 mEgCIR3782 198 mEgCIR3785 199 mEgCIR3787 200 mEgCIR3788 201 mEgCIR3792 202 mEgCIR3807 203 mEgCIR3808 Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. Molecular pre-screen to exclude heterozygotes Molecular pre-screen to exclude heterozygotes DNA was isolated from leaf tissue using DNeasy 96 Plant Kit (Qiagen, UK). Initial heterozygosity screens used 15 microsatellites (Table 1) yielding alleles readily distinguished by agarose gel electrophoresis (Figure 7). 10 μl PCR mixes comprised 1.0 μl 10× NH4 buffer (Bio- line), 0.3 μl MgCl2 (10 mM), 0.4 μl dNTPs (10 mM), 0.2 μl each primer (10 mM), 1-5 ng DNA and 1U Taq poly- merase (Bioline). Thermocycling conditions: 2 min at 94°C followed by 35 cycles of 94°C for 30 s, 52-58°C for 30 s and 72°C for 45 s, with a final extension of 72°C for 7 min. Candidates presenting two allelic bands after fractionation by (2-3% w/v metaphor) agarose gel elec- trophoresis were discarded. DH candidate 0644-219/05049582C was found to be homozygous across all 48 loci that were heterozygous in its maternal parent. Of these 48 loci, 36 have been mapped by Billotte et al. [27] (Table 5). We first consid- ered the probability of obtaining the observed homozyg- osity levels via independent assortment using only the unlinked markers from this group. For unlinked loci, the probability of homozygous offspring arising by inde- pendent assortment is 0.5 per locus. Given that hetero- zygous loci were secured from 14 of the 16 linkage groups, with the addition of a further unlinked (unas- signed) marker, the probability of these markers all becoming homozygous by chance is therefore: P = 0.515 = 0.000030517578125. DH candidate verification To verify DH candidate 0644-219/05049582C we screened 212 microsatellites (Table 4) for heterozygosity in the maternal parent (BL013/12-06). 10 μl PCR mixes comprising: 5 μl BioMix™(Bioline, UK), 0.05 μl forward primer plus M13 adaptor (10 μM), 0.2 μl labelled M13 (-29) (10 μM) (Sigma Genosys, UK), 0.2 μl reverse primer (10 μM) and 5-10 ng DNA were subjected to: 2 min at 94°C, followed by 35 cycles of 30 s at 94°C, 30 s at 52°C, 45 s at 72°C, with a final extension of 72°C for 7 min. Amplicons were surveyed for heterozygosity by high- resolution melt (HRM) analysis according to Croxford et al. [26] using the candidate as the reference comparator. Samples with amplicons variable between the maternal parent and candidate DH were fractionated by capillary electrophoresis as above. 48 markers identified as hetero- zygous in the maternal parent (Table 5) were applied to the DH candidate to assess homozygosity. Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Published by Billotte et al. [27] Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 14 of 25 Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) 204 mEgCIR3809 Published by Billotte et al. [27] 205 mEgCIR3813 Published by Billotte et al. [27] 206 mEgCIR3819 Published by Billotte et al. [27] 207 mEgCIR3825 Published by Billotte et al. [27] 208 mEgCIR3826 Published by Billotte et al. [27] 209 mEgCIR3828 Published by Billotte et al. [27] 210 mEgCIR3847 Published by Billotte et al. [27] 211 mEgCIR3850 Published by Billotte et al. [27] 212 mEgCIR3869 Published by Billotte et al. [27] e markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH -219/05049582C) (Continued) identification of candidate DHs where seedling morphol- ogy screening was followed by homozygosity/hemizygosity assessment using microsatellites. H/DHs were then distin- guished by flow cytometry and DHs subjected to an exten- sive homozygosity screen (Figure 6). Table 4: Microsatellite markers used to screen for heterozygosity on the maternal parent (palm BL013/12-06) of DH candidate palm (0644-219/05049582C) (Continued) As spontaneous DH frequency was low, later screens emphasized H recovery where the morphological screen was followed by flow cytometry; homozygosity of candidate Hs was thereafter confirmed with microsatellites. identification of candidate DHs where seedling morphol- ogy screening was followed by homozygosity/hemizygosity assessment using microsatellites. H/DHs were then distin- guished by flow cytometry and DHs subjected to an exten- sive homozygosity screen (Figure 6). As spontaneous DH frequency was low, later screens emphasized H recovery where the morphological screen was followed by flow cytometry; homozygosity of candidate Hs was thereafter confirmed with microsatellites. microsatellites (Table 3) with 150 seedlings of normal phe- notype and 24 heterozygous tenera palms as controls. PCR conditions were as described above and resultant products were fractionated on an ABI3730XL capillary sequencer (Applied Biosystems, USA) by Macrogen Inc (Korea). Allele size was determined (Genemapper v4.0) against a GS400HD standard. Individuals with two alleles at any locus were discarded. Seed morphological screen For seed storage, mesocarps were removed from freshly harvested seed, and seeds air-dried at ambient tempera- ture (24 h). Seeds were thereafter stored at 25°C with 15-18% moisture content. To induce germination, stored seeds were re-hydrated over 3 d to 18-20% moisture content, followed by 38-40°C incubation (40-60 d). Seeds were then re-hydrated for a further 5 d to >22% moisture content, and air-dried at ambient temperature (4 h). Seeds were germinated at ambient temperature (7 d to 3 months after treatment) and examined for aty- pical germination morphology (Figure 1). Extended molecular screen 62 55 88 95 87 LG6 9 LG7 93 LG8 52 LG1 × × × × × ( ) × ( ) × ( ) × 0 0 0 0 0 0 0 0 ( ) × × × × ( ) × ( ) × ( ) × . . . . . . . 93 94 87 83 LG12 5 LG14 5 LG15 6 LG16 ( ) = × − 0 0 . . . 51 8 72 1 8 Confirmation of Hs by chromosome squashes Harvested roots were pre-treated in iced water (24 h), then fixed in 3:1 v/v alcohol: glacial acetic acid at 4°C (24 h). They were then rinsed in water, softened in 1N HCl (20 min), rinsed in water (2 min) and stained in saturated aceto-orcein (1 min). The root tip was then squashed, mounted onto a glass slide, and examined using a compound photomicroscope. Extended molecular screen Candidate DHs and some Hs were subjected to an exten- sive assay for heterozygosity using 97 fluorescently-labelled Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 15 of 25 Table 5 Markers shown to be heterozygous in the maternal parent (palm BL013/12-06) and homozygous in the DH candidate (0644-219/05049582C) No Marker Linkage Group 1 mEgCIR0268 1 2 mEgCIR0874 1 3 mEgCIR3847 1 4 mEgCIR2149 2 5 mEgCIR2518 3 6 mEgCIR0425 3 7 mEgCIR3544 3 8 mEgCIR3716 4 9 mEgCIR1917 4 10 mEgCIR3535 4 11 mEgCIR3310 4 12 mEgCIR3705 4 13 mEgCIR3477 4 14 mEgCIR0059 4 15 mEgCIR3557 4 16 mEgCIR2813 5 17 mEgCIR3543 6 18 mEgCIR0195 6 19 mEgCIR0894 7 20 mEgCIR0905b 7 21 mEgCIR0774 8 22 mEgCIR2440 8 23 mEgCIR0825 10 24 mEgCIR3826 10 25 mEgCIR0788 10 26 mEgCIR2628 10 27 mEgCIR0146 10 28 mEgCIR0878 11 29 mEgCIR1773 12 30 mEgCIR3311 12 31 mEgCIR0779 14 32 mEgCIR0588 14 33 mEgCIR3737 15 34 mEgCIR3850 15 35 mEgCIR3639 16 36 mEgCIR0905a 16 37 mEgCIR3739 unlinked 38 mEgCIR3160 unmapped 39 mEgCIR3360 unmapped 40 mEgCIR0801 unmapped 41 mEgCIR2577 unmapped 42 OPSSR14 unmapped 43 OPSSR30 unmapped 44 OPSSR32 unmapped 45 mEgUWA44 unmapped 46 mEgUWA50 unmapped 47 mEgUWA07 unmapped 48 VS1 unmapped Linkage group assigned according to Billotte et al. [27]. Table 5 Markers shown to be heterozygous in the maternal parent (palm BL013/12-06) and homozygous in the DH candidate (0644-219/05049582C) This figure was further reduced by the inclusion of the remaining 21 markers that had been assigned a map position [27]. Here, linkage was accommodated by mul- tiplying by 1-(distance in cM/100). Thus the inclusion of a new marker 10 cM from an existing marker would mean multiplying the cumulative total by 1- (10/100) = 1-0.1 = 0.9 (rather than 0.5 for an unlinked marker). This reduced the probability as follows: P = × 0 0000 0 . , 3 517578125 extra markers from Linkage Group 1 LG11 92 92 extra markers from LG3 81 93 LG4 86 ( ) × × × × ( ) × 0 0 0 0 0 . . ( ) . . . 00 0 0 0 0 0 0 0 . . . . . . . . Flow Cytometry l d Newly matured leaflets or radicles from candidate H/DH palms were subjected to flow cytometry according to Anumaganathan & Earle [29] to establish ploidy level. Commercial tenera palms were included as diploid con- trols. For high-throughput mass screening, tissue samples were bulked at a rate of five individual tissue samples per bulk. Bulked samples (about 0.5 cm2 for radicles and 1 cm2 for leaf material (per each individual) were sliced by chopping with a sharp clean razor-blade (20-30 chops), in a plastic 9 cm diameter Petri dish containing 1.5 ml of cold (5°C) CyStain® UV Ploidy solution (Partec, Germany) modified by addition of 6.48 mM dithiothreitol (DTT) and 1% (v/v) polyvinylpyrrolidone (PVP-40) (Sigma- Aldrich, USA). The addition of DTT and PVP-40 were found to reduce background counts (’noise’) in output histograms of particle fluorescence in the analyte. Linkage group assigned according to Billotte et al. [27]. Principal Coordinates Analysis The genetic affinity of 270 Hs was compared with 95 representative diploids (Table 6) using 28 microsatel- lites (Table 7) by Principal Coordinates Analysis (PCoA). The PCoA was constructed using GenAlEx v6 [30]. Genetic distance option ‘codominant-genotypic’ was applied, where pairwise, individual-by-individual (N × N) genetic distances are calculated for codomi- nant data. For a single-locus analysis, with i-th, j-th, k- th and l-th different alleles, a set of squared distances is defined as d2(ii, ii) = 0, d2(ij, ij) = 0, d2(ii, ij) = 1, d2 (ij, ik) = 1, d2(ij, kl) = 2, d2(ii, jk) = 3, and d2(ii, jj) = 4. The algorithm used in GenAlEx is based on Orloci Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 16 of 25 able 6 Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates nalysis No Label no in PCO Sample name in PCO Palm Id Ploidy level 1 1 haploid 05020271_0001 x 2 2 haploid 05050099_0001 x 3 3 haploid 05050099_0002 x 4 4 haploid 05020961_0001 x 5 5 haploid 05020511_0001 x 6 6 haploid 05020946_0001 x 7 8 haploid 05030147_0001 x 8 9 haploid 05030462_0001 x 9 10 haploid 05020420_0002 x 10 11 haploid 05020361_0001 x 11 12 haploid 05030060_0001 x 12 13 haploid 05020558_0001 x 13 14 haploid 05020631_0001 x 14 15 haploid 05040748_0003 x 15 16 haploid 05030308_0001 x 16 18 haploid 05080318_0003 x 17 19 haploid 06020186_0001 x 18 20 haploid 05110212_0001 x 19 21 haploid 05120555_0001 x 20 22 haploid 06011022_0001 x 21 23 haploid 05020059_0001 x 22 24 haploid 06020320_0004 x 23 25 haploid 06020571_0004 x 24 26 haploid 06020381_0001 x 25 27 haploid 05060119_0001 x 26 28 haploid 05090172_0001 x 27 30 haploid 05100321_0001 x 28 31 haploid 06010670_0006 x 29 32 haploid 06010842_0004 x 30 33 haploid 05050228_0001 x 31 34 haploid 05110260_0001 x 32 35 haploid 05110260_0002 x 33 36 haploid 05110162_0001 x 34 37 haploid 05101030_0001 x 35 38 haploid 05040273_0001 x 36 39 haploid 05110003_0001 x 37 40 haploid 05120002_0001 x 38 41 haploid 05080095_0001 x 39 43 haploid 06110122_0002 x 40 44 haploid 05110716_0001 x 41 45 haploid 05010836_0001 x 42 46 haploid 05120155_0001 x 43 47 haploid 05110875_0001 x 44 48 haploid 05070553_0001 x 45 49 haploid 05070466_0001 x 46 50 haploid 06010650_0001 x codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 17 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates nalysis (Continued) 47 51 haploid 05110718_0001 x 48 52 haploid 05110496_0001 x 49 53 haploid 06010107_0001 x 50 54 haploid 05120429_0002 x 51 55 haploid 06010953_0001 x 52 56 haploid 05030686_0001 x 53 57 haploid 05060107_0001 x 54 58 haploid 05030791_0001 x 55 59 haploid 05080585_0001 x 56 60 haploid 05020375_0001 x 57 61 haploid 05121048_0001 x 58 62 haploid 05055090_0001 x 59 63 haploid 05121004_0002 x 60 64 haploid 06030064_0001 x 61 65 haploid 05121061_0004 x 62 66 haploid 05060276_0001 x 63 67 haploid 05100988_0001 x 64 68 haploid 05060315_0001 x 65 69 haploid 06030324_0003 x 66 70 haploid 05080506_0001 x 67 71 haploid 06010813_0001 x 68 72 haploid 05110881_0001 x 69 73 haploid 05100717_0001 x 70 74 haploid 06020169_0009 x 71 75 haploid 05110134_0001 x 72 76 haploid 05030196_0001 x 73 77 haploid 05050220_0001 x 74 78 haploid 06011195_0001 x 75 79 haploid 05120725_0001 x 76 80 haploid 05100510_0001 x 77 81 haploid 05060624_0001 x 78 82 haploid 05060712_0001 x 79 83 haploid 05030150_0001 x 80 84 haploid 06030180_0001 x 81 85 haploid 06020915_0001 x 82 86 haploid 05101150_0003 x 83 87 haploid 05101152_0001 x 84 88 haploid 05020415_0001 x 85 89 haploid 05040029_0002 x 86 90 haploid 05040035_0003 x 87 91 haploid 06020573_0001 x 88 93 haploid 05121112_0008 x 89 94 haploid 05090078_0001 x 90 95 haploid 05060495_0001 x 91 96 haploid 05070484_0001 x 92 97 haploid 06020455_0001 x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Analysis (Continued) Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 18 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Analysis (Continued) 93 98 haploid 05075185_0001 x 94 99 haploid 05090522_0004 x 95 100 haploid 06020625_0002 x 96 101 haploid 05100812_0002 x 97 102 haploid 05100862_0001 x 98 103 haploid 05030224_0002 x 99 104 haploid 05040439_0001 x 100 105 haploid 05040317_0003 x 101 106 haploid 05080030_0001 x 102 107 haploid 05070703_0003 x 103 108 haploid 05080485_0001 x 104 109 haploid 05110470_0002 x 105 110 haploid 05100423_0001 x 106 111 haploid 05110423_0001 x 107 112 haploid 05080362_0003 x 108 113 haploid 05110625_0001 x 109 114 haploid 05120719_0001 x 110 115 haploid 05121073_0002 x 111 116 haploid 06050726_0002 x 112 117 haploid 06060063_0001 x 113 119 haploid 06121220_0001 x 114 120 haploid 06080516_0001 x 115 121 haploid 06090505_0002 x 116 122 haploid 06090407_0004 x 117 123 haploid 06051133_0002 x 118 124 haploid 06060740_0031 x 119 125 haploid 06060740_0077 x 120 126 haploid 06060740_0090 x 121 127 haploid 06120178_0001 x 122 128 haploid 06090960_0003 x 123 129 haploid 06090657_0001 x 124 130 haploid 06120377_0001 x 125 131 haploid 06070208_0001 x 126 132 haploid 07010308_0001 x 127 133 haploid 06121125_0001 x 128 134 haploid 06121125_0002 A x 129 135 haploid 06121125_0002 B x 130 136 haploid 06019052_0005 x 131 137 haploid 06129197_0001 x 132 138 haploid 06079077_0001 x 133 139 haploid 07019130_0003 x 134 140 haploid 06075474_0001 x 135 141 haploid 06075474_0003 x 136 142 haploid 06075544_0001 x 137 143 haploid 06045801_0001 x 138 144 haploid 06065285_0001 x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Analysis (Continued) Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 19 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Analysis (Continued) 139 145 haploid 06081027_0001 x 140 146 haploid 06090264_0001 x 141 147 haploid 06090264_0002 x 142 148 haploid 06070430_0001 x 143 149 haploid 06090861_0001 x 144 150 haploid 06051245_0001 x 145 151 haploid 06070716_0001 x 146 152 haploid 06051468_0001 x 147 153 haploid 06075617_0001 x 148 154 haploid 06040273_0001 x 149 155 haploid 06080584_0001 x 150 156 haploid 06070825_0001 x 151 158 haploid 06110390_0015 x 152 159 haploid 06031385_0001 x 153 160 haploid 06045657_0001 x 154 161 haploid 06110204_0008 x 155 162 haploid 06050161_0001 x 156 163 haploid 06071068_0010 x 157 164 haploid 06100785_0002 x 158 165 haploid 06010987_0028 x 159 166 haploid 07010166_0001 x 160 167 haploid 06100730_0001 x 161 168 haploid 06080681_0001 x 162 169 haploid 06080532_0005 x 163 170 haploid 06040024_0001 x 164 172 haploid 06080217_0010 x 165 173 haploid 06120975_0001 x 166 174 haploid 06070581_0002 x 167 175 haploid 06060477_0001 x 168 176 haploid 06120852_0001 x 169 177 haploid 06091392_0001 x 170 178 haploid 06060344_0001 x 171 179 haploid 06090211_0001 x 172 180 haploid 06100858_0001 x 173 181 haploid 06080272_0007 x 174 182 haploid 06050493_0004 x 175 183 haploid 06101033_0002 x 176 184 haploid 06081043_0001 x 177 185 haploid 07011057_0001 x 178 186 haploid 06070921_0001 x 179 187 haploid 06111210_0002 x 180 188 haploid 06121495_0001 x 181 189 haploid 06110610_0001 x 182 190 haploid 06090772_0001 x 183 191 haploid 06090318_0002 x 184 192 haploid 06121313_0001 x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Analysis (Continued) Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 20 of 25 Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Analysis (Continued) 185 193 haploid 06085027_0001 x 186 194 haploid 06090109_0001 x 187 195 haploid 06080157_0001 x 188 196 haploid 06121316_0001 x 189 197 haploid 06110900_0001 x 190 198 haploid 06070228_0002 x 191 199 haploid 06101174_0001 x 192 200 haploid 06060805_0001 x 193 201 haploid 06085063_0001 x 194 202 haploid 06101037_0001 x 195 203 haploid 06110444_0002 x 196 204 haploid 06101487_0001 x 197 205 haploid 06100937_0001 x 198 206 haploid 06090820_0002 x 199 207 haploid 06070039_0001 x 200 208 haploid 06070772_0001 x 201 209 haploid 07011408_0001 x 202 210 haploid 07011408_0002 x 203 211 haploid 06100319_0001 x 204 212 haploid 06070468_0001 x 205 213 haploid 06121385_0002 x 206 214 haploid 06100537_0001 x 207 215 haploid 06120726_0001 x 208 216 haploid 06070883_0001 x 209 217 haploid 06040041_0001 x 210 218 haploid 06100263_0001 x 211 219 haploid 06040043_0009 x 212 220 haploid 06101232_0001 x 213 221 haploid 06060189_0003 x 214 222 haploid 06091275_0002 x 215 223 haploid 06060097_0001 x 216 224 haploid 06100873_0001 x 217 225 haploid 06050038_0001 x 218 226 haploid 06100025_0001 x 219 227 haploid 06100940_0002 x 220 228 haploid 06040800_0001 x 221 229 haploid 06071007_0002 x 222 230 haploid 06020043_0026 x 223 231 haploid 06060811_0153 x 224 232 haploid 06080751_0001 x 225 233 haploid 06050178_0068 x 226 234 haploid 06040287_0001 x 227 236 haploid 06101496_0001 x 228 237 haploid 06040643_0001 x 229 238 haploid 06045788_0003 x 230 239 haploid 06050326_0001 x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 21 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Analysis (Continued) 231 240 haploid 06080649_0002 x 232 241 haploid 06080649_0003 x 233 242 haploid 06080601_0001 x 234 243 haploid 06101247_0001 x 235 244 haploid 06111271_0001 x 236 245 haploid 06090337_0001 x 237 246 haploid 06050125_0002 x 238 247 haploid 06050331_0001 x 239 248 haploid 06060728_0002 x 240 249 haploid 06080109_0001 x 241 250 haploid 06101048_0001 x 242 251 haploid 06051077_0001 x 243 253 haploid 06041067_0003 x 244 254 haploid 06040302_0002 x 245 255 haploid 06110121_0001 x 246 256 haploid 06090845_0001 x 247 257 haploid 06060375_0001 x 248 258 haploid 06070494_0001 x 249 259 haploid 06040938_0003 x 250 260 haploid 06081010_0001 x 251 261 haploid 06070415_0003 x 252 263 haploid 07010776_0001 x 253 264 haploid 06120890_0001 x 254 265 haploid 06120316_0001 x 255 266 haploid 06121413_0001 x 256 267 haploid 06090247_0001 x 257 268 haploid 06090247_0002 x 258 269 haploid 06090801_0001 x 259 270 haploid 06041160_0002 x 260 271 haploid 06031248_0001 x 261 272 haploid 07010075_0001 x 262 273 haploid 07011039_0001 x 263 274 haploid 06041232_0001 x 264 275 haploid 06101271_0002 x 265 276 haploid 06060506_0001 x 266 277 haploid 06080566_0001 x 267 278 haploid 06060124_0001 x 268 279 haploid 07020168_0001 x 269 281 haploid 06090909_0002 x 270 282 haploid 06080869_0001 x 271 1 commercial pisifera BL605/39-04 2x 272 2 commercial pisifera BL607/91-10 2x 273 3 commercial pisifera BL612/84-05 2x 274 4 commercial pisifera BL1120/75-07 2x 275 5 commercial pisifera BL143/04-10 2x 276 6 commercial pisifera BL147/21-05 2x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Analysis (Continued) Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 22 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Analysis (Continued) 277 7 commercial pisifera BL148/05-08 2x 278 8 commercial pisifera BL158/A2-13 2x 279 1 commercial tenera BL10452/207-02 2x 280 2 commercial tenera BL10323/104-06 2x 281 3 commercial tenera BL1177/184-09 2x 282 1 commercial dura BL10887/08-22 2x 283 2 commercial dura BL10885/08-27 2x 284 3 commercial dura BL1221/51-14 2x 285 4 commercial dura BL1222/32-02 2x 286 5 commercial dura BL1224/14-19 2x 287 6 commercial dura BL1231/02-01 2x 288 7 commercial dura BL1235/14-01 2x 289 8 commercial dura BL1125/03-02 2x 290 9 commercial dura BL1124/17-09 2x 291 10 commercial dura BL1136/01-02 2x 292 11 commercial dura BL10868/12-10 2x 293 12 commercial dura BL10868/12-11 2x 294 13 commercial dura BL10868/12-13 2x 295 14 commercial dura BL10879/08-06 2x 296 15 commercial dura BL10879/08-07 2x 297 16 commercial dura BL10879/08-09 2x 298 17 commercial dura BL10883/04-06 2x 299 18 commercial dura BL10883/04-08 2x 300 19 commercial dura BL10883/04-09 2x 301 20 commercial dura BL10883/05-06 2x 302 21 commercial dura BL10891/04-23 2x 303 22 commercial dura BL10891/04-24 2x 304 23 commercial dura BL10891/05-22 2x 305 24 commercial dura BL10891/05-23 2x 306 25 commercial dura BL10873/52-18 2x 307 26 commercial dura BL10873/52-19 2x 308 27 commercial dura BL10873/52-21 2x 309 28 commercial dura BL10873/53-19 2x 310 29 commercial dura BL1229/48-15 2x 311 30 commercial dura BL1230/42-15 2x 312 31 commercial dura A1122/04-01 2x 313 32 commercial dura A1122/12-05 2x 314 33 commercial dura A1122/12-08 2x 315 34 commercial dura A1122/36-02 2x 316 35 commercial dura A1123/01-02 2x 317 36 commercial dura A1123/01-06 2x 318 37 commercial dura A1123/01-07 2x 319 38 commercial dura A1123/01-12 2x 320 39 commercial dura A1130/02-02 2x 321 40 commercial dura A1130/02-06 2x 322 41 commercial dura A1130/02-10 2x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 23 of 25 able 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Analysis (Continued) 323 42 commercial dura A1130/02-16 2x 324 43 commercial dura A1127/08-16 2x 325 44 commercial dura A1127/08-06 2x 326 45 commercial dura A1127/05-11 2x 327 46 commercial dura A1127/05-03 2x 328 47 commercial dura B1134/35-09 2x 329 48 commercial dura B1133/07-10 2x 330 49 commercial dura B1136/21-11 2x 331 50 commercial dura B1136/21-12 2x 332 51 commercial dura C1128/07-14 2x 333 52 commercial dura C1121/13-08 2x 334 53 commercial dura BL11508/111-1 2x 335 54 commercial dura BL11396/11-21 2x 336 1 Ghana wild K31-1/GHANA/1-1 2x 337 2 Ghana wild K31-1/GHANA/41-498 2x 338 3 Ghana wild K31-1/GHANA/39-875 2x 339 4 Ghana wild K31-1/GHANA/31-430 2x 340 5 Ghana wild K31-1/GHANA/26-629 2x 341 6 Ghana wild K31-1/GHANA/24-1164 2x 342 7 Ghana wild K31-1/GHANA/56-1185 2x 343 8 Ghana wild K31-1/GHANA/29-1087 2x 344 9 Ghana wild K31-1/GHANA/38-1193 2x 345 10 Ghana wild K31-1/GHANA/43-994 2x 346 11 Ghana wild K31-1/GHANA/8-1100 2x 347 12 Ghana wild K31-1/GHANA/11-1192 2x 348 13 Ghana wild K31-1/GHANA/35-1190 2x 349 14 Ghana wild K31-1/GHANA/3-46 2x 350 15 Ghana wild K31-1/GHANA/5-102 2x 351 16 Ghana wild K31-1/GHANA/7-121 2x 352 17 Ghana wild K31-1/GHANA/12-239 2x 353 18 Ghana wild K31-1/GHANA/14-350 2x 354 19 Ghana wild K31-1/GHANA/18-368 2x 355 20 Ghana wild K31-1/GHANA/19-245 2x 356 21 Ghana wild K31-1/GHANA/21-1180 2x 357 22 Ghana wild K31-1/GHANA/32-1141 2x 358 23 Ghana wild K31-1/GHANA/37-1124 2x 359 24 Ghana wild K31-1/GHANA/45-448 2x 360 25 Ghana wild K31-1/GHANA/47-1175 2x 361 26 Ghana wild K31-1/GHANA/50-1037 2x 362 27 Ghana wild K31-1/GHANA/52-547 2x 363 28 Ghana wild K31-1/GHANA/53-1167 2x 364 29 Ghana wild K31-1/GHANA/54-1196 2x 365 30 Ghana wild K31-1/GHANA/57-1153 2x Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Principal Coordinates Analysis (Continued) Table 6: Identification codes, oil palm type and ploidy level of oil palm genotypes used in the Analysis (Continued) Dunwell et al. Principal Coordinates Analysis BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Page 24 of 25 Table 7 Primer pairs used in the Principal Coordinates Analysis to compare the genetic diversity and affinities of Hs compared with a representative sample of commercial and wild diploid palms (listed in Table 6) No Primer Forward (5’-3’) Reverse (5’-3’) 1 1996 CACTGGGGTCATCTTCATCT TCGTTCTCTTTCCTTTTGTC 2 2215 GAACTTGGCGTGTAACT TGGTAGGTCTATTTGAGAGT 3 2427 GAAGGGGCATTGGATTT CAGGTGACCAAGTGTAAT 4 2569 TAGCCGCACTCCCACGAAGC CCAGAATCATCAGACTCGGACAG 5 2595 TCAAAGAGCCGCACAACAAG ACTTTGCTGCTTGGTGACTTA 6 2600 GGGGATGAGTTTGTTTGTTC GGCAACATGAAGGTAAG 7 3282 GTAACAGCATCCACACTAAC GCAGGACAGGAGTAATGAGT 8 3298 GACTACCGTATTGCGTTCAG TTTATCAGGAGTTTTTGTTTGAGAG 9 3311 AATCCAAGTGGCCTACAG TCCCTACAATAGCCATCTC 10 3321 CAAGGAGGAGCAGGTGAG TACGGCCTCGGTTCTACAC 11 3399 AGCCAATGAAGGATAAAGG CCACTTAGAGGTAAAACAACAG 12 3400 CAATTCCAGCGTFAFTATAG AGTGGCAGTGGAAAAACAGT 13 3433 GGTTCAATGGCATACAT ACTCCCCTCTTTGACAT 14 3538 TCAAGCCACATCCTAACTAC CTCATAGCCTTTGTTGTGT 15 3544 AGCAGGGCAAGAGCAATACT TTCAGCAGCAGGAAACATC 16 3546 GCCTATCCCCTGAACTATCT TGCACATACCAGCAACAGAG 17 3574 AGAGACCCTATTTGCTTGAT GACAAAGAGCTTGTCACAC 18 3711 GTCTCATGTGGCTACCTCTC GCTAGGTGAAAAATAAAGTT 19 3819 CCTCCTTTGGAATTATG GTGTTTGATGGGACATACA 20 219 TTTGCTCGGCGGATACAT GGAGGGCAGGAACAAAAAGT 21 257 GCAGCTAGTCACCTGAAC GACGAGACTGGAAAGATG 22 782 CGTTCATCCCACCACCTTTC GCTGCGAGGCCACTGATAC 23 783 GAATGTGGCTGTAAATGCTGAGTG AAGCCGCATGGACAACTCTAGTAA 24 882 TTGATCTTAGACATAACATACTGTA AAAGCGCGTAATCTCATAGT 25 894 TGCTTCTTGTCCTTGATACA CCACGTCTACGAAATGATAA 26 3213 GCTCTTTGTATTTCCTGGTTC AGCAGCAAACCCTACTAACT 27 3691 GCATCATTGGACTATCATACC TTGTGAACCAGGGAACTATC 28 vs1 GAGATTACAAAGTCCAAACC TCAAAATTAAGAAAGTATGC All primers except VS1 were taken from Billotte et al. [27]. Table 7 Primer pairs used in the Principal Coordinates Analysis to compare the genetic diversity compared with a representative sample of commercial and wild diploid palms (listed in Table 6) All primers except VS1 were taken from Billotte et al. [27]. [31] using distance matrix with standardization (by dividing the distance inputs by the square root of n-1). Here, Hs were treated as the DHs they were assumed to generate; thus genotypes were homozygous not hemizygous. weekly intervals. The resultant pollen (0.03 g) was applied to a targeted section of the female inflorescence of a diploid dura palm. The inflorescence was then bagged to prevent inadvertent wind pollination. In addition, some untreated H plants contained up to 30% fully stained pollen using Fluorescein diacetate (FDA) that was presumed to be viable. Pollen from these plants and from palms with apparently inviable pollen (unstained) was applied to targeted sections of a female inflorescence of diploid dura palms in the same way as above. Colchicine treatment Roots of confirmed haploid seedlings were washed and immersed in 2.5, 5.0, 7.5, or 10 mM aqueous colchicine for 5 h. Seedlings were then rinsed with water and planted (2:1:1 v/v compost, sand and soil). g This work was funded by Sumatra Bioscience as part of their R&D programme in oil palm. The authors are grateful for the assistance of all staff of the Breeding Department and Seed Production Unit at Bah Lias Research Station, Indonesia. Author details 1 20. Germana MA: Haploids and doubled haploids in fruit trees. In Advances in Haploid Production in Higher Plants. Edited by: Touraev A, Forster BP, Jain SM. The Netherlands: Springer-Verlag; 2009:241-263. 1School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK. 2Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK. 3Sumatra Bioscience Pte Ltd, 8 Eu Tong Sen Street, #16-94/95 The Central, 059818, Singapore. 4PT Sumatra Bioscience, Bah Lias Research Station, North Sumatra, Indonesia. 5BioHybrids International Ltd, Earley, Reading, RG6 5FY, UK. 6Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685, Talca, Chile. 1School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK. 2Institute of Biological, Environmental and Rural Sciences, 21. Lim W, Earle ED: Enhanced recovery of doubled haploid lines from parthenogenetic plants of melon. Plant Cell Tiss Org 2009, 98:351-356. 22. Finkel E: With ‘phenomics,’ plant scientists hope to shift plant breeding into overdrive. Science 2009, 325:380-381. 23. Reijnders L, Huijbregts MAJ: Palm oil and the emission of carbon-based greenhouse gases. J Clean Product 2008, 16:477-482. 24. Parveez GKA: Biolistic mediated production of transgenic oil palm. Method Mol Biol 2009, 477:301-320. Received: 2 June 2010 Accepted: 7 October 2010 Published: 7 October 2010 29. Arumuganathan K, Earle ED: Estimation of nuclear DNA content of plants by flow cytometry. Plant Mol Biol Rep 1991, 9:221-231. Acknowledgements h k f d d A developing male inflorescence of a confirmed H at the PMC stage was treated with 2.5 mM colchicine via injection into the spathe. This treatment was repeated at This work was funded by Sumatra Bioscience as part of their R&D programme in oil palm. The authors are grateful for the assistance of all staff of the Breeding Department and Seed Production Unit at Bah Lias Research Station, Indonesia. Page 25 of 25 Page 25 of 25 Dunwell et al. BMC Plant Biology 2010, 10:218 http://www.biomedcentral.com/1471-2229/10/218 Authors’ contributions JMD, PDSC, SN and MJW conceived the project. SN, BPF and ACS supervised the phenotypic screen and flow cytometry. MJW supervised the molecular analysis conducted by SW, AEC, CSF and YA, and the cytology conducted by DM. JMD and MJW wrote the manuscript and all authors discussed the results and commented on the manuscript. 25. Persson UM, Azar C: Preserving the world’s tropical forests - a price on carbon may not do. Environ Sci Technol 2010, 44:210-215. JMD, PDSC, SN and MJW conceived the project. SN, BPF and ACS supervised the phenotypic screen and flow cytometry. MJW supervised the molecular analysis conducted by SW, AEC, CSF and YA, and the cytology conducted by 26. Croxford AE, Rogers T, Caligari PDS, Wilkinson MJ: High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar. New Phytol 2008, 180:594-607. y 27. Billotte N, Marseillac N, Risterucci AM, Adon B, Brottier P, Baurens FC, Singh R, Herran A, Asmady H, Billot C, Amblard P, Durand-Gasselin T, Courtois B, Asmono D, Cheah SC, Rohde W, Ritter E, Charrier A: Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq.). Theor Appl Genet 2005, 110:754-765. References Stone R: Ecology - Can palm oil plantations come clean? Science 2007, 317:1491. 11. Wilcove DS, Koh LP: Addressing the threats to biodiversity from oil-palm agriculture. Biodivers Conserv 2010, 19:999-1007. 11. Wilcove DS, Koh LP: Addressing the threats to biodiversity from oil-palm agriculture. Biodivers Conserv 2010, 19:999-1007. 12. Koh LP, Wilcove DS: Cashing in palm oil for conservation. Nature 2007, 448:993-994. 12. Koh LP, Wilcove DS: Cashing in palm oil for conservation. Nature 2007, 448:993-994. 13. Clements R, Posa MRC: Conservationists could slip up in oil-palm enterprise. Nature 2007, 449:403. 13. Clements R, Posa MRC: Conservationists could slip up in oil-palm enterprise. Nature 2007, 449:403. 14. Venter O, Meijaard E, Wilson K: Strategies and alliances needed to protect forest from palm-oil industry. Nature 2008, 451:16. 14. Venter O, Meijaard E, Wilson K: Strategies and alliances needed to protect forest from palm-oil industry. Nature 2008, 451:16. 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: Submit your next manuscript to BioMed Central and take full advantage of: 15. Corley RHV: Potential productivity of tropical perennial crops. Exp Agric 1983, 19:217-237. 15. Corley RHV: Potential productivity of tropical perennial crops. Exp Agric 1983, 19:217-237. 16. Murphy DJ: Oil palm: future prospects for yield and quality improvements. Lipid Technology 2009, 21:257-260. 16. Murphy DJ: Oil palm: future prospects for yield and quality improvements. Lipid Technology 2009, 21:257-260. 17. Jones LH: Prospects for biotechnology in oil palm (Elaeis guineensis) and coconut (Cocos nucifera) improvement. Biotech Genet Engin Rev 1989, 7:281-296. 18. Whitehead RA, Chapman GP: Twinning and haploidy in Cocos nucifera. Nature 1962, 195:1228-1229. 18. Whitehead RA, Chapman GP: Twinning and haploidy in Cocos nucifera. Nature 1962, 195:1228-1229. 19. References 30. Peakall R, Smouse PE: GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 2006, 6:288-295. 1. Duvick DN: Biotechnology in the 1930s: the development of hybrid maize. Nature Rev Genet 2001, 2:69-73. 1. Duvick DN: Biotechnology in the 1930s: the development of hybrid maize. Nature Rev Genet 2001, 2:69-73. 1. Duvick DN: Biotechnology in the 1930s: the development of hybrid maize. Nature Rev Genet 2001, 2:69-73. 2. Horie T, Shiraiwa T, Homma K, Katsura K, Maeda S, Yoshida H: Can yields of lowland rice resume the increases that they showed in the 1980s? Plant Prod Sci 2005, 8:259-274. 2. Horie T, Shiraiwa T, Homma K, Katsura K, Maeda S, Yoshida H: Can yields of lowland rice resume the increases that they showed in the 1980s? Plant Prod Sci 2005, 8:259-274. 31. Orloci L: Multivariate analysis in vegetation research Boston: The Hague, 2 1978. 31. Orloci L: Multivariate analysis in vegetation research Boston: The Hague, 2 1978. 3. Forster BP, Thomas WTB: Doubled haploids in genetics and plant breeding. Plant Breeding Rev 2005, 25:57-88. 3. Forster BP, Thomas WTB: Doubled haploids in genetics and plant breeding. Plant Breeding Rev 2005, 25:57-88. doi:10.1186/1471-2229-10-218 Cite this article as: Dunwell et al.: Production of haploids and doubled haploids in oil palm. BMC Plant Biology 2010 10:218. 4. Cook RR: A haploid Marglobe tomato. J Hered 1936, 27:433-435. 5. Maluszynski M, Kasha KJ, Szarejko I: Published protocols for other crop plant species. In Doubled Haploid Production in Crop Plants: A Manual. Edited by: Maluszynski M, Kasha KJ, Forster BP, Szarejko I. Dordrecht: Kluwer; 2003:309-335. 6. Dunwell JM: Haploids in flowering plants: origins and exploitation. Plant Biotech J 2010, 8:377-424. 6. Dunwell JM: Haploids in flowering plants: origins and exploitation. Plant Biotech J 2010, 8:377-424. 7. Kelly-Yong TL, Lee KT, Mohamed AR, Bhatia S: Potential of hydrogen from oil palm biomass as a source of renewable energy worldwide. Energ Policy 2007, 35:5692-5701. 8. Basiron Y: Palm oil production through sustainable plantations. Eur J Lipid Sci Technol 2007, 109:289-295. 8. Basiron Y: Palm oil production through sustainable plantations. Eur J Lipid Sci Technol 2007, 109:289-295. 9. Food and Agriculture Organization of the United Nations. Agricultural Production Statistics. [http://faostat.fao.org/]. 9. Food and Agriculture Organization of the United Nations. Agricultural Production Statistics. [http://faostat.fao.org/]. 10. Stone R: Ecology - Can palm oil plantations come clean? Science 2007, 317:1491. 10. Competing interests JMD, MJW, AEC and CSF have received research funding from BioHybrids International Ltd; SN, SW, ACS, DM and YA are employed fully or in part by Sumatra Bioscience; BPF is contracted to BioHybrids International Ltd; PDSC is Managing Director of BioHybrids International Ltd. 28. Billotte N, Risterucci AM, Barcelos E, Noyer JL, Amblard P, Baurens FC: Development, characterisation, and across-taxa utility of oil palm (Elaeis guineensis Jacq.) microsatellite markers. Genome 2001, 44:413-425. Received: 2 June 2010 Accepted: 7 October 2010 Published: 7 October 2010 References Bouvier L, Zhang YX, Lespinasse Y: Two methods of haploidization in pear, Pyrus communis L.: greenhouse seedling selection and in situ parthenogenesis induced by irradiated pollen. Theor Appl Genet 1993, 87:229-232. 19. Bouvier L, Zhang YX, Lespinasse Y: Two methods of haploidization in pear, Pyrus communis L.: greenhouse seedling selection and in situ parthenogenesis induced by irradiated pollen. Theor Appl Genet 1993, 87:229-232.
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Transplantation of Autologous Minced Bladder Mucosa for a One-Step Reconstruction of a Tissue Engineered Bladder Conduit
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Gisela Reinfeldt Engberg,1,2 Johan Lundberg,3 Clara Ibel Chamorro,1 Agneta Nordenskjöld,1,2 and Magdalena Fossum1,2 1 Department of Women’s and Children’s Health and Center of Molecular Medicine, Karolinska Institutet, Q3:03 Astrid Lindgren Children’s Hospital, 171 76 Stockholm, Sweden 2 Pediatric Surgery, Unit of Urology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 171 76 Stockholm, Sweden 3 Department of Clinical Neuroscience, Karolinska Institutet and Department of Neuroradiology, Karolinska University Hospital, 171 76 Stockholm, Sweden 1 Department of Women’s and Children’s Health and Center of Molecular Medicine, Karolinska Institutet, Q3:03 Astrid Lindgren Children’s Hospital, 171 76 Stockholm, Sweden 2 Pediatric Surgery, Unit of Urology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 171 76 Stockholm, Sweden 3 Department of Clinical Neuroscience, Karolinska Institutet and Department of Neuroradiology, Karolinska University Hospital, 171 76 Stockholm, Sweden orrespondence should be addressed to Magdalena Fossum; magdalena.fossum@ki.se Received 29 April 2013; Revised 12 August 2013; Accepted 18 September 2013 Received 29 April 2013; Revised 12 August 2013; Accepted 18 September 2013 Academic Editor: Esmaiel Jabbari Academic Editor: Esmaiel Jabbari Copyright © 2013 Gisela Reinfeldt Engberg 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. Surgical intervention is sometimes needed to create a conduit from the abdominal wall to the bladder for self-catheterization. We developed a method for tissue engineering a conduit for bladder emptying without in vitro cell culturing as a one-step procedure. In a porcine animal model bladder, wall tissue was excised and the mucosa was minced to small particles. The particles were attached to a tube in a 1 : 3 expansion rate with fibrin glue and transplanted back by attaching the tube to the bladder and through the abdominal wall. Sham served as controls. After 4-5 weeks, conduits were assessed in respect to macroscopic and microscopic appearance in 6 pigs. Two pigs underwent radiology before termination. Gross examination revealed a patent conduit with an opening to the bladder. Histology and immunostaining showed a multilayered transitional uroepithelium in all cases. Up to 89% of the luminal surface area was neoepithelialized but with a loose attachment to the submucosa. No epithelium was found in control animals. CT imaging revealed a patent channel that could be used for filling and emptying the bladder. Animals that experienced surgical complications did not form conduits. Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 212734, 10 pages http://dx.doi.org/10.1155/2013/212734 Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 212734, 10 pages http://dx.doi.org/10.1155/2013/212734 Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 212734, 10 pages http://dx.doi.org/10.1155/2013/212734 Gisela Reinfeldt Engberg,1,2 Johan Lundberg,3 Clara Ibel Chamorro,1 Agneta Nordenskjöld,1,2 and Magdalena Fossum1,2 Minced autologous bladder mucosa can be transplanted around a tubular mold to create a conduit to the urinary bladder without in vitro culturing. Research Article Transplantation of Autologous Minced Bladder Mucosa for a One-Step Reconstruction of a Tissue Engineered Bladder Conduit Gisela Reinfeldt Engberg,1,2 Johan Lundberg,3 Clara Ibel Chamorro,1 Agneta Nordenskjöld,1,2 and Magdalena Fossum1,2 1 Department of Women’s and Children’s Health and Center of Molecular Medicine, Karolinska Institutet, Q3:03 Astrid Lindgren Children’s Hospital, 171 76 Stockholm, Sweden 2 Pediatric Surgery, Unit of Urology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 171 76 Stockholm, Sweden 3 Department of Clinical Neuroscience, Karolinska Institutet and Department of Neuroradiology, Karolinska University Hospital, 171 76 Stockholm, Sweden 2. Materials and Methods Eleven 15–25 kg (11-12 weeks old) female Yorkshire-Swedish Country Pigs (Vallrum, Sala, Sweden) were initially used in this study. The protocol was pre-approved by the Stockholm County Committee on Animals and all procedures con- formed to the regulations for animal use, as well as relevant federal statutes.h 2.2. Mincing the Bladder Mucosa and the Preparation of Tubes. The excised bladder wall was washed in Dulbecco’s modified Eagle medium (Sigma-Aldrich, Steinheim, Germany) twice, and the detrusor muscle was removed mechanically with curved scissors for dissection (Figures 1(e) and 1(f)). The mucosal tissue was stretched on a cutting board and thickness was measured with a caliper to approximately 0,2 mm and appropriate amount of bladder mucosa was removed. As we aimed for a 3-fold expansion rate for regeneration of a confluent mucosa in vivo, we estimated the area of the inner surface of the conduit by calculating the outer surface of the tubular mold (18 Fr) (Figure 2(b)). Five cm2 was therefore separated for use in the study (remaining bladder tissue was used for other studies). Immediately prior to transplantation, the graft was minced with a mincing device that has been developed for this purpose [12, 13] (Figure 2(a)). Briefly, the device cuts with 30 rotating cutting disks placed with 0.8 mm distance from each other. By running the device twice over the tissue in perpendicular directions, small square particles measuring approximately 0.2 × 0.8 × 0.8 mm in size were formed (Figure 1(g)). The pigs were stalled in pairs in every box except for a few hours postoperatively when they were kept single until they regained full normal activity. They had full supply of fresh water and were fed according to standard protocols at the animal institution where they were stalled. Heat lamps were used and the ground was covered with straw for rooting and toys for enrichment. Protocols were held to ensure normal urination pre- and postoperatively. Dressings and wounds were checked at least twice daily postoperatively to ensure early action if signs of infection, hernias, or other unpredictable events. Animals were euthanized at study endpoint up to 5 weeks posttransplantation. 2.1. Surgical Procedures. After a 12-hour fasting, an intra- muscular injection of azaperone 2 mg/kg (Stresnil, Janssen- Cilag, Pharma, Austria) was administered as premedica- tion. 1. Introduction and it can serve as a conduit for catheterization of the bladder [3, 4]. Drawbacks with using intestinal tissue for reconstructive urology include the need for laparotomy and high risk of mucus and stone formations as well as infections [5]. If the use of appendix is contraindicated, removal of distal small intestine can lead to secondary malabsorption of bile acids that induce diarrhea and malabsorption of liposoluble vitamins leading to malnutrition [6, 7]. Autologous tissue from the urinary system for tissue engi- neering would be an appealing approach for tissue recon- struction in pediatric urology. Conditions with lack of bladder tissue as well as low compliance and high pressure bladders, often need surgical intervention with an abdominal conduit for self-catheterization and/or a bladder augmenting approach, to reduce the risk of secondary renal failure.t For tissue engineering, the algorithm for clinical studies in the urinary pathway and for skin replacements has so far mostly included in vitro cell culturing for tissue expansion [8–11]. This procedure is however time consuming, demands high standard laboratory facilities, and is associated with high costs and will demand highly specialized centers. To date, reconstructions in the urinary pathway often use autologous intestinal tissue. Primarily, the appendix is used for self-catheterization of the bladder [1]. If nonexisting, or if the appendix is preferred for the creation of a stoma for antegrade enemas [2], the small intestine can be reconfigured 2 BioMed Research International 2 applications of chlorhexidine (Klorhexidin 5%, Fresenius Kabi, Sweden). The urinary bladder was catheterized using a 10-French silicone catheter, emptied and then filled with ster- ile saline solution (approximately 8 mL/kg of body weight). After exposure of the bladder by midline incision below the umbilicus, a lenticular area of the bladder dome measuring 12 cm longitudinally and 9 cm transversally (approximately a forth of the total bladder surface area) was marked, removed, and partly used in this study (Figures 1(c) and 1(d)). In previous studies, we transplanted small particles of skin or urothelium by attaching the minced tissue to three- dimensional tubular molds into the subcutaneous tissue in pigs [12, 13]. 1. Introduction After withdrawing the mold, a continuous epithelium in the luminal surface of subcutaneous tunnels was formed already after 2 weeks.h t The objective of the present study was to reconstruct such a three-dimensional conduit through the abdominal wall into the bladder in a large animal experimental model in order to catheterize the bladder through the canal. For postoperative analgesia, buprenorphine 45 micro- grams/kg (Temgesic, RB Pharmaceuticals, Great Britain) was administered by intramuscular injections in single doses. For infection prophylaxis, an intra-operative dose of trimetoprim 4 mg/kg and sulfonamide 20 mg/kg (Tribrissen vet, Intervet, Sweden) was administered by intramuscular injection and followed by injections twice daily for three days and then once daily for 5 days (total of 9 days). 2. Materials and Methods A combination of tiletamine hypochloride 2,5 mg/kg, zolazepam hypochloride 2,5 mg/kg (Zoletil, Virbac, France), and medetomidine 25 micrograms/kg (Domitor, Orion Pharma, Sweden) was then administered for induction of anesthesia together with atropine 25 micrograms/kg (Atropin, Mylan Inc, Canonsburg, PA) as intramuscular injections. Analgesic treatment was initiated peroperatively by administrating buprenorphine 45 micrograms/kg (Tem- gesic, RB Pharmaceuticals, Great Britain), carprofen 3 mg/kg (Rimadyl, Orion Pharma, Sweden) intravenously and by local injection of lidocaine (Xylocaine, AstraZeneca, Sweden) before skin incisions. 18 Fr latex catheters covered with a silicone elastomer (Bard Foley Catheter, C.A. Bard Inc, Covington, GA) were cut into 10 cm long tubes. Each end was closed with a 3- cm long segment of 16 Fr latex catheters sutured with 4- 0 nylon (Ethilon, Ethicon, Johnson & Johnson, Sweden) at right angles (stopping end) in order to secure the tubes into the bladder and to lower the risk of movement in the subcutaneous tissue (Figures 1(a) and 1(b)). To minimize the risk of infection during take of the transplants, the conduit was blocked until sedation for radiology studies and termination. Phenobarbiturate 15 mg/kg (Pentobarbital, APL, Sweden) was given prior endotracheal intubation and general anes- thesia was maintained with 0, 8–2% isoflurane (Isoflurane, Baxter, Deerfield, IL). Glucose 25 mg/mL (Baxter, Deerfield, IL) was administered intravenously and body temperature, saturation, blood pressure, and pulse were monitored during the whole procedure. 2.3. Transplantation. The 8 cm long outer surface (14.5 cm2) of the tube was covered with two thin layers of the sealer pro- tein concentrate (fibrinogen) from a two-component tissue sealant (Tisseel VH, Baxter, Westlake village, CA). Immedi- ately after the second application, the thrombin component was added and particles of minced bladder mucosa were applied evenly and randomly orientated. Two pigs underwent With the pig turned to a supine position, the abdominal skin was cleaned with chlorhexidine gluconate (Hibiscrub 40 mg/mL, Regent Medical, England) and with successive 3 3 BioMed Research International ed Research International (a) (b) (c) (d) (e) (f) (g) ∗ (h) e 1: (a) Cartoon demonstrating a cross-section of the pig urinary bladder and abdominal wall with a tube place inary bladder, through the abdominal muscle wall and to the cutaneous tissue. (b) Tube used for transplant sa showing stopping ends used to hold the tube still. (c) The pig urinary bladder exposed through the surgica er wall being removed. 2. Materials and Methods (b) Formula for calculating area of implanted mold and expected inner area of conduit. (c) Cross-section of conduit on slide with marking of inner surface with epithelial lining. No magnification. (a) L = 80mm D = 7mm D × 𝜋× L = area (b) (b) (a) (c) (c) Figure 2: (a) Side view of mincing device and insert demonstrating frontal aspect of central part of device with 30 parallel rotating cutting discs. (b) Formula for calculating area of implanted mold and expected inner area of conduit. (c) Cross-section of conduit on slide with marking of inner surface with epithelial lining. No magnification. For radiological assessment of the conduit, reconstruc- tion algorithm called Xper-CT, where the flat detector C-arm can perform volume acquisitions through back projection computed tomography (CT) reconstructions with a 0.5 mm slice thickness, was used [14]. Image stacks were then trans- ferred to a working station, postprocessed and analyzed in Osirix v 4.1.1 software (Open Source, OsiriX Foundation, Geneva, Switzerland). 3D surface rendering was used for gross anatomical illustration after examining CT stacks in axial, frontal, and sagittal planes. To illustrate the entire tract including the intact conduit, 3D curved multiplanar reconstructions (MPR) were performed as illustrated in the figure (Figure 3(d)). Animals were euthanized after radiolog- ical assessments. Johnson, Sweden) (Figures 1(a) and 1(h)). Thereafter, the wall of the urinary bladder and the abdomen were repaired. The subcutaneous tissue was closed in two layers with absorbable braided sutures (Polysorb, Tyco Healthcare, Mansfield, MA) and the skin with interrupted 3-0 nylon sutures (Ethilon, Ethicon, Johnson & Johnson, Sweden). 2.4. Catheterization and Radiological Assessment of 3D Con- duit. At 4 and 5 weeks after transplantation, two pigs (one each week) were sedated with sodium pentothal (Pentobarbi- talnatrium vet. 60 mg/mL, APL, Sweden) and fentanyl (Fen- tanyl vet. 50 𝜇g/mL, Braun, Germany) and placed in scanning equipment for angiography (XD20, Philips Medical System, Netherlands). In order to analyze the conduit for filling, emptying, and radiology, the transversal end of the tube, lying in the subcutaneous fat, was localized, skin was incised, and the end was cut off with scissors (Figures 1(a), 1(b), and 1(h)). The remaining tube was pushed into the bladder and the conduit was assessed from the newly created opening in the skin. An 8 Fr tube could be inserted through the conduit for filling and emptying the bladder. 2. Materials and Methods The detrusor muscle has been marked for easy identification and for measuring of tissu ation of bladder mucosa from the detrusor. (f) Bladder mucosa mounted to the left and separated detrusor les of bladder mucosa. (h) Tube with minced particles being placed in the surgical wound. In the top one, the tive bladder (upper arrow). Middle part of tube is resting on the abdominal muscle (asterix) and in the outer e r arrow). (a) (b) (a) (b) (d) (c) (d) (c) (e) (f) (f) (e) (g) ∗ (h) (g) (h) Figure 1: (a) Cartoon demonstrating a cross-section of the pig urinary bladder and abdominal wall with a tube placed to form a conduit from the urinary bladder, through the abdominal muscle wall and to the cutaneous tissue. (b) Tube used for transplantation of minced bladder mucosa showing stopping ends used to hold the tube still. (c) The pig urinary bladder exposed through the surgical wound. (d) Part of the bladder wall being removed. The detrusor muscle has been marked for easy identification and for measuring of tissue biopsy. (e) Mechanical separation of bladder mucosa from the detrusor. (f) Bladder mucosa mounted to the left and separated detrusor to the right. (g) Minced particles of bladder mucosa. (h) Tube with minced particles being placed in the surgical wound. In the top one, the end is coming out from the native bladder (upper arrow). Middle part of tube is resting on the abdominal muscle (asterix) and in the outer end placed under the skin (lower arrow). sham procedure with same size excision of bladder tissue and thereafter implantation of the same type of tubing covered with fibrin glue but without minced particles. inside). The tube was placed tangential through the abdom- inal wall, thus penetrating the abdominal rectus muscle and the oblique muscles before placement of the other end in the subcutaneous tissue, immediately under the skin, and sutured with 4-0 nylon to stay in place (Ethilon, Ethicon, Johnson & i Each tube was placed in the bladder with a purse string suture around the end of the tube (3 cm right angle part 4 BioMed Research International (a) L = 80mm D = 7mm D × 𝜋× L = area (b) (c) Figure 2: (a) Side view of mincing device and insert demonstrating frontal aspect of central part of device with 30 parallel rotating cutting discs. 3. Results the basal lamina, connective tissue, and mucus, according to standard protocols.h All pigs tolerated the excision and removal of bladder tissue (approximately 1/4 of bladder) and voided shortly after surgery and none developed postoperative fever or signs of strain or pain when voiding. The first four animals were affected by midline hernia. Two had to be euthanized due to incarceration of the small intestine 2 and 4 days postoperatively. The surgical technique was changed for the next animals so that bladder conduit was placed from the side of the dome, to the left of the midline, through the rectus muscles, and not through the midline incision. One pig was euthanized the second day postoperatively due to signs of pain. Autopsy showed a perforated ulceration of the ventricle. The two surviving animals with midline hernia ful filled the study protocol and were euthanized four weeks after trans- plantation. In these subjects, the midline hernia including small intestines was encountered by the tube, no conduit had been formed and no epithelium could be detected in the surrounding tissue on histological examination. By these means, a total of five animals were excluded due to surgical complications. The tissue specimens were evaluated by immunostaining with primary antibodies against various cytokeratins (1 : 300) (pancytokeratins 1–7, 10, 13–16 and 19, DakoCytomation, Cat# M0821, clone: MNF 116, Denmark) and uroplakin III (1 : 400) (Fitzgerald Industries, Clone AU1, CatRDI-PRO610108, Con- cord, MA). Biotinylated secondary antibodies were detected by using ABC-HRP kit (Vectastain Elite ABC kit, Vector Labs, UK) and all sections were developed employing 3,3󸀠- diaminobenzidine (DAB) (Sigma Chemical Co., St. Louis, MO) substrate according to standard routine and manufac- turer instructions. Mayer’s hematoxylin solution was used for counter staining. 2.6. Measurements of Neo-Epithelialization. Mean, standard deviation, and full range were used to evaluate planimetric data from tissue sections. All measurements were performed under 100x magnification in a light microscope (Axioscope 2 MOT Zeiss microscope) using a built in ruler. We calculated the mean epithelialized area of 5 serial sections for each biopsy specimen at four different levels of each conduit; at the junction to the bladder (0 cm), 3 (in the abdominal muscle), 5 (between muscle and subcutaneous fat), and 8 cm (in the subcutaneous fat) from the junction. The percentage was calculated for each level by linear measurement of the epithelium in relation to the total inner luminal surface (18 Fr) (Figures 2(b)-2(c)). 2. Materials and Methods Intravenous contrast agent, iohexol (Omnipaque 240 mg/mL, GE Healthcare, Sweden) and diuretics furosemide (Furix 10 mg/mL, Takeda Pharma, Sweden) were given in order to visualize the urinary excretory pathway including the kidneys, ureters, the urinary bladder, and the conduit. 2.5. Histological Examination. At 4 (6 animals) and 5 (2 animals) weeks posttransplantation, a lethal dose of sodium thiopental (Sodium Pentothal, Abbott Laboratories, North Chicago, IL) was administrated for termination. Tissue spec- imens including the whole conduit, from the subcutaneous tissue to the bladder were excised and fixed in 10% formalin solution prior to dehydration, embedding in paraffin and slicing into 5 𝜇m-thick sections. Slides were stained with haematoxylin-eosin (H&E) for routine histology, van Gieson for evaluation of collagen and other connective tissue, and periodic acid shift (PAS) for staining of carbohydrates in BioMed Research International 5 (a) (a) (b) (c) (d) (e) (E) (F) (G) (f) (g) Figure 3: In order to visualize the anatomical properties of the conduit an XD20 imaging system was used. (a) 3D reconstruction showing the gross anatomical conditions. (b) The concomitant side projection. (c) A 0.5 mm thick CT reconstructed slice is shown. In order to illustrate the conduits passage to the bladder, a MultiPlanar (MP) reconstruction was performed through the CT stack illustrated in (d). Arrows in (d) indicate orthogonal projections along the MP reconstruction. In (e), (f), and (g) showing orthogonal projections along the MP reconstruction illustrating functioning ureters filling the bladder and intact conduit. (d) (e) (E) (F) (G) (f) (g) (d) (E) (F) (G) (e) (b) (a) (e) (f) (b) (c) (f) (g) (d) (a) (c) (g) Figure 3: In order to visualize the anatomical properties of the conduit an XD20 imaging system was used. (a) 3D reconstruction showing the gross anatomical conditions. (b) The concomitant side projection. (c) A 0.5 mm thick CT reconstructed slice is shown. In order to illustrate the conduits passage to the bladder, a MultiPlanar (MP) reconstruction was performed through the CT stack illustrated in (d). Arrows in (d) indicate orthogonal projections along the MP reconstruction. In (e), (f), and (g) showing orthogonal projections along the MP reconstruction illustrating functioning ureters filling the bladder and intact conduit. 3. Results Two of the animals were sedated and the 18 French latex tubes did not adhere to the adjacent tissue and could easily be pushed into the bladder (not removed through the skin due to the stopping end). The remaining conduit was easy to catheterize using 8 Fr catheters and lidocaine anesthetic gel (2% Xylocaine gel, AstraZeneca, Sweden) for lubrication. Xper-CT reconstructions clearly showed an intact con- duit with contrast agent passage into the bladder both in the 6 BioMed Research International 6 (a) (b) Figure 4: Macroscopic appearance at removal of conduit. (a) Looking from inside the bladder that has been cut open. Inner opening to conduit is exposed. (b) Macroscopic appearance of transsection of conduit with catheter still in place in the lumen. (a) (b) (a) (b) Figure 4: Macroscopic appearance at removal of conduit. (a) Looking from inside the bladder that has been cut open. Inner opening to conduit is exposed. (b) Macroscopic appearance of transsection of conduit with catheter still in place in the lumen. bladder. At three and five centimeters from the junction, only transplanted conduits revealed epithelium (61, 22, 38, and 17%). At five centimeters, only half presented with epithelium (0, 0, 89, and 44%). From the most lateral part of the conduit, surrounded by subcutaneous fat, only traces of urothelial cells could be found in transplanted specimens. Conduit from control specimens had no epithelial lining in any tissue sections except at the junction to the bladder (Figures 6(e)– 6(h)). CT stacks reconstructed in three planes and in 3D surface rendered volumes (Figure 3). To illustrate the entire tract including the intact conduit 3D curved MPR, reconstructions were performed as illustrated in the figure (Figure 3(d)). This reconstruction clearly shows that the conduit is allowing fluid passage without leakage (Figures 3(a) and 3(b)). The bladder could be completely emptied by insertion of the catheter (not shown). Gross examination of the bladder revealed a scar in the frontal midline with no signs of inflammation. When opening the bladder, the mucosa had a normal appearance and the opening into the conduit revealed an orifice placed on the left side of the bladder dome with a normal mucosal lining (Figure 4(a)). 4. Discussion In this porcine, large animal study, we have created catheter- izable conduits by placing autologous urinary tissue around a three-dimensional mold (a tube) into the urinary bladder. The surgical technique is easy and fast forward and after removal of the mold, the conduit could be used for filling and emptying of the bladder. Advantages with the porcine model include a good-sized bladder for tissue harvesting and good tolerance for reduction of its size. No complications occurred in respect to infection. Histological assessments were obtained at 4 (4 samples including one control) and 5 weeks (2 samples including one control) after transplantation (Table 1). Routine histology of full thickness biopsies of the wall of the constructed conduit demonstrated a continuous epithelium covering the inner surface of the conduit in all cases except controls (Figure 5(a)). Morphology revealed a transitional cell epithe- lium up to 4 or 5 cell layers thick. Submucosal tissue revealed signs of inflammation with infiltration of mononucleated cells and less mature extracellular matrix in comparison to bladder biopsies (Figures 5(b) and 5(c)). PAS reaction revealed a supporting basal lamina underlying the neoepithe- lium (Figure 5(d)). We could document a patent conduit by administrating intravenous contrast and diuretics and performing 3D recon- structions of computed tomography images [14]. Kidneys excreted contrast and ureters and bladder were filled and then emptied through the tissue engineered bladder conduit. The use of 3D curved MPR was in accordance with CT urography guidelines used for high-definition visualization of an entire urinary tract albeit the use of angiographic equipment as primary imaging modality is not standard [15]. However, the Xper-CT algorithms give a high enough resolution to clearly provide an unambiguous image of the continuity of the open channel.h Immunostaining of cytokeratins and uroplakin showed that the cells covering the inner lumen were of uroepithelial origin (Figures 5(e) and 5(f)). Histology at 4 and 5 weeks after transplantation revealed up to 90% uroepithelial lining but the area with epithelium varied between samples, and regenerated mucosa was more loosely adhering than in native bladder mucosa (Figures 6(a)–6(d)). The two specimens that were subjected to catheterization before histology revealed loose epithelium in the lumen. 3. Results Gross appearance of conduit revealed that the tube used for transplantation was lying loose inside the conduit and that the wall surrounding had an even inner tubular shape with a glossy surface under some nonadhering debris (Figure 4(b)). 4. Discussion All samples (including con- trols) showed some urothelial cells at the junction to the The rationale for transplanting small parts of minced tissue for epithelial cells expansion by using the patients own body as a bioreactor has been discussed in previous publications [12, 13, 16]. For this study, we used a similar expansion rate as described before for creating epithelium around tubular molds (approximately 1 : 3 expansion), how- ever, under optimal conditions in a full-thickness wound BioMed Research International 7 Table 1: Table summarizing results from the analyses of conduits at different distances from the bladder junction. Animals numbered 1–4 were transplanted with minced urothelial particles, and animals 1 and 4 underwent radiological assessment before termination. At the junction, (0 cm) part of the native bladder was included in the biopsy. Biopsies from conduit running through the abdominal muscle (3 cm) reveal a median urothelial lining of 6 mm, SD 2.5 mm (33 ± 13%). Biopsy at the boarder between abdominal muscle and subcutaneous fat (5 cm) demonstrates a median urothelial lining of 6 mm, SD 6 mm (33 ± 33%). Table 1: Table summarizing results from the analyses of conduits at different distances from the bladder junction. Animals numbered 1–4 were transplanted with minced urothelial particles, and animals 1 and 4 underwent radiological assessment before termination. At the junction, (0 cm) part of the native bladder was included in the biopsy. Biopsies from conduit running through the abdominal muscle (3 cm) reveal a median urothelial lining of 6 mm, SD 2.5 mm (33 ± 13%). Biopsy at the boarder between abdominal muscle and subcutaneous fat (5 cm) demonstrates a median urothelial lining of 6 mm, SD 6 mm (33 ± 33%). Pig Weeks after transplantation 0 cm (mm) 3 cm (mm) 3 cm (%) 5 cm (mm) 5 cm (%) 8 cm (mm) Inner lumen (mm) 1 X-ray 4 18 11 61 + + + 18 2 4 18 4 22 + + + 18 3 4 18 6 33 17 89 + 18 4 X-ray 5 18 3 17 8 44 + 18 5 Control 4 16 0 0 0 0 0 18 6 Control 5 16 0 0 0 0 0 18 All transplanted conduits demonstrated some urothelial cells at the most distal part of the conduit but none in controls. 4. Discussion Marking with (+) indicates the presence of urothelial cells but not as confluent epithelium at the inner luminal surface. All transplanted conduits demonstrated some urothelial cells at the most distal part of the conduit but none in controls. Marking with (+) indicates the presence of urothelial cells but not as confluent epithelium at the inner luminal surface. 25𝜇M (a) 100 𝜇M (b) 100 𝜇M (c) 50𝜇M (d) 100 𝜇M (e) 50𝜇M (f) Figure 5: Microscopic analyses of tissue sections from conduit and from native bladder. (a) Wall of conduit covered with epithelium toward lumen after 4 weeks and submucosal capillaries (∗) (H&E). (b) Staining of submucosal tissue from conduitwall (Van Gieson). (c) Staining of submucosal tissue from native pig bladder wall (Van Gieson). (d) Basal membrane under the epithelial cells (arrows) (PAS). (e) Immunostaining of cytokeratins (MNF116) in epithelial lining of conduit wall. (f) Immunostaining of Uroplakin III in epithelial lining of conduit wall. 100 𝜇M (c) 100 𝜇M (b) 25𝜇M (a) (c) (b) (a) 50𝜇M (d) 50𝜇M (f) 100 𝜇M (e) (f) (d) (e) Figure 5: Microscopic analyses of tissue sections from conduit and from native bladder. (a) Wall of conduit covered with epithelium toward lumen after 4 weeks and submucosal capillaries (∗) (H&E). (b) Staining of submucosal tissue from conduitwall (Van Gieson). (c) Staining of submucosal tissue from native pig bladder wall (Van Gieson). (d) Basal membrane under the epithelial cells (arrows) (PAS). (e) Immunostaining of cytokeratins (MNF116) in epithelial lining of conduit wall. (f) Immunostaining of Uroplakin III in epithelial lining of conduit wall. healing model, a 100-fold expansion rate was successful after only 14 days [17]. This indicates that further improvements of the healing conditions in our experimental model could result in successful take and regeneration also with smaller amounts of tissue at initiation. glycosaminoglycans normally residing on the surface of the bladder mucosa [18]. Until now, we have not tried removing this mucous layer before mincing and transplantation. Histology at 4 and 5 weeks posttransplantation demon- strated a multilayered transitional uroepithelium along the inside of the newly formed conduit (Figure 5). The histol- ogy revealed that during this time period, the transplanted minced autologous urothelial transplants had reorganized from a random placement on the mold to a well-organized, continuous layer of mature epithelium facing the lumen and without adherence to the mold [13]. 4. Discussion The basal membrane Due to the mincing device, particle size was basically uniform although for urothelium, it is sometimes hard to get 100% dissociation between the particles in comparison to minced skin epithelium. Sometimes 2–5 mucosa particles attach to each other even though they had been mechan- ically separated, the reason for this is probably the sticky 8 BioMed Research International 8 (a) (b) (c) (d) (e) (f) (g) (h) Figure 6: H and E staining of cross-sections from different parts of a conduit. (a)–(d): transplanted conduit. (e)–(h): sham operated control. (a) and (e) at junction between bladder and conduit. (b) and (f) 3 cm from junction. (c) and (g) 5 cm from junction. (d) and (h) 8 cm from junction. (a) (d) (b) (c) (c) (d) (a) (b) (h) (f) (e) (g) (f) (g) (h) (e) Figure 6: H and E staining of cross-sections from different parts of a conduit. (a)–(d): transplanted conduit. (e)–(h): sham operated control. (a) and (e) at junction between bladder and conduit. (b) and (f) 3 cm from junction. (c) and (g) 5 cm from junction. (d) and (h) 8 cm from junction. of the neo-epithelium covered the newly created channel. At the same time, tissue had expanded by division of cells from the transplanted tissue, most probably from the edges of the minced transplants according to the theory of Meek [19]. Histology from control animals showed no epithelium, which excludes that urothelium derived by migration from the bladder.fi be an acceptable material for implantation, in particular not in the group of patients that could potentially benefit from its application, we need to further study alternative materials in the molds before clinical application. Also, with longer time of exposure, 4-5 weeks, latex might have had a negative effect on the newly formed epithelium. We also found that only half of the amount of conduits demonstrated urothelium at 5 cm from the bladder junction and only traces of urothelial cells were found at 8 cm (Table 1). One reason for this could be that the fatty tissue surrounding this part of the conduit had lower vascularization and poorer conditions for take of transplant than the medial part that passed through the abdominal muscles. The most lateral part might also be more susceptible for trauma by outer pressure to the skin as well as friction due to movements of the skin. 4. Discussion In this porcine in vivo study, we encountered difficulties that influenced the outcome negatively. Differences in pig anatomy, compared to human, include the intraperitoneal position of the urinary bladder. The animals had a risk of developing incarcerated intestinal midline hernias and the four animals that experienced this also had undesirable out- comes (two early terminations and two negative results). In this matter, we experienced a learning curve and by creating the conduit in a paramedian location through the abdominal rectus muscle, this problem was solved. Additionally, one pig was terminated due to acute peptic ulcer of unclear etiology. At the end of the study, a total of six conduits could be analyzed including two sham operated controls.f Histology of the two conduits that had been exposed to radiological examinations and catheterizations revealed urothelium in the lumen that had detached from the surface. The mechanical trauma from expelling the inner tube and insertion of a catheter most probably eroded the surface. This suggests that the neoepithelium is not strong enough for longstanding duration. In studies of transplanted cul- tured skin epithelium for treatment of severe burn injuries, the subepithelial tissue of the dermis seems imperative for good mechanical strength, stability, and to reduce the risk of peeling off and infection [21]. This might be a factor for bad attachment of the urothelium also in our cases. Although some submucosal tissue from the lamina propria is transplanted within the minced tissue, the regenerative properties of the cells and structures are not the same as for epithelium and thereby the supporting mechanical structures might not be strong enough in our study model. Differences in body physiology including the resting and natural standing positions of the pig in combination with a fast increase in body weight (20 to 60 kg in 4 weeks) might also exert high-mechanical stress on the conduit [20]. The changes in histological appearance with inflammatory submucosal infiltration and loosely attached epithelium com- pared to native urothelium might be due to these factors. In this study, we chose latex covered with a thin silicon elastomer to form the mold for guided tissue regeneration. The rationale for this was that previous studies showed a more favorable outcome in respect to neoepithelialization when compared to silicone molds [12]. After ten days in vivo, latex tubes demonstrated a significantly larger area of neoepithelialization in comparison to the silicon tube counterparts. References l Although we found that minced urothelium expands and regenerates and that submucosal capillary networks develop that support epithelial nutrition, further improvements need to be undertaken in order for the newly formed tissue to withstand catheterizations several times a day. Most likely lack of appropriate lamina propria and a reduced amount of anchoring filaments and normal junctions between basal cells and the submucosa is the key problem for mechanical durability as the conduit runs through muscular and fatty tissue of the abdominal wall in analogy to problems related to transplanted cultured skin [22]. One mode of action might be to add minced bladder submucosal tissue with the minced bladder mucosa. We also hypothesize that a collagen carrier could support further submucosal tissue regeneration [23]. Preliminary studies have shown that a collagen-PCL hybrid construct does support migration, reorganization, and expansion of minced bladder mucosa in vitro and this could be next step for addressing this problem and further improving the method [24]. [1] P. Mitrofanoff, “Trans-appendix continent vesicostomy in treat- ment of neurogenic bladder in children,” Chirurgie Pediatrique, vol. 21, no. 4, pp. 297–305, 1980 (French). [2] P. S. Malone, P. G. Ransley, and E. M. Kiely, “Preliminary report: the antegrade continence enema,” The Lancet, vol. 336, no. 8725, pp. 1217–1218, 1990. [3] J. A. Leslie, A. M. Dussinger, and K. K. Meldrum, “Creation of continence mechanisms (Mitrofanoff) without appendix: the Monti and spiral Monti procedures,” Urologic Oncology, vol. 25, no. 2, pp. 148–153, 2007. [4] I. D. Sugarman, P. S. Malone, T. R. Terry, and M. A. Koyle, “Transversely tubularized ileal segments for the Mitrofanoff or Malone antegrade colonie enema procedures: the Monti principle,” British Journal of Urology, vol. 81, no. 2, pp. 253–256, 1998. [5] M. Gibbons, “Urinary problems after formation of a Mitrofanoff stoma,” Professional Nurse, vol. 10, no. 4, pp. 221–224, 1995. [6] J. Fitchner, “Follow-up after urinary diversion,” Urologia Inter- nationalis, vol. 63, pp. 40–45, 1999. [7] B. A. Vanderbrink, M. P. Cain, S. King et al., “Is oral vitamin B12 therapy effective for vitamin B12 deficiency in patients with prior ileocystoplasty?” Journal of Urology, vol. 184, supplement 4, pp. 1781–1785, 2010. In future studies, we would add a supportive matrix that could promote submucosal tissue regeneration and strengthen the anchorage of the neo-epithelial to the under- lying tissue [16]. In a human setting, one of the advantages would be an extraperitoneal placement. 4. Discussion As a proof of principle, we therefore chose latex in this animal model. However, as latex is not considered to In our previous studies using minced epithelium in the subcutaneous tissue, we also noted a tendency of loosening of the epithelial lining with time in vivo [12, 13]. Due to these findings, we hypothesized that contact with the bladder BioMed Research International 9 Swedish Brain Foundation, the Swedish Research council, and Karolinska Institutet, supported this work. Swedish Brain Foundation, the Swedish Research council, and Karolinska Institutet, supported this work. Swedish Brain Foundation, the Swedish Research council, and Karolinska Institutet, supported this work. cavity and filling of urine would overcome the problem of placing a foreign body (the tube) in a blind cavity. However, as we still experience histological results with loosely adhering epithelium, we conclude that this mode of action was not enough for reducing the inflammatory reaction. References Postoperatively, the patient would not be resting on the transplanted area and neither would a significant change of body weight be expected during the course of a month. [8] M. Fossum and A. Nordenskj¨old, “Tissue-engineered trans- plants for the treatment of severe hypospadias,” Hormone Research in Pædiatrics, vol. 73, no. 2, pp. 148–152, 2010. [9] A. Raya-Rivera, D. R. Esquiliano, J. J. Yoo, E. Lopez-Bayghen, S. Soker, and A. Atala, “Tissue-engineered autologous urethras for patients who need reconstruction: an observational study,” The Lancet, vol. 377, no. 9772, pp. 1175–1182, 2011. In conclusion, we demonstrate that it is possible to create conduits to the urinary bladder by randomly transplanting small particles of autologous urothelial tissue on a tubular mold placed in a surgically created canal through the abdom- inal wall. The method is easy to perform and the transplanted tissue specimens have capacity to expand around the mold without requiring any ex vivo cell culturing. Further studies are needed in order to evaluate the mechanical strength of the neo-epithelium in the newly formed conduits, in particular after injury that may occur when catheterizing the stoma. With further success, this could be of value for a large group of patients needing bladder emptying by catheterization through an abdominal stoma. [10] A. Atala, S. B. Bauer, S. Soker, J. J. Yoo, and A. B. Retik, “Tissue-engineered autologous bladders for patients needing cystoplasty,” The Lancet, vol. 367, no. 9518, pp. 1241–1246, 2006. [11] L. Mart´ınez-Santamar´ıa, S. Guerrero-Aspizua, and M. del R´ıo, “Skin bioengineering: preclinical and clinical applications,” Actas Dermo-Sifiliogr´aficas, vol. 103, no. 1, pp. 5–11, 2012. [12] M. Fossum, B. Zuhaili, T. Hirsch et al., “Minced skin for tissue engineering of epithelialized subcutaneous tunnels,” Tissue Engineering A, vol. 15, no. 8, pp. 2085–2092, 2009. [13] M. Fossum, B. Zuhaili, J. Bergmann, M. Spielmann, T. Hirsch, and E. Eriksson, “Minced urothelium to create epithelialized subcutaneous conduits,” Journal of Urology, vol. 184, no. 2, pp. 757–761, 2010. Conflict of Interests [14] M. S¨oderman, D. Babic, S. Holmin, and T. Andersson, “Brain imaging with a flat detector C-arm: technique and clinical interest of XperCT,” Neuroradiology, vol. 50, no. 10, pp. 863–868, 2008. No financial conflict of interests exists for any of the authors. Acknowledgments [15] A. J. Molen, N. C. Cowan, U. G. Mueller-Lisse, C. C. A. Nolte- Ernsting, S. Takahashi, and R. H. Cohan, “CT urography: definition, indications and techniques. A guideline for clinical practice,” European Radiology, vol. 18, no. 1, pp. 4–17, 2008. The authors thank Professor Elof Eriksson, Harvard Med- ical School, for the kind provision of the mincing device. Grants from the Swedish Society for Medical Research, the Promobilia Foundation, the Crown Princess Lovisa Founda- tion, the Freemason Foundation for Children’s Welfare, the Solstickan Foundation, the Swedish Society of Medicine, the [16] T. Svensj¨o, B. Pomahac, F. Yao, J. Slama, N. Wasif, and E. Eriks- son, “Autologous skin transplantation: comparison of minced skin to other techniques,” Journal of Surgical Research, vol. 103, no. 1, pp. 19–29, 2002. BioMed Research International 10 [17] F. Hackl, J. Bergmann, S. R. Granter et al., “Epidermal regen- eration by micrograft transplantation with immediate 100-fold expansion,” Plastic and Reconstructive Surgery, vol. 129, no. 3, pp. 443e–452e, 2012. [18] J. C. Nickel and J. Cornish, “Ultrastructural study of an antibody-stabilized bladder surface: a new perspective on the elusive glycosaminoglycan layer,” World Journal of Urology, vol. 12, no. 1, pp. 11–14, 1994. [19] C. P. Meek, “Successful microdermagrafting using the Meek- Wall microdermatome,” The American Journal of Surgery, vol. 96, no. 4, pp. 557–558, 1958. [20] P. Geutjes, L. Roelofs, H. Hoogenkamp et al., “Tissue engineered tubular construct for urinary diversion in a preclinical porcine model,” The Journal of Urology, vol. 188, no. 2, pp. 653–660, 2012. [21] M. Meuli and M. Raghunath, “Tops and flops using cultured epithelial autografts in children,” Pediatric Surgery Interna- tional, vol. 12, no. 7, pp. 471–477, 1997. [22] M. Raghunath and M. Meuli, “Cultured epithelial autografts: diving from surgery into matrix biology,” Pediatric Surgery International, vol. 12, no. 7, pp. 478–483, 1997. [23] J. L. Pariente, B. S. Kim, and A. Atala, “In vitro biocompatibility assessment of naturally derived and synthetic biomaterials using normal human urothelial cells,” Journal of Biomedical Materials Research, vol. 55, no. 1, pp. 33–39, 2001. [24] F. Ajalloueian, S. Zeiai, R. Rojas, M. Fossum, and J. Hilborn, “One-stage tissue engineering of bladder wall patches for an easy-to-use approach at the surgical table,” Tissue Engineering C, vol. 19, no. 9, pp. 688–696, 2013.
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Introduction to the special issue: “Natural Product Discovery and Development in the Genomic Era: 2019”
Journal of industrial microbiology and biotechnology/Journal of industrial microbiology & biotechnology
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Introduction to the special issue: “Natural Product Discovery and Development in the Genomic Era: 2019” Published online: 7 February 2019 © Society for Industrial Microbiology and Biotechnology 2019 Republic, Denmark, Germany, Italy, Netherlands, Spain, Switzerland, and United Kingdom). The Honorary Co-chairs for the meeting were Professors Heinz Floss and Christopher Walsh. This Special Issue is dedicated to Professors Floss and Walsh for their outstanding contributions to the under- standing of the fundamental enzymology of natural product biosynthesis in microorganisms that has helped establish the basis for current advances on genome mining and combina- torial biosynthesis for drug discovery. Their contributions are described in more detail in the accompanying Dedication prepared by Rolf Müller and Gerry Wright. This special issue of the Journal of Industrial Microbiol- ogy and Biotechnology contains reviews, original articles, and perspectives describing recent scientific advances in natural product discovery and development. The volume is composed primarily of information presented at the 2nd International Conference on “Natural Product Discovery and Development in the Genomic Era” held in Clearwater, Florida, in January of 2018. The conference was co-spon- sored by the Society for Industrial Microbiology (SIMB), the Korean Society for Microbiology and Biotechnology (KMB), and the Society for Actinomycetes Japan (SAJ), and was attended by 175 scientists from North America (USA and Canada), South America (Brazil and Chile), Asia (Japan, South Korea, and China), and Europe (Czech Publisher’s Note  Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. * Richard H. Baltz rbaltz923@gmail.com rbaltz923@gmail.com 1 CognoGen Biotechnology Consulting, 7636 Andora Drive, Sarasota, FL 34238, USA 2 Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113‑0033, Japan 3 Department of Biological Engineering, Inha University, Incheon 402‑751, Korea 4 Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany 5 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Introduction to the special issue: "Natural Product Discovery and Development in the Genomic Era: 2019". Item Type Editorial Authors Baltz, Richard H; Abe, Ikuro; Kim, Eung-Soo; Müller, Rolf; Van Lanen, Steven G; Wright, Gerry Citation J Ind Microbiol Biotechnol. 2019 Mar;46(3-4):249. doi: 10.1007/ s10295-019-02138-w. DOI 10.1007/s10295-019-02138-w Publisher Springer Journal Journal of industrial microbiology & biotechnology Rights Attribution 4.0 International Download date 24/10/2024 04:05:03 Item License http://creativecommons.org/licenses/by/4.0/ Link to Item http://hdl.handle.net/10033/622732 Journal of Industrial Microbiology & Biotechnology (2019) 46:249 https://doi.org/10.1007/s10295-019-02138-w EDITORIAL EDITORIAL EDITORIAL Introduction to the special issue: “Natural Product Discovery and Development in the Genomic Era: 2019” Limestone Street, Lexington, KY 40536, USA 6 Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada 1 CognoGen Biotechnology Consulting, 7636 Andora Drive, Sarasota, FL 34238, USA 2 Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113‑0033, Japan 3 Department of Biological Engineering, Inha University, Incheon 402‑751, Korea 4 Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany 5 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY 40536, USA 6 Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada :(0123456789) 1 3 :(0123 1
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Metabolic signatures of germination triggered by kinetin in Medicago truncatula
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Metabolic signatures of germination triggered by kinetin in Medicago truncatula Received: 11 March 2019 Accepted: 1 July 2019 Published: xx xx xxxx Susana Araújo   1, Andrea Pagano2, Daniele Dondi3, Simone Lazzaroni3, Eduardo Pinela Anca Macovei2 & Alma Balestrazzi2 In the present work, non-targeted metabolomics was used to investigate the seed response to kinetin, a phytohormone with potential roles in seed germination, still poorly explored. The aim of this study was to elucidate the metabolic signatures of germination triggered by kinetin and explore changes in metabolome to identify novel vigor/stress hallmarks in Medicago truncatula. Exposure to 0.5 mM kinetin accelerated seed germination but impaired seedling growth. Metabolite composition was investigated in seeds imbibed with water or with 0.5 mM kinetin collected at 2 h and 8 h of imbibition, and at the radicle protrusion stage. According to Principal Component Analysis, inositol pentakisphosphate, agmatine, digalactosylglycerol, inositol hexakisphosphate, and oleoylcholine were the metabolites that mostly contributed to the separation between 2 h, 8 h and radicle protrusion stage, irrespective of the treatment applied. Overall, only 27 metabolites showed significant changes in mean relative contents triggered by kinetin, exclusively at the radicle protrusion stage. The observed metabolite depletion might associate with faster germination or regarded as a stress signature. Results from alkaline comet assay, highlighting the occurrence of DNA damage at this stage of germination, are consistent with the hypothesis that prolonged exposure to kinetin induces stress conditions leading to genotoxic injury. At the onset of germination, the transition from a dry quiescent state to a fully hydrated state is associated with extensive metabolic changes1,2. This is a crucial phase for seed viability and vigor since water up-take causes increased ROS (reactive oxygen species)-mediated oxidative injury3,4, and exacerbates genotoxic damage5,6. These deleterious effects are counterbalanced by effective ROS scavenging mechanisms that limit the damage within the cellular environment7 whereas the removal of DNA lesions is carried by dedicated repair pathways that contrib- ute to safeguard genome integrity8–11. The successful mitigation of oxidative damage towards macromolecules, including genotoxic insults correlates with enhanced seed vigor11,12. DNA repair represents a distinctive feature of the seed pre-germinative metabolism and the work by Waterworth et al.6 has clearly highlighted the cru- cial role of the DNA checkpoint kinase ATM (ATAXIA TELANGIECTASIA MUTATED) and ATR (ATM AND RAD3-RELATED) as major determinants of seed viability and vigor in the model plant Arabidopsis thaliana. www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 Metabolic signatures of germination triggered by kinetin in Medicago truncatula Studies carried in the model legume Medicago truncatula have demonstrated that the DNA damage response triggered during early seed imbibition features the up-regulation of key BER (base excision repair) genes, as OGG1 (8-oxoguanine glycosylase/lyase) and FPG (formamidopyrimidine DNA glycosylase) required to remove the DNA oxidative lesions under physiological and stress conditions9,10,13.hf p y g The positive correlation between an effective antioxidant and DNA repair response within the pre-germinative metabolism and the degree of seed vigor is the driving force of priming, a pre-sown technique that allows to carry seed imbibition under controlled conditions, in order to boost the seed repair and protective activities14–16. Additional benefits can rise by adding bioactive molecules, e.g. phytohormones, however the treatment must be stopped before radicle protrusion occurs otherwise desiccation tolerance will be lost17,18. In the case of ‘hormo- priming’, phytohormones are added to boost germination and seedling robustness, as in the case of gibberellic acid that promotes antioxidant response and abiotic stress tolerance in white clover and wheat19. 1Instituto de Tecnologia Química e Biológica António Xavier - Universidade Nova de Lisboa (ITQB-NOVA), Av. da República, 2780-157, Oeiras, Portugal. 2Department of Biology and Biotechnology ‘L. Spallanzani’, via Ferrata 9, 27100, Pavia, Italy. 3Department of Chemistry, Viale Taramelli 12, 27100, Pavia, Italy. Susana Araújo and Andrea Pagano contributed equally. Correspondence and requests for materials should be addressed to A.B. (email: alma. balestrazzi@unipv.it) Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 1 www.nature.com/scientificreports/ Exogenous applications of phytohormones generally ameliorate the stress response in planta, allowing to bet- ter regulate and integrate the growth process in changing environments. Cytokinins have been implicated in fruit and seed development20 and transgenic plants overexpressing the ipt (isopentenyl transferase) gene, essential for cytokinin biosynthesis, were characterized by increased seed yield and quality20. Initial studies revealed the ‘per- missive’ role of cytokinins in seed germination21 while more recently it has been reported that, at the onset of ger- mination, cytokinin counteracts the inhibitory role of ABA by downregulating the expression of the ABI5 (ABA INSENSITIVE) gene22. The effects of cytokinins, including kinetin (6-furfurylaminopurine), as priming agents to improve seed germination and seedling robustness have been described and possibly related to enhanced cell division rates23,24. As for legumes, cytokinins are engaged in the intricated networking underlying symbiotic nod- ulation, as shown in the model plant M. Results Ki ti Kinetin promotes seed germination while impairing root growth. To select the most suitable kine- tin dose, preliminary work was carried out using 0.25, 0.5, and 0.75 mM kinetin. As shown in Supplementary Fig. 1, a significant increase (P < 0.01) in germination percentage was observed in response to 0.5 mM and 0.75 mM kinetin, with estimated values of 72.00 ± 15.24% (0.5 mM kinetin) and 76.00 ± 15.57% (0.75 mM kine- tin), respectively. Additionally, the T50 parameter (number of days required to reach half maximal germination, see Materials and Methods) was significantly reduced when comparing the 0.5 mM and 0.75 mM kinetin doses with control samples imbibed with water (W) (Supplementary Table 1). On the other hand, inhibition of root growth was observed in four-day-old M. truncatula seedlings developed in presence of kinetin (Supplementary Table 1 and Supplementary Fig. 2). The lowest dose able to anticipate germination, 0.5 mM kinetin (hereby named Kin), was selected for further investigation.hi g The Kin treatment resulted in accelerated radicle emergence (Fig. 1a) and anticipation of the first true leaf appearance was also observed (Fig. 1b). The phenotype of four-day-old M. truncatula seedlings developed from seeds imbibed with 0.5 mM kinetin is shown in Fig. 1c. The growth impairment caused by prolonged exposure to kinetin is particularly evident at the root level. The 0.5 mM concentration was chosen among the tested ones because this was the lowest dose that could anticipate germination. In view of further applications of these results to design new priming protocols, this also represents the most cost-effective concentration. f To better understand the molecular mechanisms behind the observed phenotype induced by this treatment, the kinetin-triggered changes in metabolite profiles were investigated. Thereby, the metabolite composition was analyzed in M. truncatula seeds imbibed with water (W) or with 0.5 mM kinetin (Kin) collected at: (i) 2 h (hereby named W2 and Kin2) and (ii) 8 h (hereby named W8 and Kin8) of imbibition, as well as at the (iii) radicle pro- trusion stage (radicle length ≤ 3 mm; hereby named WRD and KinRD). With this experimental design (Fig. 2a), attention was focused on two pre-germination timepoints (2 h and 8 h of imbibition), as well as on the develop- mental stage of radicle protrusion, previously reported to undergo extensive metabolic changes1,2,13. Metabolic signatures of germination triggered by kinetin in Medicago truncatula truncatula25 and have been included, among other phytohormones, in culture media formulations tailored for in vitro regeneration via somatic embryogenesis. However, information about the effects of kinetin in the context of seed germination, namely about the potential use of this growth reg- ulator to stimulate germination, is still scanty. In this context, legumes represent an attractive system to explore and assess the possible benefits of kinetin-mediated priming. A major issue of grain legumes is the need to stabi- lize yields in water-limited environments since, compared to other crops, they have higher water requirements. Legumes are used in rotational and intercropping systems during the post-rainy season or in lands unsuitable for the main crop and the availability of seeds primed by controlled hydration before sown improves seedling emer- gence and establishment26. Indeed, reduced field performance generally results from the variability in number and speed of seedling emergence, thus reflecting poor seed vigor27. These unfavorable features can be mitigated by means of tailored priming protocols that require, however, a deeper technical knowedge tightly linked to a better comprehension of the molecular aspects of the pre-germinative metabolism28.f p p p g Metabolomics studies are very useful approaches to retrieve overall metabolites differentially accumulated during the different germination phases and possibly linked to seed vigor13,29–31. The aim of the present study was to elucidate the physiological and metabolic signatures of M. truncatula seed germination in response to exogenously applied kinetin. Besides being a reference legume for functional biology, and for the study of the rhizobia-legume symbiosis as well as the integrated stress and growth responses, M. truncatula is also a pasture species used first in Australia in the wheat/sheep rotation32 and more recently in South Africa in rotation with wheat, barley and canola33. As for other pulses, M. truncatula seed and seedling vigor is among the selection criteria used in breeding programmes finalized to the development of novel annual medics34. In the attempt to improve germination performance and stand establishment, a further step is required, namely a deeper dissection of the molecular determinants of seed vigor that might possibly include metabolites able to alleviate genotoxic stress. In this work, a multidisciplinary approach, combining non-targeted metabolite profiling, gene expression analysis, electron paramagnetic resonance, and comet assay has been used to gain an in-depth picture of the response to kinetin in legume seeds. Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 Metabolic signatures of germination triggered by kinetin in Medicago truncatula Attention was focused on the impact of exogenously applied kinetin on seed germination as well as on the stress conditions resulting from prolonged exposure to the phytohormone. This work contributes to the current state of the art regarding the issues of seed vigor in legumes, and adds another piece of information useful to decipher the complex molecular network and specific hallmarks underlying the seed response to stress. Due to the high synteny of this model species with other legumes, the results of this investigation can impact research on seed biology in other economically relevant legume crops, such as pulses. Results Ki ti Due to the reduced T50 value observed in the phytohormone-treated seeds, the sampling procedure for the radicle protru- sion stage was conducted earlier than for water-imbibed seeds. Thus, the majority of kinetin-treated seeds were collected starting from the 25th hour from the beginning of imbibition whereas the water-treated seeds were collected subsequently, starting from the 40th hour (Fig. 1a). The phenotype of W and Kin seeds at the radicle protrusion stage is shown in Fig. 2b. 2 www.nature.com/scientificreports/ Figure 1. Impact of kinetin on seed germination in M. truncatula. Imbibition with 0.5 mM kinetin (Kin) accelerates radicle protrusion (a) and anticipates the occurrence of the first true leaf (b), compared to control seeds imbibed with water (W). (c) Phenotype of four-day-old M. truncatula seedlings developed from seeds imbibed with water (W) and 0.5 mM kinetin (Kin), respectively. Values are expressed as mean ± SD of three independent replications with 20 seeds for each replication. Asterisks indicate statistically significant differences determined using Student’s t-test (P < 0.05). Bar = 0.5 cm. Figure 1. Impact of kinetin on seed germination in M. truncatula. Imbibition with 0.5 mM kinetin (Kin) accelerates radicle protrusion (a) and anticipates the occurrence of the first true leaf (b), compared to control seeds imbibed with water (W). (c) Phenotype of four-day-old M. truncatula seedlings developed from seeds imbibed with water (W) and 0.5 mM kinetin (Kin), respectively. Values are expressed as mean ± SD of three independent replications with 20 seeds for each replication. Asterisks indicate statistically significant differences determined using Student’s t-test (P < 0.05). Bar = 0.5 cm. Kinetin affects nucleotide, amino acid, lipids, and carbohydrate metabolism during germina- tion. A total of 412 metabolites with known structures were identified (Supplementary Dataset S1). Among these, kinetin was only detected in kinetin-treated samples and thus removed from the pool of metabolites to be further studied. A Principal component analysis (PCA) was applied to the 411 metabolites identified in the metab- olomic study (Fig. 3) in order to investigate the differences between samples, the similarity between replicates, and which metabolites (variables) contributed mostly to this difference. The two main factors/components extracted accounted for 65.1% of the variance. Principal component one (PC1) accounted for 53.4% of the total variance and, according to the respective loadings plot (Fig. Results Ki ti Changes in the mean metabolite contents in seeds imbibed with kinetin for 2 h and untreated seeds were noticed (7 up- and 26 down-accumulated metabolites) based on P ≤ 0.05 but they did not meet the q significance threshold imposed (q ≥ 0.1). Nevertheless, it is worth to mention the accumulation of deoxycarnitine (FC = 1.82, P = 0.001, q = 0.115) and 1-palmitoyl-2-linoleoyl-GP (FC = 3.34, P = 0.0033, q = 0.1531) as well as the depletion of 2-hydroxymyristate (FC = 0.6, P = 0.0043, q = 0.1651), 5-methylcytidine (FC = 0.8, P = 0.003, q = 0.1531), and salicylate (FC = 0.8, P = 0.0022, q = 1531) observed in seeds imbibed for 2 h with kinetin over untreated seeds, which are borderline with the significance threshold imposed. A reduced number of metabolites showing changes in content was noticed (1 up- and 8 down-accumulated metabolites, based on P ≤ 0.05) in seeds imbibed with kinetin for 8 h and untreated seeds, although these changes also did not meet the threshold imposed for q significance.i g g p q gi At the radicle protrusion stage, the majority of metabolites with significant fold changes induced by kine- tin treatment belonged to the amino acid, nucleotide and carbohydrate super-pathways (Fig. 4). The most significant changes were noticed in the amino acid super-pathway, in which saccharopine (FC = 0.18) and 3-(4-hydroxyphenyl)lactate (FC = 3.51) were the metabolites with the highest variations in their levels in response to the treatment applied (Supplementary Dataset S1). As for the lipid metabolism, significant changes in the rel- ative metabolite levels were observed for caprate (FC = 0.25). Interestingly, significant changes in relative levels of metabolites belonging to the nucleotide super-pathway were detected for cytidine 2′, 3′-cyclic monophos- phate (FC = 0.5), orotidine (FC = 0.5) and xanthine (FC = 2.06). Significant changes were also noticed in the carbohydrate metabolism, namely regarding maleate (FC = 1.21) and tartronate (hydroxymalonate, FC = 1.42). Indeed, the heatmap generated (Fig. 5) with all the samples and the 27 differentially accumulated metabolites hierarchical clustering (Euclidean distance, Ward clustering algorithm) corroborated the earlier results obtained by PCA for samples collected at the radicle protrusion stage. The dendrogram shows that the replicates for each treatment cluster together, based on the changes observed in detected metabolites (Fig. 5). Results Ki ti 3a), inositol pentakisphosphate (0.21), agmatine (0.17), diga- lactosylglycerol (0.15), inositol hexakisphosphate (0.14), and oleoylcholine (−0.14) were the metabolites that mostly contributed to the separation between 2 h, 8 h and radicle protrusion stage, irrespective to the treatment applied. PC2 accounts for 11.7% of the variation and, according to the respective loadings plot (Fig. 3b), creatine (0.29), caprate (0.26), saccharopine (0.24), 1-linoleoyl-GPI 182 (0.23), UDP-glucose/UDP-galactose (0.20), and orotate (−0.13) were the metabolites that mostly contributed to the separation in this axis. No major differences in metabolomic profiles were detected between untreated and kinetin-treated samples at 2 h and 8 h of imbibition since these samples clustered together. Nevertheless, PCA indicated that the effects of kinetin on metabolomic profiles were relevant at the radicle protrusion stage, where the separation of kinetin-treated and untreated sam- ples was unveiled. The univariate analysis allowed to identify 27 metabolites showing significant changes in the Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 3 www.nature.com/scientificreports/ Figure 2. (a) Experimental design. Metabolite composition was investigated in M. truncatula seeds imbibed with water (W) and 0.5 mM kinetin (Kin), respectively, collected at 2 h and 8 h of imbibition, and at the radicle protrusion stage (RD). (b) The phenological stage of radicle protrusion occurred faster in kinetin-treated seeds (KinRD) compared to control seeds imbibed with water (WRD). Kinetin-treated seeds were collected starting from the 25th hour from the beginning of imbibition whereas water-treated seeds were collected subsequently, starting from the 40th hours. Bar = 1 mm. Figure 2. (a) Experimental design. Metabolite composition was investigated in M. truncatula seeds imbibed with water (W) and 0.5 mM kinetin (Kin), respectively, collected at 2 h and 8 h of imbibition, and at the radicle protrusion stage (RD). (b) The phenological stage of radicle protrusion occurred faster in kinetin-treated seeds (KinRD) compared to control seeds imbibed with water (WRD). Kinetin-treated seeds were collected starting from the 25th hour from the beginning of imbibition whereas water-treated seeds were collected subsequently, starting from the 40th hours. Bar = 1 mm. mean relative contents triggered by kinetin treatment (herein defined as P ≤ 0.05 and q ≤ 0.1), exclusively at the radicle protrusion stage (RD) (Supplementary Dataset S1). Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 Results Ki ti Also, the metabolites were grouped into two major clusters, one representing four metabolites significantly more accumulated in seeds imbibed with kinetin ((3–4-hydroxyphenyl)lactate, maleate, tartronate, xanthine) while another major cluster gathers the 23 metabolites significantly accumulated in water-imbibed seeds at the radicle protrusion stage. In summary, this highlights a significant reduction of the relative metabolite contents in kinetin-treated seeds when compared to untreated samples.i Quantitative enrichment analysis was also conducted over the 27 metabolites that revealed significant changes induced by the experimental conditions at the radicle protusion stage (KinRD vs WRD). These results evidenced the major metabolic pathways whose response was significantly triggered by the experimental conditions. The top and most significant metabolite sets (pathways) are lysine degradation (P = 0.000006, FDR = 0.0002), purine metabolism (P = 0.00005, FDR = 0.0008), phenylalanine and tyrosine metabolism (P = 0.0002, FDR = 0.0023), methionine metabolism (P = 0.0008, FDR = 0.0023) and valine/leucine/isoleucine degradation (P = 0.0009, FDR = 0.0023) (Supplementary Dataset S1). Based on the reported data, metabolomic analyses highlighted that most of the differentially accumulated metabolites were reduced at the radicle protrusion stage. Such results reflect a metabolite depletion resulting from faster germination, or a stress situation. However, the observed growth impairment in the kinetin-treated seeds leans towards the occurrence of stress conditions. Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 4 www.nature.com/scientificreports/ Figure 3. Principal Component Analysis (PCA) of the 411 metabolites detected in response to Kin and W treatments, sampled at 2 h and 8 h of imbibition, and at radicle protrusion stage (RD). The log-transformed raw scaled imputed value for each metabolite in response to experimental conditions was used for computation. (a) PCA score plot explaining 65.1% of the variance of metabolite profiles, in which PC1 accounts for 53.4%, while PC2 accounts for 11.7% of the variance. (b) Loading plots highlighting the metabolites contributed to the differences observed among samples. W2, seeds imbibed with water for 2 h. W8, seeds imbibed with water for 8 h. WRD, seeds imbibed with water collected at the radicle protrusion stage. Kin2, seeds imbibed with 0.5 mM kinetin for 2 h. Kin8, seeds imbibed with 0.5 mM kinetin for 8 h. KinRD, seeds imbibed with 0.5 mM kinetin collected at the radicle protrusion stage. Figure 3. Results Ki ti Principal Component Analysis (PCA) of the 411 metabolites detected in response to Kin and W treatments, sampled at 2 h and 8 h of imbibition, and at radicle protrusion stage (RD). The log-transformed raw scaled imputed value for each metabolite in response to experimental conditions was used for computation. (a) PCA score plot explaining 65.1% of the variance of metabolite profiles, in which PC1 accounts for 53.4%, while PC2 accounts for 11.7% of the variance. (b) Loading plots highlighting the metabolites contributed to the differences observed among samples. W2, seeds imbibed with water for 2 h. W8, seeds imbibed with water for 8 h. WRD, seeds imbibed with water collected at the radicle protrusion stage. Kin2, seeds imbibed with 0.5 mM kinetin for 2 h. Kin8, seeds imbibed with 0.5 mM kinetin for 8 h. KinRD, seeds imbibed with 0.5 mM kinetin collected at the radicle protrusion stage. Kinetin triggers genotoxic stress at the radicle protrusion stage. DNA damage during early seed imbibition has been reported as a consequence of ROS accumulation during rapid water uptake5,6,8. Although it is still difficult to figure out the presence of metabolic signatures of genotoxic stress during seed germination, changes in nucleotide super-pathway were reported by Pagano et al.13 and linked to the occurrence of DNA dam- age induced by sodium butyrate. In the present work, significant changes in the nucleotide super-pathway were detected at the radicle protrusion stage, notably an increase in the levels of xanthine, an intermediate of purine degradation. Linked to xanthine overproduction, a study in animals pinpointed this metabolite as a hallmark of DNA damage in irradiated cells35. Hence, to investigate the levels of DNA damage in our system, an alkaline comet assay was carried out on radicles collected at the radicle protrusion stage. The results showed a signifi- cant (P = 0.009) increase in DNA strand breaks in Kin treatments (125.98 ± 20.67 a.u.), compared to W samples (62.89 ± 18.40 a.u.) (Fig. 6a). Additionally, a qRT-PCR analysis was carried out to monitor the expression profiles of specific genes with known roles in DNA damage repair. Nonetheless, no significant changes were detected in the expression of MtOGG1 (8-OXOGUANINE GLYCOSYLASE/LYASE) and MtFPG (FORMAMIDOPYRIMIDINE GLYCOSYLASE/LYASE), genes involved in the removal of oxidative DNA lesions during imbibition5,10,36 (Fig. 6b). Results Ki ti (a) Alkaline comet assay was used to measure the accumulation of DNA strand breaks in M. truncatula seeds collected at the radicle protrusion stage. (b) Transcript levels of MtOGG1 and MtFPG genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses. (c) EPR spectrum generated by kinetin-treated M. truncatula seeds collected at the radicle protrusion stage. The enlargement of the central part of the same EPR spectrum shows those regions corresponding to reactive oxygen species (ROS) and organic radicals, respectively. The EPR spectrum was recorded at low field. For the iron region (range from 100 to 550 mT) an applied microwave power of 10 mW with a modulation amplitude of 0.5 mT was used. For organic radicals and Mn2+, a range from 331 to 341 mT and an applied microwave power of 10 mW and a modulation amplitude of 0.2 mT were applied. (d) Transcript levels of MtAPX, MtMT2, MtTRH1 and MtTRH2 genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses.Values are expressed as mean ± SD of three independent replications with 20 seeds for each replication. Asterisks indicate statistically significant differences determined using Student’s t-test (P < 0.05). a.u., arbitrary units. W, control seeds imbibed with water. Kin, seeds imbibed with 0.5 mM kinetin. APX, ascorbate peroxidase. FPG, formamidopyrimidine-DNA glycosylase. MT2, type 2 metallothionein; OGG1, 8-oxoguanine DNA glycosylase. TRH, thioredoxin. mT, milliTesla. protrusion stage, untreated and kinetin-treated seeds were frozen and the radical concentration was determined at 120 K. At this temperature, radicals are blocked inside the icy matrix (hence, stable) allowing their detection and quantification. For each sample, EPR analyses were performed at a low field to detect iron (Fe3+), while for the quantification of organic radicals and manganese (Mn2+) the measurements were centered on 225 mT. A representative example of the EPR spectrum generated in M. truncatula seeds imbibed with kinetin collected at the radicle protrusion stage is shown in Fig. 6c. The enlargement of the central part of the EPR spectrum allows to evidence regions corresponding to ROS and organic radicals, respectively. Since no spin traps were used, the measured quantity represents the free radical steady-state concentration. No significant differences were observed between EPR spectra generated by untreated and kinetin-treated seeds collected at the radicle protrusion stage, suggesting that the exogenous application of kinetin does not impact the free radical species profiles. Results Ki ti On the other hand, both MtOGG1 and MtFPG transcripts were progressively accumulated during seed imbibition Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 5 www.nature.com/scientificreports/ Figure 4. Metabolic super-pathways significantly (P ≤ 0.05 and q ≤ 0.1) changed in response to kinetin treatment at the radicle protrusion stage compared. The number of metabolites significantly up- and down- accumulated is depicted. Figure 4. Metabolic super-pathways significantly (P ≤ 0.05 and q ≤ 0.1) changed in response to kinetin treatment at the radicle protrusion stage compared. The number of metabolites significantly up- and down- accumulated is depicted. Figure 5. Hierarchical clustering (Euclidean distance measure and Ward clustering algorithm) of 27 metabolites with significant changes (P ≤ 0.05 and q ≤ 0.1) in response to kinetin treatment at radicle protrusion stage (RD). The color (from red to blue) represents the log-transformed raw scaled imputed value for each metabolite from high to low, respectively. Figure 5. Hierarchical clustering (Euclidean distance measure and Ward clustering algorithm) of 27 metabolites with significant changes (P ≤ 0.05 and q ≤ 0.1) in response to kinetin treatment at radicle protrusion stage (RD). The color (from red to blue) represents the log-transformed raw scaled imputed value for each metabolite from high to low, respectively. n W and Kin samples, respectively (Supplementary Table 2 and Supplementary Fig. 3), possibly revealing tha DNA repair was required to the same extent, independently of treatments. in W and Kin samples, respectively (Supplementary Table 2 and Supplementary Fig. 3), possibly revealing that DNA repair was required to the same extent, independently of treatments. Kinetin does not impact the free radical steady-state levels in M. truncatula seeds. Electron paramagnetic resonance (EPR) spectroscopy is a sensitive technique used for the qualitative and quantitative detection of free radical species in seeds37. To assess the free radical profile of M. truncatula seeds at the radicle Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 6 www.nature.com/scientificreports/ Figure 6. (a) Alkaline comet assay was used to measure the accumulation of DNA strand breaks in M. truncatula seeds collected at the radicle protrusion stage. (b) Transcript levels of MtOGG1 and MtFPG genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses. (c) EPR spectrum generated by kinetin-treated M. truncatula seeds collected at the radicle protrusion stage. The enlargement of the central part of the same EPR spectrum shows those regions corresponding to reactive oxygen species (ROS) and organic radicals, respectively. Results Ki ti The EPR spectrum was recorded at low field. For the iron region (range from 100 to 550 mT) an applied microwave power of 10 mW with a modulation amplitude of 0.5 mT was used. For organic radicals and Mn2+, a range from 331 to 341 mT and an applied microwave power of 10 mW and a modulation amplitude of 0.2 mT were applied. (d) Transcript levels of MtAPX, MtMT2, MtTRH1 and MtTRH2 genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses.Values are expressed as mean ± SD of three independent replications with 20 seeds for each replication. Asterisks indicate statistically significant differences determined using Student’s t-test (P < 0.05). a.u., arbitrary units. W, control seeds imbibed with water. Kin, seeds imbibed with 0.5 mM kinetin. APX, ascorbate peroxidase. FPG, formamidopyrimidine-DNA glycosylase. MT2, type 2 metallothionein; OGG1, 8-oxoguanine DNA glycosylase. TRH, thioredoxin. mT, milliTesla. Figure 6. (a) Alkaline comet assay was used to measure the accumulation of DNA strand breaks in M. Figure 6. (a) Alkaline comet assay was used to measure the accumulation of DNA strand breaks in M. truncatula seeds collected at the radicle protrusion stage. (b) Transcript levels of MtOGG1 and MtFPG genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses. (c) EPR spectrum generated by kinetin-treated M. truncatula seeds collected at the radicle protrusion stage. The enlargement of the central part of the same EPR spectrum shows those regions corresponding to reactive oxygen species (ROS) and organic radicals, respectively. The EPR spectrum was recorded at low field. For the iron region (range from 100 to 550 mT) an applied microwave power of 10 mW with a modulation amplitude of 0.5 mT was used. For organic radicals and Mn2+, a range from 331 to 341 mT and an applied microwave power of 10 mW and a modulation amplitude of 0.2 mT were applied. (d) Transcript levels of MtAPX, MtMT2, MtTRH1 and MtTRH2 genes in seeds collected at the radicle protrusion stage determined by qRT-PCR analyses.Values are expressed as mean ± SD of three independent replications with 20 seeds for each replication. Asterisks indicate statistically significant differences determined using Student’s t-test (P < 0.05). a.u., arbitrary units. W, control seeds imbibed with water. Kin, seeds imbibed with 0.5 mM kinetin. APX, ascorbate peroxidase. FPG, formamidopyrimidine-DNA glycosylase. MT2, type 2 metallothionein; OGG1, 8-oxoguanine DNA glycosylase. TRH, thioredoxin. mT, milliTesla. Figure 6. Discussion h Under our controlled experimental conditions, neither light conditions nor the applied temperature did not seem to affect the process since after-ripening increases the temperature range compatible with germination43. The 0.5 mM concentration was the lowest dose that accelerated germination, thus the most cost-effective considering the possibility of future applications for priming protocols. In our previous works on M. truncatula, we have characterised the temporal window from the beginning of imbibition until the radical protrusion stage in terms of antioxidant and DNA repair response by monitoring gene expression profiles under conditions that challenge germination5,9,10,13,36. This was done in the attempt to figure out the most informative timepoints of the pre-germinative metabolism to be selected for more in-depth investigations, namely ‘omics’. In the case of M. truncatula seeds challenged with the stress agents trichostatin A36 and sodium butyrate13, respectively, the timepoints corresponding to 2 h and 8 h of imbibition were found to be representative of the seed response in terms of significant up-regulation of antioxidant and DNA repair genes. These two informative timepoints were also maintained for investigating the impact of kinetin on the pre-germinative metabolism of M. truncatula seeds. According to the definition provided by Bewley44, the 2 h timepoint corresponds to the early imbibition status (stage I) while at the later timepoint (8 h) the seed is fully imbibed (early stage II).hii y g The impact of the phytohormone on the seed metabolomic profiles resulted in significant changes only at the radicle protrusion stage and the overall reduction in metabolites levels, observed in kinetin-treated seeds when compared to water imbibed samples, can be regarded as a consequence of the accelerated degradation of the seed reserves required to support faster germination rate and fulfill the process41. Among the differentially accumulated compounds found at the radicle protrusion stage, 3-(4-hydroxyphenyl)lactate, member of the amino acid super-pathway, showed the highest variations in response to kinetin. This phenolic acid with ROS scaveng- ing properties45 was also differentially accumulated in M. truncatula seeds under genotoxic stress conditions induced by the histone deacetylase inhibitor sodium butyrate13. It is possible that this metabolite represents a recurrent metabolic signature of the seed response to genotoxic stress as well as xanthine, also accumulated in response to kinetin at the radicle protrusion stage. It is worth noting that xanthine is a recurrent hallmark of DNA damage in irradiated cells, as revealed by studies on the radiation-responsive metabolome35. Discussion h Despite the well-known role of cytokinins in promoting cell division23,24 and morphogenesis, very few stud- ies have explored the potentialities of kinetin treatments to enhance seed vigor and germination in legumes39. Kinetin has been tested, alone or in combination with other phytohormones/chemicals to improve germination, however the limited number of reports so far available provide only a fragmentary picture of its potential use as priming agents compared to other phytohormones frequently used, as gibberellins40. To address this gap of knowledge, we investigated the effect of kinetin during M. truncatula seed germination to evaluate its suitability as priming agent in legumes. We found that the treatment with 0.5 mM kinetin, applied thorughout germination, was able to speed-up germination but caused radicle growth impairment. Using multidisciplinary analyses that combines untargeted metabolomics, EPR, and gene expression, we investigated the metabolites, along with ROS and gene profiles, that were disturbed during germination in response to 50 mM kinetin. T k l d h h fi l h l b l d d f l d i To our knowledge, this is the first report in legumes that exploits metabolomics to provide evidence of selected metabolites associated with exposure to kinetin and evaluates the effects of the phytohormone not only as growth inducer but also as stress agent. Our results showed that the Kin treatment accelerated the germination process, but the prolonged exposure to the phytohormone led to seedling growth impairment especially at the root level. Considering the impact that phytohormones (including cytokinins) can have on seed dormancy and germina- tion41, we need to specify that the M. truncatula seeds used in this study represent freshly harvested material kept under dry storage conditions at room temperature for more than ten months, defined as after-ripening. Such treatment was reported to be effective in releasing dormancy and promoting seed germination in M. trun- catula42,43. Independently of treatments, fully after-ripened seeds always germinated within two days from the beginning of imbibition, reaching a maximum germination percentage of 80%. This suggests that there was no physiological dormancy in the M. truncatula seed lot whereas the fraction (20%) of seeds that were not able to uptake water and failed to germinate might be associated with physical dormancy, a trait that follows distinct kinetics compared to those occurring during after-ripening43. Other parameters that can affect M. truncatula seed germination include temperature and light conditions43. Results Ki ti It should be noticed that similar results were obtained with seeds collected at 2 h and 8 h of imbibition (data not shown). Overall, the reported data reflect the invariance of the steady-state concentration of radicals and show that the treatment with kinetin did not trigger ROS accumulation in M. truncatula seeds at the radicle protrusion phase. To further investigate the status of the antioxidant defence, a set of antioxidant genes (MtAPX, ASCORBATE PEROXIDASE; MtMT2, TYPE 2 METALLOTHIONEIN; MtTRH1 and MtTRH2, THIOREDOXIN) that mark the pre-germinative metabolism5,9,13,36 was also investigated (Fig. 6d). No significant changes in MtAPX and MtMT2 transcript levels were detected in Kin seeds at the radicle protrusion stage. On the other hand, MtTRH1 and MtTRH2 genes, encoding h-type thioredoxins that act as ROS scavengers to prevent oxidative damage upon imbibition38, were significantly down-regulated in Kin samples, compared to W control (Fig. 6d). The reduced antioxidant response well corroborated the results from the EPR analysis (Fig. 6c), showing that treatment with Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 7 www.nature.com/scientificreports/ kinetin does not impact the free radical steady-state levels in M. truncatula seeds at the radicle protrusion stage. As previously observed for the DNA repair genes MtOGG1 and MtFPG, for all the tested antioxidant genes the transcripts were progressively accumulated during seed germination in both W and Kin samples throughout imbibition (2 h and 8 h) until the radicle protrusion stage (Supplementary Table 2 and Supplementary Fig. 2), thus indicating that the antioxidant response triggered during the imbibition phase was somewhat sufficient to cope with any perturbation caused by the application of exogenous kinetin. Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 www.nature.com/scientificreports/ www.nature.com/scientificreports/ 5-methylcytidine, and salicylate. All these metabolites, whose levels are perturbated in response to kinetin at 2 h of imbibition, deserve further investigation to assess their possible involvement in the seed response to kinetin-based priming. 5-methylcytidine, and salicylate. All these metabolites, whose levels are perturbated in response to kinetin at 2 h of imbibition, deserve further investigation to assess their possible involvement in the seed response to kinetin-based priming. p g Aside from the metabolite depletion, further proof that extended exposure to kinetin results in stress con- ditions is also given by the comet assay-based profiles of DNA damage that highlighted the overall genotoxic- ity induced by the exogenous application of the phytohormone (Fig. 6a). The genotoxic effects of cytokinins have been investigated in animals, where it was seen that exposure to high concentrations (500 nM) of kinetin induced significant DNA damage, as evidenced by a comet assay carried out on in HL60 cells, HaCaT human keratinocyte cells, NRK rat epithelial kidney cells and human peripheral lymphocytes49. In another study, Cabello et al.50 tested the effect of cytokinins and cytokinin nucleosides in various human cancer cell lines and observed that the accumulation of DNA damage was associated with rapid upregulation of DNA damage associated genes, e.g. CDKN1A (CYCLIN DEPENDENT KINASE INHIBITOR 1A) or GADD153 (GROWTH ARREST AND DNA DAMAGE-INDUCIBLE PROTEIN). Nonetheless, under the experimental conditions of our study, the kinetin-induced DNA damage did not trigger significant up-regulation of the BER associated genes MtOGG1 and MtFPG. This suggests that the BER pathway may not be required in this case, while the implica- tion of other DNA repair pathways cannot be ruled out. Within this context, the cross-talk between DDR and cytokinins is still poorly explored even in planta, although there is evidence of interplay. For instance, Davis et al.51 demonstrated that double-strand breaks accumulation in Arabidopsis lateral root primordia not only triggers the SOG1(SUPPRESSOR OF GAMMA RESPONSE)-mediated up-regulation of DNA repair genes but also stimulates the expression of cytokinin biosynthesis/signaling genes leading to the inhibition of cell division. Kataya et al.52 also highlighted a link between DNA repair and cytokinins by investigating the Arabidopsis PSY2L (PLATINUM SENSITIVE 2 LIKE) mutant. Besides metabolite depletion and evident genotoxic injury, exposure to kinetin did not result in enhanced accumulation of free radical species nor into increased antioxidant gene expression, implying a global diminishment of the cellular metabolic activities. www.nature.com/scientificreports/ Indeed, other studies also evi- denced that, although exogenously applied cytokinins could prevent senescence and positively impacted the plant antioxidant response53, the prolonged cytokinin exposure or high concentration resulted in impair growth54. It should be also noted that kinetin itself plays a role as ROS scavenger55 and that it has an anti-glycating activity that protects proteins against reactive aldehydes56. This may also be among the reasons why no changes in ROS profiles and antioxidant gene expression were observed under the Kin treatment in our experimental conditions, compared to control. On the other hand, DNA repair and antioxidant genes were upregulated in Kin-treated seeds throughout the tested timepoints with profiles similar to those recorded in W samples. Apparently, kinetin did not influence this specific aspect of seed metabolism Conclusions In the present work, we demonstrate that the treatment of M. truncatula seeds with 50 mM kinetin applied throughout germination, accelerated radicle protrusion but causes radicle growth impairment. This shows the dual role of kinetin as a growth inducer and stress agent, likely due to the long exposure to the phytohormone. Seed metabolomics has provided a list of metabolites and metabolic pathways affected by kinetin during M. truncatula germination. Most of the changes observed were linked to the faster metabolic depletion associ- ated with a faster germination. The study highlighted the differential accumulation of two metabolites, namely 3-(4-hydroxyphenyl)lactate and xanthine, potentially linked to stress. With additional and more targeted studies, these metabolites could be used to monitor stress-mediated events during germination and to figure out, for instance, the timepoint when priming treatments should be stopped to prevent toxicity towards seeds. Discussion h This sug- gests that changes in xhantine levels occurring during seed germination might be related to peaks in genotoxic damage, although in-depth studies will be necessary to further support such hypothesis. Differences were also revealed in UDP-glucose/UDP-galactose inositol polyphosphates with roles in sucrose and starch metabolism as well as in signaling46,47, agmatine and orotic acid, intermediates in polyamine and pyrimidine biosynthesis, respectively. Saccharopine, an intermediate in lysine degradation48 is also included in this set of metabolites. Protein turnover and amino acid degradation are also required at the onset of germination since the carbon skel- etons of amino acids are directed into the TCA cycle whereas oxidation of lysine and other amino acids releases electrons that enter the mitochondrial electron transport chain. Overall, the profiles observed at 2 h and 8 h of imbibition, reflect the contribution of the different metabolic super-pathways to those essential physiological and biochemical changes that require ex novo biosynthesis or degradation to support germination. Moreover, when considering the possible changes observed during imbibition, it is worth to mention a relevant but not statistically significant accumulation of deoxycarnitine and 1-palmitoyl-2-linoleoyl-GP and depletion of 2-hydroxymyristate, Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 8 Methods l Principal component analysis (PCA), quantitative enrichment analysis, heatmaps, and clustering analysis were conducted using the software resources available at Metaboanalyst 3.0 (www.metaboanalyst.ca) following user´s guide specifications62. While PCA was conducted over all identified metabolites, the remaining analyses were conducted only over DA metabolites pres- ent at least in one of the three comparisons studied. RNA extraction, cDNA synthesis, and quantitative real-time polymerase chain reaction. RNA isolation was carried out from water- and kinetin-imbibed M. truncatula seeds, respectively, collected at 2 h and 8 h (W2, Kin2; W8, Kin8) and seeds collected at the radicle protrusion stage (WRD, KinRD) as previ- ously described63. cDNAs were obtained using the RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, Milan, Italy) according to the manufacturer’s suggestions. qRT-PCR was carried out with the Maxima SYBR Green qPCR Master Mix (2×) (ThermoFisher Scientific) according to supplier’s indications, using a Rotor-Gene 6000 PCR apparatus (Corbett Robotics Pty Ltd, Brisbane, Australia). Amplification conditions were as follows: denaturation at 95 °C for 10 min, and 45 cycles of 95 °C for 15 s and 60 °C for 60 s. Oligonucleotide primers were designed using the Real-Time PCR Primer Design program from GenScript (https://www.gen- script.com/ssl-bin/app/primer) and validated through the online software Oligo Analyzer (https://eu.idtdna. com/calc/analyzer) (Supplementary Table 1). Sequences were retrieved using the NCBI gene database (https:// www.ncbi.nlm.nih.gov/). For each oligonucleotide set, a no-template water control was used. Quantification was carried out using the MtPDF2-PROTODERMAL FACTOR 2 (Medtr6g084690) as reference gene64 for the experi- mental conditions (treated versus untreated) used in this work. The raw, background-subtracted fluorescence data provided by the Rotor-Gene 6000 Series Software 1.7 (Corbett Robotics) was used to estimate PCR Efficiency (E) and threshold cycle number (Ct) for each transcript quantification. The Pfaffl method65 was used for relative quan- tification of transcript accumulation and statistic analysis performed with REST2009 Software V2.0.13 (Qiagen GmbH, Hilden, Germany). Comet assay. For Comet assay analyses, water- and kinetin-imbibed seeds were collected at the radicle pro- trusion stage (WRD, KinRD). Kinetin-treated seeds were collected starting from the 25th hour from the beginning of imbibition whereas water-treated seeds were collected subsequently, starting from the 40th hour. Radicles were cut with a razor blade and immediately frozen in liquid N2. Methods l (Durham, NC, U.S.A.) (www.metabolon.com), based on three independent platforms: ultra-high-performance liquid chro- matography/tandem mass spectrometry (UHLC/MS/MS2) optimized for basic species, UHLC/MS/MS2 opti- mized for acidic species, and gas chromatography/mass spectrometry (GC/MS), as described in Evans et al.59. Global metabolomic profiling was performed on methanol extracts from powdered frozen samples (100 mg) of seeds imbibed with water for 2 h (W2), 8 h (W8) and seeds at the radicle protrusion stage (W_RD). Samples from seeds imbibed with 0.50 mM kinetin for 2 h and 8 h (Kin2, Kin8), and seeds at the radicle protrusion stage (Kin_ RD) were also profiled. Metabolomic analyses were conducted onto biological triplicates. Each biological replicate corresponds to a pool of at least 20 seeds. Data from seeds imbibed with water was previously described13 since the kinetin treatment was part of a larger experimental design. Metabolites were identified by automated com- parison of the ion features of the experimental samples with a reference library of chemical standard entries that included retention time, molecular weight (m/z), preferred adducts, and in-source fragments as well as associated MS/MS2 spectra and curated by visual inspection for quality control using an in-house resources59,60. Raw area counts for each biochemical compound were normalized by dividing each sample value per sample fresh weight. Then, this value was rescaled by dividing each sample value by the median value for the specific biochemical. For missing data (nulls), the minimum observed values for that compound was imputed. Prior to data analysis, scaled imputed data was log transformed. Metabolites were also mapped onto general biochemical pathways, as provided in the Kyoto Encyclopedia of Genes and Genomes (KEGG) (www.genome.jp/kegg) and Plant Metabolic Network (PMN) (www.plantcyc.org/).i y g For metabolomic profiling, Welch’s two-sample t-tests were used to determine whether or not each metabolite had a significant change in abundance, focusing on comparisons between treated and non-treated samples for the same timepoint (Kin2 versus W2; Kin8 versus W8 and KinRD versus WRD). Prior to statistical computations, scaled imputed data were log transformed (natural logarithm). An estimate of false discovery rate for the list of all identified compounds was also provided, taking into account the multiple comparison tests conducted in metabolomic-based studies61. Metabolites that achieved statistical significance (P ≤ 0.05 and q ≤ 0.1) were con- sidered differentially accumulated (DA) and selected for further analysis. Methods l Plant materials, treatments, and phenotyping. For imbibition, M. truncatula seeds (Jemalong culti- var, kindly provided by Dr. Ana Barradas, Fertiprado L.d.a., Vaiamonte-Monforte, Portugal) were sown in Petri dishes (9 cm diameter) containing two filter papers moistened with 2.5 mL distilled water (control, W) or with 2.5 mL of 0.5 mM kinetin (6-furfurylaminopurine, Sigma-Aldrich, Milan, Italy) for phytohormone treatments. For germination tests, seeds were kept in a growth chamber at 22 °C under light conditions with a photon flux density of 150 μmol m−2 s−1, photoperiod of 16/8 h and 70–80% relative humidity. For each treatment, five inde- pendent replications with 20 seeds per replication were analyzed. Seeds with protrusion of the primary radicle were considered germinated. Germination percentage, scored along two consecutive days after imbibition, and the time to reach 50% germination (T50) were calculated as previously reported57. The time to obtain 50% germi- nation (T50) was calculated according to the following formula of Coolbear et al.58, as modified by Farooq et al.57: = + − − − N T t ( /2 n )(t t ) (n n ) 50 i i j i j i where N is the final number of germinating seeds and nj and ni are the cumulative number of seeds germinated by djacent counts at times tj and ti, respectively, when ni < N/2 < nj. h j j N values were annotated for each replicate until a plateau was reached, choosing the 10th day as the standard timepoint to annotate them. The appearance of the first leaf on the resulting seedlings was scored during 14 days. Fresh and dry weights of imbibed seeds and seedlings were also measured. For molecular analyses, seeds were harvested at the indicated time points, namely 2 h and 8 h of imbibition with water or with 0.5 mM kinetin and at the post-germination stage (radicle protrusion; radicle length ≤ 3 mm). Due to the reduced T50 value observed in the phytohormone-treated seeds, the sampling procedure for the radicle protrusion stage was conducted earlier than for water-imbibed seeds. Kinetin-treated seeds were collected starting from the 25th hour from the beginning Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 9 www.nature.com/scientificreports/ of imbibition whereas water-treated seeds were collected subsequently, starting from the 40th hour. All the sam- ples were weighed and stored in liquid N2. Metabolomic profiling. Non-targeted metabolomic profiling was performed by Metabolon Inc. Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 Methods l For each sample, 300 μL TE buffer (0.4 M Tris HCl pH 7.4, 1 mM EDTA) was added to the frozen tissues that were quickly and gently chopped with a sharp razor blade to release the nuclei as described by Macovei et al.66. For each treatment, two independent experiments were car- ried out with three independent replications (10 radicles per replication). Nuclei were extracted from M. truncat- ula radicles as reported13. The suspension containing the purified nuclei and a solution containing 1% low melting point agarose (Sigma-Aldrich) in phosphate-buffered saline (PBS) at 37 °C were mixed in equal volume. Aliquots (120 μL each) were pipetted onto agarose pre-coated slides and solidified on ice. Slides were incubated for 20 min at room temperature in high salt lysis buffer (2.5 M NaCl, 100 mM Tris-HCl pH 7.5, 100 mM EDTA) to disrupt the nuclear membrane. Nuclei were denatured in alkaline buffer (1 mM Na2EDTA, 300 mM NaOH, pH > 13) for 30 min at 4 °C and then electrophoresed in the same buffer for 25 min at 0.72 V cm−1 in a cold chamber. After electrophoresis, slides were washed twice in 0.4 M Tris-HCl pH 7.5 for 5 min, rinsed once in 70% ethanol (v/v) for 12 min at 4 °C and dried at room temperature overnight. Exposure to alkaline conditions causes DNA unwind- ing and visualization of strand breaks. Slides were stained with 20 μL DAPI (4′-6-Diamidine-2′-phenylindole Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 10 www.nature.com/scientificreports/ dihydrochloride; 1 μg mL−1, Sigma-Aldrich). For each slide, one hundred nucleoids were scored, using a fluores- cence microscope (Olympus BX51, Olympus Italia S.R.L.) with an excitation filter of 340–380 nm and a barrier fil- ter of 400 nm. Nucleoids were classified and results were expressed in arbitrary units (a.u.) according to Collins67. Electron paramagnetic resonance. EPR analyses were carried out as reported13 on the water- and kinetin-treated seeds collected at 2 h, 8 h of imbibition and at the radicle protrusion stage. Seeds were transferred in quartz tubes, quickly frozen with liquid N2 and then stored in liquid N2. EPR spectra were recorded at 120 K with a Bruker EMX-10/12 spectrometer (Bruker BioSpin GmbH, Karlsruhe, Germany) operating in X-band, equipped with an ER4119HS cavity and a temperature controller. Two different instrument settings were used to better characterize iron and other radicals. References J Exp Bot 66 3549–58 (2015) p p g y , ( ) 1. Waterworth, W. M., Bray, C. M. & West, C. E. The importance of safeguarding genome integrity in germination and seed longevity J. Exp. Bot. 66, 3549–58 (2015). 11. Waterworth, W. M., Bray, C. M. & West, C. E. The importance of safeguarding genome in J. Exp. Bot. 66, 3549–58 (2015). p 12. Rajjou, L. et al. Seed germination and vigor. Annu. Rev. Plant Biol. 63, 507–33 (2012). jj g g 3. Pagano, A. et al. Metabolic and gene expression hallmarks of seed germination uncovered by sodium butyrate in Medicago truncatula. Plant Cell Environ. 2018, 1–11 (2018). 13. Pagano, A. et al. Metabolic and gene expression hallmarks of seed germination uncover truncatula. Plant Cell Environ. 2018, 1–11 (2018). 4. Heydecker, W. J., Heydecker, J., Higgins & Gulliver, K. Accelerated germination by osmotic seed treatment. Nature 246, 42–46 (1973). ( ) 5. Burgass, R. W. & Powell, A. A. Evidence for repair process in the invigouration of seeds by hydration. Ann. Bot. 53, 735–757 (1984) g p p g y y ( ) 16. Bailly, C., Benamar, A. & Corbineau, F. Antioxidant systems in sunflower (Helianthus annuus L.) seeds as affected by priming. Seed Sci. Res. 10, 35–42 (1998). 17. Paparella, S. et al. Seed priming: state of the art and new perspectives. Plant Cell Rep. 34, 1281–1293 (2015).f 18. Wojtyla, L., Lechowska, K., Kubala, S. & Garnczarska, M. 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Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 11 Acknowledgementsh g This work was supported by Regione Lombardia D.G. Attività Produttive Ricerca e Innovazione - Struttura Asse 1 POR FSE 2007-2013, Project ID 4344853 and CARIPLO Foundation (Action 3, Code 2013-1727) ‘Advanced Priming Technologies for the Lombardy Agro-Seed Industry-PRIMTECH’. The research was also supported by CARIPLO Foundation in the frame of the WAKE-APT project (Code 2016-0723) (‘Seed Wake-up with Aptamers: a New Technology for Dormancy Release and Improved Seed Priming’) and by the Italian Ministry of Education, Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 12 www.nature.com/scientificreports/ University and Research (MIUR): Dipartimenti di Eccellenza Program (2018–2022) - Dept. of Biology and Biotechnology “L. Spallanzani”, University of Pavia (to A.P., A.M., A.B.). The financial support from Fundação para a Ciência e a Tecnologia (Lisbon, Portugal) is acknowledged through research unit GREEN-it “Bioresources for Sustainability” (UID/Multi/04551/2013) and S.A. Post-Doctoral Grant (SFRH/BPD/108032/2015) and present S.A. Ph.D. holder contract (DL57). Sponsorship from COST Action FA1306: ‘The quest for tolerant varieties: phenotyping at plant and cell level’ is gratefully acknowledged. A.P. has been awarded by a Ph.D. Fellowship from IUSS-Scuola Universitaria Superiore Pavia. The authors would like to thank Dr. Danny Alexander (Metabolon, US) for his support during the preparation of this manuscript. Author Contributions A.B., A.M. and Sd.S.A. conceived the work and wrote the manuscript. A.P., D.D., S.L. and E.P. contributed to the experimental data. D.D. and S.L. carried out EPR analyses. A.P. and Sd.S.A. performed bioinformatic analyses. A.B., A.M., Sd.S.A., A.P. and D.D. contributed to the discussion of data. All authors read and agreed with the final version of the manuscript. Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 Additional Information Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-019-46866-6 Competing Interests: The authors declare no competing interests. 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 Cre- ative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not per- mitted 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 license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2019 Scientific Reports | (2019) 9:10466 | https://doi.org/10.1038/s41598-019-46866-6 13
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Inference of missing data in photovoltaic monitoring datasets
IET renewable power generation
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CC BY 3.0 CC BY 3.0 http://dx.doi.org/10.1049/iet-rpg.2015.0355 http://dx.doi.org/10.1049/iet-rpg.2015.0355 PUBLISHER © The Authors. Published by Institution of Engineering and Technology (IET) VERSION VoR (Version of Record) This item was submitted to Loughborough's Research Repository by the author. Items in Figshare are protected by copyright, with all rights reserved, unless othe This item was submitted to Loughborough's Research Repository by the author. Items in Figshare are protected by copyright, with all rights reserved, unless other This item was submitted to Loughborough s Research Repository by the author. Items in Figshare are protected by copyright, with all rights reserved, unless otherwise indicated. PUBLISHER STATEMENT This work is made available according to the conditions of the Creative Commons Attribution 3.0 Unported (CC BY 3.0) licence. Full details of this licence are available at: http://creativecommons.org/licenses/by/3.0/ This work is made available according to the conditions of the Creative Commons Attribution 3.0 Unported (CC BY 3.0) licence. Full details of this licence are available at: http://creativecommons.org/licenses/by/3.0/ LICENCE LICENCE 1 Introduction specific system performance need to be taken into account. Thus, it is not sufficient to just replace missing data with previous data, or any alternative method that does not consider actual meteorological conditions as this may introduce significant errors. Rather, the method presented here considers local weather phenomena and their relationship to performance variations of the actual PV systems. This requires two elements, assessing meteorological as well as electrical data as both systems may fail independently. The number of photovoltaic (PV) installations in the UK has increased from a few tens of MWp in 2010 to more than 6 GWp in June 2015 [1], indicating that PV is a rapidly growing industry. The majority of these systems will operate as financial investments, and in order to manage investment risk associated with system yield shortfalls, many larger scale PV systems are covered by energy performance guarantees. These are commonly based on attaining a specified performance ratio (PR), as this allows for location-specific variations in meteorological conditions. Energy yield, and to a lesser extent, PR are key performance indicators for owners, investors and operators and they can only be obtained through effective monitoring of PV systems, as highlighted in several studies [2–5]. However, due to malfunctions such as power outages, communication failures or component faults, data may be incomplete. This will affect, as shown below, the PR calculated for the system and may hide incidents that would trigger warranty cases or cause unnecessary warranty claims. There are no validated strategies that deal with this issue, particularly in maritime climates such as the UK, and any attempts to backfill data using previous dates or days from previous years are at best temporary with very high uncertainty attached to these methods. This is because such strategies do not take into account variable weather systems or PV component degradation. Utilising average values from dates close to the missing period may give an estimation of PR, but such methods are not adequate to estimate long-term energy yields of the system, especially when missing periods are extended from a few weeks to even months. Therefore, an issue remains of how to back-fill lost data values, and to arrive at a valid monthly or annual PR which is required in order to verify the warranties or to predict return on investment. REPOSITORY RECORD Koumpli, Elena, Diane Palmer, Paul Rowley, and Ralph Gottschalg. 2016. “Inference of Missing Data in Photovoltaic Monitoring Datasets”. Loughborough University. https://hdl.handle.net/2134/20351. IET Renewable Power Generation Research Article IET Renew. Power Gener., pp. 1–6 This is an open access article published by the IET under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) Inference of missing data in photovoltaic monitoring datasets ISSN 1752-1416 Received on 30th July 2015 Revised on 1st October 2015 Accepted on 9th November 2015 doi: 10.1049/iet-rpg.2015.0355 www.ietdl.org ISSN 1752-1416 Received on 30th July 2015 Revised on 1st October 2015 Accepted on 9th November 2015 doi: 10.1049/iet-rpg.2015.0355 www.ietdl.org ane Palmer, Paul Rowley, Ralph Gottschalg ergy Systems Technology (CREST), School of Electronic, Electrical and Systems Engineering, Loughborough h, LE11 3TU, UK Eleni Koubli ✉, Diane Palmer, Paul Rowley, Ralph Gottschalg Centre for Renewable Energy Systems Technology (CREST), School of Electronic, Electrical and Systems Engineering, Loughborough University, Loughborough, LE11 3TU, UK ✉E-mail: E.Koumpli@lboro.ac.uk Eleni Koubli ✉, Diane Palmer, Paul Rowley, Ralph Gottschalg Centre for Renewable Energy Systems Technology (CREST), School of Electronic, Electrical and Systems Engineering, Loughborough University, Loughborough, LE11 3TU, UK ✉E-mail: E.Koumpli@lboro.ac.uk Eleni Koubli ✉, Diane Palmer, Paul Rowley, Ralph Gottschalg Centre for Renewable Energy Systems Technology (CREST), School of Electronic, Electrical and Systems Engineering, Loughborough University, Loughborough, LE11 3TU, UK ✉E-mail: E.Koumpli@lboro.ac.uk Abstract: Photovoltaic (PV) systems are frequently covered by performance guarantees, which are often based on attaining a certain performance ratio (PR). Climatic and electrical data are collected on site to verify that these guarantees are met or that the systems are working well. However, in-field data acquisition commonly suffers from data loss, sometimes for prolonged periods of time, making this assessment impossible or at the very best introducing significant uncertainties. This study presents a method to mitigate this issue based on back-filling missing data. Typical cases of data loss are considered and a method to infer this is presented and validated. Synthetic performance data is generated based on interpolated environmental data and a trained empirical electrical model. A case study is subsequently used to validate the method. Accuracy of the approach is examined by creating artificial data loss in two closely monitored PV modules. A missing month of energy readings has been replenished, reproducing PR with an average daily and monthly mean bias error of about −1 and −0.02%, respectively, for a crystalline silicon module. The PR is a key property which is required for the warranty verification, and the proposed method yields reliable results in order to achieve this. (i) Root-mean-square error (RMSE) (ii) Mean absolute error (MAE) (iii) Mean bias error (MBE) The RMSE describes the random error in a distribution and tends to increase with outliers, MAE describes the absolute error and MBE indicates whether the model overestimates or underestimates the measurement value, which is also expressed as the ‘systematic’ error of the distribution. MBEs close to zero signify an unbiased distribution. It should be noted that, although the word ‘error’ is commonly used in statistical analysis, ‘difference’ would here be 1 Introduction Meteorological data for the missing period is obtained here from interpolating from a network of about 80 meteorological monitoring stations operated by the UK met-office [6]. The local irradiance is calculated from interpolating these using Kriging [7] and correcting the horizontal irradiance to the site installation by employing separation, into beam and diffuse, and translation, into plane of the array, algorithms. The same interpolation technique is applied for ambient temperature. Ambient temperature is corrected to module temperature by employing a simple thermal model. The method is described in more detail in Sections 2.1 and 2.2. The energy output of missing periods is estimated using an empirical electrical model. The underlying coefficients are obtained by ‘training’ the model with the available past data (see Section 2.3), i.e. determining system specific characteristics. The validity of the proposed method is assessed using the following metrics: 2.1 Irradiance and temperature interpolation The analysis is based on meteorological data, namely global horizontal irradiation and ambient temperature, acquired from more than 80 ground meteorological stations on a national scale through Met Office Integrated Data Archive System (MIDAS) [6]. The PR of a PV system depends on the irradiation (H in Wh/m2) received according to (1) PR = (E · GSTC) (H · PSTC) (1) (1) where E is the energy output (Wh), PSTC (W) and GSTC (W/m2) are the nominal power of the system and irradiance at Standard Testing Conditions (STC), respectively. Horizontal irradiance is interpolated to a grid of points. The nearest point of the PV system is selected and separation (Ridley et al. [9]) and translation algorithms (Hay et al. [10] with Reindl correction [11]) are employed to calculate in-plane irradiance given that the location, orientation and tilt of the system are known. The specific separation model was chosen based on empirical observations, which demonstrated that it delivered the best results in comparison with several separation algorithms for UK [7]. Similarly, a previous work in Loughborough [12] has shown that the all-sky model by Reindl et al. delivers the best results for the UK climate. Both the horizontal irradiation and the ambient temperature data are interpolated using Kriging, which has been proven to perform well in comparison with various climate data interpolation methods [7, 13]. IET Renew. Power Gener., pp. 1–6 This is an open access article published by the IET under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) 2.3 Extraction of the fitting coefficients Quality checks are a critical step in every data analysis, the aim of which is to identify outliers that could corrupt the training process. Thus, the quality checks applied here focused on module temperature, irradiation and maximum power output. Graphical representation of the above parameters as well as logical controls based on (1) and (2) were employed according to the analyses described in [22, 23]. Only unshaded and fault-free systems were considered for this study. The training algorithm is key for the acquisition of the optimum system’s coefficients, as it has been shown that device-specific characteristics, and thus implicitly the system characteristics, are one of the two uncertainties determining the model accuracy [20]. The requirements for the training need to be determined in terms of optimal training set’s size and how recent it should be with respect to the missing period of data, in order to achieve maximum agreement. System performance is affected by both meteorological seasonal variations as well as by module technology [24, 25]. This seasonal nature of system performance is expected to have an impact upon the determination of the optimum training set. This study concluded that in all cases, the training set should maintain close proximity to the missing period, as this provides a better fit. More specifically, an average of 20 days before and 20 days after the missing set was found to be a sufficient data pool for the particular location, regardless of the position of the missing set throughout the year (i.e. during summer or winter etc.). here has the following form [19] here has the following form [19] more appropriate since the true values are not actually known, as sensor uncertainty is not taken into account. P′(G′, T′) = G′ · (1 + k1ln(G′) + k2ln(G′)2 + k3T′ m + k4T′ mln(G′) + k5T′ mln(G′)2 + k6T′2 m ) (3) y Real measurements of in-plane irradiation, ambient and module temperature, as well as energy output were used for the validation. The datasets used were specifically from two PV modules from CREST’s outdoor monitoring system (COMS3) [8] whose properties are listed in Table 1. (3) where P′ = PMP/PSTC, G′ = G/GSTC and T ′ m = Tm–TSTC (STC = Standard Testing Conditions) and PMP is the maximum power. The model yields a ‘3D power surface’. This model has been compared with a number of other models [20] where it was found that it performed well for a range of PV module technologies, on predicting annual energy output and it is also possible to combine measured data from many PV modules to obtain a general model for a given PV technology [19]. By changing the PSTC, (3) can be used to describe an entire PV system. In this study, defining the coefficients for a specific system is essentially training the model based on the specific system characteristics and re-using the coefficients to predict the output of the missing period. Energy generation is calculated using sums of hourly averaged maximum power output. For the training process, past data are fed into the model and the coefficients (k1–k6) are determined by means of a Marquardt–Levenberg optimisation algorithm [21]. To assess the reliability of the results, data quality checks and a training algorithm were used to determine the optimum training set for the model. 2 Methodology development and validation Given the aim is to back-fill missing periods appropriately, then in order to infer data reliably, actual weather patterns as well as 1 1 Name Module type Tilt angle, o Orientation Nominal power, W Mounting type Data origin module A crystalline silicon (c-Si) 32.5 south 245.0 open-rack CREST outdoor monitoring system module B polycrystalline silicon (pc-Si) 32.5 south 245.0 open-rack CREST outdoor monitoring system 2.2 Thermal and electrical model Module temperature is calculated from in-plane irradiance and ambient temperature using the thermal model presented in [14] Tm = Ta + k · G (2) (2) where Tm (K), Ta (K) and G (W/m2), are module temperature, ambient temperature and in-plane irradiance, respectively. The k, or Ross coefficient is the modified thermal resistance of the module, modified in terms of influence of the mounting configuration of the array [15] a typical value of which is 0.02 (K·m2/W) for free-standing modules [16]. Ross’s model is a good choice in cases where irradiance and ambient temperature are the only available weather data. Furthermore, k can be readily obtained using outdoor measurements of module and ambient temperature and horizontal irradiance. In this work, k was obtained experimentally for each module by linear fitting of (Tm–Ta) against G for one year’s worth of data. Equation (2) was used by taking the hourly values of irradiance as proposed in [17]. The training algorithm was applied separately for each one of the PV modules in Table 1. For the training process, past data were analysed using (3). The optimal training set was chosen based upon the lowest RMSE achieved and R2 values, in combination with the size of the training set. The training size was defined as the number of days before (noted as negative, going backwards in time) and after (noted as positive, going forwards in time) the missing period. The input training data were hourly measurements of power, module temperature and in-plane irradiance. Here, 1 The electrical model was chosen based on both the available input data and its training capability. The chosen electrical model plays the role of the ‘learning machine’. It is based on a simplified King’s model for the maximum power point [18] and the formula used 2 Fig. 1 Plots of a Training sets around the missing period taking as starting points the 31st of May and the 1st of July 2014, and going backwards and forwards in time, respectively b Fitting curve for the optimum training set (15 days backwards and 26 days forwards) for module A It can be seen in Fig. 1a that although RMSE does not vary significantly across different training sets, there is a specific (red) area where it showed its lowest values. This area includes points that are closer to the missing period, which can be justified as seasonal dependence. 2.2 Thermal and electrical model The results also showed that very small training sets yielded the highest RMSE, e.g. using only several days before and after the missing period was not a sufficient data pool. This seems to be due to location and the local weather phenomena, whereas smaller training sets, are expected to suffice for less variable weather systems (for example, a Mediterranean summer). The choice of the training set’s size plays an important role as it must be large enough in order to obtain the optimal model coefficients which are then used to predict the energy output for the missing period. The training algorithm defined the best set of coefficients (k1–k6) which then provided the power surface shown in Fig. 1b. The optimal training size for this case was found to be 41 days in total. Finally, the training process yields valid results if no significant changes (i.e. component failures) have occurred in the PV system during its operation while no data are available (i.e. during the missing period). IET Renew. Power Gener., pp. 1–6 This is an open access article published by the IET under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) 3.1 Analysis of interpolated climatic data The following analysis is carried out for 1 year (2014). Irradiation (horizontal and in-plane) and ambient temperature comparisons with real measurements are shown in Figs. 2a and b and the statistical results are presented in Table 2. The method works well for horizontal irradiation, with a monthly RMSE of 2.8% and MBE of 1.5%. Ambient temperature is also well described with RMSE and MBE of 0.15 and −0.14% (in Kelvin), respectively. Fig. 1 Plots of a Training sets around the missing period taking as starting points the 31st of May and the 1st of July 2014, and going backwards and forwards in time, respectively b Fitting curve for the optimum training set (15 days backwards and 26 days forwards) for module A a Training sets around the missing period taking as starting points the 31st of May and the 1st of July 2014, and going backwards and forwards in time, respectively b Fitting curve for the optimum training set (15 days backwards and 26 days forwards) for module A A noticeable deterioration in the statistic metrics is noted for in-plane irradiation, which is primarily due to the sub-models used in the process of translation of global horizontal irradiation into the plane of array. This is to be anticipated, as separation month of missing data was considered (June 2014). This period was removed from the training set and was used as the validation set for the training algorithm. Fig. 2 Comparison of a Global horizontal (GHI) and plane-of-array irradiation (POA) b Ambient temperature for measured and interpolated data throughout a year (2014) Fig. 2 Comparison of a Global horizontal (GHI) and plane-of-array irradiation (POA) b Ambient temperature for measured and interpolated data throughout a year (2014) Table 2 Statistical results for annual analysis with measured and interpolated climatic data Ambient temperature, K POA irradiation, kWh/m2 GHI, kWh/m2 Monthly Annual Monthly Annual Monthly Annual RMSE 0.43 0.40 8.92 97.4 2.13 14.3 MAE 0.40 0.40 8.12 97.4 1.75 14.3 MBE −0.40 −0.40 −8.12 −97.4 1.20 14.3 RMSE, % 0.15 0.14 9.79 8.91 2.79 1.54 MAE, % 0.14 0.14 8.91 8.91 2.30 1.54 MBE, % −0.14 −0.14 −8.91 −8.91 1.56 −1.54 IET Renew. Power Gener., pp. 1–6 3 This is an open access article published by the IET under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) Fig. 2 Comparison of Fig. IET Renew. Power Gener., pp. 1–6 3 This is an open access article published by the IET under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) 3.2 Inferring missing meteorological and electrical data 3.2 Inferring missing meteorological and electrical data (global irradiance to beam and diffuse) and translation algorithms add a high percentage random and bias error, which varies amongst different models and locations [26]. However, there is potential for improvement in determining the optimum separation model for the UK climate. Thus generally, the results depend strongly on the climatic profile of the location and the choice of models. In-plane irradiation is generally underestimated, with some days giving better results than others. A further analysis based on different irradiation bins and clearness indices shows that the random error derives mainly for low irradiation and partly cloudy days as seen in Figs. 3a and b. Clearness index was calculated using [27] and the days were classified according to Gul et al. [28]. Concurrent energy yield readings and a climatic dataset were utilised containing a 1 month period of missing data (June 2014), during which neither of the above information was available. In order to validate the modelling results, this period was completely removed from the initial dataset and was treated as the ‘missing’ period. To calculate energy output, (3) is employed twice. Initially, it is used with hourly measured data of in-plane irradiation, module temperature and energy output to extract the model coefficients using a training period as defined using the training algorithm described in 0. Then, it is applied again to calculate the energy output for the missing month, using interpolated climatic data only for this period. Aggregated irradiation is calculated using hourly sums of irradiance. Module temperature for the missing period is calculated using (2) with interpolated irradiation and ambient temperature as input parameters. Comparisons between the obtained results and actual measurements for the missing period are shown in Figs. 4 and 5, followed by the statistical results in Tables 3 and 4. The width and the number of the irradiation bins were adjusted considering the frequency of irradiation values, so that RMSE in different bins is affected by the same number of observations. Lower irradiation values present a higher percentage RMSE which however is small in terms of absolute energy yield (Wh). The data points in Fig. 3a represent the calculation bias, which changes according to clearness index. , pp This is an open access article published by the IET under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) 3.1 Analysis of interpolated climatic data 2 Comparison of a Global horizontal (GHI) and plane-of-array irradiation (POA) b Ambient temperature for measured and interpolated data throughout a year (2014) a Global horizontal (GHI) and plane-of-array irradiation (POA) b Ambient temperature for measured and interpolated data throughout a year (2014) Table 2 Statistical results for annual analysis with measured and interpolated climatic data Ambient temperature, K POA irradiation, kWh/m2 GHI, kWh/m2 Monthly Annual Monthly Annual Monthly Annual RMSE 0.43 0.40 8.92 97.4 2.13 14.3 MAE 0.40 0.40 8.12 97.4 1.75 14.3 MBE −0.40 −0.40 −8.12 −97.4 1.20 14.3 RMSE, % 0.15 0.14 9.79 8.91 2.79 1.54 MAE, % 0.14 0.14 8.91 8.91 2.30 1.54 MBE, % −0.14 −0.14 −8.91 −8.91 1.56 −1.54 Table 2 Statistical results for annual analysis with measured and interpolated climatic data IET Renew. Power Gener., pp. 1–6 3 This is an open access article published by the IET under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) IET Renew. Power Gener., pp. 1–6 Fig. 3 Statistical analysis on hourly irradiation bins Fig. 3 Statistical analysis on hourly irradiation bins a %RMSE and %MBE b Normalised contribution to RMSE of hours with different clearness index Kt Fig. 3 Statistical analysis on hourly irradiation bins a %RMSE and %MBE b Normalised contribution to RMSE of hours with different clearness index Kt Fig. 3 Statistical analysis on hourly irradiation bins Fig. 3 Statistical analysis on hourly irradiation bins a %RMSE and %MBE b Normalised contribution to RMSE of hours with different clearness index Kt IET Renew. Power Gener., pp. 1–6 This is an open access article published by the IET under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) 3.2 Inferring missing meteorological and electrical data It seems that the method tends to underestimate higher irradiance (negative MBE) which present a higher bias error, whereas for irradiance values lower than 100 W/ m2 the result is slightly overestimated (positive MBE). This is due to the separation into beam and diffuse algorithms which tend to overestimate diffuse radiation for days with higher clearness index. Partly cloudy days contribute significantly to the overall error for the majority of the bins. The results for ambient temperature show that it can be interpolated to the location of interest with a very small MBE and RMSE. This is to be expected, as temperature is temporally and spatially more homogeneous than irradiance over the same distance for the UK climate. MBE increases for module temperature due to error propagation from both in-plane irradiation (inherent underestimation) and ambient temperature, but the effect Fig. 4 Comparison of daily results for the missing month (June 2014) for modelled and measured in-plane irradiation (POA) and average module temperature for a Module A Fig. 4 Comparison of daily results for the missing month (June 2014) for modelled and measured in-plane irradiation (POA) and average module temperature for Fig. 4 Comparison of daily results for the missing month (June 2014) for modelled and measured in-plane irradiation (POA) and average module temperature for a Module A b Module B Fig. 4 Comparison of daily results for the missing month (June 2014) for modelled and measured in-plane irradiation (POA) and average module temperature for a Module A b Module B a Module A b Module B 4 Fig. 5 Comparison of daily modelled and measured energy output and PR for the missing month (June 2014) for a Module A b Module B Fig. 5 Comparison of daily modelled and measured energy output and PR for the missing month (June 2014) for a Module A Fig. 3.2 Inferring missing meteorological and electrical data 5 Comparison of daily modelled and measured energy output and PR for the missing month (June 2014) for a Module A b Module B Table 3 Statistical results for in-plane irradiation and module temperature comparisons Table 3 Statistical results for in-plane irradiation and module temperature comparisons In-plane irradiation (kWh/m2) Module temperature, K Module A Module B Daily Monthly Daily Monthly Daily Monthly RMSE 0.70 8.3 2.78 2.24 2.67 2.31 MAE 0.50 8.3 2.35 2.24 2.33 2.31 MBE −0.28 −8.3 −0.76 −2.24 −0.89 −2.31 RMSE, % 14.9 5.9 0.93 0.75 2.31 0.77 MAE, % 10.5 5.9 0.78 0.75 2.31 0.77 MBE, % −5.9 −5.9 −0.76 −0.75 −2.31 −0.77 Table 4 Statistical results for energy output and PR for the two modules Energy output, kWh Performance ratio, PR Module A Module B Module A Module B Daily Monthly Daily Monthly Daily Monthly Daily Monthly RMSE 0.15 1.81 0.14 1.50 0.040 0.0002 0.042 0.007 MAE 0.11 1.81 0.11 1.50 0.026 0.0002 0.030 0.007 MBE −0.06 −1.81 −0.05 −1.50 −0.009 −0.0002 −0.0024 −0.007 RMSE, % 14.5 5.92 14.4 5.09 4.39 0.016 4.85 0.86 MAE, % 10.8 5.92 10.8 5.09 2.90 0.016 3.44 0.86 MBE, % −5.92 −5.92 −5.09 −5.09 −0.97 −0.016 −0.28 −0.86 Fig. 6 Scatter diagrams for module A, of hourly modelled and measured for the missing month (June 2014) a In-plane irradiation b Energy output Table 4 Statistical results for energy output and PR for the two modules Fig. 6 Scatter diagrams for module A, of hourly modelled and measured for the missing month (June 2014) a In-plane irradiation b Energy output IET Renew. Power Gener., pp. 1–6 This is an open access article published by the IET under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) 5 is very small with a maximum deviation of about 5° and average deviation of about 2°. Infrastructure and Society’ project which is funded by the RCUK’s Energy Programme (contract no: EP/K02227X/1). Infrastructure and Society’ project which is funded by the RCUK’s Energy Programme (contract no: EP/K02227X/1). The results for energy output errors are a propagation of irradiation and module temperature. The negative bias which arises primarily due to irradiation is evident also in energy output and in terms of absolute RMSE for energy output, that is 1.8 and 1.5 (in kWh) for modules A and B, respectively. 4 Conclusions 13 Hofstra, N., Haylock, M., New, M., et al.: ‘Comparison of six methods for the interpolation of daily, European climate data’, J. Geophys. Res., 2008, 113, (D21), doi:10.1029/2008JD010100 A method to replenish missing meteorological and electrical data (not) obtained during PV system operation was developed and validated for a polycrystalline and a monocrystalline PV module. The method is based on interpolating meteorological data and translating it to the local climate (namely in-plane irradiation and module temperature) governing the device performance. The local climate data are then used to calculate the electrical output of the system. This approach is validated against data from a precision measurement system. 14 Ross Jr., R.G.: ‘Interface design considerations for terrestrial solar cell modules’. 12th Photovoltaic Specialists Conf., Baton Rouge, LA, USA, November 1976, pp. 801–806 15 Skoplaki, E., Palyvos, J.A.: ‘Operating temperature of photovoltaic modules: a survey of pertinent correlations’, Renew. Energy, 2009, 34, (1), pp. 23–29 16 Nordmann, T., Clavadetscher, L.: ‘Understanding temperature effects on PV system performance’, Energy Convers., 2003, 3, pp. 2–5 17 Segado, P.M., Carretero, J., Sidrach-de-Cardona, M.: ‘Models to predict the operating temperature of different photovoltaic modules in outdoor conditions’, Prog. Photovolt. Res. Appl., 2014, 23, (10), pp. 1267–1282 There are noticeable differences in terms of the absolute energy production, while the estimation of the PR shows excellent agreement for both PV technologies. This means that the key property for assessing system quality can be replenished accurately with the given method and thus this is sufficient for evaluating real-time continuous performance. The PR is the key parameter required for warranty verification, and the method is highly successful for achieving this. Detailed investigation of the relative underestimation of the energy yield of a system identified that the error is almost exclusively due to the irradiance translation to plane of array and thus further efforts will focus on this. The largest bias is seen for high irradiance conditions, while the highest scatter is seen for lower irradiances but the reasons for this are not yet entirely clear. 18 Kratochvil, J.A., Boyson, W.E., King, D.L.: ‘Photovoltaic array performance model’. SAND2004-3535, Sandia National Laboratories (SNL), 2004 19 Huld, T., Friesen, G., Skoczek, A., et al.: ‘A power-rating model for crystalline silicon PV modules’, Sol. Energy Mater. Sol. Cells, 2011, 95, (12), pp. 4 Conclusions 3359–3369 pp 20 Dittmann, S., Friesen, G., Williams, S., et al.: ‘Results of the Third modelling round robin within the European project performance’ – comparison of module energy rating methods’. 25th European Photovoltaic Solar Energy Conf. and Exhibition/Fifth World Conf. on Photovoltaic Energy Conversion, Valencia, Spain, September 2010, pp. 4333–4338 p p pp 21 Lourakis, M.I.A.: ‘A brief description of the Levenberg–Marquardt algorithm implemented by levmar’, Found. Res. Technol., 2005, 4, pp. 1–6 22 Strobel, M.B., Betts, T.R., Friesen, G., et al.: ‘Uncertainty in photovoltaic performance parameters – dependence on location and material’, Sol. Energy Mater. Sol. Cells, 2009, 93, (6–7), pp. 1124–1128 ( ) pp 23 Firth, S.K., Lomas, K.L., Rees, S.J.: ‘A simple model of PV system performance and its use in fault detection’, Sol. Energy, 2010, 84, (4), pp. 624–635 Finally, the next step is to scale this study up to a specific set of data, such as a number of PV systems in close geographic proximity, for example, over a given urban area. This will require simulation of the entire PV system, i.e. take into consideration inverter and shading effects. This task is currently ongoing [29] and together with the work carried out in this study, it will enable automated analysis of domestic systems over a larger area. 24 Carr, A.J., Pryor, T.L.: ‘A comparison of the performance of different PV module types in temperate climates’, Sol. Energy, 2004, 76, (1–3), pp. 285–294 yp p gy ( ) pp 25 Gottschalg, R., Betts, T.R., Eeles, A., et al.: ‘Influences on the energy delivery of thin film photovoltaic modules’, Sol. Energy Mater. Sol. Cells, 2013, 119, pp. 169–180 26 Lave, M., Hayes, W., Pohl, A., et al.: ‘Evaluation of global horizontal irradiance to plane-of-array irradiance models at locations across the united states’, IEEE J. Photovolt., 2015, 5, (2), pp. 597–606 , , , ( ), pp 27 Iqbal, M.: ‘An introduction to solar radiation’ (Academic Press, London, 1983) 28 Gul, M., Muneer, T., Kambezidis, H.: ‘Models for obtaining solar radiation from other meteorological data’, Sol. Energy, 1998, 64, (98), pp. 99–108 28 Gul, M., Muneer, T., Kambezidis, H.: ‘Models for obtaining solar ra 3.2 Inferring missing meteorological and electrical data Crucially, the monthly PR can be predicted with a very small error for both cases and more specifically, with RMSE of about 0.0002 and 0.007 for modules A and B, respectively. A comparison of the above graphs, shows that for days where temperature is particularly low, measured PR is high and may slightly exceed 1.0, leading to a small deviation from the modelled value. Module temperature plays a significant role in modelling the energy output, which however is not directly evident in the PR. Namely, if in-plane irradiation is overestimated (Fig. 4), modelled energy output (Fig. 5) is affected by both in-plane irradiation and module temperature rise. The modelled result is very close to the measured energy output (where actual in-plane irradiation is lower) and thus, modelled PR is slightly lower than the measured value. This behaviour is particularly evident for days with lower average of module temperature (i.e. low ambient temperature and/or windy days). 6 References 1 ‘Solar photovoltaics deployment – Department of Energy & Climate Change’: https://www.gov.uk/government/statistics/solar-photovoltaics-deployment, accessed: 22 September 2015 2 IEC standard 61724: ‘Photovoltaic system performance monitoring – guidelines for measurement, data exchange and analysis’, 1998 3 Barbose, G., Wiser, R., Bolinger, M.: ‘Designing PV incentive programs to promote performance: a review of current practice in the US’, Renew. Sustain. Energy Rev., 2008, 12, pp. 960–998 4 Woyte, A., Richter, M., Moser, D., et al.: ‘Analytical monitoring of grid-connected photovoltaic systems’, IEA-PVPS T13-03:2014, 2014 5 Blaesser, G., Munro, D.: ‘Guidelines for the assessment of photovoltaic plants document B: analysis and presentation of monitoring data’, EUR 16339 EN, 1995 6 ‘Met Office Integrated Data Archive System (MIDAS) Land and Marine Surface Stations Data (1853-Current)’, http://catalogue.ceda.ac.uk/uuid/220a65615218d5c 9cc9e4785a3234bd0, accessed 24 April 2015 ( ) p g 9cc9e4785a3234bd0, accessed 24 April 2015 7 Rowley, P., Leicester, P., Palmer, D., et al.: ‘Multi-domain analysis of photovoltaic impacts via integrated spatial and probabilistic modelling’, IET Renew. Power Gener., 2015, 9, (5), pp. 424–431 In Figs. 6a and b, the scatter diagrams of modelled and predicted in-plane irradiation and energy output show that the discrepancy is low with a relatively small number of outliers in both cases being the main reason for the higher RMSE values for in-plane irradiation and energy output. This discrepancy is largely diminished with regards to the daily and monthly results for PR (see (1)). ( ) pp 8 ‘Centre for Renewable Energy systems Technology (CREST)’, http://www.lboro. ac.uk/research/crest/, accessed 23 July 2015 , y 9 Ridley, B., Boland, J., Lauret, P.: ‘Modelling of diffuse solar fraction with multiple predictors’, Renew. Energy, 2010, 35, (2), pp. 478–483 10 Hay, J.E., Perez, R., McKay, D.C.: ‘Estimating solar irradiance on inclined surfaces: a review and assessment of methodologies’, Int. J. Sol. Energy, 1986, 4, (5), pp. 321–324 11 Reindl, D., Beckman, W., Duffie, J.: ‘Evaluation of hourly tilted surface radiation models’, Sol. Energy, 1990, 45, (1), pp. 9–17 12 Zhu, J., Betts, T., Gottschalg, R.: ‘Accuracy assessment of models estimating total irradiance on inclined planes in Loughborough’. Fourth Photovoltaic Science Application and Technology (PVSAT-4), Bath, UK, April 2008, pp. 207–210 IET Renew. Power Gener., pp. 1–6 This is an open access article published by the IET under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) 5 Acknowledgments other meteorological data’, Sol. Energy, 1998, 64, (98), pp. 99–108 29 Palmer, D., Betts, T.R., Gottschalg, R.: ‘Assessment of potential for photovoltaic roof installations by extraction of roof slope from Lidar data and aggregation to census geography’. 11th Photovoltaic Science Application and Technology (PVSAT-11), Leeds, UK, April 2015, pp. 165–166 This work has been conducted as part of the research project ‘PV2025 - Potential Costs and Benefits of Photovoltaic for UK 6
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English
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Dermoscopy features of acquired reactive perforating collagenosis: a case series
Dermatology practical & conceptual
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Received: December 4, 2017; Accepted: April 20, 2018; Published: October 31, 2018 Received: December 4, 2017; Accepted: April 20, 2018; Published: October 31, 2018 Copyright: ©2018 Ormerod 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: None. Competing interests: The authors have no conflicts of interest to disclose. Competing interests: The authors have no conflicts of interest to disclose. All authors have contributed significantly to this publication. All authors have contributed significantly to this publication. Corresponding author: Emma Ormerod, MA, MRCP, Bristol Dermatology Unit, Bristol Royal Infirmary, Marlborough Street, Bristol BS2 8HW. Email: Emma.ormerod@uhbristol.nhs.uk collagen fibers accumulate in dermal papillae and epidermal hyperplasia may be seen. In more established lesions a cup- shaped depression of the epidermis develops with an overlying keratin plug containing inflammatory cells, keratinous debris, and collagen fibers [4,5]. Vertically oriented collagen fibers, stained red by elastic van Gieson staining or blue by Masson’s trichrome stain, are extruded through the epidermis and there may be a mild perivascular lymphohistiocytic infiltrate. Introduction Reactive perforating collagenosis (RPC) is a rare disorder in which abnormal collagen fibers extrude through the epider­ mis. In the acquired form, erythematous keratotic papules and plaques with firmly adherent central crust and ulceration develop, commonly on the trunk and extremity extensor surfaces, and often at sites of superficial trauma [1]. Intense itch is common. Acquired RPC is often associated with long- standing diabetes and chronic renal failure, particularly in patients undergoing dialysis [2,3]. Dermoscopy is a noninvasive technique which is now a standard tool used in the preoperative clinical diagnosis of skin tumors [6]. It is also increasingly used to aid in the diagnosis in other dermatological conditions including inflammatory dermatoses [7,8]. To our knowledge, the der­ moscopic features of RPC have been described in 2 previous case reports [9,10]. Here we report the dermoscopic findings in a series of 5 patients with RPC. However, because RPC is uncommon, the clinical presen­ tation can vary between patients, and it can be difficult to differentiate clinically from other conditions, the true diagno­ sis is often missed or delayed. Differential diagnosis includes ecthyma, prurigo nodularis, perforating granuloma annulare, dermatitis artefacta, and other perforating diseases [4]. Clini­ cal diagnosis of RPC is supported or confirmed by charac­ teristic histopathological features in most cases, although repeated biopsies may be required. Histological features vary according to stage of disease; in the early stages degenerate Dermoscopy features of acquired reactive perforating collagenosis: a case series Emma Ormerod1, Ausama Atwan2, Laszlo Intzedy3, Natalie Stone2 1 Dermatology Department, Bristol Royal Infirmary, Bristol, UK Key words: dermoscopy, perforating collagenosis, acquired, diagnostics Key words: dermoscopy, perforating collagenosis, acquired, diagnostics Citation: Ormerod E, Atwan A, Intzedy L, Stone N. Dermoscopy features of acquired reactive perforating collagenosi Dermatol Pract Concept. 2018;8(4):303-305. DOI: https://doi.org/10.5826/dpc.0804a11 Case Presentations We identified 5 patients with a diagnosis of acquired RPC in our department over the past 2 years. Case notes, pathology 303 Letter | Dermatol Pract Concept 2018;8(4):11 Figure 1. Macroscopic images of the rash in each of the 5 patients (patients 1-5, labeled A-E). [Copyright: ©2018 Ormerod et al.] Figure 1. Macroscopic images of the rash in each of the 5 patients (patients 1-5, labeled A-E). [Copyright: ©2018 Ormerod et al.] Figure 2. Dermoscopic images of a typical lesion from the rash in each of the 5 patients (patients 1-5, labeled A-E). [Copyright: ©2018 Ormer­ od et al.] Figure 2. Dermoscopic images of a typical lesion from the rash in each of the 5 patients (patients 1-5, labeled A-E). [Copyright: ©2018 Ormer­ od et al.] onset of his skin problems; he subsequently started a regi­ men of low molecular weight heparin. Routine blood values, including renal function, were normal. Skin biopsy showed ulceration of epidermis, acute and chronic inflammation at the ulcer base with leukocytoclasis, and a perivascular chronic inflammatory infiltrate in the mid-dermis. reports, and dermoscopy pictures were analyzed. Dermo­ scopic images were taken using a digital dermoscopy system (Nikon D33S camera [Nikon, Tokyo, Japan]; Heine Delta® 20T Dermatoscope [Heine Optotechnik, Herrsching, Ger­ many]). Minimal pressure was applied and ultrasound gel was used during the process to help preserve vessel morphology as much as possible. Patient 3. A 58-year-old man with a previous diagnosis of sarcoidosis was taking no regular medications. Routine blood values at the time of presentation were normal. Skin biopsy from an ulcer showed florid reactive changes and vertically oriented collagen fibers at the ulcer base consistent with RPC. Renal function was normal. There were 3 female and 2 male patients, with age rang­ ing from 53 to 83 years. All of them gave a history of a very itchy rash, affecting the trunk and/or lower limbs. The rash had a similar appearance in all patients, with erythematous nodules of varying sizes and central keratin plug (Figure 1). The diagnosis of RPC was suspected clinically in all patients and confirmed histologically in 4 of the 5 cases (in 1 patient, biopsy was felt to be inappropriate). Patient 4. An 83-year-old woman was housebound and unable to attend the dermatology clinic. She was referred via teledermatology for review of her images and clinical history. References nicorandil, candesartan, and atenolol. Blood values were nor­ mal apart from an elevated HbA1c in keeping with her known diabetes. Histology showed focal necrosis, ulceration and epidermal inflammation, with perivascular chronic inflamma­ tory cell infiltrate in the dermis. Dermoscopic images showed almost identical features in all 5 patients (Figure 2). 1. Millard PR, Young E, Harrison DE, Wojnarowska F. Reactive perforating collagenosis: light, ultrastructural and immunohisto­ logical studies. Histopathology. 1986;10:1047-1056. 1. Millard PR, Young E, Harrison DE, Wojnarowska F. Reactive perforating collagenosis: light, ultrastructural and immunohisto­ logical studies. Histopathology. 1986;10:1047-1056. 2. Morton CA, Henderson IS, Jones MC, Lowe JG. Acquired perfo­ rating dermatosis in a British dialysis population. Br J Dermatol. 1996;135:671-677. The 3 clear, consistent features were (1) a yellow-brown structureless area in the center of the lesion in keeping with surface crust; (2) a white rim surrounding the crust which can vary in thickness between patients and in a single lesion, possibly correlating to epidermal invagination or keratinous debris; and (3) an outer pink circle of inflammation with visible vessels, commonly short looped vessels centrally and dotted vessels peripherally. These features are similar to those previously described in 2 separate reports of single cases with RPC [9,10]. 3. Poliak SC, Lebwohl MG, Parris A, Prioleau PG. Reactive perforat­ ing collagenosis associated with diabetes mellitus. N Engl J Med. 1982;306:81-84. 4. Kim SW, Kim MS, Lee JH, et al. A clinicopathologic study of thirty cases of acquired perforating dermatosis in Korea. Ann Dermatol. 2014;26:162-171. 4. Kim SW, Kim MS, Lee JH, et al. A clinicopathologic study of thirty cases of acquired perforating dermatosis in Korea. Ann Dermatol. 2014;26:162-171. 5. Cerio R, Calnan CD, Wilson-Jones E. A clinic-pathological study of reactive perforating collagenosis: report of 10 cases. Br J Der­ matol. 1987;117:16-17. 6. Argenziano G, Soyer HP, Chimenti S, et al. Dermoscopy of pigmented skin lesions: results of a consensus meeting via the internet. J Am Acad Dermatol. 2003;48:679–693. 6. Argenziano G, Soyer HP, Chimenti S, et al. Dermoscopy of pigmented skin lesions: results of a consensus meeting via the internet. J Am Acad Dermatol. 2003;48:679–693. 7. Goncharova Y, Attia EA, Souid K, Protzenko O, Koktishev I. Dermoscopic features of clinically inflammatory dermatoses and their correlation with histopathologic reaction patterns. Arch Dermatol Res. 2015;307:23-30. Case Presentations She had a history of an aortic aneurysm, hypertension, atrial fibrillation, and transient ischemic attack. Blood tests revealed microcytic anemia but normal renal function. Biopsy was not felt to be appropriate for this patient; the diagnosis was made from classic clinical and dermoscopy features. Patient 1. A 53-year-old woman had a 20-year history of type 2 diabetes mellitus, peripheral vascular disease, and ischemic heart disease. Her medications included metformin, clopidogrel, bisoprolol, and lisinopril. Routine blood values, including renal function, were normal, and skin biopsy was consistent with RPC, showing vertical collagen orientation. Patient 5. An 80-year-old woman had a history of long- standing type 2 diabetes mellitus, ischemic heart disease, and hypertension. Medications included lercanidipine, furosemide, Patient 2. A 67-year-old man was diagnosed with bilateral pulmonary embolism at approximately the same time as the 304 etter | Dermatol Pract Concept 2018;8(4):11 Letter | Dermatol Pract Concept 2018;8(4):11 Conclusions RPC is an unusual condition that can mimic other conditions and is often initially misdiagnosed. The dermoscopic find­ ings in our cases reinforce the features described in previous reports [9,10] and indicate that dermoscopy in RPC gives a very characteristic, consistent appearance and can therefore be a useful and quick aid to make the diagnosis. Dermoscopy of RPC is particularly helpful in cases in which biopsy is not possible or is nondiagnostic. 8. Lallas A, Kyrgidis A, Tzellos TG, et al. Accuracy of dermoscopic criteria for the diagnosis of psoriasis, dermatitis, lichen planus and pityriasis rosea. Br J Dermatol. 2012;166:1198-1205. 9. Kittisak P, Tanaka M. Dermoscopic findings in a case of reactive perforating collagenosis. Dermatol Pract Concept. 2015;5:75-77. 10. Ramirez-Fort MK, Khan F, Rosendahl CO, Mercer SE, Shin-Chang H, Levitt JO. Acquired perforating dermatosis: a clinical and der­ matoscopic correlation. Dermatol Online J. 2013;19:18958. 305 305 Letter | Dermatol Pract Concept 2018;8(4):11 Letter | Dermatol Pract Concept 2018;8(4):11
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The Wellness Economy: A Comprehensive System of National Accounts Approach
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The Wellness Economy: A Comprehensive System of National Accounts Approach Rafael Martin M. Consing III (rconsing.consultant@adb. org), Michael John M. Barsabal (mbarsabal.consultant@ adb.org), Julian Thomas B. Alvarez (jalvarez.consultant@ adb.org) are consultants at the Economic Research and Regional Cooperation Department (ERCD) of the Asian Development Bank (ADB). Mahinthan J. Mariasingham (mmariasingham@adb.org) is a senior statistician in ERCD, ADB. Rafael Martin M. Consing III, Michael John M. Barsabal, Julian Thomas B. Alvarez, and Mahinthan J. Mariasingham No. 631 | December 2020 Rafael Martin M. Consing III, Michael John M. Barsabal, Julian Thomas B. Alvarez, and Mahinthan J. Mariasingham No. 631 | December 2020 Rafael Martin M. Consing III, Michael John M. Barsabal, Julian Thomas B. Alvarez, and Mahinthan J. Mariasingham This analysis was used in the Asian Development Outlook 2020 Update. The team would like to thank Julieta Magallanes, Ana Francesca Rosales, Angelo Jose Lumba, Clara Torelli, and Elaine Tan for their valuable insights. ASIAN DEVELOPMENT BANK ADB Economics Working Paper Series Creative Commons Attribution 3.0 IGO license (CC BY 3.0 IGO) © 2020 Asian Development Bank 6 ADB Avenue, Mandaluyong City, 1550 Metro Manila, Philippines Tel +63 2 8632 4444; Fax +63 2 8636 2444 www.adb.org Some rights reserved. Published in 2020. ISSN 2313-5867 (print), 2313-5875 (electronic) Publication Stock No. WPS200433-2 DOI: http://dx.doi.org/10.22617/WPS200433-2 The views expressed in this publication are those of the authors and do not necessarily reflect the views and policies of the Asian Development Bank (ADB) or its Board of Governors or the governments they represent. ADB does not guarantee the accuracy of the data included in this publication and accepts no responsibility for any consequence of their use. The mention of specific companies or products of manufacturers does not imply that they are endorsed or recommended by ADB in preference to others of a similar nature that are not mentioned. By making any designation of or reference to a particular territory or geographic area, or by using the term “country” in this document, ADB does not intend to make any judgments as to the legal or other status of any territory or area. This work is available under the Creative Commons Attribution 3.0 IGO license (CC BY 3.0 IGO) This work is available under the Creative Commons Attribution 3.0 IGO license (CC BY 3.0 IGO) https://creativecommons.org/licenses/by/3.0/igo/. By using the content of this publication, you agree to be bound by the terms of this license. For attribution, translations, adaptations, and permissions, please read the provisions and terms of use at https://www.adb.org/terms-use#openaccess. This CC license does not apply to non-ADB copyright materials in this publication. If the material is attributed to another source, please contact the copyright owner or publisher of that source for permission to reproduce it. ADB cannot be held liable for any claims that arise as a result of your use of the material. Please contact pubsmarketing@adb.org if you have questions or comments with respect to content, or if you wish to obtain copyright permission for your intended use that does not fall within these terms, or for permission to use the ADB logo. Corrigenda to ADB publications may be found at http://www.adb.org/publications/corrigenda. Notes: In this publication, “$” refers to United States dollars. ADB recognizes “China” as the People’s Republic of China. Creative Commons Attribution 3.0 IGO license (CC BY 3.0 IGO) The ADB Economics Working Paper Series presents data, information, and/or findings from ongoing research and studies to encourage exchange of ideas and to elicit comment and feedback about development issues in Asia and the Pacific. Since papers in this series are intended for quick and easy dissemination, the content may or may not be fully edited and may later be modified for final publication. CONTENTS TABLES, FIGURES, AND BOX iv ABSTRACT v I. INTRODUCTION 1 II. METHODOLOGY 3 A. Identifying the Wellness Sector 3 B. Data 3 C. Disaggregation of Input–Output Tables 4 D. Direct Computation of Wellness Sector Gross Value Added 5 E. Tracing the Production Linkages of the Wellness Sector 5 F. Integration of Gross Fixed Capital Formation in Wellness Gross Domestic Product 7 G. Measuring the Employment Attributable to the Wellness Economy 8 H. Hypothetical Extraction Method 9 I. Gross Domestic Product Loss Decomposition 10 J. Employment Loss Decomposition 10 III. RESULTS AND DISCUSSION 11 A. The Wellness Economy 11 B. Wellness Employment 22 IV. CONCLUSION AND MOVING FORWARD 27 APPENDIX 29 REFERENCES 33 33 TABLES, FIGURES, AND BOX TABLES 1 Size of the Wellness Economy for Selected Asian Economies 12 2 Size of the Wellness Economy in Per Capita Terms for Selected Asian Economies 16 3 Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted 21 4 Wellness Employment for Selected Asian Economies 23 5 Wellness Economy Labor Productivity for Selected Asian Economies 24 6 Decomposition of Employment Loss When Wellness Sector is Extracted 27 A.1 List of Industries and Activities Considered Part of the Wellness Economy 29 A.2 Data Sources 31 A.3 Data Sources for Input–Output Table Disaggregation 31 TABLES TABLES 1 Size of the Wellness Economy for Selected Asian Economies 12 2 Size of the Wellness Economy in Per Capita Terms for Selected Asian Economies 16 3 Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted 21 4 Wellness Employment for Selected Asian Economies 23 5 Wellness Economy Labor Productivity for Selected Asian Economies 24 6 Decomposition of Employment Loss When Wellness Sector is Extracted 27 A.1 List of Industries and Activities Considered Part of the Wellness Economy 29 A.2 Data Sources 31 A.3 Data Sources for Input–Output Table Disaggregation 31 FIGURES 1 Structure of the Wellness Sector: Share of the Top Five Wellness Industries 17 2 Disaggregation of Wellness Employment by Country, by Period 18 3 Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted by Country, by Period 20 4 Disaggregation of Wellness Employment by Country, by Period 25 5 Decomposition of Employment Loss When Wellness Sector is Extracted 26 by Country, by Period BOX Wellness Economies and Aging 13 FIGURES 1 Structure of the Wellness Sector: Share of the Top Five Wellness Industries 17 2 Disaggregation of Wellness Employment by Country, by Period 18 3 Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted by Country, by Period 20 4 Disaggregation of Wellness Employment by Country, by Period 25 5 Decomposition of Employment Loss When Wellness Sector is Extracted 26 by Country, by Period BOX Wellness Economies and Aging 13 13 Keywords: economy, employment, input–output, national accounts, wellness JEL codes: E01, C67, D57, I39, R15 ABSTRACT This paper provides a comprehensive discussion on different, interconnected methods of using the system of national accounts to measure the relevance of a country’s wellness sector to its overall economy. Procedures are discussed for using input–output analysis to derive the production and employment linkages between wellness and nonwellness sectors. We also discuss procedures for using the hypothetical extraction method to derive and decompose the production and employment losses that may arise when a country’s wellness sector is removed from the economy. These procedures are then used to provide estimates for ten countries in developing Asia across two time periods which together provide a proxy for the region (Asia-10), along with a discussion on how these wellness economies have grown and how each one's labor productivity and wellness sector structure have evolved between the two periods. Keywords: economy, employment, input–output, national accounts, wellness JEL codes: E01, C67, D57, I39, R15 I. INTRODUCTION Wellness goes beyond a lack of physical illness. It often means thriving holistically and living a well- rounded life, and so people engage in diverse activities to help themselves feel and become well. The World Health Organization (WHO) defines wellness as: “…the optimal state of health of individuals and groups. There are two focal concerns: the realization of the fullest potential of an individual physically, psychologically, socially, spiritually, and economically, and the fulfillment of one’s role expectations in the family, community, place of worship, workplace and other settings.” (WHO 2006) “…the optimal state of health of individuals and groups. There are two focal concerns: the realization of the fullest potential of an individual physically, psychologically, socially, spiritually, and economically, and the fulfillment of one’s role expectations in the family, community, place of worship, workplace and other settings.” (WHO 2006) While many of these activities do not necessarily involve monetary transactions, there are wellness-related activities which are also economic in nature. In a developing world, the volume and economic value of these activities are expected to increase as people become increasingly conscious of and able to meet their need for wellness. This paper contributes to wellness and economic literature by showing how the system of national accounts (SNA) framework can be used to measure the wellness sector’s relevance to the overall economy and then demonstrating this for selected Asian Development Bank (ADB) developing member countries (DMCs) over two time periods. The main advantage of this approach is that most countries follow the SNA framework when preparing their national accounts, and theoretically this allows any country to estimate and analyze its own wellness economy, defined here as the linkages of an economy attributable to the production of wellness goods and services with monetary transactions attached to them. As nations develop, it becomes increasingly important to be able to measure the wellness economy. From a policy perspective, this provides a better understanding of how relevant wellness activities have become to the economy, which ones are the biggest economic contributors, and which ones are potentially underdeveloped in the context of country-specific unmet social needs. For policymakers interested in maximizing the wellness of their constituents, a measure of the wellness economy becomes another analytical tool for socioeconomic development. There have been past attempts to measure wellness economies. 1 In national accounting, gross output is equal to the sum of intermediate consumption and value added. Because of the former, it is typically larger than GDP. I. INTRODUCTION The multidimensionality of wellness trends into the next century, with Miller and Foster (2010) stating that the broadening scope of wellness is meant to create a “theoretical framework that views individuals within a holistic perspective and consists of many dimensions.” Wellness is also commonly viewed as both a state and the active pursuit of that state, and this appears in the GWI (2018) definition of wellness as “the active pursuit of activities, choices, and lifestyles that lead to a state of holistic health.” The WHO definition introduced earlier is the most explicitly comprehensive so far as it includes an economic dimension to wellness as well as the other commonly cited dimensions and recognizes wellness as both a state and an activity. As this definition shares similarities with and encompasses many others covered, this is the definition for wellness primarily being referred to in this paper. In the endeavor to estimate how much of an economy can systematically be attributed to the production of wellness goods and services, the most inclusive definition is correspondingly adopted. Given the established multidimensionality of wellness, economic activities that fall under wellness cannot be limited to just the consumption of medical services and pharmaceutical goods. Potentially, wellness includes all economic activities and industries that help people feel and become well, such as those relating to travel, recreation, outdoor, sporting, and personal care activities. The specific economic activities considered as wellness are described further in section II and enumerated in Table A.1 of the Appendix. In this paper, the industries engaged in the production of such wellness goods and services are referred to collectively as the wellness sector.2 As economies are complex systems with interconnected sectors, the wellness sector is itself supported by activities in other sectors of the economy. In the context of economic productivity, the wellness economy is measured in terms of gross value added (GVA).3 Therefore, the objective of the paper is to show how much of a country’s GVA is attributable to those wellness goods and services with monetary transactions attached to them. This refers to two main components: (i) the GVA from the wellness sector itself, such as the GVA from hospitals; and (ii) the contribution from supporting nonwellness sectors, such as the GVA from the energy sector used to produce hospital services. I. INTRODUCTION The Global Wellness Institute (GWI) is one of the largest institutions to attempt to estimate wellness economies, and it estimates the value of the global wellness economy at $4.2 trillion as of 2017. However, its methodology is proprietary and does not appear to follow international standards of national accounting. For example, it is unclear what the $4.2 trillion figure mentioned in GWI (2018) refers to. It appears to be in terms of gross domestic product (GDP) as it’s described as “representing 5.3% of global economic output” (world GDP was over $80 trillion in 2017), but GDP is not necessarily the same as gross output.1 Any attempt to relate metrics and wellness starts with the most important question: What is wellness? As a naturally desirable state of health, wellness as a concept has been around potentially as long as humanity has. The desire for a better life is fundamentally a desire for wellness. As is common with such concepts, the term “wellness” can seem nebulous and imprecise, often grasped intuitively ADB Economics Working Paper Series No. 631 2 rather than scholastically. For the wellness economy to be measured, however, wellness must be defined explicitly. rather than scholastically. For the wellness economy to be measured, however, wellness must be defined explicitly. In the modern academe, numerous definitions for wellness have been proposed, with one of the earliest coming from Dunn (1959) who defines it as “a health condition which includes general well-being of body, mind, and spirit.” A review by Roscoe (2009) indicates similarities in definitions across wellness literature in the decades following Dunn (1959) but with more dimensions added, the most prevalent being those related to social, emotional, physical, intellectual, and spiritual well-being. 3 There is a small difference between a country’s GVA and its GDP. A country’s GDP is equal to its GVA plus nonrefundable product or sales taxes. These taxes constitute a very small percentage of GDP and are a function of product-specific value added. Therefore, for all analytical purposes, this paper assumes that GVA is almost equal to GDP and use the terms interchangeably (Consing et al. 2020). In this context, wellness industries and wellness subsectors may be treated synonymously. I. INTRODUCTION It’s important to emphasize that measuring the wellness economy is not the same as measuring the welfare, wellness, or well-being of people in a country. For example, a pandemic might increase spending on hospital activities which might, holding other factors constant, mean a larger measurement of the wellness economy, yet a population’s well-being could actually decline as more people fall ill or into anxiety and poverty due to the pandemic. Similarly, a wellness economy might be The Wellness Economy 3 The Wellness Economy growing due to high production of wellness goods and services, yet the population’s welfare may remain low if only a wealthy minority of the population is able to consume these goods and services. This paper focuses only on using input–output analysis to measure wellness economies and not welfare. growing due to high production of wellness goods and services, yet the population’s welfare may remain low if only a wealthy minority of the population is able to consume these goods and services. This paper focuses only on using input–output analysis to measure wellness economies and not welfare. Besides measuring the wellness economy in GVA terms, there are other ways by which the relevance of the wellness sector to the overall economy can be estimated under the SNA framework. One is to estimate wellness employment, defined here as the employment linkages attributable to the production of wellness goods and services with monetary transactions attached to them, and another is to estimate the production and employment losses that may occur if the wellness sector were extracted from the economy. Conceptually, these all fall under input–output analysis, and so they neatly relate to each other and are discussed as such in the methodology. Estimates for the wellness economy, the GVA lost from hypothetical extraction, and wellness employment are then produced for selected countries in developing Asia with available data over two time periods to show a practical application of this framework. A. Identifying the Wellness Sector A. The first step is to identify which economic industries produce wellness goods and services. Using the fourth revision of the International Standard Industrial Classification of All Economic Activities (ISIC Rev. 4), 35 industrial codes were identified as composing the wellness sector. These codes were selected to be as inclusive as reasonably possible of the various dimensions of wellness embodied in WHO’s definition. These are likewise consistent with wellness activities discussed in the literature, such as in Kickbusch and Payne (2003), Pilzer (2007), and GWI (2018). Some codes are included to expand the scope of commonly recognized wellness activities. For example, these ISIC codes include hospital activities for ill patients (excluded in some definitions of wellness, such as GWI 2018), under the assumption that ill patients engage in hospital activities with the intention of becoming well. As in Consing et al. (2020), these ISIC codes capture a variety of wellness goods and services from various industries, such as human health, residential care, social work, tourism, amusement, recreation, sports, creative, arts, entertainment, culture, and personal care activities as well as the construction of wellness-related structures, such as health and sports facilities and the manufacture and retail trade of wellness goods such as pharmaceutical, beauty, and sports products. Table A.1 of Appendix A contains the list of ISIC codes covering the wellness sector. C. Disaggregation of Input–Output Tables While a country’s IOT provides information necessary in computing for sectoral GVA, the industries of the wellness sector are often grouped into various sectoral aggregates making the identification and computation of the GDP attributable to the wellness sector difficult. This is resolved by disaggregating or breaking down the IOT industries. With several methods available, this paper uses information extrapolated from supply tables, administrative, and secondary data. The first method of disaggregating an IOT involves the use of the supply table. This is the preferred method as it involves using SNA components as a basis for disaggregation. This entails identifying wellness products and the total amount of wellness products supplied by the sector to be broken down. The total amount of wellness products that is supplied by the aggregated industry is then divided by the total output of the aggregated sector to obtain the disaggregator. This ratio is then multiplied to the relevant GVA in the IOT. This process is repeated to generate a set of disaggregators that are used to break down the aggregated sectors of interest. Once the wellness component has been separated, these are summed up to create a separate account for the wellness sector in the IOT. Underlying the first method is the need for a highly disaggregated row accounts in the supply table. That is, for the first method to be viable, the supply products must include numerous products. Hence, if a country’s supply table is not detailed enough to produce disaggregators, an alternative method of disaggregation is to use firm-level data coming from a secondary source. Here, the firm- level data from Orbis database was used. After applying the methods on filtering firms in the database as prescribed in Kalemli-Ozcan et al. (2019), data on the operating revenue of each firm for each country is collected. The operating revenues are aggregated at the four-digit ISIC level and based on the sectoral groupings in the IOT. 4 The set of disaggregators were then computed by taking the ratio of the operating revenue of ISIC industry codes for wellness industries to the operating revenue of the sector being disaggregated. If a detailed supply table is unavailable and data from secondary sources are limited for disaggregation, the donor imputation method for deriving disaggregators was employed. The objective is to use the disaggregators from a donor country. ADB Economics Working Paper Series No. 631 4 into IOT is the assumption that without any regard to the producing industry, each product has its own sale-specific structure (Eurostat 2008). Table A.2 of Appendix A contains a summary of the data sources used for estimating the wellness economy in each country. into IOT is the assumption that without any regard to the producing industry, each product has its own sale-specific structure (Eurostat 2008). Table A.2 of Appendix A contains a summary of the data sources used for estimating the wellness economy in each country. 4 Since firms in the Orbis database are classified according to the European Classification of Economic Activities Rev. 2, a concordance table was used to convert these codes into ISIC Rev. 4 industry codes. 5 It is a requirement that the sector aggregation in the IOTs of the donor and imputed economies be the same. It is a requirement that the sector aggregation in the IOTs of the donor and imputed economies be the s Data The main data source used in computing for the contribution of the wellness sector to GDP are national input–output tables (IOTs). Symmetric IOTs summarize the flow of transactions across industries operating in the economy. These contain information on intermediate consumption, gross output, and GVA for each production sector. When IOTs are not readily available, supply and use tables (SUTs) from various national statistical offices were converted into industry-by-industry IOTs using the transformation model prescribed by Eurostat (2008). Inherent in the transformation of SUTs ADB Economics Working Paper Series No. 631 C. Disaggregation of Input–Output Tables The donor country is chosen based on the expectation that the economic structure of the imputed country closely resembles that of the donor.5 Economic factors such as similarity in market structure, share of agriculture, industry and services to GDP, income group and major commodities produced were the main consideration in choosing a donor for a recipient country. Aside from these economic factors, similarities in geographical location, historical experience and values in different developmental indices such as the Human Development Index and unemployment rates were also taken into account in selecting the donor country. For example, the economic structure of Malaysia was used as a donor for Sri Lanka since both countries are upper middle-income economies with comparable market structure in terms of share of agriculture, manufacturing, and services to GDP. Similarly, both countries share the same colonial experience and geographical attributes. The type of disaggregation for each country IOT used in this paper is elaborated in Table A.3 of the Appendix. 5 The Wellness Economy Once disaggregators are estimated from the methods described above, these were further verified with available administrative data for each country of interest to ensure that the disaggregators are reliable and intuitive. The disaggregators are then used to dissect the aggregated sectors in each country’s IOT. Since IOTs are characteristically symmetric, these disaggregators are multiplied to both the rows and columns corresponding to the industries in the IOT which contain the wellness activities of interest. In effect, the symmetric IOT is expanded for each disaggregator being applied as the corresponding industry being disaggregated is split into the part of it containing wellness activities and the part of it containing nonwellness activities. For example, an IOT containing a single entry encompassing all ISIC codes starting with 47 (retail trade, except motor vehicles and motorcycles) would be split row- and column-wise using a relevant disaggregator to create a separate entry just for ISIC code 4763 (retail sale of sporting equipment in specialized stores), which is considered part of wellness. D. Direct Computation of Wellness Sector Gross Value Added D. Given that a country’s IOT is disaggregated following the procedure described in the previous subsection, the wellness components of each sector were summed up to compute the country’s GVA directly generated by its wellness industries, also referred to here as wellness sector GVA. Assuming that there are n sectors in the economy and q of which are wellness industries, equation (1) describes a formula for the GVA of the wellness sector that is consistent with the SNA framework. Wellness sector GVA = pᇱ(x −z) = p′va (1) (1) where p is a n x 1 indicator vector whose value is 1 if the entry corresponds to a wellness industry and 0 otherwise.6 x, z and va are n x 1 vectors of output, total intermediate consumption, and gross value added, respectively. Throughout the paper, the prime symbol (′) denotes matrix transposition. where p is a n x 1 indicator vector whose value is 1 if the entry corresponds to a wellness industry and 0 otherwise.6 x, z and va are n x 1 vectors of output, total intermediate consumption, and gross value added, respectively. Throughout the paper, the prime symbol (′) denotes matrix transposition. 6 As a check, the sum of each entry in p must be equal to q. Another way of aggregating values in each wellness industry is through the multiplication of an aggreg components of the IOT. See Torelli and Lumba (2020) for a detailed exposition on the aggregator matri As a check, the sum of each entry in p must be equal to q. As a check, the sum of each entry in p must be equal to q. 7 Another way of aggregating values in each wellness industry is through the multiplication of an aggregator matrix to the components of the IOT. See Torelli and Lumba (2020) for a detailed exposition on the aggregator matrix. E. Tracing the Production Linkages of the Wellness Sector E. The wellness GVA derived in equation (1) captures the direct economic contribution of the sector. However, the wellness economy also includes GVA from supporting nonwellness industries used to produce wellness goods and services. These contributions are not encapsulated in the previous equations. To account for these contributions when estimating the size of the wellness economy, we use Leontief’s insight in Leontief (1936) to derive the wellness sector’s product linkages which contain the contribution from supporting nonwellness industries. To trace the production linkages of the wellness sector, the first step is to convert the disaggregated n x n IOT into a table with n-(q-1) x n-(q-1) dimension. This ensures that there is only a single account dedicated for the wellness sector and there is no double-counting that comes from the interaction of wellness industries with each other. Resizing the IOT entails that each entry of the wellness industry in the disaggregated IOT is added to a single account.7 Once the values for each wellness industry are aggregated into a single account, the matrix of technical coefficients, A = [aij] which gives the share of inputs from sector j to total output of sector i, is obtained. This matrix is derived by post-multiplying the matrix of intermediate consumption, ADB Economics Working Paper Series No. 631 6 Z = [zij], with the inverse of a diagonalized matrix of gross output, X෡-1.8 Subtracting A to an identity matrix and taking its inverse yields equation (2), the Leontief Inverse. Z = [zij], with the inverse of a diagonalized matrix of gross output, X෡-1.8 Subtracting A to an identity matrix and taking its inverse yields equation (2), the Leontief Inverse. B = (I −A)ିଵ= [bij] (2) (2) The Leontief Inverse summarizes the output requirements from each sector to meet final demand given a specific time period. bij represents the entry in the ith row and jth column of the matrix represented in equation (2). Similarly, we also construct the direct value-added coefficient matrix V෡ by placing the elements of a n-(q-1) × 1 vector of direct value-added coefficients, v = [vaj xj ⁄ ], into the diagonal entries. Each entry in v is obtained by dividing Sector j’s gross value added by the gross output of the same sector. Pre-multiplying B to V෡ gives us V෡B, the total value-added matrix. 8 For notational purposes, a hat (i.e., X෡) represents a diagonal matrix with elements of vector x on the diagonal. 9 This decomposition performed in this framework is based on the work of Wang, Wei, and Zhu (2013) and Wang et al. (2017) which decomposes the value added into various component in a multiregional input–output model. notational purposes, a hat (i.e., X෡) represents a diagonal matrix with elements of vector x on the diagonal. composition performed in this framework is based on the work of Wang, Wei, and Zhu (2013) and Wa which decomposes the value added into various component in a multiregional input–output model. This decomposition performed in this framework is based on the work of Wang, Wei, and Zhu (2013 (2017) which decomposes the value added into various component in a multiregional input–output mod E. Tracing the Production Linkages of the Wellness Sector This matrix indicates the value added each sector directly and indirectly required to produce a unit of its final demand. Thus, when Y෡, a diagonal matrix of the final demand, is post-multiplied to V෡B, equation (3) is derived. V෡BY෡= ቎ v1b11y1 ⋯ v1b1,n-(q-1),yn-(q-1) ⋮ ⋱ ⋮ vn-(q-1)bn-(q-1),1y1 ⋯ vn-(q-1)bn-(q-1),n-(q-1)yn-(q-1) ቏ (3) V෡BY෡= ቎ v1b11y1 ⋯ v1b1,n-(q-1),yn-(q-1) ⋮ ⋱ ⋮ vn-(q-1)bn-(q-1),1y1 ⋯ vn-(q-1)bn-(q-1),n-(q-1)yn-(q-1) ቏ (3) (3) The matrix in equation (3) with dimension n-൫q-1൯ × n-൫q-1൯, traces the production linkages of each sector in the economy by decomposing the value added made by each sector in the economy.9 Each element in the matrix is interpreted as the value added from each sector that is directly or indirectly used in the production of final goods and services of a specific sector (Wang, Wei, and Zhu 2013; Wang et al. 2017). Therefore, the sum of each entry of the V෡BY෡ matrix, as shown in equation (4), gives the total GDP of the entire economy. Total GDP = iᇱV෡BY෡i (4) (4) For notational purposes, a hat (i.e., X) represents a diagonal matrix with elements of vector x on the diagonal. 9 This decomposition performed in this framework is based on the work of Wang, Wei, and Zhu (2013) and Wang et al. (2017) which decomposes the value added into various component in a multiregional input–output model. where i is a unit vector. where i is a unit vector. Alternatively, the entries along the rows of equation (3) can be interpreted as the distribution of the value added created from a sector across all other industries in the economy. For example, the entry in the ith- row and jth-column, vibijyj, represents the value-added contribution of sector i that is used in the production of sector j’s final goods and services. Thus, the sum of each entry in the row accounts would yield the GVA that is directly created in the sector, tracing all forward linkages across all downstream sectors from a producer’s perspective (Wang, Wei, and Zhu 2013). Conversely, the entries along the column, correspond to the breakdown of value-added contributions from all sectors in the economy used in the production of a particular sector’s final goods and services. Thus, looking at the entries column-wise traces the backward linkages of a particular industry across all upstream sectors from a user’s perspective (Wang, Wei, and Zhu 2013). To measure the wellness economy, the value-added contribution attributable to the wellness sector from equation (3) is estimated. This is done by including the sum of all entries in the row for the The Wellness Economy The Wellness Economy 7 wellness sector in equation (3). The row sum, iᇱV෡BY෡𝛆, can be easily obtained by pre-multiplying a unit row vector and post-multiplying ε to equation (3). The vector ε is an indicator vector for the wellness sector where each element of the vector is 0 except for the row corresponding to the wellness sector with a value of 1. This term captures the value-added contributions from the wellness sector that enable production in all sectors in the economy. The term iᇱV෡BY෡𝛆 also encapsulates the forward linkages of the wellness sector across all downstream sectors. Furthermore, this term is exactly equal to the result derived in equation (1). The measure for the size of the wellness economy also includes the backward linkages of wellness sector. This is computed by taking the sum of the column dedicated for the wellness sector in equation (3). Operationally, the value for the backward linkage is derived by post-multiplying 𝛆 to iᇱ൫V෡BY෡൯ ᇱ. With the inclusion of iᇱ൫V෡BY෡൯ ᇱ𝛆 to the new estimate of wellness GDP, the value-added contribution from supporting nonwellness sectors that enables the production of the wellness sector is accounted. where i is a unit vector. Adding these two terms while adjusting for the intersection term, ൣdiag൫V෡BY෡൯൧′, which is double- counted, gives a GDP measure of the wellness economy based on its production linkages as shown in equation (5). Wellness GDP = iᇱV෡BY෡𝛆+ iᇱ൫V෡BY෡൯ ᇱ𝛆 −ൣdiag൫V෡BY෡൯൧′𝛆 (5) (5) ( ) 11 In the application of this estimation procedure, the donor country is Canada due to data limitations. However, another economy with available data can be used as a donor country. Consequently, if the matrix product is not filtered out, 𝚲 becomes an identity matrix. 10 The wellness GFCF matrix (W) is extrapolated from the GFCF vector in the IOT by multiplying the corresponding ratio of the gross output of each wellness industry to total output with the row entry in the GFCF vector. In matrix notation, ′ W = gt′, where g is a n-(q-1) x 1 GFCF vector and t is a qx1 vector of gross output ratios. Integration of Gross Fixed Capital Formation in Wellness Gross Domestic Product While the wellness GDP stated in equation (6) captures all contemporaneous input–output transactions with respect to the exogenous final demand, it does not include the capital goods purchased by the wellness sector for future production. To account for the gross fixed capital formation (GFCF) attributable to the wellness sector but distributed in other industries, equation (6) is adjusted as follows: ellness GDP = iᇱV෡BY෡𝛆+ iᇱ൫V෡BY෡൯ ᇱ𝛆 −ൣdiag൫V෡BY෡൯൧ ᇱ𝛆+ (i −𝜺)ᇱV෡BY෡R෡𝚲(i −𝜺) (6) (6) equation (6) is almost identical to equation (6) except that a fourth term was added, where the V෡BY෡ matrix is post-multiplied with R෡. The post-multiplied matrix is a n-(q-1) x n-(q-1) diagonal matrix of the ratio of use of wellness GFCF to the total final use of each sector in the economy. Each ratio is computed by dividing the sum of each row in the wellness GFCF matrix by the corresponding total final demand.10 The matrix product V෡BY෡R෡ is again post-multiplied with a filter matrix, 𝚲= 𝜶ෝ. The diagonalized vector 𝜶, is an indicator vector whose value is 1 if the same industry in a donor country11 uses wellness GFCF products and 0 otherwise. The post-multiplication of 𝚲 to the matrix product V෡BY෡R෡ effectively ADB Economics Working Paper Series No. 631 8 filters out industries that might be providing wellness GFCF, but whose counterparts in the donor economy do not. filters out industries that might be providing wellness GFCF, but whose counterparts in the donor economy do not. The sum of all entries in the resulting matrix less the entries corresponding to the wellness sector itself is the term representing the part of GDP attributable to the wellness sector’s purchase of capital goods from other sectors in the economy. Thus, equation (6) is the key equation in measuring the size of the wellness economy. G. Measuring the Employment Attributable to the Wellness Economy Besides measuring the economy attributable to wellness in terms of GVA, the economic relevance of wellness can be characterized through its contribution to total employment. The key step in performing this analysis is the collection and processing of sectoral employment data from official sources. Since sources of labor data are likely to release employment figures at an aggregated level, different techniques are applied to further disentangle the number of jobs attributable to each sector in the economy. The first method in disaggregating employment data uses the unit labor cost approach where the sectoral unit labor cost (ULC) is defined as the ratio of total labor cost to real output by sector (Ernst and Sarabia 2015). Since the total labor cost is the product of real wages and the total number of employees in each sector, the sectoral ULC can be multiplied to the inverse of the wage-to-output ratio to recover total employment by industry. This step is operationalized in equation (7). Employmenti=ULCj× Total Outputj Real Wagej = Real Wagej × Employmentj Total Outputj × Total Outputj Real Wagej (7) Employmenti=ULCj× Total Outputj Real Wagej = Real Wagej × Employmentj Total Outputj × Total Outputj Real Wagej (7) (7) Given that the unit labor cost approach requires data that might not be readily available from official sources, another method in deriving sectoral employment is to use the of distribution of Compensation of Employees (COE) by sector. Often, COE is provided in the SUT of a particular country. If COE is not available, the distribution of GVA can be an alternative in further dividing aggregated employment figures. Once data on employment are processed to the desired sectoral disaggregation, the effects of the sector on jobs is determined by executing a procedure analogous to the method described in section II.E is performed. Unlike in equation (4) where V෡ is pre-multiplied to BY෡, V෡ is replaced with an employment matrix, E෡, which is a n-൫q-1൯ × n-൫q-1൯ diagonal matrix with labor coefficients as its diagonal entries. Labor coefficients represent the total number of persons needed to produce a unit of output and are computed by dividing the total number of jobs for each sector to the gross output of the corresponding sector (i.e.: ej= jobsJ/xj). Pre-multiplying E෡ with BY෡ yields to the matrix equation below. G. Measuring the Employment Attributable to the Wellness Economy E෡BY෡= ቎ e1b11y1 ⋯ e1b1,n-(q-1),yn-(q-1) ⋮ ⋱ ⋮ en-(q-1)bn-(q-1),1y1 ⋯ en-(q-1)bn-(q-1),n-(q-1)yn-(q-1) ቏ (8) E෡BY෡= ቎ e1b11y1 ⋯ e1b1,n-(q-1),yn-(q-1) ⋮ ⋱ ⋮ en-(q-1)bn-(q-1),1y1 ⋯ en-(q-1)bn-(q-1),n-(q-1)yn-(q-1) ቏ (8) (8) The n-൫q-1൯ × n-൫q-1൯ matrix represented in equation (8) shows the number of jobs created in each sector due to the final demand. Particularly, eibijyj is the number of jobs created in Sector i due to the final demand of Sector j. Thus, summing up all entries in equation (8) results into the total number of jobs in the economy. Mathematically, the total number of jobs in the economy is expressed as The Wellness Economy 9 Total employment = iᇱE෡BY෡i (9) (9) Total employment = iᇱE෡BY෡i To derive the employment attributable to the wellness economy, entries in the column and row vectors of equation (8) corresponding to the wellness sector are added together. This procedure is summarized in equation (10). Wellness employment = iᇱE෡BY෡𝛆+ iᇱ൫E෡BY෡൯ ᇱ𝛆 −ൣdiag൫E෡BY෡൯൧′𝛆 (10) (10) The first term of equation (11) shows the total number of jobs created in the wellness sector due to the demand of all sectors in the economy. Similarly, the difference between the second and third terms of the preceding equation indicates the number of jobs induced by the final demand for wellness goods and services in all other sectors in the domestic economy. H. Another way of measuring the importance of wellness industries to the economy is by tracing the GDP and jobs that are lost when the sector is nullified in the economy (Miller and Blair 2009). One way of doing this is through the hypothetical extraction method (HEM). HEM is almost identical to the analysis discussed in section II.E except that in this method, the row and column elements of the wellness sector in the matrix of technical coefficients are deleted by replacing them with zeroes to generate a new matrix, Aഥ. By doing so, the interdependence between the wellness sector and the rest of the economy is canceled out (ADB 2018). It also follows that there is no final demand for wellness goods and services, yതk = 0, and no primary inputs, va തതതk = 0 for the wellness sector. Since the input requirements of other sectors are unaltered, HEM assumes that the inputs originally provided by the wellness sectors are satisfied by additional imports after extraction (Dietzenbacher, van Burken, and Kondo 2019). Moreover, HEM further assumes that once the inputs for the wellness sector are extracted, these resources do not shift to other activities and therefore, remain unemployed. This assumption is valid in the short run. With the matrix of technical coefficients altered, the entries in the Leontief Inverse are also changed (i.e.: Bഥ= (I −Aഥ)ିଵ). Similarly, new matrices of direct value-added coefficients, Vഥ, and final demand, Yഥ, are derived. Pre-multiplying Vഥ with Bഥ and post-multiplying Yഥ with the matrix product gives us the new GDP of the economy when the wellness sector is nullified. The new GDP is summarized in equation (11). tal GDP തതതതതതതതതതത= iᇱVഥBഥYഥi (11) Total GDP തതതതതതതതതതതതതത= iᇱVഥBഥYഥi (11) When HEM is also applied, the jobs that the wellness sector generates are lost. This means that the labor coefficient for the wellness sector becomes zero (i.e.: eതk = 0) implying that a new employment matrix, Eഥ, is derived. Matrix Eഥ is almost identical to matrix E described in section II.G, except that the diagonal entry corresponding to the wellness sector is now set to zero. By summing up the entries of the resulting matrix product from pre-multiplying Eഥ to BഥYഥ, the remaining jobs in the domestic economy is computed. The new level of total employment is represented mathematically in equation (12). Total Employment തതതതതതതതതതതതതതതതതതതതതതതത= iᇱEഥBഥYഥi (12) Total Employment തതതതതതതതതതതതതതതതതതതതതതതത= iᇱEഥBഥYഥi (12) Total Employment തതതതതതതതതതതതതതതതതതതതതതതത= iᇱEഥBഥYഥi (12) ADB Economics Working Paper Series No. 631 10 I. Gross Domestic Product Loss Decomposition The difference between the total GDP prior extraction (equation [4]) and the hypothetical situation (equation [11]) gives us the potential GDP lost when the wellness sector is extracted. Formally, this is written as GDP Loss = iᇱV෡BY෡i −iᇱVഥBഥYഥi (13) (13) Since HEM assumes no reallocation among domestic inputs and the extracted inputs used by the wellness sector is completely substituted by imports as a result of extraction, the estimate produced from equation (13) is an upper bound estimate in the short run. Alternatively, equation (14) can be re-written as GDP Loss = vak + yk ෍brk vak xr r + ෍var(brr-bതrr) yr xr + 𝒓 ෍෍var(brs-bതrs) ys xr s≠r r≠s (14) (14) where r and s are indices for all industries except for the wellness sector with index k.12 Equation (14) shows that the GDP lost can be decomposed into direct (first and second terms) and indirect losses (third and fourth terms). The direct losses comprise of the lost incurred due to removal of production linkages of the wellness sector. Specifically, the first term represents the GVA loss attributed to the wellness sector that is used in the production of final goods and services by all sectors in the economy, while the second term is the total GVA lost from other industries that were previously used in the production of final wellness goods and services in the pre-extraction scenario. These correspond to the linkages of the wellness economy described in section II.E. Similarly, the indirect losses are incurred due to the resulting changes in the sensitivity of the output of the remaining sectors because of a change in the final demand. Specifically, the third term is the loss incurred due to own-industry output elasticities and the fourth term represents the loss due to changes in cross-industry output elasticities. The third and fourth term together are the difference between the estimated GDP lost from the hypothetical extraction of wellness industries and the estimated size of the wellness economy from its linkages in equation (6). 12 See Barsabal, Alvarez, and Consing (2020) for the detailed derivation of the GDP lost after hypothetical extraction. J. Like in section II.I, the total jobs lost after extracting the wellness sector from the domestic economy is the difference between the total employment prior extraction (equation [9]) and the new level of employment described in equation (12). In matrix form, the loss in employment is expressed as follows. Employment Loss = iᇱE෡BY෡i −iᇱEഥBഥYഥi (15) (15) Note that equation (15) is a maximum estimate of the total jobs lost in the short run since the HEM assumes no redistribution of production inputs to remaining sectors. Furthermore, the total employment loss can be decomposed as shown in equation (16). Employment Loss = jobsk + yk ෍brk jobsk xr r + ෍jobsr(brr-bതrr) yr xr + ௥ ෍෍jobsr(brs-bതrs) ys xr s≠r r≠s (16) Employment Loss = jobsk + yk ෍brk jobsk xr r + ෍jobsr(brr-bതrr) yr xr + ௥ ෍෍jobsr(brs-bതrs) ys xr s≠r r≠s (16) (16) 12 See Barsabal, Alvarez, and Consing (2020) for the detailed derivation of the GDP lost after hypothetical extraction. 11 The Wellness Economy The Wellness Economy The first term in equation (16) is equal to the jobs lost as a result of the nullification of the demand for wellness final goods and services from all remaining sectors. Similarly, the second term computes the jobs induced by the final demand for wellness goods and services in all other sectors in the domestic economy that are now lost, while third and fourth terms represent the losses in jobs due to the changes in output elasticities of the remaining industries. In particular, the third term represents the jobs lost due to changes in own-industry output elasticities while the fourth term shows the losses in employment due to changes in cross-industry output elasticities. By convention, the sum of the first two terms is referred as the direct employment losses and is equal to the employment losses generated by equation (16). Adding the third and fourth terms of equation (16) gives the indirect employment losses incurred. 1. Size of the Wellness Economy Table 1 shows the estimates of the wellness economy in ten of ADB’s DMCs, as measured in millions United States dollars at constant 2010 prices. The wellness economies are calculated using equation (6). The estimates are presented for two periods for each country, and the annualized growth rate for each wellness economy is also shown in the last column. As a caveat, the estimates are dependent on the data sources used for disaggregation shown in Table A.3 in the appendix. Breaking down of national IOTs to disaggregate the wellness sector from the other sectors is implemented using Orbis firm-level data for the People’s Republic of China (PRC), India, Philippines, Thailand, and Viet Nam. Supply table is used for Kazakhstan and Malaysia as these two countries have detailed products in their SUTs. When the other two sources are insufficient, the structure of donor country is used to approximate the disaggregation for another country. The choice is based on the similarity in economic structure (i.e., share of agriculture, industry, and services to GDP), level of development (i.e., income classification, HDI), geographic proximity, and historical context. Malaysia is used as the donor country both for Fiji and Sri Lanka, while the structure of the PRC is used for Mongolia. Table 1: Size of the Wellness Economy for Selected Asian Countries ($ million, constant 2010 prices) Country Period 1 Period 2 Real Wellness GDP Growth Rate (annualized, %) Real GDP Growth Rate (annualized, %) Asia-10 756,800 1,460,166 10.7 7.2 Fiji 105 171 10.2 4.6 India 90,902 171,070 13.5 7.4 Kazakhstan 8,811 9,237 1.2 2.6 Malaysia 11,044 20,545 13.2 5.3 Mongolia 333 622 9.3 8.2 People’s Republic of China 585,508 1,176,330 10.5 7.6 Philippines 14,410 21,802 8.6 6.6 Sri Lanka 8,783 9,351 1.3 4.3 Thailand 29,118 37,437 5.2 2.8 Viet Nam 7,786 13,601 11.8 6.2 GDP = gross domestic product. Notes: Real GDP data are based on World Bank’s estimates. The growth rate for Asia-10 is the average growth rate of all countries’ wellness economies weighted by each one’s real GDP in the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017); Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. Real GDP data are based on World Bank’s estimates. A. The Wellness Economy A. Based on data for the previous decade, the wellness economy’s prospects in developing Asia have generally been positive, demonstrating potential for high growth. Wellness traditions in the region have their roots in centuries-old practices and have deeply embedded themselves in its peoples’ lives and cultures. Asian economies have successfully assimilated some of these practices even in contemporary markets, notwithstanding significant changes in their economic structure. Even the wellness economy itself witnessed drastic changes in recent periods, resulting from changes in technology and changes in demographic composition. The advancements in technology, for example, have enabled greater volumes of wellness products to be more accessible to a wide array of consumers. At the same time, the aging population in several economies in developing Asia also influenced wellness consumption patterns, as societies divert more resources toward meeting the demands of the elderly population. The sharp increases in per capita income in developing Asia has been accompanied by a rapidly growing middle class (ADB 2019, Kharas 2017). As a consequence, large segments of the population have been able to integrate wellness goods and services into their daily consumption pattern. Moreover, there is an increasing recognition that wellness-oriented policies are needed to complement people’s transitions toward improved and healthier lifestyles (ADB 2020). Given these developments, there is also growing demand for a framework by which to measure the wellness economy and to trace its evolution across countries and over time. This section presents and discusses estimates of the wellness economy in selected countries in developing Asia using the procedures described in section II. The discussion in this section is outlined as follows: section III.A.1 discusses the size of wellness economy in aggregate and in per capita terms, while section III.A.2 highlights the structure and industry composition of the wellness sector. Section III.A.3 decomposes the wellness economy into forward and backward linkages, and wellness GFCF component. Finally, section III.A.4 presents the results of the hypothetical extraction method, where the wellness sector is hypothetically removed from the economy, and the resulting loss in GDP is calculated. ADB Economics Working Paper Series No. 631 12 Notes: Real GDP data are based on World Bank’s estimates. The growth rate for Asia-10 is the average growth rate of all countries’ wellness economies weighted by each one’s real GDP in the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017); Thailand (2012, 2017); Viet Nam (2012, 2017). ( , ); ( , ) Source: Authors’ calculations. Real GDP data are based on World Bank’s estimates. The growth rate for Asia-10 is the average growth rate of all countries’ wellness economies weighted by each one’s real GDP in the second period. Box: Wellness Economies and Aging Intuitively, spending on wellness goods and services may share a relationship with a country’s demographic structure. As the share of the elderly population increases, the demand for goods and services which constitute the wellness sector also increases. These include health-care services, residential care services, manufacture of pharmaceuticals, among other wellness products consumed by the elderly population. Hence, it is interesting to compare the size of wellness economy as a percentage share of GDP with the share of elderly population to the economy’s total population, as shown in Box Figure 1 for each of the two periods. Intuitively, spending on wellness goods and services may share a relationship with a country’s demographic structure. As the share of the elderly population increases, the demand for goods and services which constitute the wellness sector also increases. These include health-care services, residential care services, manufacture of pharmaceuticals, among other wellness products consumed by the elderly population. Hence, it is interesting to compare the size of wellness economy as a percentage share of GDP with the share of elderly population to the economy’s total population, as shown in Box Figure 1 for each of the two periods. In general, economies with higher percentage share of elderly population also have larger wellness economy as a percentage share of GDP (i.e., Sri Lanka, the People’s Republic of China, and Thailand). In contrast, economies with lower percentage share of elderly population also have lower share of wellness economy as a percentage of GDP (i.e., Mongolia and Fiji). The upward- sloping fitted line suggests a positive correlation between wellness economy and aging. As a caveat, the scatterplot shown in the Box Figure 1 below does not imply causality. For comparison, a red line is also shown which indicates a one-to-one correlation between wellness economy as a percentage of GDP and elderly population as a percentage of total population. Notice that the fitted line deviates from the red line, indicating that there are factors, other than changes in the demographic structure that also influence the size of wellness economy. Correlation between the Size of Wellness Economy and Aging FIJ = Fiji, GDP = gross domestic product, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. 1. Size of the Wellness Economy The growth rate for Asia-10 is the average growth rate of all countries’ wellness economies weighted by each one’s real GDP in the second period. Table 1: Size of the Wellness Economy for Selected Asian Countries ($ million, constant 2010 prices) g p Notes: Real GDP data are based on World Bank’s estimates. The growth rate for Asia-10 is the average growth rate of all countries’ wellness economies weighted by each one’s real GDP in the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017); Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. Real GDP data are based on World Bank’s estimates. The growth rate for Asia-10 is the average growth rate of all countries’ wellness economies weighted by each one’s real GDP in the second period. The Wellness Economy 13 Box: Wellness Economies and Aging Notes: Periods: FIJ (2012, 2017); IND (2012, 2017); KAZ (2013, 2017); MAL (2010, 2015); MON (2010, 2017); PHI (2012, 2017); PRC (2010, 2017); SRI (2012, 2017); THA (2012, 2017); VIE (2012, 2017). Source: Authors’ calculation using demographic data from the online ADB Key Indicators Database. https://kidb.adb.org/kidb/ (accessed 28 October 2020). continued on next page SRI Period 1 Period 2 16 14 12 10 8 6 4 4 5 6 7 8 9 10 11 12 13 14 PRC Wellness economy as % of GDP THA KAZ VIE PHI Elderly population as % of total population MON MAL IND FIJ SRI 16 14 12 10 8 6 4 4 5 6 7 8 9 10 11 12 13 14 PRC Wellness economy as % of GDP THA KAZ VIE PHI Elderly population as % of total population MON FIJ MAL IND ASIA–10 ASIA–10 Correlation between the Size of Wellness Economy and Aging SRI Period 1 Period 2 16 14 12 10 8 6 4 4 5 6 7 8 9 10 11 12 13 14 PRC Wellness economy as % of GDP THA KAZ VIE PHI Elderly population as % of total population MON MAL IND FIJ SRI 16 14 12 10 8 6 4 4 5 6 7 8 9 10 11 12 13 14 PRC Wellness economy as % of GDP THA KAZ VIE PHI Elderly population as % of total population MON FIJ MAL IND ASIA–10 ASIA–10 Correlation between the Size of Wellness Economy and Aging of Wellness Economy and Aging Period 2 SRI 16 14 12 10 8 6 4 4 5 6 7 8 9 10 11 12 13 14 PRC Wellness economy as % of GDP THA KAZ VIE PHI Elderly population as % of total population MON FIJ MAL IND ASIA–10 SRI Period 1 16 14 12 10 8 6 4 4 5 6 7 8 9 10 11 12 13 14 PRC Wellness economy as % of GDP THA KAZ VIE PHI Elderly population as % of total population MON MAL IND FIJ ASIA–10 FIJ = Fiji, GDP = gross domestic product, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Box: Wellness Economies and Aging Notes: Periods: FIJ (2012, 2017); IND (2012, 2017); KAZ (2013, 2017); MAL (2010, 2015); MON (2010, 2017); PHI (2012, 2017); PRC (2010, 2017); SRI (2012, 2017); THA (2012, 2017); VIE (2012, 2017). Source: Authors’ calculation using demographic data from the online ADB Key Indicators Database. https://kidb.adb.org/kidb/ (accessed 28 October 2020). continued on next page ADB Economics Working Paper Series No. 631 14 Box continued Alternatively, one can also compare the growth rate of wellness economy and the growth rate of elderly population between two periods, as illustrated in Box Figure 2. In Asia-10, the annualized growth rate of population aged 65 years and above is at 4%, which is far below the 10.7% annual rate of expansion of wellness economy in recent years. This pattern is observed for almost all of ADB DMCs. The most notable gap between growth rate of wellness economy and growth rate of elderly population is seen for India (13.5% vs. 3.8%), Viet Nam (11.8% vs. 2.8%), and Fiji (10.2% versus 1.9%). Meanwhile in the People’s Republic of China, the annual growth rate of wellness economy is 10.5%, which also exceeds the 4.1% annual growth rate of elderly population. Growth of Wellness Economy versus Growth of Elderly Population FIJ = Fiji, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Notes: Periods: FIJ (2012, 2017); IND (2012, 2017); KAZ (2013, 2017); MAL (2010, 2015); MON (2010, 2017); PHI (2012, 2017); PRC (2010, 2017); SRI (2012, 2017); THA (2012, 2017); VIE (2012, 2017). Source: Authors’ calculations. The estimates for Asia-10 are the weighted average growth rate for the 10 economies. Box: Wellness Economies and Aging 10.7 10.2 13.5 1.2 13.2 9.3 8.6 10.5 1.3 5.2 11.8 4.0 1.9 3.8 2.7 5.7 2.7 4.5 4.1 5.4 4.4 2.8 0 2 4 6 8 10 12 14 16 Growth rate (%) Wellness economy Elderly population SRI PRC ASIA–10 THA KAZ VIE PHI MON MAL IND FIJ Growth of Wellness Economy versus Growth of Elderly Population 10.7 10.2 13.5 1.2 13.2 9.3 8.6 10.5 1.3 5.2 11.8 4.0 1.9 3.8 2.7 5.7 2.7 4.5 4.1 5.4 4.4 2.8 0 2 4 6 8 10 12 14 16 Growth rate (%) SRI PRC ASIA–10 THA KAZ VIE PHI MON MAL IND FIJ Growth of Wellness Economy versus Growth of Elderly Population Elderly population FIJ = Fiji, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Notes: Periods: FIJ (2012, 2017); IND (2012, 2017); KAZ (2013, 2017); MAL (2010, 2015); MON (2010, 2017); PHI (2012, 2017); PRC (2010, 2017); SRI (2012, 2017); THA (2012, 2017); VIE (2012, 2017). Source: Authors’ calculations. The estimates for Asia-10 are the weighted average growth rate for the 10 economies. FIJ = Fiji, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Notes: Periods: FIJ (2012, 2017); IND (2012, 2017); KAZ (2013, 2017); MAL (2010, 2015); MON (2010, 2017); PHI (2012, 2017); PRC (2010, 2017); SRI (2012, 2017); THA (2012, 2017); VIE (2012, 2017). Source: Authors’ calculations. The estimates for Asia-10 are the weighted average growth rate for the 10 economies. ( , ); ( , ); ( , ); ( , ) Source: Authors’ calculations. The estimates for Asia-10 are the weighted average growth rate for the 10 economies. Overall, Box Figures 1 and 2 suggest that the increase in the size of wellness economy is also largely driven by factors other than the country’s aging population. These factors capture shift in preferences which could relate to wellness consumption patterns as well as changes in behaviors toward healthy and well-rounded lifestyles. Overall, Box Figures 1 and 2 suggest that the increase in the size of wellness economy is also largely driven by factors other than the country’s aging population. Box: Wellness Economies and Aging These factors capture shift in preferences which could relate to wellness consumption patterns as well as changes in behaviors toward healthy and well-rounded lifestyles. 15 The Wellness Economy The Wellness Economy Countries in developing Asia have made significant strides in the expansion of the wellness economy. In absolute terms, the PRC experienced the most significant expansion of the wellness economy, doubling its size from $585.5 billion to $1.18 trillion in just 7 years. This is equivalent to an average annual growth rate of about 10.5%. The annualized growth rate of the wellness economy has also been double digit for India (13.5%), Malaysia (13.2%), Viet Nam (11.8%), and Fiji (10.2%). If these growth rates are sustained, these countries’ wellness economies can be expected to double in size in less than 7 years. Mongolia and the Philippines also experienced a significant increase in the size of the wellness economy, growing annually at an average of 9.3% and 8.6%, respectively. Together, these 10 economies demonstrate rapid growth, from an estimated $756.8 billion in the first period to $1.46 trillion in the second period in constant 2010 prices.13 Except for Kazakhstan and Sri Lanka, the estimated annual growth rate of the wellness economy is much higher compared to the growth of the entire economy. This implies that the expansion of the wellness economy generally outpaced the other sectors. In Malaysia, for example, the annualized growth rate of the wellness economy is 7.9 percentage points higher compared to the average annual growth of its real GDP. In India this difference is as much as 6.1 percentage points. The same pattern is also observed in the case of Fiji and Viet Nam, where the estimated growth of the wellness economy is at least 5.6 percentage points higher relative to the entire economy. For Mongolia, Thailand, the PRC, and the Philippines, the difference is between 1 to 3 percentage points. Collectively for Asia-10, wellness gross value added has expanded in recent years at an estimated average of 10.7% annually, which is 3.5 percentage points higher compared to the 7.2% annual expansion of its overall GDP in constant prices. These estimates are consistent with earlier findings from GWI (2018) which suggests that the expansion of the wellness economy is relatively faster than the expansion of the overall economy. 13 The two periods estimated for each country are not necessarily the same due to data limitations. However, looking at these figures together as a proxy for developing Asia can give an idea of how big the region’s wellness economy has become. This is done by summing the GVA attributable to wellness for all countries and dividing by the sum of their total GVA in each of the two periods (Consing et al. 2020). Box: Wellness Economies and Aging Table 2 shows the size of the wellness economy in per capita terms, expressed in United States dollars at constant 2010 prices. In this table, wellness is measured to take into account the differences in population. These estimates can be interpreted as the annual spending on wellness per individual. While the aggregate size of the wellness economy, shown in Table 1, is comparable for Malaysia and the Philippines in period 2, the corresponding estimates in per capita terms differ significantly. Malaysia’s wellness per capita in 2015 is 3.3 times the wellness per capita in the Philippines in 2017, and the latter’s estimate is much closer to that of Mongolia ($200) and Fiji ($195) in the more recent period. Notably, wellness per capita spending is comparable for the PRC, Sri Lanka, and Thailand in period 1: $438 (2010), $430 (2012), and $429 (2012), respectively. However, stark differences are observed between their annual growth rates thereafter. Table 2 indicates that wellness per capita in Thailand grew at 4.7% annually, which is less than half the annual growth rate of wellness per capita in the PRC. In Sri Lanka, wellness per capita barely increased by $6 for a period of 5 years, while Kazakhstan experienced a $5 decline in wellness per capita between 2013 and 2017. In contrast, the double-digit annual growth rate in Malaysia and Viet Nam increased wellness per capita by $287 (73%) and $57 (65%), respectively, and each expansion occurred within a span of 5 years. Despite having a population comparable in size to that of the PRC, India’s wellness per capita grew the fastest, expanding at an average annual growth rate of 12.2%—from $78 in 2012 to $128 in 2017. 13 The two periods estimated for each country are not necessarily the same due to data limitations. However, looking at these figures together as a proxy for developing Asia can give an idea of how big the region’s wellness economy has become. This is done by summing the GVA attributable to wellness for all countries and dividing by the sum of their total GVA in each of the two periods (Consing et al. 2020). ADB Economics Working Paper Series No. Box: Wellness Economies and Aging 631 16 Table 2: Size of the Wellness Economy in Per Capita Terms for Selected Asian Countries ($, constant 2010 prices) Country Period 1 Period 2 Real wellness GDP Per Capita Growth Rate (annualized, %) Real GDP Per Capita Growth Rate (annualized, %) Asia-10 259 476 6.7 3.9 Fiji 122 195 9.9 4.3 India 72 128 12.2 6.2 Kazakhstan 517 512 (0.2) 1.2 Malaysia 392 679 11.6 3.8 Mongolia 122 200 7.2 6.1 People’s Republic of China 438 848 9.9 7.1 Philippines 148 207 6.9 5.0 Sri Lanka 430 436 0.3 3.3 Thailand 429 541 4.7 2.4 Viet Nam 87 144 10.6 5.1 GDP = gross domestic product. Notes: Population and Real GDP per capita data are based on World Bank’s estimates. The wellness economy in per capita terms for Asia-10 is the average in each period weighted by each country’s total population. The growth rate for Asia-10 is the average growth rate of all countries’ wellness economies per capita weighted by each one’s real GDP per capita in the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017); Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. Table 2: Size of the Wellness Economy in Per Capita Terms for Selected Asian Countries ($, constant 2010 prices) GDP = gross domestic product. Notes: Population and Real GDP per capita data are based on World Bank’s estimates. The wellness economy in per capita terms for Asia-10 is the average in each period weighted by each country’s total population. The growth rate for Asia-10 is the average growth rate of all countries’ wellness economies per capita weighted by each one’s real GDP per capita in the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017); Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. 2. Structure of the Wellness Sector Including medical and dental practice industries, as well as other human health activities, health care- related industries comprise a significant portion of wellness sector, even accounting for over or nearly half of the wellness GVA in Fiji and Viet Nam. In the case of the PRC, Sri Lanka, and Thailand, the biggest contributors to the wellness sector after human health activities are amusement and recreation activities. In Kazakhstan, Malaysia, and the Philippines, the biggest contributors, after human health activities, are those activities relating to the manufacture and retail trade of pharmaceutical products. In Fiji, India, and Viet Nam, tourism- supporting activities related to short-term accommodation are the biggest contributors after human health activities. Even when the size of wellness economies relative to total economies are similar for some ADB DMCs, their structures can vary significantly from one another. Figure 1: Structure of the Wellness Sector: Share of the Top Five Wellness Industries (as a % of wellness sector GVA) FIJ = Fiji, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. 2. Structure of the Wellness Sector Figure 1 shows the structure of the GVA coming from just the wellness sector itself (also called the forward linkage as discussed in section II.E) for the selected ADB DMCs. This figure highlights the top five wellness industries for each country by year, as measured by their percentage share to total GVA from wellness industries. Results suggest that the top five wellness industries alone comprise at least 50% of the wellness sector for all countries. In most economies, the share of the top five wellness industries is as high as 80%. For example, in Fiji, the top five wellness industries comprise 82.3% of its wellness sector in 2012, which increased to 88% in 2017. This proportion was even higher in India for both years, at about 90%. In Kazakhstan, the top five wellness industries comprised 60.7% of its wellness sector in 2012, but this share declined to 53.7% in 2017, indicating that other wellness industries had increased their share to the country’s GVA from wellness industries. Most of the top five wellness industries consistently appear in both years, suggesting that there is no major change in the structure of the wellness sector between the two periods. In the PRC, health care-related services, amusement parks and other recreation activities, as well as wellness-related construction activities consistently appear in the top five wellness industries for both years. These industries also dominate the wellness sector in the case of Mongolia and India for both years. Meanwhile, Malaysia’s wellness sector is dominated by retail of pharmaceutical goods, health care-related industries, as well as wellness tourism-related sectors including short-term accommodation and travel agency services. While these industries consistently dominate the country’s 17 The Wellness Economy wellness sector, each industry’s relative importance, expressed as a share of the wellness sector GVA, does not remain constant. wellness sector, each industry’s relative importance, expressed as a share of the wellness sector GVA, does not remain constant. Health care-related industries consistently make up a large part of the wellness sector for all countries in both years. Specifically, hospital activities account for at least 10% of the wellness sector. This share is higher for Fiji, Mongolia, Philippines, Thailand, and Viet Nam, where hospital services alone comprise at least 30% of the country’s wellness sector GVA, at least in the latter period. 3. Forward and Backward Linkages As discussed in the methodology, the production of the wellness sector is interconnected with other sectors in the economy through its forward and backward linkages. Here, the forward linkage refers to the GVA from wellness industries used in the production of all goods and services, and this corresponds to the first term in equation (6). Intuitively, production in the wellness sector and the demand for wellness goods and services used in the production of other goods and services (including within the wellness sector itself) move together. The length of the forward linkage of the wellness sector measures its relative significance in terms of the overall productive activities that the wellness sector could support (Miller and Blair, 2009). On the other hand, the backward linkage refers to the GVA from all industries used in the production of wellness goods and services, and this corresponds to the second term in equation (6). Intuitively, a rise in the production in the wellness sector is associated with an increase in demand for goods and services used in the production of wellness goods and services. The length of the wellness sector’s backward linkage can be interpreted as its relative importance in the economy in terms of the overall productive activities that it generates. The total linkage of the wellness sector is the sum of the sector’s forward and backward linkages less their intersection (to remove the double-count). Figure 2 presents the estimates for these linkages in terms of their percentage share to the country’s total GVA, as indicated by the bars of different colors. Figure 2: Disaggregation of Wellness Economy by Country, by Period (as % of GDP) FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. The estimates for Asia-10 is the average GVA share to total GVA of each country weighted by each one’s real GDP in the second period. 2. Structure of the Wellness Sector 44 53 37 36 23 14 13 12 24 35 34 35 13 26 18 17 40 34 19 33 8 12 11 8 15 10 9 9 8 30 11 16 8 4 3 5 9 10 5 15 16 2 5 12 23 6 14 11 24 18 10 10 24 9 39 6 7 7 7 4 18 8 8 6 25 55 44 24 24 5 9 9 10 11 1 8 15 16 26 10 5 7 5 12 9 8 5 6 4 8 6 24 14 5 6 10 8 8 7 2 8 18 12 10 11 39 46 36 29 14 22 28 30 17 28 16 28 17 22 34 22 0 10 20 30 40 50 60 70 80 90 100 2012 2017 2012 2017 2013 2017 2010 2015 2010 2017 2012 2017 2010 2017 2012 2017 2012 2017 2012 2017 % Share to wellness GVA (%) Hospital activities Medical and dental practice activities Other human health activities Travel agency activities Tour operator activities Other reservation service and related activities Short term accommodation activities Creative, arts and entertainment activities Activities of amusement parks and theme parks Other amusement and recreation activities n.e.c. Sports and recreation education Hairdressing and other beauty treatment Manufacture of pharmaceuticals, etc. Retail sale of pharmaceuticals, etc. Construction of buildings Construction of other civil engineering projects Others FIJ IND KAZ MAL MON PHI PRC SRI THA VIE FIJ = Fiji, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. ADB Economics Working Paper Series No. 631 18 3. Forward and Backward Linkages 3.3 3.9 2.5 3.6 2.3 3.0 3.2 2.5 2.0 3.0 2.7 3.0 3.2 3.4 3.5 4.1 8.2 7.3 4.6 4.9 3.3 4.8 3.5 4.5 0.8 1.0 1.6 2.3 1.8 2.1 1.4 1.7 1.4 1.1 1.8 2.1 4.5 5.2 3.0 2.8 2.0 2.3 1.9 2.5 1.1 1.3 0.6 0.5 0.5 0.8 0.3 0.3 0.8 1.3 0.7 0.9 1.0 1.2 1.3 1.5 1.5 1.3 1.3 1.3 0.7 0.7 0.6 0.7 0.1 0.2 0.5 0.8 0.3 0.2 0.2 0.4 0.4 0.3 0.5 0.6 0.6 0.8 1.1 1.0 0.8 0.7 0.4 0.5 8.5 10.5 4.0 5.3 5.0 6.8 5.6 5.2 4.4 6.4 5.2 5.4 6.5 7.3 9.9 11.5 13.9 12.4 8.6 9.3 6.3 8.4 0.0 2.0 4.0 6.0 8.0 10.0 12.0 14.0 16.0 % share to total GVA Forward and backward linkage (intersection) Pure backward linkage Pure forward linkage Wellness gross fixed capital formation KAZ MAL MON PHI PRC IND FIJ Asia-10 Period 1 Period 2 2012 2017 2012 2017 2013 2017 2010 2015 2010 2017 2012 2017 2013 2017 2012 2017 2013 2017 2012 2017 SRI THA VIE FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. The estimates for Asia-10 is the average GVA share to total GVA of each country weighted by each one’s real GDP in the second period. FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. The estimates for Asia-10 is the average GVA share to total GVA of each country weighted by each one’s real GDP in the second period. 19 The Wellness Economy The Wellness Economy The orange bars represent the pure backward linkage, while the green bars represent the pure backward linkage. The blue bar indicates the intersection between forward and backward linkages, which is equivalent to the double-count. Hence, the pure backward linkage together with the intersection represent the total backward linkage. In the same manner, the pure forward linkage together with the intersection indicate the total forward linkage. 3. Forward and Backward Linkages Finally, yellow bars represent the gross fixed capital formation (GFCF) that is relevant to the wellness sector. Wellness GFCF represents the investments made by the economy for the future production of wellness goods and services, and this could be in the form of construction of buildings and infrastructure, purchase of machineries and equipment, or procurement of intellectual property rights. The total height of the bars indicates the size of wellness economy as a percentage of total GVA, corresponding to equation (6). Figure 2 exhibits these estimates for ten ADB DMCs. With the exception of Sri Lanka and Kazakhstan, the share of the wellness economy increased between the two time periods for each country. As shown in Table 1, this translates to a wellness economy that generally expands faster than the total economy. Notice that the wellness economy’s share in Sri Lanka and Kazakhstan actually decreased between the two time periods, and correspondingly, the wellness economy grew slowly relative to the total economy. In the PRC, the share of wellness economy increased from 9.9% (2010) to 11.5% (2017). Considering that the PRC has a population of more than 1.3 billion, and being one of the largest economies in the world, this rapid growth translates to a huge leap on the productive activities that constitute the wellness economy. It is also worth mentioning that India experienced a significant increase in the size of its wellness economy, growing from 5.0% to 6.8% of its GDP in just a span of 5 years. For the four Southeast Asian economies included, the share of wellness economy is at least 6% in the latter period. In Thailand, the share of wellness gross value added increased from 8.6% (2012) to 9.3% (2017), while in the Philippines, the size of the wellness economy grew from 6.5% (2012) to 7.3% (2017). Viet Nam and Malaysia experienced sharp increase in the size of wellness economy. In Viet Nam, this share increased from 6.3% (2012) to 8.4% (2017), while in Malaysia, the share of wellness economy grew from 4.4% (2010) to 6.4% (2015). Mongolia’s share of wellness GVA moderately increased by 0.2 percentage point, from 5.2% in 2010 to 5.4% in 2017. Likewise, the share of wellness GVA in Fiji increased from 4.0% in 2012 to 5.3% in 2017. In Sri Lanka, the share of wellness GVA is 13.9% in 2012. 4. Hypothetical Extraction of the Wellness Sector The hypothetical extraction of the wellness sector allows us to gauge its relative importance to the country’s total economy. In this process, both the backward and forward linkages of wellness sector are nullified, creating a hypothetical scenario where the wellness-producing and wellness-supporting industries are inexistent. This method therefore measures how much of the country’s GDP is lost when the wellness sector is extracted, both directly and indirectly. Figure 3 illustrates the results of the hypothetical extraction method as applied to ten of ADB’s DMCs. The estimated loss from nullifying the wellness sector is expressed as a percentage of GDP, decomposed into direct and indirect loss as described in equation (14). The direct loss is exactly the same as the sum of the forward and backward linkages, less the double-count, as shown in Figure 2. Results consistently indicate that the GDP lost is greater than the share of wellness to GDP. That is, extracting wellness economy has a synergistic effect on the economy, as it does not only directly remove the contribution of the wellness sector to the gross value added, but it also entails some decline in the output of other sectors. Notice that the indirect GDP loss is largest in the PRC, where it accounts for 1.7% in 2010, and 1.9% in 2017. For the rest of the economies, the indirect loss is less than 1%, ranging from 0.1% to 0.7%. Figure 3: Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted by Country, by Period (as % of GDP) FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. ADB Economics Working Paper Series No. 631 Finally, wellness GFCF as a percentage of GVA is largest in Sri Lanka (1.1% in 2012, and 1% in 2017). This reflects the economic boost driven by the public investment to rebuild after ending its 3- decade conflict in 2009. However, this source of growth is not sustainable in the long run (World Bank 2015), which could also explain the declining share of wellness GFCF in the latter period. In the other economies, the share of wellness GFCF is less than 1%. In level, the PRC’s wellness GFCF stands at $95.1 billion in 2017, and this is more than three times higher than the wellness GFCF of the other nine economies combined. 3. Forward and Backward Linkages This share had moderately declined by 1.5 percentage points in 2017. The same trend is observed in the case of Kazakhstan, where the wellness economy moderately shrank by 0.4 percentage point, from 5.6% in 2013 to 5.2% in 2017. The decrease in the share of wellness economy for these two countries, however, does not imply that the levels of wellness GDP decreased over time. Rather, this trend only indicates that the rest of the economy grew faster than the wellness economy. Results indicate that the backward linkage of the wellness sector is longer than its forward linkage for all countries for both periods. In the context of input–output analysis, a strong backward linkage is indicative of heavy reliance on interindustry supply. This is usually evident in the case of services sector, where inputs from other industries are required for its production. Since a huge proportion of wellness economy is comprised of services, as in health care, amusement and entertainment, and tourism activities, the interconnection with the upstream sectors is also expected to be much more significant compared to the downstream sectors. The gap between the backward linkage and the forward linkage is largest in the case of the PRC for both periods, between which it increased. This reflects the “rebalancing of the economy” in the PRC, where services sector now comprising a bigger share of the economy than industry (World Bank 2017). 20 ADB Economics Working Paper Series No. 631 4. Hypothetical Extraction of the Wellness Sector –3.9 –5.1 –4.5 –6.0 –5.3–5.0 –4.2 –6.0 –4.8–5.0 –6.0 –6.7 –9.3 –10.8 –12.7 –11.4 –7.9 –8.5 –5.9 –8.0 –0.2 –0.1 –0.4 –0.6 –0.2–0.3 –0.5 –0.8 –0.4–0.4 –0.6 –0.7 –1.7 –1.9 –0.6 –0.5 –0.6 –0.6 –0.4 –0.4 –4.0 –5.2 –4.9 –6.6 –5.5 –5.2 –4.7 –6.8 –5.2 –5.4 –6.6 –7.4 –11.0 –12.6 –13.3 –11.9 –8.4 –9.1 –6.3 –8.3 –16.0 –14.0 –12.0 –10.0 –8.0 –6.0 –4.0 –2.0 0.0 2.0 % share to GVA Direct loss Indirect loss FIJ 2012 2017 2012 2017 2013 2017 2010 2015 2010 2017 2012 2017 2010 2017 2012 2017 2012 2017 2012 2017 IND KAZ MAL MON PHI PRC SRI THA VIE Figure 3: Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted by Country, by Period (as % of GDP) FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. FIJ = Fiji, GDP = gross domestic product, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. The Wellness Economy The Wellness Economy 21 Table 3 shows the decomposition of GDP loss into direct and indirect loss. The latter is further disaggregated into own-industry elasticity effects and cross-industry elasticity effects. In all economies, own-industry elasticity effect is less than 0.1% of GDP for both periods. The aggregated cross-industry elasticity effect is much higher relative to own-industry elasticity effect, reaching as much as 1.85% of GDP as in the case of the PRC. Except for Fiji and Kazakhstan, cross-industry elasticity for the other economies ranges between 0.33% and 0.73% of GDP. Together, these elasticity effects could also be interpreted as the extent of interdependence of the other sectors when the wellness sector is hypothetically extracted in the economy. GDP = gross domestic product. B. Wellness Employment B. As discussed in the previous section, the wellness economy has a sizeable contribution to the GDP of developing economies in Asia. Hence, it should also be expected that the wellness economy generates and supports a significant portion of the overall employment. This section delves into this empirical inquiry by quantifying the size of the wellness employment in terms of the number of jobs attributable to the wellness economy (section III.B.1). Moreover, this section compares the labor productivity in the wellness economy (section III.B.2), and presents the decomposition of the wellness employment into forward and backward linkages to quantify the relative size of employment which are directly or indirectly generated by the wellness sector (section III.B.3). Finally, employment loss from a hypothetical extraction of the wellness economy is also examined, as an alternative measure for the relative significance of the wellness economy in the overall employment (section III.B.4). 4. Hypothetical Extraction of the Wellness Sector Table 3: Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted (as % of GDP) Country Period Total Loss Direct Loss Indirect Loss Own- Elasticity Effect Cross- Elasticity Effect Fiji 2012 4.04 3.86 0.18 0.00 0.18 2017 5.24 5.10 0.14 0.00 0.14 India 2012 4.87 4.50 0.37 0.00 0.37 2017 6.64 6.04 0.60 0.01 0.60 Kazakhstan 2012 5.51 5.33 0.18 0.01 0.18 2017 5.23 4.95 0.28 0.02 0.26 Malaysia 2010 4.73 4.21 0.53 0.01 0.52 2015 6.74 6.00 0.75 0.02 0.73 Mongolia 2010 5.17 4.81 0.36 0.02 0.34 2017 5.37 5.03 0.35 0.02 0.33 People’s Republic of China 2012 2017 10.96 12.64 9.26 10.76 1.70 1.18 0.02 0.03 1.68 1.85 Philippines 2012 6.66 6.00 4.28 0.04 0.55 2017 7.26 6.70 0.67 0.07 0.60 Sri Lanka 2012 13.30 12.73 3.83 0.03 0.53 2017 11.89 11.40 0.48 0.02 0.46 Thailand 2012 8.40 7.86 0.55 0.01 0.54 2017 9.15 8.53 5.04 0.01 0.60 Viet Nam 2012 6.33 5.91 7.08 0.01 0.41 2017 8.33 7.98 0.36 0.01 0.35 GDP = gross domestic product Table 3: Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted (as % of GDP) Table 3: Decomposition of Gross Domestic Product Loss When Wellness Sector is Extracted (as % of GDP) ADB Economics Working Paper Series No. 631 22 1. Size of Wellness Employment Table 4 shows the estimated wellness employment for each country and time period, containing the jobs that are both directly and indirectly attributable to the production of wellness goods and services. The annualized growth rate of wellness employment is also included in the third column where it can be compared with the growth rate of total employment for each country. Further insights on the wellness sector’s economic relevance may be derived from this. Malaysia’s wellness employment had the largest increase from 595,000 in 2010 to 1.6 million in 2015, and this is followed by the PRC where wellness employment grew from 58.7 million in 2010 to 118.5 million in 2017. Both countries experienced double-digit wellness employment growth rates of 21.9% and 10.5%, respectively. India’s wellness employment also experienced significant growth at 7.7% annually, from 21.4 million in 2012 to 30.6 million in 2017. Generally, the economies of Asia-10 have experienced a positive growth in wellness employment across the two time periods estimated in each. Collectively, wellness employment in Asia-10 expanded from 88.1 million to 159.4 million between the two periods estimated, increasing at an annual growth rate of 9.7%. Except for Malaysia and the PRC, the growth of wellness GVA is generally faster than the growth of wellness employment. Collectively for Asia-10, the weighted average annual growth rate of wellness gross value added is one percentage point higher than the weighted average annual growth rate of wellness employment. This indicates growth in labor productivity within the wellness economy in recent years, consistent with what is shown in Table 3 for most of ADB DMCs. Labor productivity in the wellness economy increased from $8,594 to $9,160 for Asia-10, ranging from $4,903 (Viet Nam) to as high as $18,891 (Sri Lanka) in period 2. The structure of the wellness sector may explain the variation in labor productivity across countries. For example, industries such as the manufacturing of pharmaceutical goods may be more productive than retail trade services. 1. Size of Wellness Employment 23 The Wellness Economy Table 4: Wellness Employment for Selected Asian Countries (Thousands) Country Period 1 Period 2 Wellness Employment Growth Rate (annualized, %) Employment Growth Rate (annualized, %) Asia-10 88,059 159,410 9.7 0.2 Fiji 10 13 5.4 2.9 India 21,139 30,628 7.7 (0.1) Kazakhstan 634 654 0.8 0.0 Malaysia 595 1,600 21.9 3.4 Mongolia 63 91 5.4 2.6 People’s Republic of China 58,742 118,536 10.5 0.3 Philippines 1,959 2,292 3.2 1.4 Sri Lanka 487 495 0.3 1.5 Thailand 2,049 2,327 2.6 (0.8) Viet Nam 2,381 2,774 3.1 1.1 Notes: The growth rate for Asia-10 is the average growth rate of all countries’ wellness employed weighted by each one’s total employment in the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017); Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. Table 4: Wellness Employment for Selected Asian Countries (Thousands) Notes: The growth rate for Asia-10 is the average growth rate of all countries’ wellness employed weighted by each one’s total employment in the second period. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017); Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. 2. Wellness Economy Labor Productivity Table 5 compares wellness economy labor productivity, expressed as wellness economy GDP per worker in the wellness economy, to economywide labor productivity, expressed as total GDP per worker in the economy, as indicated by the ratios shown in the last two columns. A ratio greater than 1 indicates that wellness labor productivity is stronger than overall labor productivity. Conversely, a ratio less than 1 indicates that wellness labor productivity is weaker than overall labor productivity, such as in Kazakhstan, Malaysia, Mongolia, and the PRC in the second period. Generally, it cannot be concluded with high certainty what the causes of these ratios are due to the limited data and sample size. Theoretically, however, there may be several explanations for these ratios. Countries with ratios less than 1 may have sufficiently advanced industrial or manufacturing sectors that produce high-value goods with relatively few laborers, and therefore workers in the wellness sector, whose goods are typically service oriented, might not be as productive relative to that. The reverse scenario implies a similar logic for the wellness sector where, supposing that its structure is oriented toward high-value goods and services that require relatively low labor, a ratio greater than 1 may arise. Similarly, countries with underdeveloped industrial sectors or are otherwise services oriented may have the average laborer being similar in productivity to workers in the wellness economy. Employment populations may also differ fundamentally between a country’s wellness economy and its overall economy due to other factors and unique social conditions that are difficult to observe or measure quantifiably. ADB Economics Working Paper Series No. 631 24 Table 5: Wellness Economy Labor Productivity for Selected Asian Countries ($, constant 2010 prices) Wellness Economy Labor Productivity Ratio of Wellness Economy Labor Productivity to Total Economy Labor Productivity Period 1 Period 2 Period 1 Period 2 Asia-10 8,594 9,160 1.3 0.9 Fiji 10,540 13,158 1.0 1.1 India 4,300 5,585 1.1 1.0 Kazakhstan 13,897 14,124 0.7 0.6 Malaysia 18,561 12,841 0.9 0.5 Mongolia 5,286 6,837 0.8 0.7 People’s Republic of China 9,967 9,924 1.2 0.8 Philippines 7,356 9,512 1.3 1.3 Sri Lanka 18,034 18,891 2.0 1.9 Thailand 14,211 16,088 1.5 1.4 Viet Nam 3,270 4,903 1.3 1.5 Note: Overall labor productivity are calculated as the ratio between Real GDP (in $, constant 2010) and total employment using World Bank data. 2. Wellness Economy Labor Productivity Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017);Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. Table 5: Wellness Economy Labor Productivity for Selected Asian Countries ($, constant 2010 prices) Note: Overall labor productivity are calculated as the ratio between Real GDP (in $, constant 2010) and total employment using World Bank data. Periods: Fiji (2012, 2017); India (2012, 2017); Kazakhstan (2013, 2017); Malaysia (2010, 2015); Mongolia (2010, 2017); People’s Republic of China (2010, 2017); Philippines (2012, 2017); Sri Lanka (2012, 2017);Thailand (2012, 2017); Viet Nam (2012, 2017). Source: Authors’ calculations. 3. Wellness Employment: Forward and Backward Linkages Figure 4 shows the disaggregation of wellness employment in terms of its forward and backward linkages. Forward linkage captures the number of jobs that are directly generated by the wellness sector, while backward linkages captures the employment that are indirectly attributed to the wellness industries, as these jobs are generated by other sectors that support wellness industries. The blue bars represent the intersection between forward and backward linkages (equivalent to what is double- counted applying the methodology). The orange bars represent the pure backward linkages, while the green bars represent the pure forward linkages. The cumulative height of the three bars is the percentage share of wellness employment to the country’s total employment. In general, the percentage share of wellness employment to total employment increased for each country over the two time periods estimated. The sharpest rise is seen in the case of the PRC and Malaysia, increasing by 7.5 and 6.4 percentage points, respectively. For other countries in Asia-10, wellness employment’s contribution varies between 3.6% to 7.6% of total employment by the second period. Collectively, Asia-10’s share of wellness employment increased rapidly between the two periods, from 6.3% to 11.2% of total employment in the region, primarily driven by the steep increase of wellness employment in the PRC. It is also observed that the backward linkage is generally higher than the forward linkage, indicating that much of the employment attributable to wellness comes from the industries supporting the wellness sector. This is generally consistent with the results shown in Figure 2, where wellness-supporting industries are shown to account for a larger share of the wellness economy relative to the wellness sector itself. The Wellness Economy 25 Figure 4: Disaggregation of Wellness Employment by Country, by Period (as % of GDP) FIJ = Fiji, GDP = gross domestic product, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam Source: Authors’ calculations. The estimates for Asia-10 is the average wellness employment share of each country weighted by each one’s total employment in the second period. 3. Wellness Employment: Forward and Backward Linkages 3.0 3.6 0.6 0.8 1.8 3.0 0.5 0.6 1.3 1.6 1.3 1.1 1.7 1.7 4.1 4.3 2.3 1.8 1.9 2.4 1.9 2.4 0.8 1.9 0.3 0.3 0.5 0.7 2.0 2.2 1.0 3.0 1.1 1.5 0.9 1.0 1.0 2.9 0.6 0.6 0.7 0.8 0.5 0.3 6.3 11.2 3.2 3.6 4.3 6.3 7.4 7.6 5.0 11.4 6.1 7.4 5.2 5.7 7.7 15.3 6.4 6.0 5.3 6.3 4.7 5.2 0.0 Period 1 Period 2 2012 2017 2012 2017 2013 2017 2010 2015 2010 2017 2012 2017 2010 2017 2012 2017 2012 2017 2012 2017 2.0 4.0 6.0 8.0 10.0 12.0 14.0 16.0 18.0 % share to total employment Forward and backward linkage (intersection) Pure backward linkage Pure forward linkage Asia–10 FIJ IND KAZ MAL MON PHI PRC SRI THA VIE 2.4 5.6 2.3 2.5 2.1 2.6 4.9 4.8 2.7 6.9 3.8 4.8 2.7 3.0 2.6 8.0 3.4 3.6 2.7 3.0 2.3 2.4 Figure 4: Disaggregation of Wellness Employment by Country, by Period (as % of GDP) FIJ = Fiji, GDP = gross domestic product, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam Source: Authors’ calculations. The estimates for Asia-10 is the average wellness employment share of each country weighted by each one’s total employment in the second period. Source: Authors’ calculations. The estimates for Asia-10 is the average wellness employment share of each country one’s total employment in the second period. 4. Potential Employment Losses from Hypothetical Extraction Similar to section III.A.4, the relative importance of the wellness sector is also measured in terms of the estimated employment loss from its hypothetical extraction. In this process, all linkages relating to the wellness economy are nullified to measure how many jobs will be lost when both forward and backward linkages of the wellness sector are extracted. Employment loss from the hypothetical extraction of the wellness sector is shown in Figure 5. Results are expressed as a percentage of total employment, and are decomposed into direct and indirect loss, similar to what is shown in Figure 3. Note that the direct loss, as indicated by the blue bars, is equivalent to the percentage share of wellness employment to total employment shown in Figure 4. Similar to the results of the hypothetical extraction method as applied to GDP, employment loss as a percentage of total employment is higher than the share of wellness employment to total employment. The difference constitutes the indirect loss, as indicated by the orange bars. The wellness employment loss as a percentage of total employment is highest for the PRC at 16.8% (2017), and Malaysia at 12.0% (2015). For the rest of Asia-10, wellness employment loss as a percentage of total employment ranges from 3.9% (Fiji) to 7.9% (Kazakhstan), in the second period. ADB Economics Working Paper Series No. 631 26 Figure 5: Decomposition of Employment Loss When Wellness Sector is Extracted by Country, by Period (as % of total employment) FIJ = Fiji, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. 4. Potential Employment Losses from Hypothetical Extraction –3.4 –3.8 –4.3 –6.3 –7.4 –7.6 –5.0 –11.4 –6.1 –7.4 –5.2 –5.7 –7.7 –15.3 –6.4 –6.0 –5.3 –6.3 –4.7 –5.2 –0.2 –0.1 –0.4 –0.8 –0.2 –0.3 –0.5 –0.7 –0.3 –0.3 –0.5 –0.6 –1.6 –1.6 –0.4 –0.3 –0.5 –0.7 –0.4 –0.4 –3.6 –3.9 –4.7 –7.1 –7.6 –7.9 –5.5 –12.0 –6.4 –7.7 –5.7 –6.3 –9.3 –16.8 –6.8 –6.3 –5.9 –6.9 –5.1 –5.5 –20.0 –18.0 –16.0 –14.0 –12.0 –10.0 –8.0 –6.0 –4.0 –2.0 0.0 2.0 % share to GVA FIJ IND KAZ MAL MON PHI PRC SRI THA VIE 2012 2017 2012 2017 2013 2017 2010 2015 2010 2017 2012 2017 2010 2017 2012 2017 2012 2017 2012 2017 Direct loss Indirect loss Figure 5: Decomposition of Employment Loss When Wellness Sector is Extracted by Country, by Period (as % of total employment) FIJ = Fiji, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. FIJ = Fiji, GVA = gross value added, IND = India, KAZ = Kazakhstan, MAL = Malaysia, MON = Mongolia, PHI = Philippines, PRC = People’s Republic of China, SRI = Sri Lanka, THA = Thailand, VIE = Viet Nam. Source: Authors’ calculations. The decomposition of indirect wellness employment into own-industry elasticity and cross- industry elasticity effects is further detailed in Table 6. Results show that own-industry elasticity effects range from 0% (Fiji) to 0.05% (Philippines), while cross-industry elasticity effects range from 0.14% (Fiji) to 1.56% (PRC). Together, the own-industry elasticity and cross-industry elasticity effects are the reason why estimated employment losses from hypothetical extraction of the wellness sector in Table 6 are greater than just the employment attributable to the wellness economy. The own-elasticity effect is the additional loss in employment caused by greater sensitivity of nonwellness sectors’ outputs (and therefore employment) to declines in each one’s own final demand post-extraction than pre- extraction. The cross-elasticity effect is the additional loss in employment caused by greater sensitivity of nonwellness sectors outputs to declines in each other’s final demand post-extraction than pre- extraction. Since production declines beyond the production attributable to the wellness economy in the current period as shown in the estimated GDP losses from section III.A.4, the corresponding estimates on employment losses are correspondingly severe. 4. Potential Employment Losses from Hypothetical Extraction 27 The Wellness Economy Table 6: Decomposition of Employment Loss When Wellness Sector is Extracted (as % of total employment) Country Period Total Loss Direct Loss Indirect Loss Own- Elasticity Effect Cross- Elasticity Effect Fiji 2012 3.59 3.43 0.16 0.00 0.16 2017 3.89 3.75 0.14 0.00 0.14 India 2012 4.75 4.34 0.41 0.01 0.40 2017 7.12 6.33 0.80 0.01 0.78 Kazakhstan 2012 7.61 7.40 0.21 0.01 0.20 2017 7.91 7.62 0.29 0.01 0.28 Malaysia 2010 5.52 5.01 0.51 0.01 0.50 2015 12.04 11.37 0.67 0.01 0.65 Mongolia 2010 6.40 6.10 0.30 0.01 0.29 2017 7.69 7.36 0.33 0.01 0.32 People’s Republic of China 2012 9.30 7.72 1.58 0.02 1.56 2017 16.84 15.27 1.57 0.02 1.55 Philippines 2012 5.74 5.20 0.54 0.03 0.51 2017 6.26 5.68 0.57 0.05 0.52 Sri Lanka 2012 6.82 6.39 0.43 0.02 0.41 2017 6.33 6.02 0.31 0.01 0.30 Thailand 2012 5.85 5.32 0.53 0.01 0.53 2017 6.93 6.27 0.66 0.01 0.65 Viet Nam 2012 5.08 4.68 0.40 0.02 0.38 2017 5.52 5.17 0.35 0.01 0.34 Source: Authors’ calculations. Table 6: Decomposition of Employment Loss When Wellness Sector is Extracted (as % of total employment) Table 6: Decomposition of Employment Loss When Wellness Sector is Extracted (as % of total employment) IV. CONCLUSION AND MOVING FORWARD This paper contributes to the literature on wellness economics and national accounting by showing how the SNA framework can be used to estimate the economy attributable to the production of wellness goods and services and then applying this methodology to selected countries in developing Asia. Through input–output analysis, it is possible to derive the production and employment linkages between the wellness sector and nonwellness sectors, the potential production and employment losses that may arise if the wellness sector were hypothetically extracted from the economy, and how these two sets of estimates relate to one another. Theoretically, this means that any country whose economic accounting is consistent with the SNA framework can estimate the economic relevance of its wellness sector. This in turn creates fertile new ground in the field of wellness economics as new 28 ADB Economics Working Paper Series No. 631 data create new possibilities for research and, eventually, policies to promote wellness. As estimates for more countries are produced over time, it becomes feasible to generate reliable figures at the regional, and eventually, global level. data create new possibilities for research and, eventually, policies to promote wellness. As estimates for more countries are produced over time, it becomes feasible to generate reliable figures at the regional, and eventually, global level. Nevertheless, there are ways to improve the quality of wellness economy estimation within the SNA framework. The main challenges are data related. Firstly, there would be no need for disaggregation if each country’s IOT were highly detailed, ideally with rows and columns for all 4-digit ISIC rev. 4 codes. In practice, however, a balanced IOT of such a size would be costly to produce. A second-best scenario would be for each country’s IOT to contain rows and columns corresponding to at least the 4-digit codes covering the production of wellness goods and services, such as those listed in Table A.1. A similar prescription applies when estimating wellness employment as employment numbers are needed for each industry in the IOT in order to estimate the wellness economy’s contribution to overall employment. Secondly, while the selected ISIC codes provide a basis for estimating the wellness economy, the process of drawing out the corresponding GVA from available SNA components often differ in practice between countries due to nonuniformity in the level of detail and aggregation. IV. CONCLUSION AND MOVING FORWARD Access to highly detailed supply tables and nationally representative firm-level data on output would allow for more reliable disaggregation of IOTs when needed, and uniformity in the level of aggregation across countries would allow for better comparisons in wellness economy estimates between countries and across time. Fortunately, uniformity can be achieved through the use of national IOTs derived from regional IOTs such as the World Input–Output Tables and the ADB Multiregional Input–Output Tables which provide annual national accounts data at a uniform level of detail for a multitude of countries across time. While the level of detail per country is highly aggregated under these regional IOTs, the fact that they are uniform in detail means that they may be subjected to a uniform process of disaggregation and allow for more reliable cross-country analyses. APPENDIX ble A.1: List of Industries and Activities Considered Part of the Wellness Economy Table A.1: List of Industries and Activities Considered Part of the Wellness Economy ISIC Rev.4 Code ISIC Industry Wellness-Related Activities 2023 Manufacture of soap and detergents, cleaning and polishing preparations Only activities related to the manufacture of personal care items (e.g., beauty, sunburn, manicure preparations, etc.) 2100 Manufacture of pharmaceuticals, medicinal chemical and botanical products All activities related to the manufacture of pharmaceutical, medicinal, and botanical products 3012 Building of pleasure and sporting boats All activities related to the manufacture of boats for recreation and wellness purposes 3230 Manufacture of sports goods All activities related to the manufacture of sporting goods 4100 Construction of buildings All activities related to the construction of wellness- related and indoor-sports facilities 4290 Construction of other engineering projects All activities related to the construction of outdoor wellness and sports facilities 4721 Retail sale of food in specialized stores All retail sale activities of fruits and vegetables 4763 Retail sale of sporting equipment in specialized stores Retail sale of sporting and wellness-related goods 4772 Retail sale of pharmaceutical and medical goods, cosmetic and toilet articles in specialized stores Retail Sale of pharmaceuticals and cosmetic articles 5510 Short-term accommodation activities Includes only the provision of short-term accommodation for holiday, wellness, and recreation purposes. APPENDIX 5520 Camping grounds, recreational vehicle parks and trailer parks Includes only the provision of accommodation in recreational camps and facilities 7721 Renting and leasing of recreational and sports goods Includes activities involving the rental and leasing services of recreational and wellness-related sports goods 7911 Travel agency activities Includes activities of agencies engaged in selling of wellness travel, tour, transportation, and accommodation services 7912 Tour operator activities Includes activities of agencies engaged in arranging and assembling wellness-related tours 7990 Other reservation service and related activities Other provisional wellness-travel reservation activities not included in 7911 and 7912 8130 Landscape care and maintenance service activities All service activities related to landscape care and maintaining wellness spaces 8541 Sports and recreation education Education services related to the pursuit of sports, recreation, and wellness (e.g., yoga, martial arts, etc.) 8610 Hospital activities All activities 8620 Medical and dental practice activities All activities Wellness-Related Activities 30 Appendix Appendix 30 ISIC Rev.4 Code ISIC Industry Wellness-Related Activities 8690 Other human health activities All activities 8710 Residential nursing care facilities All activities 8720 Residential care activities for mental retardation, mental health and substance abuse All activities 8730 Residential care activities for elderly and disabled All activities 8890 Other social work activities without accommodation All other social work activities without accommodation aimed at improving wellness 9000 Creative, arts and entertainment activities All creative, arts and entertainment services aimed at improving wellness 9101 Library and archive activities Activities related to the operation of libraries 9102 Museum activities and operation of historical sites and buildings Activities related to the operation of wellness-related sites (e.g., spiritual spaces, museums, etc.) 9103 Botanical and zoological gardens and nature reserves activities All activities related to the operation of wellness- inducing sites (e.g., botanical gardens, etc.) 9311 Operation of sports facilities All activities related to the operation of sports facilities 9312 Activities of sports clubs All activities related to the operation of sports clubs promoting fitness 9319 Other sports activities All other fitness related activities excluded in 9311 and 9312 9321 Activities of amusement parks and theme parks All activities related to the operation of amusement and theme arks 9329 Other amusement and recreation activities, n.e.c. All other wellness-related activities excluded in 9321 9602 Hairdressing and other beauty treatment All activities aimed at promoting beauty and wellness 9609 Other personal service activities, n.e.c. All activities of Turkish baths, sauna and steam baths, solarium, salons etc. ISIC = International Standard Industrial Classification of All Economic Activities, n.e.c.= not elsewhere classified. Source: United Nations. 2008. System of National Accounts. New York. ISIC = International Standard Industrial Classification of All Economic Activities, n.e.c.= not elsewhere classified. S U d N 2008 S f N l A N Y k APPENDIX ISIC = International Standard Industrial Classification of All Economic Activities, n.e.c.= not elsewhere classified. Source United Nations 2008 System of National Accounts New York Appendix 31 ix 31 Appendix 31 Appendix 31 Table A.2: Data Sources Country Table Years Available Dimension of Tables Source Fiji IOT 2012,2017 35 x 35 ADB India IOT 2012,2017 35 x 35 ADB Kazakhstan SUT 2013, 2017 698 x 114 KAZ SC Malaysia SUT 2010, 2015 68 x 86; 124 x 124 ADB; DOSM Mongolia IOT 2010, 2017 35 x 35 ADB People’s Republic of China IOT 2010, 2017 35 x 35 ADB Philippines IOT 2012, 2017 35 x 35 ADB Sri Lanka IOT 2012, 2017 35 x 35 ADB Thailand IOT 2012, 2017 35 x 35 ADB Viet Nam IOT 2012; 2017 35 x 35 ADB ADB = Asian Development Bank, DOSM = Department of Statistics Malaysia, IOT = input–output table, KAZ SC = Agency of the Republic of Kazakhstan on Statistics, SUT = supply and use table. Source: Authors’ compilation. ADB = Asian Development Bank, DOSM = Department of Statistics Malaysia, IOT = input–output table, KAZ SC = Agency of the Republic of Kazakhstan on Statistics, SUT = supply and use table. Source: Authors’ compilation. Table A.3: Data Sources for Input–Output Table Disaggregation Country Source of Disaggregators Fiji Structure of donor country (MAL) India Firm-level data (Orbis) Kazakhstan Supply table Malaysia (MAL) Supply table Mongolia Structure of donor country (PRC) People’s Republic of China (PRC) Firm-level data (Orbis) Philippines Firm-level data (Orbis) Sri Lanka Structure of donor country (MAL) Thailand Firm-level data (Orbis) Viet Nam Firm-level data (Orbis) Source: Authors’ compilation. Table A.3: Data Sources for Input–Output Table Disaggregation REFERENCES Asian Development Bank (ADB). 2018. Economic Indicators for Eastern Asia, Input-Output Tables. Manila. ————. 2019. Key Indicators for Asia and the Pacific 2019. Manila. ————. 2020. Asian Development Outlook 2020 Update: Wellness in Worrying Times. Manila. Barsabal, Michael John, Julian Thomas Alvarez, and Rafael Martin III Consing. 2020. “A Note on Losses after Hypothetical Extraction.” Unpublished. 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Wang, Zhi, Shang-Jin Wei, and Kunfu Zhu. 2013. “Quantifying International Production Sharing at the Bilateral and Sector Levels.” NBER Working Paper Series No. 19677. World Bank. 2015. Sri Lanka: Ending Poverty and Promoting Shared Prosperity, A Systematic Country Diagnostic. Washington, DC. ————. 2017. China: Systematic Country Diagnostic, Towards a More Inclusive and Sustainable Development. Washington, DC. World Health Organization (WHO). 2006. Health Promotion Glossary Update. Geneva. The Wellness Economy The Wellness Economy A Comprehensive System of National Accounts Approach This working paper explains how to derive indicators for a country’s wellness sector using the system of national accounts framework. It also provides estimates of these indicators for 10 countries in developing Asia across 2 time periods. Estimates include the wellness sector’s production and employment linkages with nonwellness sectors and potential losses in production and employment if the wellness sector were hypothetically extracted from each economy. About the Asian Development Bank ADB is committed to achieving a prosperous, inclusive, resilient, and sustainable Asia and the Pacific, while sustaining its efforts to eradicate extreme poverty. Established in 1966, it is owned by 68 members —49 from the region. Its main instruments for helping its developing member countries are policy dialogue, loans, equity investments, guarantees, grants, and technical assistance. ASIAN DEVELOPMENT BANK 6 ADB Avenue, Mandaluyong City 1550 Metro Manila, Philippines www.adb.org