Summary To register visit platform.rd-connect.eu RD-Connect: an integrated infrastructure for data sharing and analysis in rare disease research S. Beltran1,2, D. Piscia1,2, S. Laurie1,2, J. Protasio1,2, A. Papakonstantinou1,2, A. Cañada3,14, J.M. Fernández3,14, M. Thompson6, R. Kaliyaperumal6, S. Lair7, P. Sernadela8, M. Girdea9, M. Brudno9, A. Blavier7, R. Thompson10, H. Lochmüller10, D. Badowska10, V. Straub10, M. Bellgard11, J. Paschall12, M. Roos6, P.A.C. 't Hoen6, A. Valencia3,14, L. Monaco15, CM. Wang15, D. Salgado4,5, C. Béroud4,5,13, I. Gut1,2 and the RD-Connect Consortium 1Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain, 2Universitat Pompeu Fabra (UPF), Barcelona, Spain, 3Centro Nacional de Investigaciones Oncológicas (CNIO) , Madrid, Spain, 4Aix-Marseille Université, Marseille, France, 5Inserm, UMR_S 910, Marseille, France, 6Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 7Interactive Biosoftware, Rouen, France, 8DETI/IEETA, University of Aveiro, Portugal, 9Centre for Computational Medicine, Hospital for Sick Children and University of Toronto, Toronto, ON, Canada, 10John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, UK, 11Centre for Comparative Genomics, Murdoch University, Perth, Western Australia, 12European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, United Kingdom, 13APHM, Hôpital TIMONE Enfants , Laboratoire de Génétique Moléculaire, Marseille, France, 14Instituto Nacional de Bioinformática (INB), Spain, 15Fondazione Telethon, Milan, Italy Around 300 million people worldwide are affected by one of the 6000+ known rare diseases (RD). RD research faces specific challenges because patients, clinical expertise and research communities are scarce and fragmented. Data sharing between researchers is therefore crucial. Next-generation sequencing (NGS) and genomics have opened up new possibilities for gene discovery and diagnosis, but many RD expert centres lack the bioinformatics expertise and computational support to take full advantage of the new genomic paradigm. RD-Connect is an EU-funded infrastructure bringing together multiple data types used in rare disease research into a common resource for researchers and clinicians. RD-Connect consists of three systems: Genome-Phenome Analysis Platform (platform.rd-connect.eu), Sample Catalogue (samples.rd-connect.eu) and Registry & Biobank Finder (catalogue.rd-connect.eu), which are open to any RD and available free of charge. Genome-Phenome Analysis Platform provides both a repository for RD research data and a user-friendly interface for NGS analysis that has much of the same functionality as commercial analysis suites. RD researchers or clinical centres worldwide can submit data, analyse own patients and compare with data submitted by others, and find patients in external databases with matching phenotype and candidate variant in the same gene. Registry & Biobank Finder is a global directory of rare disease patient registries and biobanks, including the numbers of register cases for each disease. Sample Catalogue allows browsing biosample collections of RD biobanks and find detailed information about individual biosamples. RD-Connect ethical and legal experts provide guidance to researchers and work on optimal models for data sharing, while engagement of patient representatives at every level of the project work ensures patient-centred approach. rd-connect.eu Sample selection Inheritance filters Quality filters Population filters Annotation filters Effect prediction filters Candidate gene filters Explore Results EGA Sequencing Lab Raw data (.bam/.fastq) Clinician / researcher PhenoTips (HPO terms) Sample Clinical phenotype Genome-Phenome Analysis Platform Sta


Visualization of Precision Medicine: A Case Study of PD-1 Therapy Efficacy Evaluation through Analytical Algorithm in Triple Negative Breast Cancer Alice Jiang Havergal College, Toronto, Ontario, Canada Introduction & Background Results I would like to acknowledge the help that I received from the Rapidamic Lab and offer special thanks to my parents and advisors for their direct and indirect support and guidance throughout the project. • Future work will focus on the optimization of our algorithm and incorporating more factors to assess the correlations with the outcome to meet the large database analytics requirements of precision medicine. • The system of the analytical platform is quite versatile It can be applied and extended to other different precision medicines for diseases, especially cancer therapy. Figure 5. Correlation matrix. Values range from -1 to 1. Figure 3. Boxplots in comparison of CPS and Placebo/Pembrolizumab to survival length. An increase in combined positive score (CPS) values corresponds to a larger range and median, indicative of a longer survival length. The Pembrolizumab + chemotherapy (2) group exhibits a significantly wider range, higher median, and a more extensive IQR in contrast with the placebo + chemotherapy group (1), highlighting the salient distinctions between the two cohorts. An increased presence of the CPS positively correlates to a higher survival length of individuals for PD-1 therapy + chemotherapy. Other input factors did not display a significant influence or correlation to survival length. The analytical algorithm tool proved to be promising in processing vast datasets and was capable of generating comprehensive visualizations. Utilizing the created linear regression model, approximate survival length (y value) could be predicted from input variables. We can efficiently and precisely identify underlying factors, understanding the strength and general trend of influence. Recognizing key interactions can enable professionals to prioritize these factors when making a medical prognosis, ensuring that treatments are tailored to maximize the therapeutic efficacy and outcome for patients. This guides personalized medicine, moving away from generalized treatment protocols, by identifying influential factors but also quantifying the impact of drug efficacy on a specific individual. The importance of precise data-enhanced decision-making is emphasized. Conclusions [1] Sporikova Z, Koudelakova V, Trojanec R, Hajduch M. Genetic markers in triple-negative breast cancer. Clinical breast cancer. 2018 Oct 1;18(5):e841-50. [2] Jaber N. SACITUZUMAB earns regular FDA approval for TNBC. National Cancer Institute. Available from: https://www.cancer.gov/news-events/cancer-currents- blog/2021/sacituzumab-govitecan-tnbc-regular-approval Figure 1. Visual representation of TNBC’s missing receptors [2] Triple-Negative Breast Cancer (TNBC) is an aggressive breast cancer subtype that lacks the estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2, accompanied by a heightened metastasis and recurrence risk [1]. Treatments lack specificity and are limited by TNBC’s various molecular subtypes and chemoresistance. In this study, we explored programmed cell death protein 1 (PD-1) therapies as a novel TNBC treatment and implemented the concept of precision medicine, developed an analytical algorithm using Python to investigate the drug efficacy of PD-1 therapy based on individual TNBC profiles. There is a positive, moderately strong correlation determined between CPS (r=0.51) and Placebo/Pembrolizumab (r=0.65) with the survival length. Correlations among other variables are relatively weak. Most Breast Cancer TNBC Methodology Future Work Acknowledgements References 93% 5-year survival rate 77% 5-year survival rate Figure 2. Analytical algorithm process. In this study, a mock database was randomized and generated using Pembrolizumab + chemotherapy clinical trial summary statistics on


New perspectives, breaking up traditions! Consultancy of Publication strategies in research proposals Career development of ECR Implementing research related policies Dr. Anneke Meyer Leibniz University Hannover Research and Innovation Services www.uni-hannover/forschungsservice.de @annekemeyer2 The Role of Research Managers in the Advocacy of Open Science Dr. Reingis Hauck Leibniz University Hannover Research and Innovation Services www.uni-hannover/forschungsservice.de @rsilvia77 Radical collaboration, breaking down silos! Building teams & networks with experts What is the right mix of knowledge on individual and team level? Activities of Research Managers with links to Open Science Advocacy of Open Science by building competencies & networks 2D Framework of knowledge Open Access level 3 No more distinguishing between professions but levels of competence! Librarian EC/ Horizon 2020 level 2 FAIR Data level 1 Federal Funding level 3 Academic Prizes level 3 Responsible Metrics level 1 Open Access level 3 German Research Foundation level 3 Research Manager Level 3 - Specialist knowledge Level 2 - Core knowledge Level 1 - Basic knowledge © Foto: Michael Matthey | LUH © Foto: Michael Matthey | LUH


Slum Sisterhood, philanthropy and Sapphic dialogues in Margaret Harkness’s In Darkest London (1890) Garth Wenman-James (g.wenman-james@surrey.ac.uk) Introduction: Sisterhood, Charity, and the Slums My research focusses on three main elements of the slum novel in the late nineteenth century: New Horizons: By the mid-1890s, over half a million women in Britain were ‘occupied continuously’ in philanthropic work (Poole, 2014, p. 3). Up until this point, philanthropic efforts in the slums were often led by clergymen and doctors—typically male occupations. Known as ‘slum sisterhoods’, these groups of women crafted new horizons that made way for major re- forms of the Poor Laws as well as laying foundations for later suffrage movements. Poverty Porn: Novels like Margaret Harkness’s In Darkest London (1890) represent the social reform enacted by these women. Yet, they also act as a form of entertainment, or ‘poverty porn’, to evoke pleasure in readers. Sex and Desire in the Slums: The eroticisation of poverty in the slum novel appears in dialogue with Harkness’s use of the slum space to express ‘Sapphic desire’, an expression of sexual or emotional passion between women (Vanita, 1996). Margaret Harkness: Slum Sister, Socialist, Philanthropist  Margaret Harkness was a socialist, philanthropist, nurse, novelist and journalist working towards social reform at the end of the nineteenth centu- ry  Harkness saw the perceived divides between religious (the Salvation Ar- my) and secular (socialist) philanthropic groups as detrimental to improving the conditions of the poor, stating that the ‘two organisations ought to work more together than they do at present, they have many points of common interest’ (1888, p. 2).  In Darkest London follows the lives of women in the Salvation Army as well as socialist sisterhoods, emphasising the social progress that can be achieved with both groups working together. The title is taken from the Salvation Army manifesto In Darkest England and the Way Out (1890), further indicating the influence that this context had on Harkness’s novel writing  As a socialist herself, Harkness worked as a slum sister alongside Beatrice Webb and Eleanor Marx, both highly influential figures on social reform an economic theory (Ross, 2007, p. 90). Harkness’s experience with slum work sets her writing apart from the slum novels of Arthur Morrison and Eliz- abeth Gaskell. Sapphic desire and Masochism  In much the same way that In Darkest London operates a form of poverty porn which evokes pleasure from the reader through its im- ages of grotesque poverty, the Slum Sisters gain pleasure from their work in the slums.  Speaking of the slum sisters, an unnamed pauper states that ‘you can’t scare those girls […] it’s not good trying to scare em’, they just enjoys it’ (p. 180). A shared masochism (the experience of pleasure when faced with pain or danger) occurs among the slum sisters, who ‘enjoy’ the danger posed by the poor they attempt to as- sist.  Masochism of this form features within Sapphic, same-sex desire as a shared pleasurable experience (Prins, 1999, p. 155). The slum sisters themselves therefore experience the novel’s environment as poverty porn. Slumming together: Passionate dialogues and Sapphic relations among slum sisterhoods Slum sisters enacted social change by ‘dressing, walking, and writ- ing together’ (Rappoport, 2012, p. 136). In these same-sex commu- nities, a Sapphic dialogue was produced; according to Ruth Vanita (1996), the Sapphic mode refers to a same-sex desire created be- tween women through social action and shared sympathetic experi- ence. Harkness herself alludes to something much like Sapphic desire in a letter to Beatrice Webb, where she defined love as the mixture between ‘sympathy + kindred feeling’ (1887); this is represented throughout In Darkest London, with the protagonist Ruth managing to cross from secular to religious sisterhoods. In sharing the sympathies of both sisterhoods, Ruth


Indalo isekelwe Iindlela zokujonga zineenzuzo ezilungileyo. Kodwa indlela ezihlukeneyo zikhokelela kwimpembelel o ezimbi. Isithintelo kulawu Isithintelo kulawu Isithintelo kulawulo “Xa besebenza bebengafumani mrholo. Khange bayigqibe ikontrakthi. Basebenza iinyanga ezintandathu kodwa behlawula imali elinganayo. Omnye osebenza inyanga enye.” Imiqobbo yentlalo yenkcubeko Imida yenkqubo yoosolusapho exhaphakileyo kubafazi. “... ndaqala ndaba yinkokeli yokucoca itywabasini kodwa ngenxa yokungahloniphi kwafuneka ndiyeke umsebenzi ukuze ndifumane izibonelelo ezithile kuphela.” Imithetho eluntwini okanye eyingosi Abazange bangene naluphi na ulwazi Imiqobo yolwazi “Kukho ukunqongophala konxibelelwano. Abantu balapha batyikitya isivumelwamo Kanye ngomnyaka. Bafuna ngakumbi kumbutho wamadlelo, hayi kanye ngonyaka. Ulwazi lunyanzelela intsebenziswano engaphezulu.” Ezoqoqosho kwezentlalo isithintelo Ubusela bemfuyo bubeka esichengeni iindlela zemfuyo kunye namadlelo. kukho Akukho ntengiso yempahla eveliswayo yokupjila, kwaye abaphumezi beprojekthi abakwazi ukuzithenga ezikuluntu. Ukungavisisani phakathi kwendlela yokuphila kunye neendlela zokuphila Indlela zijongelwa phantsi kukunqongophala ukuqonda nentlonipha kunye nolwazi olungangqineniyo luhamba kumanqanaba karhulumente. Abathengi okanye masiko nezithethe ngamnye amaxesha zingqubana neendlela zisekelwe kwindalo. Ulawulo olungacacanga nolungquzulanayo “Ngamanye amaxesha abanalo ulwazi, kwaye abafuni kubandakanya abantu basekuhlaleni. Ngoko ke abantu abathile abanokuthi baxhamle bakhutshelwa ngaphandle. Oko akulunganga. Bafuna uluntu olungundoqo luxhamle umqobo wolwazi.” Imiqobo yolwazi Unxibelelwano olunqabileyo nolulodwa “Sithendabuza uxanduva lokuphendula kwii NGOs njengoko kungekho mali yokuhlwawula ingcaphpephe zalapha ekhaya.” Ufikelelo lwenkxaso-mali oluthintelweyo kunye namaxesha angekho nqgiqweni Uluntu lohlukene njengoko abanye belandela umbutho wamadlelo kwaye Ezinye iinkokeli zemveli, kwaye kukhokelela kwiyantlukwano yolumntu. Ndingathanda ukubandakanyeka ngenxa yokukhethwa kweendawo zokuphumla kwaye usibonda akayonxal; enye zentlalo nekcubeko yombutho wamadlelo. Ukuntsonkotha kwezakhiwo zemveli Imiqobbo yentlalo yenkcubeko Ke silwenza njani ubulungisa kwiindlela ezisekelwe kwindalo kuluntu kunye nabachaphazelekayo kwi projekthi? Yeyiphi imiqobo ekuphumezeni ukulingana ngokwentlalo kwiindlela ezisekelwe kwindalo eMzimvubu? Funded by Sibulela amalungu oluntu aseMatatiele naseMaclear nabo bonke abachaphazekekayo kwiprojekthi kunye no Nosi Mtati and Phumula Nyembezi. By Glynis Humphrey, Tali Hoffman and Petra Holden · August 2024 glynis.humphrey@uct.ac.za Email: https://bit.ly/3BGj0vR Website: Izithintelo zamandla oluntu Ngokutsho kwamalungu olumntu angama 71 Ngokwabaphumezi beprojekthi bangama shumi amabini anesixhenxe


Core global metrics of chronic kidney disease (CKD) prevalence Global CKD prevalence Data: Global Burden of Disease (GBD) Study, 2019 Institute of Health Metrics and Evaluation Numbers on the top indicate global CKD prevalence. Comparisson of global prevalence for selected noncommunicable diseases Country-level CKD prevalence metrics Color filling accounts for three parameters: (1) all-ages and (2) age-standardised rates in 2019, and (3) age-standardised rate change since 1990. Before mapping each parameter was normalised to the scale from 0 to 100 (representing lowest and highest value of the original parameter). This allows to visualize all parameters and to identify the predominant one for each country. Scientific-Tools.Org Data analysis and visualization The creation of these visualizations and infographics has not been financed by any funds. You can donate at https://scientific-tools.org/support-us/ to support this and other visualizations Suggested citation: Bikbov B. (Scientific-Tools.Org). Core global metrics of chronic kidney disease (CKD) mortality in the GBD 2019 Study. Zenodo. DOI https://doi.org/10.5281/zenodo.8312897 1990 2000 2010 2019 341.7 mln 437.7 mln 559.3 mln 697.3 mln Chronic respiratory diseases Diabetes mellitus Neoplasms Cardiovascular diseases Chronic kidney disease Mental disorders 0 500 1000 Prevalence of selected diseases, in 2019, million persons Neoplasms Cardiovascular diseases Chronic respiratory diseases Mental disorders Diabetes mellitus Chronic kidney disease −20% 0% 20% 40% 60% nge in age−standardised prevalence rate between 1990 and 2019, % Data: GBD 2019 revision; Visualization: Scientific−Tools.Org Cha Data: GBD 2019 revision; Visualization: Scientific−Tools.Org


Uncovering the repertoire of legume NLR immune receptors Rita Maravilha Marques1,2, Carmen Santos1, Carlota Vaz Patto1, Sophien Kamoun2, and Jiorgos Kourelis2 1Instituto de Tecnologia Química e Biológica António Xavier, NOVA University of Lisbon, Oeiras 2780-157, Portugal 2The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, UK 1. Cardoso, D. B. O. S. et al. (2013). Reconstructing the deep-branching relationships of the papilionoid legumes. SA Journal of Botany, 89, 58-75. 2. Mundt, C. C. (2014). Durable resistance: a key to sustainable management of pathogens and pests. Infection, Genetics and Evolution, 27, 446-455. 3. de Queiroz, L. P. et al. (2015). A multilocus phylogenetic analysis reveals the monophyly of a recircumscribed papilionoid legume tribe Diocleae with well-supported generic relationships. Molecular Phylogenetics and Evolution, 90, 1-19. 4. Kourelis J et al. (2021) RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family. PLOS Biology 19(10): e3001124. https:// doi.org/10.1371/journal.pbio.3001124. BUSCO Assesment Results 7. Conclusions and Outlook The number and distribution of NLR classes across legume species is variable and mostly reflects legume phylogeny Most legume species tend to have more CC-NLRs than TIR-NLRs The number of CCG10-NLRs and CCR-NLRs appears less variable Whole genome duplications and genetic erosion could be altering NLR numbers The Fabaceae NLR repertoire will be an important tool for comparative resistance mapping studies and for R gene enriched Genome-Wide Association Studies What is the nature and diversity of Legume NLRs? 2. Question and Aim Perform a comparative NLRome study 3. The completeness of legume proteomes could be improved 4. We built NLR phylogenies for each species using RefPlantNLR4 5. The abundance and distribution of NLR classes in the Fabaceae is variable 6. Legumes display expansions and contractions in NLR numbers <5% Missing = Good Assembly Max. likelihood trees - Clustal Omega Alignment - FastTree algorithm Phaseolus vulgaris NLR Phylogeny Example: Tree Scale: 1 Proteome + NLR tracker Genome Quality Control NLR Phylogenomics Fabaceae, the legume family, is a large and diverse angiosperm crop family, with much ecological and economic importance.1,3 However, biotic stress continues to seriously constrain legume yield2 Resistance breeding is considered the most sustainable plant disease management method2 Nucleotide-binding Leucine Rich genes (NLRs) are intracellular receptors that detect pathogen effectors, triggering a powerful defensive mechanism known as Hypersensitive Response4 The NLR resistance genes and their respective classes remain largely unexplored in legumes CC NBARC LRR CC NBARC LRR LRR TIR NBARC LRR LRR RPW8 NBARC NLR number according to total number of proteins Number of Protein-coding Loci Total Number of NLRs MLA36-1 MLA30-1 MLA7 MLA13 MLA12 2 MLA9 MLA10//MLA13//MLA30-1//MLA34//MLA36-1//MLA37-1//MLA7//MLA9 MLA10 MLA37-1 MLA3 MLA23 MLA35-1 MLA23//MLA3//MLA35-1 2 MLA34 MLA39-1 1 MLA39-1 2 MLA6 1 MLA6 2 MLA27-2 MLA2//MLA27-1//MLA27-2 MLA27-1 MLA2 MLA19-1 1 MLA19-1 2 MLA12 1 MLA18-2 2 MLA18-2 1 MLA31-1 1 MLA31-1 2 MLA32 1 MLA32 2 MLA22 1 MLA22 2 MLA8 MLA1//MLA8 MLA1 MLA28-1 1 MLA28-1 2 MLA25-1 1 2 MLA25-1 2 2 MLA16-1 1 2 MLA16-1 2 2 MLA18-1 1 2 MLA18-1 2 2 HcMLA1 1 HcMLA1 2 TmMLA1 1 TmMLA1 2 Sr33 1 2 Sr33 2 2 SrTA1662 2 SrTA1662 1 Sr50 2 Sr50 1 Pi36 1 Pi36 2 DES1 2 3 DES1 1 1 Sr35 2 2 Sr35 1 2 Yr-10 1 2 Yr-10 2 2 Pm1a 1 Pm1a 2 Sr22 2 2 Sr22 1 2 SrTm5 Sr22-PI190945//SrTm5 Sr22-PI190945 sr22-PI573523 2 sr22-PI573523 1 Lr10 1 Lr10 2 Sr13a Sr13a//Sr13b//Sr13c//Sr13d Sr13c Sr13d Sr13b Sr26 1 2 Sr26 2 2 NLS1 1 2 NLS1 2 2 Pbr1.b 1 Pbr1.b 2 Pbr1.c 1 2 Pbr1.c 2 2 Pm41 2 Pm41 1 Pm5b 2 4 Pm5b 1 1 Pm5e Pm5-BMDM Pm5-CS Pm5a Pm5-ND Pm5-BMDM//Pm5-CS//Pm5-ND//Pm5a//Pm5e RPG5 2 RPG5 1 YrU1 2 4 YrU1 1 1 Adnr1 2 Adnr1 1 Pi-ta 1 Pi-ta 2 RGA2a 1 RGA2a 2 Pia-2 1 1 Pi


Has the Public’s Knowledge of Anatomy Been Hamstrung? A Questionnaire-Based Exploration of Basic Anatomical Awareness Within the General Population. Todd FS1, Whiting JR1, Taylor A2, Smith CF1 1Department of Medical Education, Brighton and Sussex Medical School (BSMS), Brighton, United Kingdom 2Clinical Anatomy Learning Centre, Lancaster Medical School, Lancaster, United Kingdom Introduction Despite a recent resurgence in public interest for anatomical sciences,1 little research exists to determine the extent of their knowledge. We aimed to assess this through a questionnaire-based localisation of anatomical structures. Our findings suggest a significant gender discrepancy, as well as the presence of prevalent anatomical misconceptions which, to our best knowledge, have not been documented in the literature. These results have implications for the content and targeting of future public and clinical teaching. Methodology Recruitment: Questionnaires were distributed to attendees of a public talk delivered by BSMS Anatomy faculty as part of the September 2017 British Science Festival. Questionnaire: Developed at Lancaster Medical School, and asked participants to identify the location of 22 anatomical structures on a blank human outline (Figure 1). Demographics: 45 questionnaires were returned, of which 37 had complete demographic information. The age range was 18 to 86. Of the 45 questionnaires returned, 37 had complete demographic information (24 females and 13 males). Questionnaires with incomplete information were omitted from gender analysis, but included in the misconception analysis. Results Gender Differences Females consistently outperformed males in 18/22 anatomical structures tested. Only the prostate, rectum, cornea and kidneys were answered better by males. Large gender differences in scores were seen for several of the structures, as highlighted in figure 2. Notably, only the prostate exhibited a large gender discrepancy in favour of males. Interestingly, no males were able to correctly identify the location of the gallbladder. Figure 3 compares the remaining structures. The mean female score was 14.0, whereas the mean male score was 11.7. Anatomical Misconceptions Two consistent mistakes were highlighted amongst participants during analysis. These were: 1) The “calves” were mistakenly labelled as the “hamstrings”. 2) The adrenal glands were incorrectly identified as being located in the head or neck. The first misconception was seen on 31.1% of respondent’s questionnaires (14/45), whilst the second was seen in 20% (9/45). This includes two participants who had both misconceptions on their answer sheet. In total, 46.7% of participants (21/45) had at least one of the above anatomical misconceptions. Discussion and Conclusions Literature The mean scores for both males and females closely reflect that of prior studies by Kljakovic et al.2 (Females: 52.0%, Males: 50.0%, n=1156) and Weinman et al.3 (Females: 50.9%, Males: 45.4%, n= 722), however neither differences reached significance. Whilst the larger gender difference seen in our results may be attributed to a small sample size or baseline knowledge biases introduced by sampling attendees of a public anatomy talk, Weinman et al.3 corroborates our findings in that females outperformed males in 10/11 structures tested. The detailing of public anatomical misconceptions has, to the best of our knowledge, not been documented in the literature. Implications Miscommunication is a major source of poor outcomes in general practice5 and a significant discrepancy exists between doctor and patient interpretations of medical terms, including anatomical language.6 This study highlights the need for doctors to be aware that misconceptions are prevalent and answers such as “glands in the neck” or “hamstrings” should be clarified in the history. An awareness of the public’s lack of ability to localise organs, particularly in males, may further improve patient satisfaction and outcome


Environmental Data Initiative (EDI): enabling reproducible ecology and environmental science Information Management Training EcocomDP: • Community ecology researchers met and defined the structure of a dataset pattern that facilitates synthesis of community datasets. • EDI personnel write code to translate community observations into this pattern EDI offers several options for education about the five stages of data publishing (Organize, Clean, Describe, Upload, and Cite) • Webinars (available on YouTube) • On-site (EDI personnel go to a professor’s lab to teach multiple grad students how to archive data) • EDI Training Lab (above, a 2018 training workshop on the EML Assembly Line R tool for generating Ecological Metadata Language (EML)) Datasets and metadata are evaluated for quality and congruence before upload into the repository • Some quality checks result in a failure to upload: • Field delimiter is a single character • URL returns data • Some quality checks return a warning or information, but do not result in a failure to upload: • Geographic Coverage present • DateTime format in metadata matches data • Record delimiter is present K. Vanderbilt1, C. Gries2, M. Servilla1 , D. Costa1 , Susanne Grossman-Clarke2, P. Hanson2 , M. O'Brien3, C. Smith2, R. Waide1 1Biology, University of New Mexico, Albuquerque, NM, 2Center for Limnology, University of Wisconsin, Madison, WI, 3Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA Overview The NSF-funded Environmental Data Initiative (EDI): • Offers data curation assistance to scientists affiliated with NSF-funded programs including: • Organization of Biological Field Stations (OBFS), • Long Term Research in Environmental Biology (LTREB), • Macrosystems Biology (MSB), and • Long Term Ecological Research (LTER), as well as • Individual environmental scientists without a viable data archive. Data Repository • Built on PASTA+ software • Contains high quality, well-documented datasets • Data are documented in Ecological Metadata Language (EML), a standard that can describe many types of data in great detail Data Synthesis Support Information Management Software Development • The EML Assembly Line, an R package, makes generating EML metadata a straightforward process • The user fills out several templates and runs the program to produce EML Outreach • The six EDI Summer 2018 Fellows learned information management practices from EDI personnel before heading to their host sites to conduct information management projects • EDI hosted a “hackathon” to begin populating the Information Management Code Repository (http://imcr.ontosoft.org/) • EDI supported the 2017 AGU Data Fair and co-organized the 2018 ESA Data Help Desk. Visit us at booth 722 in the Exhibition Hall! Summer 2018 EDI Fellows & Workshop Instructors portal.edirepository.org @EDIgotdata github.com/EDIorg https://environmentaldatainitiative.org/ AGU Data Fair


Additional modes and cycle-to-cycle variations of non-Blazhko RR Lyrae stars József M. Benkő1, Johanna Jurcsik1, Aliz Derekas2,1 & Margit Paparó1 1Konkoly Observatory, MTA CSFK, Konkoly Thege u. 15-17. H-1121 Budapest, Hungary 2ELTE Eötvös Loránd University, Gothard Astrophysical Observatory, Szombathely, Hungary Questions? Comments? Let me know! benko@konkoly.hu Cycle-to-cycle variations Acknowledgements This work was supported by the Hungarian National Research, Development and Innovation Office by the Grants NKFIH K-115709 and K-119517. AD was supported by the ÚNKP 17 4 New National Excellence Program of the Ministry of Human Capacities. AD would like to thank the City of Szombathely for support under Agreement No. 67.177 21/2016. Reality of cycle-to-cycle variation Appearing additional modes Data handling origin? The local instrumental trends was handled three different ways. We applied both (i) our moving average subtraction method described in Benkő et al. (2014) and (ii) a method in which we adjust each pulsation cycle to a common zero point. Moreover, (iii) if there were no evident instrumental trend in the flux curves, the data without further processing were also investigated. These two (or three) data sets show qualitatively similar C2C variations. Photometric problems? We choose high and low maxima pairs from the light curves and plotted the flux in the pixel maps either at the high maxima phase or the flux differences between the high and low maxima phases. In Fig. 2 can be seen such a plot pairs for NR Lyr. The figure shows that (1) the amplitude difference is connected to the star itself and there is no other source of flux, and (2) the position of the star is unchanged in the pixel mask. These detection make doubts any serious photometric defects as an origin of the C2C variation. Unknown instrumental effects? For testing unknown instrumental effects as an explanation of C2C variations similar observations from a different instrument is the best chance. Currently the only independent instrument which observed high precision time series for non-Blazhko RR Lyrae stars is the CoRoT satellite (Baglin et al. 2016). Three non-Blazhko stars were observed with the so-called oversampled mode (32 sec sampling) during the CoRoT runs. Two of them proved to be bright enough for our purpose: CM Ori (CoRoT 617282043, rCoRoT= 12.64 mag, Benkő et al. 2016) and the BT Ser (CoRoT 105173544, rCoRoT=12.99 mag). Investigating the CoRoT light curves as we did for Kepler stars' data we found C2C variation for the two brighter stars CM Ori and BT Ser. Fig. 3 shows their amplitude variation as panel c) of Fig. 1. Even though for these stars the scatter is evidently higher than NR Lyr the amplitude variations are obvious. The maximal difference between high and low amplitude maxima is about 0.005-0.006 mag. This value is the same as we estimated for Kepler stars. Figure 3. The amplitude difference of consecutive cycles in CoRoT non- Blazhko stars CM Ori and BT Ser. The purple plus signs mean the original light curve points while the green `x' symbols show the light curve points shifted one pulsation cycle. Figure 2. The pixel mask of NR Lyr during the SC (Q11.1) observation. The left panel shows the flux in `high' maxima signed by `C' in Fig. 1, while the right-hand-side panel contains the flux difference between the `high' (`C') and `low' (`B') maxima points. Figure 4. Sample spectra showing additional modes around the main pulsation frequency f0 and its first harmonic 2f0. In the left-hand-side and in the middle: The black curves show the LC spectra. Spectra computed from the SC data are signed red and blue curves (see also labels in panels). Providing comparable spectra either we divided the frequency scales with the actual f0 and also the flux scales are normalized to the signal to noise ratio of the LC spectra. In the right hand side: Typical time-frequency plots. The colour scales show the power values. The C2C behaviour of NR Lyr


Constraining stellar cores in the main sequence mass-transition zone Benard Nsamba, Marion Asasira, and Ronald Ssembatya Core evolution of stars in the main-sequence transition zone How long does core overshoot sustain a convective core on the main sequence? Radiation Vs. Convection We implemented core overshoot using the exponential decay recipe with a diffusion coefficient described by Herwig (2000), Model with no overshoot Model with overshoot *** Depending on the core extension implemented via the overshoot parameter, the mass transition region varies from [1.02 – 1.14] Solar masses. We note that metallicity also impacts on the probability of models being convective along the main-sequence phase*** Dov = D0exp( z f . H p) , where f is the overshoot parameter, Hp is the pressure scale height, z is the distance from the boundary of the convective region, and Do is the diffusion coefficient of the unstable convective region. Convective core evolution of models in the mass transition zone *** Hydrogen profile and sound speed profile are the best indicators of a uniformly mixed core region***


The European Testing and Experimentation Facilities for Agrifood Innovation Swedish node There are two fantastic facilities for your tests: Testbed Digitalized Agriculture and AstaZero. In addition, RISE has more than 130 test & demo facilities that can also be used depending on what you want to test. By combining our capabilities and competencies in agriculture with other areas such as AI, digitization and autonomous vehicles, we help companies between prototype and market introduction and to build trust for new AI and robotics solutions in the agricultural sector. A network of test and experimentation infrastructures in Europe that supports Agri-Food technology companies to do near product validation of their AI and Robotics solutions, using real-world facilities. AgrifoodTEF Swedish Node AgrifoodTEF Swedish Node AgrifoodTEF Sweden aims to promote technology development in agriculture and offers opportunities to test new technology in realistic environments before market introduction. The goal is to introduce AI and robotics solutions in agriculture that strengthen the sustainability of food production in an era of climate change and global competition. What is AgrifoodTEF? What is AgrifoodTEF? Main Objectives Main Objectives


Rosa M. González Delgado1, Julio E. Rodríguez Martín1, Ginés Martínez-Solaeche1, André de Amorim2, Luis Díaz García1, Rubén García Benito1, Matteo Maturi3,4 and J-PAS collaboration In this presentation, we report the results derived from analyzing the J-NEP field observed using the Pathfinder camera. We characterize the properties of stellar populations by fitting the J-PAS data with the parametric code BaySeAGal, focusing on galaxy members of groups detected by AMICO, as well as a sample of galaxies situated in filaments from the entire J-NEP sample down to an apparent magnitude limit of r < 22.75 (AB). We identify blue, red, quiescent, and transition (blue quiescent or green valley) galaxy populations based on their intrinsic colors and specific star formation rates. Furthermore, we estimate the fraction of red galaxies within groups, the excess fraction of quenched galaxies, and the evolution of the quenching rate within groups. These findings are compared with those from other fields, allowing us to assess the efficiency of group galaxy quenching as a function of the group or cluster mass. Introduction Galaxies in dense environments, such as galaxy clusters and groups, are more likely to interact among themselves and with the gas in the medium among themselves. These interactions lead to the suppression of the star formation of galaxies, by either heating or removing the cold gas reservoirs from galaxies, through mechanisms such as the ram-pressure stripping (Gunn et al., 1972), the tidal stripping (Malumuth & Richstone, 1984), or the harassment (Moore et al., 1996). This process is commonly referred to as environment quenching (Peng et al., 2010, Ilbert et al., 2013). Additionally, the populations and the distribution of the properties of the galaxies found in clusters and groups is different from those found in the field (see e.g. Dressler 1980; Bower et al. 1990; Lewis et al., 2002; Balogh et al., 2004; Kauffmann et al., 2004) The J-PAS survey has already started its science verification. Thanks to its photometric filter system, composed of 56 narrow-band filters, which provide an spectral resolution R~60, allowing for SED-fitting, as well as its large FoV (4.2 deg2), which allows for the unbiased detection of galaxies in galaxy clusters and groups, it will be an excellent survey to study the role of environment on galaxy evolution. In fact, works using data from the miniJPAS survey have already proven these capabilities (see González Delgado et al., 2022 and Rodríguez-Martín et al., 2022). In this work, we use the data from the J-NEP field, observed with J-PAS’ photometric filter system to further delve into this matter. Data The selected sample consists of 3257 galaxies with photo_z ≤ 1. We selected those objects with total_prob_star < 0.5. Galaxies in the sample reach a depth of 24 AB magnitudes in the rSDSS band. Most galaxies are dimmer than 18 AB magnitudes (peaking at ~23 mag) with an error lower than 0.1 mag. The distribution of the redshift of galaxies peaks at ~0.5. The brightness of galaxies decreases with redshift, and the median S/N decreases with the AB magnitude. Methodology SED fitting In order to retrieve the stellar population properties of galaxies we use BaySeAGal (de Amorim et al., in prep.; González Delgado et al., 2021), a bayesian SED-fitting code that uses a Markov Chain Monte Carlo approach. This way, we can estimate the errors of the properties and parameters as the standard deviation of the values of the chains, as well as retrieving the PDF of the properties. The code assumes parametric SFH. For our analysis, we choose a delayed-tau model, this is: Galaxy clusters and groups detections The classification of the galaxies into galaxies in groups and clusters and galaxies in the field was done using the AMICO code (Maturi et al., 2005; Bellagamba et al., 2018). This code is based on the Optimal Filtering technique and it was adapted by Maturi et al. (2023) in order to work with data using the J


THE NEED TO CLASSIFY MOON SOILS: PROPOSAL FOR A FIRST STEP FOR PLANETARY PEDOLOGY CONTEXT The Industrial Revolution during the 19th spurred the development of standards and methodologies in the search of mineral resources. Likewise, the first step in space resources utilization is the identification and assessment of the distribution, composition, and quantity of extra-terrestrial material, i.e. the mapping of the so-called regolith or real soil [1]. The creation of a lunar resource cartography requires to agree on a standardized language to communicate about the different soil layers or “horizons” of the upper regolith. This consensus is a prerequisite to ensure effective communication, accurate interpretation, proper classification and reliable mapping of the lunar soils. This proposal provides a starting point for discussions among lunar scientists and soil scientists to establish a foundation for Moon Soil Sciences Mapping methods in the context of space resources. REFERENCES: [1] Certini, G. and Scalenghe, R. (2010) Do soils exist outside Earth? Planet. Space Sci. 58, 1767– 1770. [2] IUSS Working Group WRB. (2022). World Reference Base for Soil Resources. International soil classification system for naming soils and creating legends for soil maps. 4th edition. International Union of Soil Sciences (IUSS), Vienna, Austria. [3] Morris, R.V. (1978) Proc. LPSC 9th, 2287-2297. [4] Laul J.C. and Papike J.J. (1980) The Apollo 17 drill core: Chemistry of size fractions and the nature of the fused soil. Proc. 11th Lunar Planet. Sci. Conf. 1395-1413 [5] Taylor G.J., Warner R.D. and Keil K. (1979) Stratigraphy and depositional history of the Apollo 17 drill core. Proc. 10th Lunar Planet. Sci. Conf. 1159-1184. Jérôme Juilleret1, Abigail Calzada-Diaz 1,2, Riccardo Scalenghe 3, Giacomo Certini 4 1Luxembourg Institute of Science and Technology, 2European Space Resources Innovation Centre 3Universita degli Studi di Palermo, 4Universita degli Studi Firenze EARTH EXPERIENCE Terrestrial pedologists have developed an international nomenclature of soil horizons based on interpretive symbols, which link soil description to properties and/or genesis of the layers [2]. This system facilitated the parallel development of pedological classification and soil mapping in the 20th century, allowing for systematic interpretation of soil properties and genesis. For example, the World Reference Base for Soil Resources International soil classification system uses capital letters (master symbol), often followed by one or more lowercase letters (suffixes) to label soil horizons [2]. PROPOSAL FOR THE MOON We propose to use a combination of the Is/FeO maturity index of Morris [3] (i.e., the amount of single-domain and nanophase Fe0 (Is) normalized for total FeO content), and the agglutinate content to differentiate soil reference horizons, as these variables reflect the surface exposure time of lunar soils to weathering. In addition, we suggest using a labelling system inspired by Earth’s pedology concept but adapted to the Moon context. To avoid confusion with terrestrial soils horizons, we have chosen to use the degree symbol ° (Unicode U+00B0) as a prefix to the master horizon designation. We have defined 4 master horizons (°A,°B, °C, °D) based on the agglutinates content, and these, combined with the Is/ FeO maturity index, allow us to define 12 reference soil horizons (see Table below). We suggest naming the °A horizon the Agglutinic Master Horizon, as it has the highest content of agglutinates. Finally, we recommend integrating rock fragment cover, texture and other important features for in-situ resource utilization (ISRU) as diagnostic properties. Agglutinates (%) Master Horizon Is/Fe (%) Reference Horizons Comments > 30 °A > 60 °Am Mature °A 30 - 60 °As Submature °A < 30 °Ai Immature °A 15 - 30 °B > 60 °Bm Mature °B 30 - 60 °Bs Submature °B < 30 °Bi Immature °B 5 - 15 °C > 60 °Cm Mature °C 30 - 60 °Cs Submature °C < 30 °Ci Immature °C < 15 °D > 60 °D


CHARACTERIZATON OF A HOLLOW-CATHODE LAMP TO MEASURE ACCURATE TRANSITION PROBABILITIES OF RARE EARTH ELEMENTS P. R. Sen Sarma, M. T. Belmonte, S. Mar , N. Lorenzana Universidad de Valladolid, Department of Theoretical and Atomic Physics and Optics, Paseo de Belén 7,47011 Valladolid, Spain. WHAT DO WE DO AND HOW IS IT DONE? The quality and quantity of atomic data, like transition probabilities of rare-earths, is a major hindrance for astrophysicists to accurately calculate chemical abundances of stars[1]. Thus it is of utmost importance to produce new improved atomic data. Spectral Range: 200 nm to 800 nm Resolving Power: 150 000 at 450 nm ACKNOWLEDGEMENTS: P. R. Sen Sarma thanks the University of Valladolid for his PhD grant. M. T. Belmonte acknowledges the funding provided by the Spanish government through projects PID2021-127786NA-100 and a Beatriz Galindo Fellowship. PRATYUSH RANJAN SEN SARMA pratyushranjan.sen-sarma@uva.es MARIA TERESA BELMONTE SAINZ EZQUERRA mariateresa.belmonte@uva.es In order to report transition probabilities (Aki) of Nd III in the UV-visible range, we use a diffraction grating spectrometer (2400 lines/mm) to measure the branching fractions (BFi). Using this BFi and lifetimes (τk), Aki is calculated. VOLTAGE-CURRENT CHARACTERISTIC OF THE HOLLOW-CATHODE LAMP (HCL) STABILITY OF THE HCL OVER TIME We measure intensities of Ar II lines at different wavelengths for transitions from different upper energy levels over a period of almost two hours. Current and pressure are 300 mA and 150 Pa, respectively. To make sure that our Hollow-cathode Lamp is operating in the abnormal glow region of its discharge curve, the voltage-current characteristic is obtained for low pressures in order to get “nice spectroscopic property” [2]. The resistance of the lamp decreases with an increase in pressure due to the increase in Ar atoms. Wavelength (nm) Transition Probability (*108s-1) Upper Energy Level (eV) Intensity Variation 349.1 2.31 [3][4] 22.8 10% 423.72 0.112 [3][4] 21.4 7% 611.5 0.2 [3][5] 21.1 3% Hollow-Cathode lamp is operated in the abnormal glow region of the gas-discharge curve of Ar II. We have used standard Tungsten and Deuterium lamps to obtain the response function. We measure the same response using the branching ratio (BR) method [6]. This method takes the transmittance of the lamp’s front window into consideration. RESPONSE FUNCTION OF OUR SETUP REFERENCES [1] Banerjee, Smaranika, et al. ApJ 934.2 (2022): 117. [2] B. Barbieri, N. Beverini and A. Sasso, Rev. Mod. Phys. 62, 603 (1990). [3] Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2022). NIST Atomic Spectra Da- tabase (ver. 5.10), [Online]. Available: https://physics.nist.gov/asd [2023, June 21]. National Insti- tute of Standards and Technology, Gaithersburg, MD. DOI: https://doi.org/10.18434/T4W30F [4] W. R. Bennett, Jr., P. J. Kindlmann, and G. N. Mercer, in Chemical Lasers: Applied Optics Supplement 2, 34 (Edited by J. N. Howard, Opt. Soc. America, 1965) [5] R. Schnapauff, Z. Astrophys. 68, 431 (1968) (Ger.) [6] Whaling, W., M. T. Carle, and M. L. Pitt. JQSRT 50.1 (1993): 7-18. [6] Ical : Calibrated Intensity; Imeasured : measured Intensity Ɛ(λ) : Response function of the setup at wavelength λ


OPEN, FREE & FAIR DATA GUIDE CHEAT SHEET FOR NASA-FUNDED EARTH SCIENCE DATA PRODUCTS § Keep a holistic view with FAIR core concepts. § Follow NASA established processes and practices. § Utilize NASA enterprise systems and tools. § Leverage community standards and practices. F1 IDENTIFIER F2 RICH METADATA F4 RESOURCE A1, A1.1 PROTOCOL A1.2 PROCEDURE R1 ATTRIBUTE R1.1 LICENSE R1.2 PROVENANCE R1.3 STANDARD Obtain and use unique, persistent, and resolvable identifiers: § Data product: DOI from DataCite (via a DAAC) or Zenodo. § Metadata records: UUID or ARKs. Additionally, use these IDs if appropriate: § Person (Data producer and (meta)data curator): ORCID. § Organization: ROR ID. § Data center or Repository: re3data ID. § Instrument/Platform: PIDInst § Other artifacts: RRID § Use CMR UMM-C schema. § Ensure inclusion of required UMM-C metadata elements such as: DOI, Title, Abstract, Creator and/or Publisher [Data Centers], Version, Platform, Spatial Extent, Temporal Extents, Processing Level, Science Keywords, and Metadata Specification. When publicly releasing data products and associated metadata records: § Include an open license, following practices in R1.1. § Include data provenance, following practices in R1.2. Additionally, § include those in I3 if appropriate. § Review and include relevant attributes from Appendices D and E in DPDG (Ramapriyan et al. 2024). § Use CC0 1.0 + Attribution for mission data products. § Use CC0 1.0 + Attribution or CC-BY 4.0 for NASA-funded scientific data products. § Make it both human and machine-readable* and include recommended citation in metadata and on DOI/data product landing pages. * See the side panel on the right for examples. § Use UMM-C metadata fields (Version, Data Dates, Metadata Dates, DOI/PreviousVersion, RelatedURL, Data Center, Collection Citation/Creator). § Use global attributes in netCDF data files for source data, algorithm used, and data producer and/or publisher. WHAT YOU SHOULD KNOW Making data FAIR is a multi-dimensional, multi-layered, and multi- faceted problem (Figure 1) that requires multi-domain information and knowledge. § FAIR Principles consist of 15 FAIR sub-principles in 4 quality dimensions (Findability, Accessibility, Interoperability, and Reusability), covering three categories (Data, Metadata, and Infrastructure) (Figure 2). § The FAIR principles can be mapped to 28 category-specific requirements (Figure 3) and 21 unique category-specific unique core concepts (Figure 2). FAIR ID / CORE CONCEPT Integrate with NASA’s Earth data publication process: § Register data product DOIs and UMM-C/G metadata records in CMR § Integrate to Earthdata Search Portal Ensure integration to additional searchable resources, including: § DataCite, if it minted DOI § Google Search Engine § Register for an Earthdata account. § Use Earthdata Search Portal for retrieving metadata records. § Download data with Earthdata Login. § Use Earthdata (Cloud/GIS) login for data access. § Use Earthdata Search Portal or CMR API for metadata access. Figure 2. FAIR dimensions and sub-principles IDs (filled circles); categories (filled ovals) for data (D), metadata (M), and infrastructure (IS); and core concepts (round triangles). The pink-filled core concepts are FAIRness quality measures. Source: Peng et al. (2024a). License: CC-BY 4.0 DEVELOPED BY NASA ESDS O’FAIR Working Group Recommended Citation: Peng. G., R.R. Downs, H. K. Ramapriyan, and NASA ESDS O’FAIR WG, 2024: Open, Free & FAIR Data Guide Cheat Sheet for NASA-funded Earth Science Data Products. Version: v01r00-20240926. DOI: https://doi.org/10.5281/zenodo.11520035. License: CC0 1.0 + Attribution. Acknowledgement: The work for this cheat sheet and the O’FAIR data guide document (i.e., Peng et al. 2024b) was carried out across multiple United States government-funded institutions under contracts with NASA (see details in Peng et al. 2024b). Government sponsorship is acknowledged. § Follow a standard for enabling data identifiers globall


4 4 4 4 When it comes to measuring the quality of an open access repository, it is not the size that matters but the sum of its characteristics. The Open Access Repository Ranking (OARR) is a ranking that lists all German open access repositories according to a metric that evaluates a certain set of criteria that are summarized in categories. The OARR metric is open, transparent and developed in accordance with the open access community. The data for the current ranking was collected in the course of the 2014 Census project seminar at the BLIS. The ranking is planned to be published annually at the Open-Access-Tage conference in September. The preceding January each open access repository that meets the OARR definition will be contacted to submit their data via an online form. The OARR team reviews all submissions assuring its quality and validity. What? For now OARR is a ranking limited to Germany. We are planning to extend it to other countries. OARR is a research project based at the Information Management Department of Professor Peter Schirmbacher at the Berlin School of Library and Information Science (BSLIS), Humboldt-Universität zu Berlin (HU Berlin). If you have any ideas (e.g. cooperations) of how to work on the future of OARR we encourage you to contact us. For whom? OARR aimes primarily at repository managers and institutions that host, run or plan to build a repository. With OARR funders and repository managers get an overview of the (technical) developments within the open access repository community. Finally OARR enables researchers to identify the open access repository that suits best their needs when looking for a proper place to deposit their publications. Where to? Ranking Proﬁle Page Metric REPOSITORY RANKING OPEN ACCESS 2014 RANKING METRIC STATISTICS SUBMIT Team: Paul Vierkant, Maxi Kindling, Dennis Zielke, Thomas Hartmann


• At the end of each trial, the correct category was revealed and the subjects recorded the accuracy of their category guess. Investigating the effects of a non-native salamander on the native salamander community at Mountain Lake Biological Station, Pembroke, Virginia. Alexander J. Novarro1 and August Blackman2 Background Results Literature Cited Methods 1. Rissler et al. 2000. Spatial and behavioral interactions between a native and introduced salamander species. Behavioral Ecology and Sociobiology, 48, 61-68. 2. Hairston, N.G. 1983. Alpha selection in competing salamanders: experimental veriﬁcation of an a priori hypothesis. The American Naturalist., 122, 105-113. 3. Fiske, I. and R. Chandler. 2011. An R package for ﬁtting hierarchical models of wildlife occurrence and abundance. Journal of Statistical Software, 43, 1-23. 1Department of Biology, University of Maryland, College Park, MD; 2Department of Biology, Oberlin College, Oberlin, OH Discussion @TheSalexmander Plethodon cinereus and Plethodon glutinosus naturally co-occur at Mountain Lake Biological Station. In the 1930s-40s, a third Plethodon species, P. montanus, was introduced1. Although these species coexist elsewhere, the introduction of novel salamander species is known to negatively impact the abundance of naïve species2. We hypothesized that the abundance of P. cinereus and P. glutinosus would be lower in the presence of P. montanus than in the absence of P. montanus. Has the introduction of Plethodon montanus affected the abundance of native Plethodon species at Mountain Lake Biological Station? Our study shows that a non-native Plethodon salamander may persist in a community of ecologically similar species without negatively impacting the abundance of the native species. However, an increase in the number of P. montanus is likely to have a negative impact on the dominant native species, P. cinereus. To our knowledge, this is the only human-introduced population of lungless salamanders. Our study provides insight to the community-level effects of human- and climate-induced range shifts in Plethodon salamanders. Anova1@umd.edu Our results suggest that the non-native P. montanus has not reached high enough densities to negatively impact the native salamander community at Mountain Lake Biological Station. We performed three nocturnal visual encounter surveys in 48 15x3m transects at sites where P. montanus was either absent, introduced, or native. We used N- mixture models in the R package unmarked to estimate abundance while accounting for imperfect detection3. Table 1. Beta estimates, standard error, conﬁdence intervals, and P-values for the best-supported abundance models. Fig. 3. Mean abundance of Plethodon salamanders in a 45m2 transect at sites where P. montanus is absent, introduced, and native. a b c Fig. 1. Photos of Plethodon species at Mountain Lake Biological Sta9on: (a) P. cinereus, (b) P. glu1nosus, and (c) P. montanus. Fig. 2. Predicted relationship between the abundance of P. montanus and the abundance of P. cinereus in a 45m2 transect. Fig. 2. Map showing the loca9on of study sites in Giles County, Virginia where surveys were conducted. Circles are color coded to represent the state of P. montanus. 0 20 40 60 80 100 Absent Introduced Native State of P.montanus Estimated Abundance Species P. cinereus P. glutinosus P. montanus 0 10 20 30 40 50 60 70 0 50 100 150 200 P. montanus P. cinereus Fitted Regression Line 95% Confidence Interval (SE) β SE 95% CI P-value P. cinereus Detection covariates: Precipitation 0.019 0.003 0.012 0.026 < 0.001 Time of survey -0.003 0.001 -0.004 -0.002 < 0.001 Understory cover 0.005 0.004 -0.004 0.013 0.275 Abundance covariates: Distance to stream -0.001 0.000 -0.002 < 0.001 0.118 Understory cover -0.007 0.005 -0.017 0.002 0.149 Estimated abundance of P. montanus -0.027 0.005 -0.036 -0.017 < 0.001 P. glutinosus Detection covariates: Precipitation -0.019 0.011 -0.041 0.002 0.088 Time of survey -0.003 0.001 -0.006 -0.001 0


RESEARCH POSTER PRESENTATION DESIGN © 2015 www.PosterPresentations.com Long-baseline neutrino oscillation sensitivity with Theia Guang Yang1 , Michael Wilking1, Elizabeth Worcester1,2 on behalf of the Theia collaboration 1.Stony Brook University, 2. Brookhaven National Lab Neutrino detection and reconstruction Long-baseline sensitivity Theia detector Neutrino mixing and oscillation Background reduction PMNS matrix: - A non-zero Ɵ₁₃ has been measured. - Different appearance probability between ν and anti-ν indicates the CP phase. Theia has proposed two possible masses of 25 kt and 100 kt with features: - large-scale water-based liquid scintillator - Advanced photo-sensor technology with improvements in time resolution, light collection, spatial granularity etc. - Multiple complementary and advanced reconstruction techniques - Main neutrino interaction channels at GeV: - CCQE: νe 0 decay electrons ; νμ typically 1 decay electron - CCπ+ : 1, 2 or 3 rings; νe 1 decay electron ; νμ 2 decay electrons - NC π : NCπ0 can be mis-ided as an electron ; NC π+ can be mis-ided as either μ or e. - As a reconstruction package, FiTQun is now exclusively used for all T2K oscillation analysis -For any hypothesis of final state particles, predict the charge and hit recorded by every PMT Theia 25 Theia 100 -FiTQun can handle any number of reconstructed tracks in the water detector -Event hypotheses are distinguished by comparing best-fit likelihoods. - BDT has been used for the background reduction for each i-ring j-decay sample (i from 1-3, j from 0-1). - T2K-like fully contained fiducial volume cuts have been applied as pre-cuts. - Variables with FiTQun after the pre-cuts: - vertex, distance to wall, direction - pi0 fit momenta, likelihood, angle, mass - 1-ring fit: momenta, likelihood - 2-ring fit: kinematics, differences between the best fit likelihoods of each combination (e-like or pi-like) - 3-ring fit: similar to the 2 ring case, with all possible differences between the best fit likelihood of each combination (e-like and pi-like) - Energy-dependent BDT cuts are applied to the samples after the pre-cuts. FHC 1 ring 0 decay FHC 1 ring 0 decay - There are totally 9 samples included in the sensitivity study. - FHC: - 1-ring, 0 or 1-decays - 2-rings, 0 or 1-decays - 3-rings, 0 or 1-decays - RHC: - 1-ring, 0-decay - 2-rings, 0-decay - 3-rings, 0-decay - Full set of spectra: Eur. Phys. J. C 80, 416 (2020). https://doi.org/10.11 40/epjc/s10052-020-7977-8 - The CP and mass hierarchy sensitivities with a 25 kt (fiducial) Theia module are comparable to a 10 kt (fiducial) DUNE module. guang.yang.1@stonybrook.edu


Stephanie Werner (Darmstadt University of Applied Sciences): stephanie.werner@h-da.de ORCID: 0000-0002-0468-8856 Arnela Balic (Frankfurt University of Applied Sciences): arnela.balic@fit.fra-uas.de ORCID: 0000-0002-7049-5737 1.5 hours per module 6 modules published reusable materials individual adjustments 20-80 attendees per module about 400 registrations The HeFDI universities and universities of applied sciences What is HeFDI? Various different infrastructures and services are needed to support researchers in managing their digital research data. Led by the Philipps-University of Marburg, eleven Hessian universities and universities of applied sciences collaborate to establish common research data services fit for the needs at hand. HeFDI offers, amongst many other products, training courses targeted towards PhD students at Hessian universities and universities of applied sciences. Decentralized and collaborative: Data School RDM training HeFDI Data School HeFDI Publications HeFDI Website HeFDI Data School in the future Future plans for the HeFDI Data School include the possibility of granting credit points for participation as well as improving workflows and planning processes. Up-to-date-content regarding RDM is continuously fed into the materials and the quality of those materials is improving based on growing expertise as well as feedback of the attendees. English modules and materials are currently being discussed as well. Advantages The idea of the Data School comes with many advantages such as opportunities for individual adjustment of focus for each institution. On top of that, the whole HeFDI network works together to evolve its contents, enabling especially smaller institutions to develop and take advantage of this training concept while significantly conserving staff efforts. The attendance of the HeFDI Data School is possible from anywhere with a stable internet connection offering maximum flexibility to speakers and attendees alike, allowing for increased attendance rates. Attendees can also request a certificate of participation after completing the courses. All in all, the HeFDI Data School is a popular training offer with consistently high registration numbers, also attracting registrations from outside the HeFDI community. Formation of the HeFDI Data School The HeFDI Data School started as a decentralized online offer in the beginning of the COVID-19 pandemic. The mostly digital environments during the time of the pandemic led to an accelerated productivity in the planning process. A working group on this topic was established that still continues its activities. Initially it was carried out by volunteers of universities of applied sciences in the HeFDI network to reduce individual workloads when educating about Research Data Management on a local scale alone. Since it has grown and shifted with every year. At this point, the fourth edition of the HeFDI Data School is being held and participants of the symposium are encouraged to register. All about the HeFDI Data School Contents The Data School consists of several modules imparting basic knowledge regarding Research Data Management such as data management plans or FAIR principles. The contents of the Data School are continuously being evaluated, developed and extended to fit the needs of the attendees as well as reflecting current developments in the RDM community. The basic Data School curriculum typically consists of six modules: • Introduction to Research Data Management • Data Management Plans (DMPs) • Data Organization and Documentation • Archiving and Publication of Research Data • Legal Aspects (Copyright and Rights of Use) • Legal Aspects (Data Protection) 16th October 30th October 13th November 27th November 11th December 15th January Data School III attendance per status group PhD students professors others students administrative staff academic staff Modules that have been taught previously as additional courses were for example: • Open Science


Design and Formalization of Blockchain Oracles By: Mohammad Shaheer Advisor: Giselle Reis • Blockchain: Decentralized, distributed ledger that stores information securely and transparently. • Ethereum: Blockchain based decentralized computing platform that allows developers to build dApps (Decentralized Applications). • Smart Contracts: Computer programs running on Ethereum that can be called by users by creating requests. • Example: Alice agrees to pay Bob X ETH if team Y wins the match. The smart contract for this match needs to obtain the results of the match. • Solution 1: Smart Contracts call the off-chain APIs themselves. Issue: Blockchain loses determinism. • Solution 2: Oracles Entities that connect blockchains to external systems 1. Background • Oracle Problem: Connecting Blockchain to off-chain systems without losing the transparency, consensus and decentralization. • Agood oracle should satisfy the following properties: 1.Confidentiality, Integrity and Availability 2.End-to-End Decentralization 3.Discourage Dishonest Behavior • Problems with current oracles: 1. No formal guarantees 2. Ad hoc 3. Prone to attacks by malicious entities 4. Uncertainty 2. Problem • Chainlink is the most trusted Oracle used in industry. • Adopts decentralization at every layer. • Issues: 1. Not Formally Verified 2.Complex Implementation 3. State of the Art • Provide guarantees through Formal Verification. • Ensure protocol is sustainable and charges consumers fairly. 4. Our Approach • Smart Contract implemented using Solidity. • Every external data source connected to an oracle smart contract on- chain. • Data Model: Subscription based model. Consumers deposit credit to obtain data. • Price setting Model: 1. Every consumer charged (weight * base fee). 2. The model tries to keep the total cost and total revenue the same by adjusting the Base Fee at periodic intervals. 3. 𝑹𝒌+ 𝝓′ ∗𝛀𝒌= 𝑪𝒌+ 𝜶𝒌∗𝑵𝒌(Solving for 𝜙′). • Under certain assumptions, total cost equals total revenue right before the next base fee adjustment. 5. Implementation • Coq (Interactive Theorem Prover) used for formalizing the Solidity smart contract. • The oracle is modeled as a state machine. • The state of oracle is formalized as an n-tuple. • Trace: Record of events ordered from least-recent to most-recent. • Using the initial oracle state and the trace we can track the evolution of the oracle state. 6. Formalization 𝑆𝑡𝑎𝑡𝑒𝑖+ 𝑃𝑎𝑟𝑎𝑚𝑒𝑡𝑒𝑟𝑠 𝐶𝑜𝑞𝐹𝑢𝑛𝑐𝑡𝑖𝑜𝑛 𝑆𝑡𝑎𝑡𝑒𝑖+1 • Theorem 1: After every action, the credit of all consumers remains non- negative. 2 helper lemmas • Theorem 2: Between any 2 data write calls, a consumer pays exactly once for obtaining data. 9 helper lemmas • Theorem 3: If the base fee is adjusted under certain assumptions, total revenue equals total cost right before the next base fee adjustment. 16 helper lemmas • Theorems proved inductively using the trace. • Desired property and assumptions expressed as Coq propositions. 7. Specifications • PID Control: Technique used in Control Theory to control the system’s behavior (controlled variable) in order to achieve the desired output (commanded variable). • Intuitively, it’s a function that receives an input and produces an output. • Objective: Over time, we want the total revenue (controlled variable) to be equal to the total cost (commanded variable) which indicates sustainability and fairness of the protocol. 8. Price Setting using PID control Total Cost Total Revenue Base Fee • We can modify the Adjust Base Fee function to implement a PID control. • Determining 𝑲𝒑,𝑲𝒊,𝑲𝒅(also known as gains) is the main challenge. • Heuristic Approach: Run input sequences and use Cohen Coon/Ziegler Nichols method for determining the gains. • Model Based Approach: Determine a model that describes how the total revenue is affected by the base fee and use it to determine gain values. • 𝑻𝒐𝒕𝒂𝒍𝑹𝒆𝒗𝒆𝒏𝒖𝒆𝒕= ׬𝟎 𝒕𝝓𝒕∗𝒓𝒕𝒅𝒕 • 𝑻𝒐𝒕𝒂𝒍𝑪𝒐𝒔𝒕𝒕= ׬𝟎 𝒕𝜶𝒕∗𝒘𝒕𝒅𝒕 Total Revenue = 𝑅𝑘 Total Cost = 𝐶𝑘 Reads = Ω𝑘 Writes = 𝑁𝑘 Latest Cost = 𝛼𝑘 Base Fee Adjustedk Total Re


Segmentation Neural Networks for Particle Identiﬁcation in ProtoDUNE Carlos Sarasty Segura for the DUNE Collaboration† †University of Cincinnati Segmentation Neural Networks for Particle Identiﬁcation in ProtoDUNE Carlos Sarasty Segura for the DUNE Collaboration† †University of Cincinnati ProtoDUNE-SP Detector The ProtoDUNE single-phase (SP) detector is the prototype of the DUNE far detector SP technology built with full scale compo- nents at the CERN neutrino platform. With a total liquid argon mass of 0.77 kt it is the world largest Liquid Argon Time Projec- tion Chamber (LArTPC) built to date. The TPC consist of a cen- tral Cathode Plane Assembly (CPA) held at 180kV that is ﬂanked by 6 Anode Plane Assemblies (APAs) at a distance of 3.6m. Each APA is 6 m long x 2.5m wide and contains a set of three planes of sense wires (tow collection planes and one induction plane) oriented at different angles. Fig. 1: Ilustration od the ProtoDUNE-SP detector Semantic Segmentation We apply sparse CNNs for semantic segmentation at a pixel level using simulated event displays in two and three dimensions in the ProtoDUNE (LArTPC) detector. We use a hybrid network of two popular architectures that are U-Net and ResNet. U-Net is an auto-encoder made of two parts where the ﬁrst part applies a series of convolution blocks that reduces the size of the feature maps and learns important properties of the image at different scales. The second part applies a series of up-sampling oper- ations and convolutions to recover the original resolution of the image. Based on ResNet architecture, we allow residual skip connections that speed learning. Fig. 2: Illustration of the UResNet architecture, ﬁgure from [1] Ground Truth The performance of any machine learning model is limited by the quality of the deﬁnition of the ground truth. In this case the ground truth is a tensor that holds the true informa- tion of the different types of particles present in each pixel (or voxel for the 3D case) of an event display. In order to deﬁne the ground truth, we use the information from the underlying simulation such as the PDG code of the particles, the track ID, the process name and the amount of energy deposited by each particle per pixel (or voxel). The different particle classes used in our training are: Mouns, pions, heavily ionizing particles (such as protons, kaons and nuclei), Michel electrons, electromagnetic showers, and diffuse electromagnetic activity. Then we record the fraction of energy deposited by each type of particle per pixel. Results We trained a sparse CNN for particle identiﬁcation using a set of 70.000 3D recon- structed samples that we split into 95% and 5% for train and test respectively. We calculated the accuracy of each particle class and we summarized those results in a confusion matrix. Moreover, we tested the capability of the neural network to correctly separate pions and protons. Fig. 3: Confusion Matrix. Fig. 5: True and classiﬁed scores for pion and proton separation. Fig. 6: The ﬁgure in the top represents the true labels. The ﬁgure in the bottom shows the classiﬁed labels Status and Future Plans • These results show a very good performance of the network for the task of semantic segmentation at a pixel level, they also show that pions can be well separated from protons. • We plan to train the network using single particles dataset. • Test the capability of the network to separate electrons and pho- tons as well as muons and pions. References [1] Laura Domine and Kazuhiro Terao. “Scalable Deep Convolutional Neural Networks for Sparse, Locally Dense Liquid Argon Time Projection Camber Data”. In: arXiv:1903.05663 (2019).


1.1. 3. 3. 4. 4. 2. 2. Could Norway supply its own P fertilizer? High-resolution analysis of the agricultural phosphorus cycle. Miguel Las Herasª, Francis Barrea, Nils Dittrichb, Avijit Panditb, Anne Falk Øgaardc, Daniel B. Müllerb a The Climate and Environmental Research Insitute NILU b Norwegian University of Science and Technology c Norwegian Institute of Bioeconomy Research 1 Cordell, Drangert, and White, (2019). The Story of Phosphorus. Global Environmental Change. 2 Jasinski, Stephen (2019). Mineral Commodity Summaries 2019. USGS. 3 Hamilton et al. (2016). Investigating Cross-Sectoral Synergies... Journal of Industrial Ecology. Project funded by NFR - Bionær Mineral P is currently the main source of P-fertilization, essential for food production1. Mineral P reserves are highly concentrated in a few regions: ~70% of global P is found in Morocco and West. Sahara2. Over half of the P fertilizer applied to cropland is wasted (runs oﬀ to water or accumulates in the soil)3. P emissions increase the risk of eutrophication. FOOD SECURITY + EUTROPHICATION RISKS FOOD SECURITY + EUTROPHICATION RISKS METHODS METHODS Farm: P flows quantification P cycles of x40 000 farms Spatial aggregation Modelling of manure management optimization P CYCLE OF NORWEGIAN FARMS P CYCLE OF NORWEGIAN FARMS mineral fertilizer biosolids & biowaste accumulation runoﬀ vegetables roughage grass animals grain products eggs milk manure B. Farm with crop production A. Farm with mixed production (livestock and crops) C. Farm with pig production P accumulation in Norway (t/yr) 0,0 - 6,0 6,1 - 16,0 16,1 - 42,0 42,1 - 112,0 112,1 - 355,0 A. B. C. * A, B and C are three example farms from the Norwegian 40,000 and are not representative of the national P cycle. If you are interested in the aggregation of ﬂows on a national level, please see the additional documentation hanging on the side. POTENTIAL REDUCTION OF MINERAL P IMPORTS POTENTIAL REDUCTION OF MINERAL P IMPORTS IN CONCLUSION, AND ANSWERING THE TITLE: YES IN CONCLUSION, AND ANSWERING THE TITLE: YES mineral P traded manure animal deposition biosolids & biowaste collected manure fertilization demand -52% -74% -78% -89% Farm Optimiz. Regional Market Municipal Market Status Quo National Market 1 2 3 4 Strategies to replace imported mineral P with secondary P from collected manure: ▪Optimizing manure and fertilizer application at the farm level (1). ▪Secondary P fertilizer markets: Implementation of processing and trading infrastructure for manure and recycled fertilizer (2, 3, 4). Fertilizer demand under diﬀerent strategies The eﬀective application of collected manure as P fertilizer by farms with livestock could reduce mineral P imports by 52%. Trade of surplus manure between neighboring farms could reduce mineral P imports by an additional 22%. A country-wide market for recycled fertilizer from surpluss manure could increase the reduction by up to 89%. An improved treatment of sewage sludge to enhance the plant uptake of P from biosolids could allow the P fertilizer independence. 0 250 500 750 1000 1250 1500 1750 Age of the cow (days) outﬂows | inﬂows 0.08 0.00 -0.06 body growth lactation mass embryo growth manure milk (feed) concentrated (feed) roughage (feed) total feed PRETTY COOL: DYNAMIC MFA OF INDIVIDUAL ANIMALS (here, dairy cow) kg P Feel free to ask! :)


0 0.5 1 TINnorm -20 -15 -10 -5 0 5 10 15 20 dbar shallower than peak dT/dz Jul-Sep Midl Shelf Composite TIN norm rel to peak dT/dz -0.2 -0.1 0 0.1 0.2 mmol N m-3 d-1 -20 -15 -10 -5 0 5 10 15 20 0 10 20 30 40 50 60 70 80 90 100 Days Since 1 July 0 5 10 15 20 25 30 35 TINdeep [ mol l-1] Deep (>50 dbar) TIN concentrations, SE Middle Shelf Jul-Sep • Researchers at NOAA PMEL and AFSC are currently working on a compendium of CTD (1974- present) and nutrient (2001- present) data based on NOAA sampling in Alaska waters. • This will include EcoFOCI and predecessor programs at PMEL, along with data from the BASIS program at AFSC. • Here, we show an example application: investigating the nutricline on the SE Bering Sea middle shelf. • A strong thermocline there is a consistent feature in summer. • The compendium data are used to demonstrate the composite structure relative to this thermocline, post-spring bloom. • We use total inorganic nitrogen TIN = NO3+NO2+NH4 to characterize the nutricline (Lomas et al. 2012). Data are referenced to the thermocline in each profile. • Composites at left are based on 991 casts in 18 years (2003-2020) of sampling on middle shelf in July-Sept (red). • E Bering Shelf is among most densely sampled areas for nutrients in the compendium. • Coverage extends into Chukchi (not shown) and Gulf of Alaska (partially shown). • Observed subsurface chl maxima – e.g., shown here at M2 site (green, above) in 2019 sampled by prawler instrument (Nielsen et al., 2023) – are often also coincident with or just above thermocline. • Confirmed in composite (right) of data in vertical coordinates relative to thermocline. Compare with profile of convergence of turb. flux at left. Conditions at M2 site in 2019 Bloom Thermocline Convergence of vertical turbulent flux, assuming constant Kz applied to composite • Composite deep concentrations (right) increase with day of year. • Suggests that replenishment due to biogeochemical processes in lower layer outpaces upward mixing. • Though, likely some geographic variability on the middle shelf that needs to be more fully accounted for in sampling. Data Compilation An Example Summer The Composite Deep Layer The Composite Nutricline Composite Fitted Data Composite Fitted (descriptive) • The composite nutricline in these profiles is almost exactly centered on depth of peak dT/dz. • Here TINnorm = TIN / TINdeep (avg of bottles ≥50 dbar in each profile). • The mean summer profile implies nutrients are being supplied to upper half of nutricline. And, being depleted in lower half. • ~0.5 mmol N per day total supplied to a 5-meter region in upper nitricline, if Kz ~ 10-5 m2 s-1 and is constant, and TINdeep ~ 15 micromol kg-1 • Results support the common assumptions that thermocline and nutricline are coincident, and that nutrients are often depleted in surface layer, and imply a vertical structure of nutrient supply under certain conditions/assumptions. Data are to be described in: Mordy C, Pelland N, Stabeno P, Bell S, Cheng W, Eisner L, Farley E, Gann J, Hermann A, Nielsen J, Proctor P, Wisegarver E. A fifty-year compendium of hydrographic data in Alaska waters by the U.S. National Oceanic and Atmospheric Administration. Data manuscript in preparation. Other references: Nielsen J, Pelland N, Bell S, Lomas M, Eisner L, Stabeno P, Harpold C, Stalin S, Mordy C (2023) Seasonal Dynamics of Primary Production in the Southeastern Bering Sea Assessed Using Continuous Temporal and Vertical Dissolved Oxygen and Chlorophyll-a Measurements. JGR: Oceans, 128, e2022JC01907. Lomas M, Moran S, Casey J, Bell D, Tiahlo M, Whitefield J, et al. (2012). Spatial and seasonal variability of primary production on the eastern Bering Sea shelf. DSR-II, 65–70, 126–140 The composite southeast Bering Sea shelf nutricline, within a multi-decade compendium of NOAA Alaska hydrography Noel Pelland1,3, Jens Nielsen1,3, Calvin Mordy1,2, Phyllis Stabeno2, Shaun Bell2, Wei Cheng1,2, Al Hermann1,2, Lisa Eisner3, Jeanette Gann3 1.


Empowering disease knowledge representation with the Disease Ontology Knowledgebase (DO-KB) J. Allen Baron, Mike Schor, Claudia Sanchez-Beato Johnson, Lynn Schriml Institute for Genome Sciences, University of Maryland School of Medicine. Let’s talk: allenbaron@som.umaryland.edu ... or msg me on the conf app! A Global Core Biodata Resource As a recognized Global Core Biodata Resource (GCBR) the Human Disease Ontology Knowledgebase is: “[O]f fundamental importance to the wider biological and life sciences community and the long term preservation of biological data.” The DO-KB and ~ 400 biomedical resources & databases are powered by the disease data and relationships in the Human Disease Ontology (DO), including many of the genomic databases at TAGC. The Disease Ontology Knowledgebase: Tools powered by data from the Human Disease See how the Alliance of Genome Resources uses the DO to organize links from alleles, genes, and models to diseases. Example: DOID:0050117 disease by infectious agent Other biomedical and genomic resources that use the DO include Reactome, CIViC and the Common Fund Data Ecosystem, along with a number of the Common Fund programs it collects data from. The DO is used for research in a variety of fields. The number publications citing a DO publication by field are shown. Courtesy lens.org. doi:10.6084/m9.figshare.25320946 TAGC disease presentations -- What could have been... Want to find all the presentations at TAGC 2024 related to neurodegenerative disease without searching for each individually? Tagging presentations with diseases from the Disease Ontology could have made that possible, as this figure shows. A larger version of this figure with presentation program numbers colored by type (poster, talk, etc.) is available on figshare to make it easier to find TAGC24 presentations by disease. Dashed lines represent simplified relationships (intermediate diseases removed). 567T - Homology and Disease curation at Saccharomyces Genome Database: Budding yeast as a model for eukaryotic biology - Stacia R Engel, et al 594F - Xenbase: latest support for genomics and disease models - Malcolm Fisher, et al Alliance presentations with the DO NIH/NHGRI U24-HG012557 NIH/NHGRI U41-HG008735 Funded by FAIR & TRUST For a detailed look at how the DO makes data FAIR-er and is managed to ensure TRUST, check out our recent poster from Rare Disease Day at NIH. doi: 10.6084/m9.figshare.25292731 Using the SPARQL query language and the DO Sandbox or endpoint it’s possible to query diffuse data across the web. Data can be pulled to or from the DO. For example, add synonyms from MeSH to the DO, hierarchically organize the disease- linked proteins in UniProt, and more. disease-ontology.org OBO & OWL Tree Browsers with (Advanced) Search DO-KB SPARQL Sandbox & Endpoint DO-KB Faceted Search Interface DO-KB SPARQL sandbox: https://disease-ontology.org/do-kb/sparql DO-KB SPARQL endpoint: https://sparql.disease-ontology.org/ SPARQL info: https://www.w3.org/TR/sparql11-query/ The browser and basic or advanced searches can be used to look up information. The OBO tree is limited to diseases, while the OWL tree includes semantically-linked terms from other ontologies. The tree selected affects basic search results. The Human Disease Ontology (DO) is an expertly curated, etiological disease classification written in OWL/RDF (Web Ontology Language). The DO has 37,000 vocabulary mappings to authoritative biomedical resources (OMIM, Orphanet, etc.) and semantically integrates disease features like inheritance, phenotypes, chemical and environmental drivers, anatomy, and infectious agents. The Human Disease Ontology Knowledgebase (DO-KB) comprises the data in the DO and the tools at disease-ontology.org that make that data easier to search or expand interoperability. Think simple! All eye diseases that involve inflammation... yep! This is just one more possible application of the DO. Enjoy the conference!


Relativistic effects in HgTe and CdTe electronic structure C. D. Hinostroza and P. H. Rivera cristhian.hinostroza2@unmsm.edu.pe priverar@unmsm.edu.pe ABSTRACT Quantum spin Hall phase, or also referred as Topological Insulator state, has been obtai- ned in 2007 in a CdTe/HgTe quantum well. These novel state is possible due to the in- verted band order near the Fermi energy, for the HgTe. These behaviour is originated becau- se there exist a non negligible correlation bet- ween valence electrons of the 5d- and 6s-orbital of Hg, and relativistic effects, speciﬁcally spin- orbit coupling. In this work, we present the electronic struc- ture of Cadmiun Telluride (CdTe) and Mercury Teluride (HgTe), obtained using the local spin density approximation, including the Hubbard correction (LSDA+U), in the density functional theory (DFT), considering non relativistic, rela- tivistic, and relativistic with spin-orbit coupling effects for each alloy. The results show that re- lativistic effects reduce the band gap for both alloys, and inverted band ordering for HgTe is only possibe if spin-orbit copupling is conside- red. THEORY Density functional theory is a method used to solve the many body problem based on the Hohemberg and Kohm theorems. Thus, the ob- servables could be calculates as a functional of the ground state energy electronic density, wich is obtained calculating the density that mini- mizes the energy expresion derived from the Kohn-Sham equation: E = N X i ϵi −EH[ρ] + Exc[ρ] − Z δExc[ρ] δρ(r) ρ(r)dr Where ϵi is related to the kinetic Kohn-Sham energy, EH to the Hartree energy, and Exc is the exchane and correlation nergy, wisch is consi- dered using the LDA approximation, as presen- ted by Perdew and Wang: EXC[n↑, n↓] = Z d3rn(r)ϵhom XC (n↑, n↓) Some systems need to consider a correction in the correlation function due to strong inter- action between electrons. This is achieved ad- ding the Hubbard correction in the LDA energy function. ELDA+U[n(r)] = ELDA[n]+EHub[nσ mm′]−Edc[nσ] Where Edc is the double counting term: Edc[nIσ mm′] = X Iσ U I 2 Tr[nIσ(1 −nIσ)] The relativistic solution is calculated using the Zero order regular aproximation: HZORA = V +p c2 2c2 −V p+ c2 (2c2 −V )2 σ·(∇V ×p) PROCEEDINGS Cadmium and Mercury Telluride are both II- VI type semiconductors. These materials have a Zinc Blende structure with lattice parameter a = 6,46Åand a = 6,48Åfor CdTe and HgTe repec- tively. Both semiconductors below to the F¯43m space group, with group number 216. Wich co- rrespond to two FCC displaced by ( 1 4, 1 4, 1 4) each other. We used the DFT method to get the band structure aplying the LAPW basis as implemen- ted in the package Exciting code. The Ex- change and Correlation energy considered was the LDA as presented by Perdew and Zhang icn- luding the Hubbard correction, and the relativis- tic effects where obtained with the Zero Order Regular Approximation of the Dirac Hamilto- nian. To appreciate the effects of relativistic con- siderations we performed calculations without any relativistic terms, with relativistic terms but without spin-orbit coupling, and within relati- vistic terms considering spin-orbit coupling. RESULTS Non relativistic L Γ X -2 -1 0 1 2 Energy (eV) Cd s L Γ X EF Te p L Γ X -2 -1 0 1 2 Energy (eV) Hg s L Γ X EF Te p Relativistic without s · L L Γ X -2 -1 0 1 2 Energy (eV) Cd s L Γ X EF Te p L Γ X -2 -1 0 1 2 Energy (eV) Hg s L Γ X EF Te p Relativistic considering s · L L Γ X -2 -1 0 1 2 Energy (eV) Cd s L Γ X EF Te p L Γ X -2 -1 0 1 2 Energy (eV) Hg s L Γ X EF Te p CONCLUSIONS From our calculations, we observe that the- re is a dependece between spin-orbit coupling and band ordering, obtained only if electron co- rrelation is considered. Relativistic effects chan- ges the band structure in a non neglible way, reducing the band gap from 3.07 and 2.87 eV to 1.05 and -0.104 eV for CdTe and HgTe res- pectively, also invreasin the velocity of charge carriers at Γ point. There must exist a value x for HgxC


The diverse history of counter-rotating galaxies Tjitske K. Starkenburg1, Laura V. Sales2, Shy Genel1,3, Christina Manzano-King2, Gabriela Canalizo2 1Center for Computational Astrophysics, the Flatiron Institute, 2University of California Riverside, 3Columbia University Introduction Galaxies containing significant counter-rotating components are particularly interesting as it can provide additional dynamical constraints (i.e. polar ring galaxies: Schweizer et al 1983; Athanassoula & Bosma 1985; Sackett & Sparke 1990) and hold clues to evolutionary history and past environment (e.g. Cappellari 2016). However, while isolated simulations have shown that mergers and smooth accretion onto gas-poor galaxies can form galaxies with counterrotating components (Thakar & Ryden 1996, Puerari & Pfenniger 2001, Algorry et al. 2014) the statistical occurrence and completeness of these origins are not clear. Moreover, there is no general prediction of the occurrence and properties of these galaxies within the cosmological framework. This poster is a first step towards a study of these issues using the Illustris cosmological simulation (Vogelsberger et al. 2014; Genel et al. 2014). We focus on the evolutionary history of 1 disky sub-L* galaxy that shows extremely clear gas disk - stellar disk counterrotation. This specific galaxies is selected as an analogue to an observational sample of counterroting dwarf galaxies carried on with Keck. Abstract Galaxies with counter-rotating gas or stars are particularly interesting. Their distinct kinematical components can provide additional dynamical constraints and possible clues to evolutionary history and past environment. These intriguing systems have since long been observed, but have rarely been studied collectively. We present a study of their occurrence, properties, and evolutionary history using the Illustris cosmological simulation. In this poster we focus in detail on the surprising evolutionary history of 1 disky sub-L* galaxy that shows clear gas disk - stellar disk counterrotation. The counter-rotation in this system is due to the system being a splashback satellite that re-accretes material. We thus show that the origin of significant counter-rotation in low mass galaxies can be diverse and unexpected. Figure 1.1: Face-on (top four panels) and edge-on (bottom four panels) of the stellar disk (left) and the gaseous disk (right) defined by the total angular momentum of the stars within 2 stellar half mass radii, where the top and third row show the projected surface density and the second and bottom row show the line-of- sight velocity. The bottom row shows clearly the opposite direction of rotation for the stellar disk and the (inclined) gaseous disk. Section 1: a counterrotating galaxy The galaxy used as an example for this poster shows clear counterrotation. The angle between the total angular momentum of the stars and the gas disks is 131 degrees, and the stellar and gaseous projected surface densities and velocities (face-on and edge-on with respect to the stellar disk) in Figure 1.1 show that the complete gas disk actually is inclined with respect to the stellar disk (by 131 degrees). Even though the stellar disk is very thick, the rotation in the stellar disk is significant. Figure 1.2 shows simple mock observational rotation curves (red: stars; blue: gas), measured assuming a slit that includes all gas and stars along the line-of- sight, with the galaxy perfectly edge-on, within a vertical distance of 1 kpc above and below the plane of the stellar disk. The points and error bars indicate the mean and standard deviation of all material along the line-of-sight. The gas and stellar velocities in this plane are similar in magnitude but exactly opposite in sign. Figure 2.1: Evolution of the angle of the total angular momentum vector of the stars and the gas within the galaxy and the gas in the halo with respect to the total angular momentum vector of the stars at the present day. The direc


TERMOGRAFIA INFRAVERMELHA MÉDICA NA DIÁFISE DISTAL DA TÍBIA EM PACIENTE COM DIAGNÓSTICO DE PSEUDOARTROSE - ESTUDO DE CASO Wally auf der Strasse1, Daniel Padro Campos1, Celso Junio Aguiar Mendonça1, Jamil Faissal Soni2, Percy Nohama1,2 1 Universidade Tecnológica Federal do Paraná, Programa de Pós-Graduação em Engenharia Elétrica e Informática Industrial 2 Pontifícia Universidade Católica do Paraná, Programa de Pós-Graduação em Tecnologia em Saúde 1. INTRODUÇÃO 2. OBJETIVO Investigar alterações no padrão térmico na fratura da tíbia com diagnóstico de pseudoartrose com o uso do fixador externo Ilisarov 4. CONCLUSÃO Pseudoartrose não consolidação de uma fratura processo de reparação óssea deixou de atuar Não uniões ósseas complicações de saúde expressiva diminuição da qualidade de vida aumento nos custos dos serviços de saúde Termografia alternativa de diagnóstico imediato na evolução clínica do paciente com pseudoartrose 3. MÉTODO Setup experimental Temperatura média da região de interesse na diáfise distal da tíbia entre os anéis do fixador Ilisarov. Gráfico de dispersão da temperatura média na diáfise distal da tíbia entre os anéis do fixador Ilisarov. Os resultados preliminares indicam Termografia como método promissor de diagnóstico em traumatologia e ortopedia Necessidade de aplicação do método em um grupo amostral maior de pessoas com diagnóstico de pseudoartrose de tíbia e uso de fixador externo Ilisarov


A Cross-Institutional, FAIR VIVO for Metabolomics Michael Conlon, Kevin S. Hanson, Taeber Rapczak, Naomi Braun, Christopher P. Barnes, University of Florida, Gainesville, Florida, USA Metabolomics Data The Metabolomics Workbench (MWB) (https://metabolomicsworkbench.org) is the National Metabolomics Data Repository of the US National Institutes of Health (NIH). Anyone can deposit data to the MWB. As of August 28, 2019, the workbench provides data from 982 publicly available studies. Another 205 studies are currently embargoed and will be available subject to their embargo dates. MWB develops and uses RefMet (http://bit.ly/2PkxY5p), a nomenclature for representing metabolites found using mass spectroscopy (MS) and nuclear magnetic resonance (NMR) techniques. Investigators upload study data to the workbench and provide metadata regarding themselves and their work. The MWB provides an API that can be used to access metadata about studies and investigators. MWB metadata has been mapped to an ontology developed by the authors to represent it as RDF and load it to VIVO. PubMed (http://pubmed.gov) is an open access index to literature in metabolomics. Its API can be used to find and retrieve publication data regarding metabolomics investigators. Many groups use PubMed data in VIVO. PubMed data has been mapped to the VIVO Ontology (http://vivoweb.org/ontology/core) Data regarding software used in metabolomics studies has been difficult to find. An index to such software will be created and curated by a group at the University of Colorado Anschutz Medical Campus funded by the NIH. This data will be in the form of a spreadsheet. The authors will use the Software Ontology (SWO) (http://www.obofoundry.org/ontology/swo.html) to represent the data as RDF and load the data into VIVO. Metabolomics Metabolomics is the scientific study of metabolites present within an organism, cell, or tissue. Human metabolites are small molecules found in human tissue that occur naturally as a result of human metabolism, or are present as a result of drugs, food components, or exposure to environmental conditions. Along with genomics (the study of DNA), transcriptomics (RNA), proteomics (proteins), metabolomics provides information regarding biochemical compounds and processes in cells, leading to a better understanding of cellular biology. “Metabolic profiling can give an instantaneous snapshot of the physiology of a cell, and thus, metabolomics provides a direct "functional readout of the physiological state" of an organism.” (Wikipedia http://bit.ly/2Pg06X3) Such profiles can be used to distinguish tissue types, disease states, and health status of individuals. Understanding the changes in profiles over time can lead to improved understanding of diseases such as cancer and diabetes, leading to potential treatments. Over 450,000 human metabolites have been identified to date. Metabolomics is considered an emerging field. Technical challenges in compound identification and data analysis are significant. The NIH Common Fund Metabolomics consortium originated in 2013 to help address these and other challenges. Fourteen investigators across the US are supported to advance metabolomics. Five are engaged in compound identification, seven in software tools and data analysis. The group at UCSD supports the Metabolomics Workbench, a data repository. The group at the University of Florida provides overall coordination for the consortium. FAIR Data Principles The FAIR Data Principles (Wilkinson, et. al https://www.nature.com/articles/sdata201618) provide a framework for creating data that can be used by groups beyond the group that created the data. The principles are difficult to achieve in practice and much has been written about implementation. VIVO supports the principles naturally, it is designed to share data. • Findable – data should be found using search engines on the Internet • Accessible – the data can be accessed without technical, legal or operational barr


Fossil Record – the palaeontological journal of the Museum für Naturkunde Berlin Constanze Bickelmann1, Stefanie Paß1, Florian Witzmann1, Xenia van Edig2, Jana Hoﬀmann1, and Johannes Müller1 1Museum für Naturkunde – Leibniz-Institut für Evolutions- und Biodiversitätsforschung Invalidenstrasse 43, 10115 Berlin 2Copernicus Publications (Copernicus GmbH), Bahnhofsallee 1e, 37081 Göttingen The Journal Fossil Record is one of three journals issued by the Museum für Naturkunde Berlin (Fig. 1). It handles palaeontological science, spanning such ﬁelds as taxonomy and systematics, biostratigraphy and biogeochemistry, palaeoecology, evolution and earth history. All taxonomic groups are covered, including vertebrates, invertebrates, plants, and microfossils. Fossil Record was founded in 1998 under the name „Mitteilungen aus dem Museum für Naturkunde in Berlin, Geowissenschaftliche Reihe“ by Prof. Hans-Peter Schultze. In 2009, the journal became ISI-listed. Since 2014, simultaneously with publication by Copernicus Publications, it has been open access, and increased its impact factor up to 1,250 in 2016. As an online open-access journal, Fossil Record closes the gap between the requirements of scientists, funders, and libraries for open access to scientiﬁc publications. Besides enjoying better visibility, scientiﬁc papers are thus much more widely distributed and available for scientiﬁc databases. We welcome international contributions dealing with fossil specimens and collections, as well as research on pa- laeobiological processes and patterns using common and innovative analytical methods. Fossil Record enjoys an internationally good reputation, resulting in submission of excellent manuscripts from all over the world (Fig. 2). We oﬀer a peer-review process with at least two independent reviews. Since 2006, Fossil Record has appea- red with two issues each year. In addition, special issues are printed on chief editors’ demand. Advantageously, comprehensive manuscripts such as (doctoral) monographs are also printed (Fig. 3). We provide opportunity for high quality illustrations (Fig. 4). Article processing charges (APCs) covering costs for the review process, ty- pe-setting, web publication and long term archiving upon publication are currently not requested from authors, instead covered by the Museum für Naturkunde. However, diﬀerent models for author contributions are current- ly evaluated and may be introduced at a later stage. Manuscripts can be uploaded on the Fossil Record website (https://www.fossil-record.net/). The Editor The Museum für Naturkunde is an integrated research museum and since 2009, the museum has been a member of the Leibniz Association, which is a non-proﬁt organization combining and promoting world-renowned research institutions. The Museum für Naturkunde conducts excellent research in biology and earth sciences. Speciﬁcally, we study the geo- logical and biological evolution and diversity of life, and transfer this knowledge to the international scientiﬁc community as well as the public. To date, our collections, comprising over 30 million zoological, palaeontological, geological and mi- neralogical specimens, are of unique cultural, historical, and scientiﬁc value inextricably linked to our research (Fig. 5). In order to provide as much free access to knowledge as possible we aim to develop an open-access strategy, oﬀering open-access advisory services to our researchers. This process is part of the science programme “Digital World and Infor- mation Science”, which combines information and communication technology, biodiversity informatics, and library and information sciences at the museum. The Publisher Copernicus Publications is a German open-access publisher based in Göttingen. It has been a partner of scientists and socie- ties since 1988 and launched its ﬁrst open-access journal in 2001. Since 2004, all journals have been open access. With a clear focus on in-house services, Copernicus Publications promot