RESEARCH POSTER PRESENTATION DESIGN © 2015 www.PosterPresentations.com Studied areas in coastal zone for SST and the preparation of the TRISHNA mission: The Mediterranean sea along the coast from the Bay of Banyuls/Mer up to Marseille : → Submesoscale processes (~ 1-10km) (link with the SWOT mission) up to the scale of mixing/dissipation (100 m-1km): → Diurnal cycle, mixing after a wind event, river discharge and plumes, groundwater discharges especially around the in situ observations for the SST: moorings (LF/HF) examples: in the Bay of Banyuls/Mer (this poster), lagoons • Côte Sud-Nord avec un canyon → difference (Airborne SST/Landsat SST – HF in situ SST) = - 0.5°C (POEM Station) And = -1°C (SOLA Station) → Difference (satellite SST at 9:20am – Airborne SST at 10am) = - 0.1°C Laboratoire d’Etudes en Géophysique et Océanographie Spatiales – Toulouse – F - France I. Dadou, B. Pagli, M. Kaouah (LEGOS, Toulouse, F)M. Irvine (INRAE, Bordeaux, F) B. Coudert, V. Rivalland (CESBIO, Toulouse, F) R. Villemain, L. Zudaire (LOMIC/OOB, Banyuls/Mer, F) F. Bourrin (CEFREM, Perpignan, F) Sea surface temperature (SST) in coastal ocean with different data: application for the TRISHNA mission Scientific context Scientific context Study thermal infrared signals (TIR) for the determination of sea surface temperature (SST) in the coastal environment (Mediterranean Sea) by different data (airborne, satellite, in situ data, model outputs) and methods, complementary in their spatio-temporal resolutions and coverage in order to prepare the TRISHNA mission (CNES/ISRO - 2025) (algorithm, products and expectations in coastal environment) Main scientific question Main scientific question Studied Area: Mediterranean Sea Studied Area: Mediterranean Sea SST data and models used with different spatial resolution SST data and models used with different spatial resolution Conclusion & perspectives Conclusion & perspectives References References Results Results Berk, A. et al. MODTRAN 5: a reformulated atmospheric band model with auxiliary species and practical multiple scattering options: update. In Proceedings of the Algorithms and Technologies for Multispectral, Hyperspectral, and Ultraspectral Imagery XI ; International Society for Optics and Photonics, 2005; Vol. 5806, pp. 662–667.Estournel, C., Marsaleix, P., & Ulses, C. (2021). A new assessment of the circulation of Atlantic and Intermediate Waters in the Eastern Mediterranean. Progress in Oceanography, 198, 102673. Estournel, C., X. Durrieu de Madron, P. Marsaleix, F. Auclair, C. Julliand, and R. Vehil (2003) Observation and modeling of the winter coastal oceanic circulation in the Gulf of Lion under wind conditions influenced by the continental orography, (FETCH experiment), J. Geophys. Res., 108(C3), 8059, doi:10.1029/2001JC000825, 2003 Feuilloley G. , Fromentin J-M, Stemmann L., Demarcq H, Estournel C, Saraux C. (2006), Concomitant changes in the environment and small pelagic fish community of the Gulf of Lions, Progress in Oceanography, Volume 186, 2020 Gatti, J., Petrenko, A., Devenon, J. L., Leredde, Y., & Ulses, C. (2006). The Rhone river dilution zone present in the northeastern shelf of the Gulf of Lion in December 2003. Continental Shelf Research, 26(15), 1794-1805. Lagouarde, J.-P., M. Bach, J.A. Sobrino, G. Boulet, X. Briottet, S. Cherchali, B. Coudert, I. Dadou, G. Dedieu, P. Gamet, O. Hagolle, F. Jacob, F. Nerry, A. Olioso, C. Ottlé, (2013). The MISTIGRI thermal infrared project: scientific objectives and mission specifications. International Journal of Remote Sensing. Volume 34, Issue 9-10, pages 3437-3466 O’Carroll, A. G., Armstrong, E. M., Beggs, H. M., Bouali, M., Casey, K. S., Corlett, G. K., ... & Wimmer, W. (2019). Observational needs of sea surface temperature. Frontiers in Marine Science, 6, 420. Schaeffer, A., Garreau, P., Molcard, A., Fraunié, P., & Seity, Y. (2011). Influence of high-resolution wind forcing on hydrodynamic modeling of the Gulf of Lions. Ocean Dynamics, 61(11)


Introduction Chronic hepatitis B infection (CHB) has diverse disease phenotypes, ranging from minimal hepatic fibrosis, to cirrhosis and hepatocellular carcinoma (HCC)1. Serum viral markers are currently measured to inform clinical management, however none directly detect the covalently closed circular DNA (cccDNA) hepatocyte reservoir. Serum hepatitis B core related antigen (HBcrAg) has been correlated with cccDNA levels, and may predict HCC development2,3, but most studies are from Asia where genotypes B and C predominate4-6, so wider utility of HBcrAg is unknown. Serum Hepatitis B core-related antigen in a diverse UK cohort of patients with Chronic Hepatitis B infection Louise O Downs1,2, Tingyan Wang1,3, Marion Delphin4, Elizabeth Waddilove4, Monique Andersson2, Geoffrey Dusheiko5, Kosh Agarwal5, Eleanor Barnes1,2 Ivana Carey5, and Philippa C Matthews1,4,6,7 1 Nuffield Department of Medicine, University of Oxford, UK, 2 Department of Infectious Diseases and Microbiology, John Radcliffe Hospital, Oxford, UK, 3 NIHR Oxford Biomedical Research Centre, University of Oxford, UK, 4 The Francis Crick Institute, London, UK, 5 Institute of Liver Studies, King’s College Hospital, London, UK, 6 Division of Infection and Immunity, University College London, UK, 7 Department of Infectious Diseases, University College London Hospital, London, UK Contact Informations: Louise Downs: louise.downs@exeter.ox.ac.uk @lou_downs Philippa Matthews: philippa.matthews@crick.ac.uk @pippa_matt References 1 GBD 2019 Hepatitis B Collaborators, 2022 (PMID: 35738290) 2 Testoni et al, 2019 (PMID:30529504) 3 Carey et al, 2020 (PMID: 31701544) 4 Tada et al, 2018 (PMID: 28914957) 5 Tada et al, 2016 (PMID: 27034253) 6 Shimakawa et al, 2020 (PMID: 31102406) Aims We measured HBcrAg in a cross-sectional cohort of 143 ethnically diverse adults with CHB from a UK teaching hospital to understand how HBcrAg varies or is associated with: Patient demographics. Liver disease. Treatment Its use as a surrogate HBV DNA marker will also be investigated and whether this applies in all subgroups. Methods Clinical Metadata Patient data were collected in outpatient clinics and from Oxford University Hospitals Electronic Patient Records (EPR). 143 patients infected with HBV enrolled in the Oxford University Hospitals NHS Foundation with broad Viral Loads (VL). Participants provided written informed consent. Serum samples Liver Biomarkers (Alanine Transferase - ALT) HBV Biomarkers (HBeAg, HBsAg, VL) HBcrAg: chemiluminescent assay (Lumipulse G HBcrAg assay, Fujirebo) Statistical analysis was conducted in R (version 4.1.1) using the ‘ggplot2’ package (version 3.3.6). Correlations were all done using Pearson’s coefficient. Acknowledgments: Oxford University Hospitals laboratories NIHR Health Informatics Collaborative Kinga A Várnai and Oliver Freeman Results Figure 1: HBcrAg correlation with patients metadata HBcrAg was significantly correlated with HBsAg (A-B) and HBV DNA levels (D-E), however this was lost with HBeAg negativity (C,F). HBcrAg was still detected in those with undetectable HBV DNA. HBcrAg did not correlate with ethnicity (A), biological sex (B) or treatment (C) but is positively correlated with serum ALT (D) and decline significantly with age (E). 2 4 6 8 0 100 200 300 ALT (IU/L) HBcrAg (U/mL) 2 4 6 8 20 40 60 Age (years) HBcrAg (U/mL) E D 2 4 6 8 Arab Asian Black African Chinese European Other Asian Unknown HBcrAg (U/ml) A Ethnic group 2 4 6 8 Female Male HBcrAg (U/ml) B Biological Sex Figure 2: HBcrAg correlation with viral parameters in patients 4 6 8 0 2000 4000 HBsAg (IU/ml) HBeAg positive patients B 2 3 4 5 0 2000 4000 6000 HBeAg negative patients C A 2 4 6 8 0.0 2.5 5.0 7.5 HBcrAg (U/mL) All Patients D 4 6 8 0.0 2.5 5.0 7.5 HBV DNA (log IU/mL) HBeAg positive patients E 2 3 4 5 0 2 4 HBeAg negative patients F HBcrAg (U/mL) All Patients 2 4 6 8 No Yes HBcrAg (U/ml) Treatment status C 0.0 2.5 5.0 7.5 0 2000 4000 6000 R = - 0.19 p = 0.023 R = - 0.42 p = 0.047 R =


hhu.de Cyanobacteria as platform organisms for biotechnology Cyanobacteria are photoautotrophic bacteria capable of photosynthesis and high rates of CO2 fixation. Their metabolic potential makes them promising candidates for biotechnological production of industrially relevant compounds such as plant secondary metabolites. Valencene - an important aroma and more Valencene is a sesquiterpene that can be found in many citrus fruits. While it can be used in various applications in industry, including cosmetics and flavor, it also serves as a precursor for nootkatone, which has been shown to act as a powerful insect repellant, but can also inhibit growth of cancer cells. ValenCell: Large-scale production of sesquiterpenes from microalgae Anna Behle1, Ilka Axmann1, Lars Bähr2, Arne Wüstenberg2 CO2BioTech Kick-Off Meeting Lars Bähr (CellDEG) Anna Behle (HHU) Heinrich-Heine-Universität Düsseldorf Institute for Synthetic Microbiology 1 Institute for Synthetic Microbiology, HHU Düsseldorf; 2 CellDEG GmbH Berlin synmikrobiologie.hhu.de CO2 CO2 CO2 NADPH Valencene A WP1: Engineering the bacterial metabolism We previously showed that increasing metabolic flux through the terpenoid biosynthesis pathway had positive effects on strain productivity. Since sesquiterpene production competes with pigment biosynthesis, it is important to supply the cell with sufficient precursor molecules, as well as cofactors. We were able to achieve, rerouting carbon supply from pigment biosynthesis towards product formation with inducible systems1. We aim to build a stable production strain without costly inducers using the following strategies. Titration of expression strength by testing multiple genetic cassettes Testing different sesquiterpene synthases Variation of cultivation conditions Reinforcement of carbon and cofactor supply by rerouting the metabolism (Fig. 1) WP3: Scaling up with CellDEG One main challenge when scaling up the cultivation volume of cyanobacterial strains is ensuring a sufficient availability of nutrients such as light and CO2. The CellDEG technology is specifically designed to enable fast growth of photoautotrophic organisms to a high cell density (Fig. 2B). To identify strains that perform best in such reactors, promising strains will be screened in HD10 reactors early on. Upscaling of the best production strains will take place in the HD1500 production platform (Fig. 2A). The final aim of this project is to achieve a strain with a growth rate of 2.5 g DCW/L/day while maintaining a production rate of 200 mg valencene / g DCW. WP2: Alternative extraction methods Valencene, along with many sesqui- and monoterpenes, is a volatile compound. This is especially advantageous for downstream processing, as it eliminates the need for expensive and time- consuming extraction from the biomass. The current state-of-the-art for quantification of valencene production makes use of a thin layer of dodecane on top of the culture, which captures the volatile product (Fig. 2C). This is favorable for analysis, as dodecane can be analyzed via GC/MS directly. In terms of cost, scalability and sustainability it is of high interest to find alternative extraction- or capturing methods for valencene. A B C Figure 1: Relevant metabolic pathways in the cyanobacterium Synechocystis sp. PCC 6803. Relevant genes for overexpression or deletion are boxed. Involvement of ATP and NADPH is shown in red and blue, respectively. Figure 2 A. From left to right: HD10, HD100, HD1500 reactor setup. B. Growth curves of Synechocystis sp. PCC 6803 WT in the three different reactors. C. Schematic setup for growth of production strains to high cell densities using the HD10 screening platform (image modified from2 Scientific reports, 10(1), 5932 https://doi.org/10.1038/s41598-020-62681-w) 1 OD₇₅₀ = 0,322 gDW L⁻¹     1Dietsch, Behle et al.: Metabolic engineering of Synechocystis sp. PCC 6803 for the photoproduction of the sesquiterpene valencene. Metab. Eng. Commun. 2021 Aug 13


U.S. Environmental Protection Agency Office of Research and Development Building an Adverse Outcome Pathway Framework through HTS Data and Literature Mining Integration Nancy C. Baker1, Nisha S. Sipes2, M. Shane Hutson3, Thomas B. Knudsen2 1Lockheed Martin, RTP, NC, 2U.S. EPA, ORD, National Center for Computational Toxicology, 3Departments of Physics and Biological Sciences, Vanderbilt University, Nashville, TN Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Footnotes Go Here Overview Literature Data Nancy Baker l baker.nancy@epa.gov l 919-541-2680 Interpreting EPA’s ToxCast in vitro assay data in the context of Adverse Outcome Pathway (AOP) development is a significant challenge. While chemical activation in these assays may shed light on the molecular initiating event, it can be difficult to identify the downstream effect of these activities at higher levels of biological organization (e.g., cellular, tissue, organ) that could potentially lead to a toxicity endpoint. In this research, we explore applications of literature mining techniques that can be readily used to build and evaluate an AOP framework from in vitro data. We use cleft palate as a prototype and focus on the ToxCast assay targets that were found to have a significant univariate association with cleft palate / cleft lip (CLP) in ToxRefDB and the literature. DISCLAIMER: does not reflect EPA policy Proteins Chemicals Effects 51 million annotations 24 million annotations 18 million annotations >22 million articles A connection Analyze the EPA’s ToxCast HTS dataset containing > 1,000 unique chemicals tested across >500 in vitro assays to identify the assays with the most significant univariate association with chemicals that cause cleft palate or cleft lip. Find the literature connections between ToxCast targets and cell-level activity/entities and tissue-level activity and entities. Connections are defined as an article co-annotation between a target protein and the cell/tissue entity. Strategy Target Tissue Level CLP Organ Cell Level Option 1. Binary relationships Option 2. Expand relationships Option 3. Bidirectional relationships Results Target Tissue Level CLP Organ Cell Level ToxCast: 56 chemicals in the ToxCast libraries were identified as CLP actives by reviewing data in ToxRefDB and the biomedical literature. A statistical analysis of the assay data identified 29 assays that correlated significantly with the CLP endpoints. (Student’s T-test (p<=0.05)) A subset of those assays with the corresponding Medical Subject Heading (MeSH) term for the target protein is found in Table 1. These statistical correlations represent potential molecular targets that have been assayed in the ToxCast portfolio and serve as a potential entry point for AOPs leading to a cleft palate/cleft lip phenotype in pregnant rats and/or rabbits. Literature: The search of EPA’s biomedical literature database using the term Cleft Palate retrieved 36 unique tissue MeSH terms, 37 cell types, 34 cellular processes, and 54 non-cellular processes. Co-annotations of these tissue or cell types and any of the MeSH terms for the ToxCast targets (Table 1) were also retrieved. The articles were counted and the results output to the database and extracted (with hyperlinks) into the spreadsheets show below. Observations deduced from the subject categories serve as a starting point to fill in the biological space between the assays and the endpoint based on what is known in the literature. Target Cell Level Tissue Level Tissue Level Tissue Level Tissue Level CLP Organ CLP Organ CLP Organ Organ CLP Organ CLP Organ Organ AOP Framework: Table 1. Selected assays with significant univariate association with cleft lip / cleft palate; Blue: nuclear receptors; Gray: GPCRs; Green: other ToxCast Assay Target - selected MeSH term NVS_ENZ_oCOX1 Cyclooxygenase 1 NVS_ENZ_hElastase Leukoc


There is increasing recognition of the scope of cultural change needed to realize the European vision for Open Science policy. Key challenges include contemporary modes of recognition and reward that are out of step with principles of open science[1] and identi@ication of numerous disincentives, at the individual level, regarding adoption of new openness practices[2]. These obstacles raise questions about implementation of top-down policy in general, and the European Commission's open science policy in particular. (mock-up) x-xxxx-xxxx-xxxx Contributor Contributions, Open Scholarship •————— •——- •————— •———— •————— •————— Openness Proﬁle (individual) Openness Proﬁle (group) Contributor x-xxxx-xxxx-xxxx Repository, (e.g. Zenodo or RAiD) individual group Research and Innovation – a vision for Europe Open Innovation Open Science Open to the World In what ways is open science policy informed by the science of science? Although evaluation of open science is gaining traction as an important dimension for implementation of open science policy, there is not yet much in the way of empirical analysis. To address this question, we begin with a targeted search in the Web of Science bibliographic database (WoS), which yields three citation networks associated with: open access, open data, and open science[3]. With a combined total of approximately @ive-thousand publication records, published between 1958 and 2018, we then use VOSviewer for analysis and visualization of keyword terms at an aggregate level. Keyword mapping illustrates the relatedness of research topics on the bases of keyword co-occurrence. —> economics of academic publishing —> transparency and accountability —> aﬀordances of digital media and computa8onal resources —> technical integrity of scien8ﬁc processes and outputs —> rapid dissemina8on of medically relevant knowledge In our analysis of the combined keyword datasets, the three queried topics largely retain their individual structures with some interlinking across networks. The keyword map also identi@ies sub-networks that reveal motivating factors associated with the broader openness movement, such as: economics of academic publishing, transparency and accountability, affordances of digital media and computational resources, technical integrity of scienti@ic processes and outputs, and rapid dissemination of medically relevant knowledge. While we identify some common ground between the European notion of open science and the keyword networks, the research topics identi@ied shed light on a more complex relationship between research practice and increased openness. In other words, the European notion of open science appears to draw on particular understandings of the sciences system, characterized by close alignment with economic activity and a clear, albeit linear, view of how science bene;its society. Open science is seen as a natural extension of existing research practices. Missing from this vision is attention to research practices that do not align so easily with economic activity and research @ields that hold a more indirect relationship with society. Within the community of policy makers and advocates of open Science, there is increasing consensus that (a) better recognition and reward of openness practices is a necessary condition for broad adoption of open scholarship, (b) top-down guidance, which is aimed at a wide range of disciplinary practices, will require substantial cultural change to shift the priority of research evaluation toward principles of open scholarship and (c) bottom-up openness initiatives and practices must emerge from local contexts to enable relevant, sustainable change [1, 2]. The Knowledge Exchange working group addressing this issue[4], proposes an Openness Proﬁle for making visible and being recognized for one’s contribu?ons to open scholarship. The aim in this endeavor is to provide complementary, boFom-up resources linked to contemporary Research Informa8on infrastructure. There are


LA CIENCIA ABIERTA EN LA UNIVERSIDAD DE PUERTO RICO OBJETIVO DE LA INVESTIGACIÓN Explorar la apertura y el intercambio de los procesos, herramientas y resultados de investigación en la Universidad de Puerto Rico (UPR), en cuatro dimensiones de la Ciencia Abierta: (I) Acceso abierto (Open Access) (II) Revisión por pares abierta (Open Peer review) (III) Recursos educativos abiertos (Open Educational Resources) (IV) Código Abierto (Open Source) METODOLOGÍA • Estudio inicial de carácter exploratorio y fundamentalmente descriptivo • Fuentes para la recogida de la información: - Política de Acceso Abierto a los resultados de la labor creativa e investigaciones producidas en la Universidad de Puerto Rico (Certificación 113, 2019-2020) - Portal de Revistas Académicas de la Universidad de Puerto Rico - Estadísticas de acceso y uso de los repositorios institucionales de la UPR - Scopus® (Elsevier's abstract and citation database) CONCLUSIONES Los resultados preliminares de este trabajo reflejan que, indudablemente, el movimiento de la ciencia abierta viene impactando notable en las políticas institucionales de la Universidad de Puerto Rico, que en los últimos años ha puesto en marcha distintas iniciativas para favorecer el proceso de apertura e intercambio de sus resultados de investigación. RESULTADOS PRELIMINARES: acceso abierto Dra. Cláudia De Souza claudia.souza@upr.edu Profesora Catedrática Auxiliar Dr. Carlos A. Suárez Balseiro carlos.suarez5@upr.edu Profesor Catedrático Universidad de Puerto Rico, Recinto de Río Piedras (UPRRP) Facultad de Comunicación e Información (FaCI) https://faci.uprrp.edu/ Programa Graduado en Ciencias de la Información 443 436 490 643 592 714 902 906 969 986 1070 974 1001 944 1017 1032 1048 1091 1071 1010 1084 13,32 60,42 0,00 5,00 10,00 15,00 20,00 25,00 30,00 35,00 40,00 45,00 50,00 55,00 60,00 65,00 70,00 75,00 80,00 85,00 90,00 95,00 100,00 0 100 200 300 400 500 600 700 800 900 1000 1100 N. docs UPR % All Open Access 28 revistas editadas o coeditadas en 5 recintos de la UPR Más de 9000 documentos disponibles a texto completo


Summarized findings Two candidate effectors, PM02_g378 and PM02_g2610, localize to the cell periphery while the remaining putative effectors localize to both the nucleus and cell periphery PM02_g1115, PM02_g7882 and PM02_g8240 consistently suppress chitin-dependent ROS production when transiently expressed in N. benthamiana PM02_g1115 suppresses Pseudomonas syringae DC3000-mediated cell death in maize \ Acknowledgments and Funding We thank Dr. Tesfaye Mengiste (Purdue University) for access to the microplate reader for ROS suppression assays, Dr. Rachel Hiles and Dr. Terri Cameron for their technical assistance, and the Purdue University Imaging Facility for access to the Zeiss LSM880 Axio Examiner upright confocal microscope. This research was funded by the USDA-ARS research project 5020-21220-014-00D. USDA is an equal opportunity provider and employer. Candidate effector proteins from from the maize tar spot pathogen Phyllachora maydis suppress immune responses Abigail Rogers1†,Namrata Jaiswal2 †, Emily Roggenkamp3, Hye-Seon Kim4, Joshua S. MacCready3, Martin Chilvers3, Steven R. Scofield2, Anjali Iyer-Pascuzzi1, and Matthew Helm2 * † these authors contributed equally to this work 1 Department of Botany and Plant Pathology, Purdue University West Lafayette, IN 47907, U.S.A. 2 Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), West Lafayette, IN 47907, U.S.A., 3 Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824 4 Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL, U.S.A. * Corresponding author: M. Helm; Email: Matthew.Helm@usda.gov Significance @LabAbbie27 To better understand the molecular mechanisms underlying the P. maydis – maize interaction, we investigated how P. maydis utilizes effectors to induce disease. Leveraging the most recent genome annotation, we identified eighteen candidate virulence (effector) proteins that are expressed during disease development and assessed whether these putative effectors suppress immune responses using heterologous expression systems, including Nicotiana benthamiana and the bacterial type III secretion system from Pseudomonas syringae DC3000. Three P. maydis effector candidates suppress chitin-mediated ROS production in N. benthamiana Figure 5. Protein structures were predicted with ColabFold v1.5.2: AlphaFold2 and visualized using the ChimeraX-1.5 modeler package. Here we present the predicted structures of three PmECs which have cell surface-triggered immune suppression activities. The coloring of the models depicts the predicted local distance different test (pLDDT) which indicates the per-residue confidence score. Higher confidence scores are depicted in cool colors while low confidence scores are depicted in warmer colors. Figure 2. Transient expression assays were performed at 48 hours post infiltration. The sub-cellular localizations of PmEC-sYFP fusions were determined by laser scanning confocal microscopy (A). Expression of full-length PmEC-sYFP fusions in N. benthamiana leaves was confirmed by western blot analysis (B). Figure 3. Transient expression of candidate effector- fluorescent protein fusions suppress reactive oxygen species (ROS) burst triggered by chitin in N. benthamiana. The indicated constructs were expressed in N. benthamiana. Forty-eight hours post-agroinfiltration, N. benthamiana leaf disks were collected, challenged with chitin, and relative luminescence was monitored for 40 minutes using a luminol-based assay. Free sYFP (3xHA:sYFP) was used as a reference control P. maydis effector candidates localize primarily to the nucleus and cell periphery Predicted protein structures of the candidate effectors as determined by AlphaFold2 An introduction to Phyllachora maydis The fungal phytopathogen Phyllachora maydis is an obligate pathogen of maize and is the causal agent of tar spot disease. It was first identifie


1. Inhibition and processing speed impaired in MCI and AD groups • Standardised tests detect cognitive changes in impaired groups, and more so in inhibition than processing speed 2. WM fibre density (FD) in SLF differed between groups, but not FC, and little for FDC • Density, rather than volume of the fibre, steadily decreased between groups • While C and SCD groups had similar cognitive performance, the SLF FD differed. The C group had greater SLF FD, while the SCD group’s SLF FD was more similar to the MCI and AD groups 3. Inhibition, and not processing speed significantly correlated with FD in the left SLF 2 and 3 • The SLF plays a critical role in inhibition processes in AD risk cohorts Funding from Brain Research New Zealand (BRNZ) We thank the participants and DPRC staff for giving their time for this study. SCD n = 60 C n = 35 mMCI n = 52 AD n = 27 aMCI n = 55 Lenore T Tahara-Eckl1,2, Reece Roberts1,2, Catherine Morgan1,2, Flavio Dell’Acqua3, Ian Kirk1,2, Tracy R Melzer4,6, John C Dalrymple-Alford4,5, Tim J Anderson4,6, Nicholas J Cutfield7, Lynette Tippett1,2 1School of Psychology, University of Auckland, New Zealand; 2Centre for Brain Research, University of Auckland, New Zealand; 3Forensic and Neurodevelopmental Sciences, King’s College, London, England; 4NZ Brain Research Institute, Christchurch, New Zealand; 5School of Psychology, Speech and Hearing, University of Canterbury, Christchurch, New Zealand; 6Department of Medicine, University of Otago, Christchurch, New Zealand; 7Department of Medicine, University of Otago, Dunedin, New Zealand Participants. n = 229 (122 F, 69.75 ± 8.25 years), recruited from the Dementia Prevention Research Clinic (DPRC) over three sites: Auckland, Christchurch, Dunedin Neuropsychological assessment. Normal Fibre Bundle Reduced FD Reduced FC Reduced FDC Fixel-based analysis (FBA) for FD, FC, and FDC5 1. Rabin, L. A., Smart, C. M., and Amariglio, R. E. 2017. Annual Review of Clinical Psychology, 13(1), 369–396. 2. Lockhart, S. N., & DeCarli, C. 2014. Neuropsychology Review, 24(3), 271–289. 3. Perry, R. J., & Hodges, J. R. 1999. Brain, 122(3), 383–404. 4. Bennett, I. J., & Madden, D. J. 2014. Neuroscience, 12(276), 187–205. 5. Sasson, E., Doniger, G. M., Pasternak, O., Tarrasch, R., and Assaf, Y. 2013. Frontiers in Neuroscience, 7(7 MAR), 1–13. 6. Cremers, L. G. M., de Groot, M., Hofman, A., Krestin, G. P., van der Lugt, A., Niessen, W. J., Vernooij, M. W., and Ikram, M. A. 2016. Neurobiology of Aging, 39, 108–117. 7. Raffelt, D. A., Tournier, J. D., Smith, R. E., Vaughan, D. N., Jackson, G., Ridgway, G. R., and Connelly, A. 2017. NeuroImage, 144, 58–73. 8. Tournier, J. D., Smith, R., Raffelt, D., Tabbara, R., Dhollander, T., Pietsch, M., Christiaens, D., Jeurissen, B., Yeh, C. H., and Connelly, A. 2019. NeuroImage, 202(August), 116137. Five participant groups (total n = 229) Poorer executive function is associated with lower white matter fibre density in the superior longitudinal fasciculus in groups at risk of Alzheimer’s disease Diffusion FOD Image acquisition and preprocessing. Diffusion-weighted MRI (100 directions, b = 1000, 2000 s/mm2). FOD estimation with multi-tissue constrained spherical deconvolution and FBA processed with MRtrix38 Six SLF tracts of interest. Left: SLF tracts coloured by direction (red = right-left, blue = superior-inferior, green = anterior- posterior). Right: SLF tracts segmented by number (SLF1, SLF2, SLF3) In groups at different levels of risk of AD… 1. Do measures of processing speed and inhibition differ? 2. Do SLF fibre properties differ? 3. Do the SLF tracts correlate with processing speed and inhibition measures? Research Questions Background Methods Processing Speed Hayling’s Congruent Sentence Set 1 Stroop Colour Naming Stroop Word Reading Trail Making Test A Inhibition Hayling’s Incongruent Sentence Set 2 Hayling Category A Error Hayling Category B Error Stroop Inhibition Category Switching Trail Making Test B Our findings suggest that specific mi


Commissariat à l’énergie atomique et aux énergies alternatives INES | 50 avenue du lac Léman | 73375 Le Bourget-du-Lac www-liten.cea.fr / www.ines-solaire.org DEVELOPMENT AND IMPROVEMENT OF METHODS FOR REDUCING CONTAMINATION OF SILICON-KERF FROM WAFER SLICING Roland RIVA, Margot LANDA-PLIQUET, Fabrice COUSTIER UNIVERSITÉ GRENOBLE ALPES, CEA, LITEN, CAMPUS INES, 73375 LE BOURGET DU LAC, FRANCE CONTACT : Roland RIVA, roland.riva@cea.fr This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 958365 CONTEXT 35% silicon-kerf loss during wafer slicing (diamond wire) recycling desirable Silicon contamination from cutting liquid (water + additives), brick holder (beam) and diamond wire CONTAMINATION REDUCTION OF SILICON-KERF 1) DURING WAFER SLICING Low concentration (Carbon Oxygen Demand) coolant decrease of carbon Beam composition (silicon-based filler) aluminum reduction 2) ON DRY RECOVERED SILICON-KERF Soft chemical treatment (HCl) followed by thermal treatment (2 hours @ 500°C) Main residual contaminant = nickel (from cutting wire coating) CONCLUSION • Raw silicon-kerf purity can be enhanced to 3N (99.9%, excluding light elements) without industrial cutting process modification thanks to cutting liquid and beam composition change • Additional soft chemical treatment, followed by thermal treatment can drastically reduce carbon concentration and increase silicon-kerf purity to 4N (99.99%) References • H. Hajjaji, F. Coustier, V. Brizé, A. Benayad, M. Benmansour, A. Chabli, “Recycling of Kerf-Loss Silicon Powder from Diamond-Wire Cutting Without Chemical Treatment”, EU PVSEC 33, 2017. • M. Vazquez-Pufleau, T.S. Chadha, G. Yablonsky, P. Biswas, “ Carbon elimination from silicon kerf: Thermogravimetric analysis and mechanistic considerations”, Scientific Reports, Volume 7, 2017. • F. Coustier, V. Brizé, H. Hajjaji, “Wire cutting support for bonded abrasives comprising an assembly of different materials, system comprising such a support and wire cutting methods”, European Patent EP 3 424 663 A1, 2017. • X. Li, G. Lv, W. Ma, T. Li, R. Zhang, J. Zhang, S. Li, Y. Lei, “Review of resource and recycling of silicon powder from diamond-wire sawing silicon waste”, Journal of Hazardous Materials, Volume 424, Part A, 2022. • Z. Hu, G. Wang, J. Li, Y. Tan, Y. liu, P. Li, “Recycling of diamond-wire sawing silicon powder by direct current assisted directional solidification”, Waste Management, Volume 157, 2023. Metals divided by 3 and carbon by 6 from raw Si-kerf 1BV.5.5


Hochschule für Gesundheit · University of Applied Sciences · Gesundheitscampus 8 · 44801 Bochum Raising awareness for RDM: The importance of multipliers within the institution anke.osterhoff@hs-gesundheit.de Osterhoff, Anke & Koch, Katharina Hochschule für Gesundheit, Bochum, Germany State of RDM at UAS Professional research data management (RDM) is becoming increasingly important not only at universities but also at universities of applied sciences (UAS). This is partly due to DFG and other authorities’ regulations regarding RDM, which means that more and more third-party funding bodies require RDM for funding. Additionally, research at UAS is often practical and application-oriented, which means that the findings and results can quickly flow into different areas of society, the economy, and culture to create innovation and transformation. Research data at UAS therefore has yet rather underutilized scientific, cultural, and economic potential, especially in terms of its subsequent applied use. Professional RDM is essential for realizing these opportunities. Researchers and institutions are becoming increasingly sensitive to its potential. Yet, UAS are burdened with high teaching loads and relatively little funds for research, while RDM is often not funded at all. Starting points Bringing RDM into practice at the institutional level and raising awareness among researchers, administrative and infrastructural stakeholders is challenging. Thus, we placed special focus on the role of voluntary multipliers within the institution. These voluntary multipliers are also referred to as “data champions” [1] and can be considered key actors for raising awareness for RDM among researchers as their peers and can serve to complement the work of professional RDM staff (such as data stewards). In our example, RDM as a concept was initially introduced by the Research and Transfer Office with the support of university leadership, which recognized RDM as strategically important. The initial situation was as follows: • no professional RDM staff • all efforts to establish RDM took place on a voluntary basis • consultation with RDM-initiatives • contacting associated working groups for guidance Strategies for increased institutional RDM awareness Our first goal was to create a trickle-down effect by making RDM a topic of discussion in several institutional committees, starting with UAS leadership. This includes regular reporting about RDM and linking RDM with other current topics, e.g. the institution's digitization strategy or establishing a local repository. Furthermore, specific measures have been initiated to establish services related to RDM, e.g. by acquiring third-party funding for RDM- related research. Thanks to said funding, a data steward (0,5 FTE) is currently developing subject-specific RDM services and providing practical support for researchers. Another important step to make RDM visible in the institution was to appoint a professorial, voluntary RDM representative. Said professor serves as an important multiplier due to their RDM-related expertise and research interests. They can be considered a sort of data champion due to their specific RDM-knowledge [2]. We selected them since they have a comprehensive understanding of the importance of well-planned research data management practice and are passionate about sharing discipline-specific expertise and advancing FAIR principles and good scientific/RDM practice [1]. In doing so, the RDM representative is one of our institution’s key actors in promoting changes in research culture towards RDM and Open Science. They work in close collaboration with the Research and Transfer Office and data steward. Additionally, their feedback and assessment have been crucial to improving our RDM services. As a long-standing professor, they are experienced, trusted, and well known at the institution. The role benefits greatly from selecting a low-threshold contact person for academic peers to ask about R


Barriers & Enablers of Intercropping and Enhanced Crop Diversification in the UK Trivett E.E¹ Bates L¹ Drummond C.J¹ ¹ LEAF (Linking Environment And Farming) CV8 2LG, UK ABSTRACT Increasingly volatile weather conditions and extreme weather events have increased challenges in pest management in single variety cropping. A need to enhance Integrated Pest Management (IPM) has led to the use of plant species mixtures or ‘plant teams’ to optimise performance, improve yield stability, reduce pest and disease damage and enhance stress resilience in agricultural systems. Combined with supporting Integrated Farm Management (IFM) practices, intercropping, in field crop mixtures and other examples of enhanced crop diversification have gained attention in recent years due to the beneficial effects of soil fertility, nutrient recycling and pest, weed and disease management. However, uptake remains limited in the UK. Barriers to and opportunities presented by enhanced crop diversification are illustrated through a series of case studies from across three projects LEAF collaborated on between 2017 and 2020. Enablers and barriers to adoption of enhanced crop diversification are illustrated, concluding that a range of approaches will be necessary to support upscaling of these practices in the UK. We are grateful to of received the support and funding from the following projects to make this study possible. The project DiverIMPACTS - "Diversification through Rotation, Intercropping, Multiple Cropping, Promoted with Actors and value-Chains towards Sustainability" is supported by the European Union's HORIZON 2020 research and innovation programme under Grant Agreement no 727482 and by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number 17.00092. The DIVERSify project has received funding from the European Union’s Horizon 2020 research and innovation programme under agreement No. 727284. The SEAMS project Funded by the Esmée Fairbairn Foundation, and coordinated by the James Hutton Institute. Enablers Barriers • Soil health and fertility • Integrated Pest Management • Mixed farming systems lend themselves well to enhanced crop diversification • Investment and availability of machinery • Seed separation • Establishment • Lack of knowledge exchange Outcomes Through H2020 projects DIVERSify , DiverIMPACTS and Esmee Fairbairn Foundation project SEAMS, LEAF has been working with a range of UK farmers and stakeholders since 2017 on enhanced crop diversification projects. A farmer engagement workshop ‘Experiences, barriers and opportunities in plant teams’ was carried out at West Gilson Mains, Fife as part of the SEAMS project. The outcome of this event was a summary of plenary discussions between farmers, agronomists and industry representatives. Two farmer led case studies were delivered as part of LEAF’s contribution to the H2020 project cluster ‘Crop Diversification’ which includes the DIVERSify and DiverIMPACTS projects. Enablers of barriers to the uptake of enhanced crop diversification approaches such as intercropping , companion cropping and rotation extension were the focus of all three outputs. Enablers were classified as site specific farm business approaches which improved access, incentive or motivation to employ enhanced crop diversification strategies. Barriers were categorised as unresolved challenges or perceived risks in the adoption of such approaches. Companion, cover and intercropping and extended rotations all have potential to enhance sustainability in UK cropping. An increase in effective knowledge exchange to highlight opportunities, and advice and support to help overcome barriers will be required. Where the balance between risks against benefits is seen to pay off, an increase in the adoption of enhanced crop diversification is more likely. Farming 300ha’s of arable ground, intercropping trials have been a particular interest in the farms diverse 9 crop wide rotation. Seed separation i


Diameters Star Sp Type (mas) 1 Diameter ( )2 NR Vul K3 I (L05) 3.04 0.1 4.12 BD+354077 M2.5 I (L05) 3.18 0.13 5.45 BI Cyg M3-M4 I (L05) 5.16 0.34 9.21 RW Cyg M3 I (L05) 5.09 0.36 11.8 AZ Cyg M3 Iab (M19) 3.74 0.18 8.41 V424 Lac M0 I (L05) 3.77 0.08 12.6 V 336 And M2Ib (KM89) 2.46 0.05 3.08 AD Per M2.5 Iab (M19) 2.39 0.15 8.39 BU Per M3 I (L05) 2.27 0.29 21.0 FZ Per M1.5 (M19) 1.8 0.24 13.7 KK Per M2 Iab-Ib (M19) 2.27 0.10 2.17 SU Per M3-M4 I (L 05) 3.20 0.21 10.9 RS Per M4 I (L 05) 2.96 0.13 5.13 S Per M4.5 I (L 05) 4.08 0.36 6.91 W Per M4.5 I (L05) 2.93 0.12 6.14 XX Per M4 Ib (M19) 2.77 0.16 5.90 6 Gem M1-M2 Ia-Iab (KM89) 4.11 0.48 49.3 TV Gem M1 I (L 05) 3.41 0.53 37.5 WY Gem M2 Iabep+ (M19) 2.68 0.03 3.96 An Interferometric Imaging Survey of Red Supergiant Stars Ryan P. Norris (New Mexico Tech) Abstract Red supergiant stars (RSGs) are an end stage of massive star evolution. Among the notable behaviors of stars during this stage are their irregular and semi- regular variability and mass-loss. In order to better understand the sources of these phenomena, we collected high resolution optical interferometric observations of 17 RSGs using the Center for High Angular Resolution Astronomy (CHARA) Array at Mount Wilson between 2015 and 2016. Here, we present stellar diameters derived from these data. We comment on evidence of surface asymmetries on those stars for which we were able to obtain closure phases and present an example image for one of these objects. In addition, we have obtained near-contemporaneous spectroscopy of these stars using SpeX on the NASA InfraRed Telescope Facility (IRTF). We have developed libraries of synthetic spectra derived from spherical MARCS, PHOENIX, and SATLAS stellar atmospheres, and are currently working to derive fundamental stellar parameters with these data. Diameter Fitting We used the OITOOLS.jl1 package to run a grid search for fitting model limb-darkened disks to the squared visibilities. Future efforts will resistrict the fit to the first two lobes of the visibility curve in order to avoid effects from large surface features. 1:https://github.com/fabienbaron/OITOOLS.jl Figure 1: Example χ2 surface for the linearally limb-darkened disk of RS Per. 1: Linear limb-darkening coefficent. 2: Using Gaia parallaxes as reported in Bailer-Jones et al. 2018 References 1)Bailer-Jones, C. A. L., Rybizki, J., Fouesneau, M.,Mantelet, G., & Andrae, R. 2018, AJ, 156, 58 2)Keenan P. C., McNeil R. C., 1989,ApJS, 71, 245 (KM89) 3)Levesque, E. M., Massey, P., Olsen, K. A. G., et al. 2005,ApJ,628, 973 (L05) 4) Norris et al. 2021. Submitted.. 5)Messineo, M., & Brown, A. G. A. 2019,AJ,158, 20 (M19) Example Imaging Image Reconstruction Of the 17 stars observed 10 have enough (u, v) coverage for image reconstruction and have closure phases suggesting surface assymetries. In Figure 2, we present an example image for RS Per. Details of the reconstruction process can be found in Norris et al. 2021. We used SQUEEZE1 and the OITOOLS.jl package to reconstruct images. 1:https://github.com/fabienbaron/squeeze Figure 2: Image reconstruction of RS Per (top) and corresponding uv coverage (bottom). Beam size is depicted in the lower right corner of the image. Image was reconstructed using SQUEEZE and total variation and Laplacian regularizers.


using the QR-Code and: your training. gaps or needs for further training and your training. Get your training if you meet at least 80% of the principles recommended by the research community. your badged training to the OS Learning Gate. reach out: buchheit@paedagogik.uni-kiel.de alavi@zke-kiel.de Help us to create an intersection of high-quality and reliable OS training in line with principles of Research Integrity, Research Ethics and Ethics of AI operating with OS tailored according to the needs of various OS learning groups. Join us in the OPEN SCIENCE LEARNING GATE 3 2 1 4 SCREEN IDENTIFY & COMMUNICATE BADGED CONNECT AMEND QUESTIONNAIRE Starting at the beginning of June 2024 ENTER NERQ_OS QUESTIONNAIRE for Julia Priess-Buchheit, Joeri K. Tijdink, Katharina Miller, Sean Lacey, Peter Eduard, Marie Alavi (and more from NERQ_OS Group)Julia Priess-Buchheit, Joeri K. Tijdink, Katharina Miller, Sean Lacey, Peter Eduard, Marie Alavi (and more from NERQ_OS Group) OPEN SCIENCE Learning Gate tailored capacity building for OS training Authors: Julia Priess-Buchheit, Marie Alavi With contribution of: Joeri K. Tijdink, Katharina Miller, Ruth Moran, Varga Orsolya, Maruxa Martinez, Ulf Tölch, Sean Lacey , Peter Eduard, Anita Lunić (and more from NERQ_OS Group)With contribution of: Joeri K. Tijdink, Katharina Miller, Ruth Moran, Varga Orsolya, Maruxa Martinez, Ulf Tölch, Sean Lacey, Peter Eduard, Anita Lunić (and more from NERQ_OS Group) SIG_OS


A Model for Interpretable High Dimensional Interactions Bhatnagar SR1,2, Yang Y3, Blanchette M4, Greenwood CMT1,2 1Department of Epidemiology, Biostatistics and Occupational Health, McGill University 2Lady Davis Institute, Jewish General Hospital, Montreal, QC 3Department of Mathematics and Statistics, McGill University, QC 4School of Computer Science, McGill University Summary • Environmental exposures may induce subtle system-wide changes in high- dimensional genomic data such as gene expression or epigenetic measures – Can such situations be exploited to improve prediction models? • Large system-wide changes are observed in many environments and hence this assumption can possibly be exploited to aid analysis of high dimensional data • We develop and implement a multivariate penalization procedure for predict- ing a continuous or binary disease outcome while detecting interactions between high dimensional data (p >> n) and an environmental factor. R software: http://sahirbhatnagar.com/eclust/ – Dimension reduction is achieved through leveraging the environmental-class- conditional correlations – Also, we develop and implement a strong heredity framework within the penal- ized model Motivation Figure 1: Microarray study of COPD. Top: Heatmap of Pearson correlations. Bottom: Heatmap of gene expression data (2,900 genes) rows are genes and columns are subjects. There are 7 subjects in each group, matched on COPD case status, gender and age. Methods Figure 3: Method overview. First step involves measuring gene similarity in both exposure groups. We then cluster these and create a cluster representation. The last step involves entering these terms in a penalization model that follows the strong heredity principle [1] Figure 4: Clustering based on Fisher’s Z transformation of exposure dependent correla- tions. Let ρijk be the correlation between genes i and j in class k. Transform the corre- lations into z values: zijk = 0.5log|(1 + ρijk)/(1 −ρijk)|. The Z-test statistic is given by |zij0 −zij1|/ p 1/(n0 −3) + 1/(n1 −3) ∼N(0, 1) • Model: g(µ) = β0 + β1X1 + · · · + βpXp + βEE | {z } main eﬀects + α1E(X1E) + · · · + αpE(XpE) | {z } interactions • Strong Hierarchy Principle [1]: ˆαjE ̸= 0 ⇒ ˆβj ̸= 0 and ˆβE ̸= 0 • Reparametrization [2]: αjE = γjEβjβE. • Variable Selection: arg minβ0,β,γ 1 2 ∥Y −g(µ)∥2 + λβ w1β1 + · · · + wqβq + wEβE  + λγ w1Eγ1E + · · · + wqEγqE  • Adaptive weights: wj = 1 ˆβj , wjE = ˆβj ˆβE ˆαjE • Why strong heredity? – Statistical Power: large main eﬀects are more likely to lead to detectable interactions than small ones – Interpretability: Assuming a model with interaction only is generally not biologically plausible – Practical Sparsity: X1, E, X1 · E (2 variables to measure) vs. X1, E, X2 · E (3 variables to measure). Simulation Study Results Figure 5: Stability of results: Average Jaccard distance from 10-fold cross validation. A Jaccard distance of 1 indicates perfect agreement between two sets while no agreement will result in a distance of 0. Figure 6: Prediction accuracy: Test set mean squared error This work was supported by the Ludmer Centre for Neuroinformatics and Mental Health. Software available at http://sahirbhatnagar.com/eclust/. References [1] Hugh Chipman. Bayesian variable selection with related predictors. Canadian Journal of Statis- tics, 24(1):17–36, 1996. [2] Nam Hee Choi, William Li, and Ji Zhu. Variable selection with the strong heredity constraint and its oracle property. Journal of the American Statistical Association, 105(489):354–364, 2010.


INCIPIT-CSIC Monte Gaias s/n, Edificio Fontán, bloque 4, 15707, Santiago de Compostela, Galicia, Spain leticia.tobalina-pulido@incipit.csic.es A thorough recording and collection of archaeological finds allows the detection of errors in the field and later on. FROM FIELD TO GIS Intensive archaeological pedestrian survey in the characterisation of Roman rural settlements BIBLIOGRAFÍA Leticia TOBALINA-PULIDO (Institute of Heritage Sciences, CSIC) The use of archaeological survey for the characterisation of Roman sites and their surroundings is not a new topic. We present here the theoretical proposal that we have carried out in recent months, emphasising an exhaustive record that allows us to assess the quality of the archaeological survey. SURVEY APPROACH It is also significant that some imported materials were found, such as a fragment of an amphora made of paste from the Lower Guadalquivir. It is curious that neither Terra Sigillata nor other fine pottery is recorded. Many loom weights were recovered too. Only common pottery and dolia were recorded. The concentration of material, moreover, shows the three concentration patches, possibly corresponding to those indicated in the literature as three archaeological sites. The distribution of archaeological material extends over almost 2ha, making it a settlement of significant size. Considering the classification of L.G. Pérez-Aguilar (2018) for the southwest of Spain, we can consider that we are dealing with a large farm-type site. Perhaps, in the event that future interventions extend the area of distribution of materials, we may be looking at a small settlement. There is very limited datable artefacts, although a fragment of a highly eroded amphora dates to the 1st century AD. The use of intensive archaeological prospection with the systematic collection of archaeological material has allowed us to characterise archaeological sites from the Roman period of lesser importance and with a complicated materiality (a lot of constructive material and little datable material). PERSPECTIVES CONTACT @dynatinc @dynatinc Firstly, we opted for an intensive archaeological survey with a spacing between surveyors of 5 metres. The intensity changes depending on the terrain. In our case, the two types of land we prospect are pasture and vineyard. In cases of poor visibility in dehesa, we choose to reduce the intensity to 3 metres. Secondly, all archaeological finds are geo-referenced in the field. In addition, all non-constructive archaeological material is collected (also from other chronologies), with the aim of being able to detect identification errors in the field due to poor visibility, for example. In the case of doubts or significant constructive material, it is also collected. Thridly, for each surveyed plot, each prospector has to fill in a sheet indicating issues such as GPS used, visibility, GPS error or field experience. Each of these factors must be indicated on the sheet with a number according to the criteria specified in the sheet's instructions. This allows for a better homogenisation of the data afterwards. APPLICATION EXAMPLE The sheet allows us to know which areas each prospector has surveyed, the previous experience he/she has in the field and the characteristics of the area he/she surveyed. A case study of an application in the municipality of Fronteira, Portugal, is presented here. It is an area previously extensively surveyed and recorded on the archaeological chart as 3 settlements. In addition, one of the problems archaeologists encountered when prospecting it was the difficulty of characterising it. The aim was to characterise the area and determine whether there are three areas of the same site or three separate sites and to characterise it LOCATION OF THE SURVEYED AREA SURVEYED AREA DISPERSION OF ARCHAEOLOGICAL FINDS During the survey we located a large amount of laterite building material. There was also a significant concentration of scoria and dolia. The collecti


In order to assess the relationship between ﬂowering time control and roots, ﬂowering time mutants and mu- tants isolated from the reverse genetic approach presented above were characterized for root architecture (ﬁg. 3a). Unexpectedly, we observed that the late ﬂowering constans (co) mutant had a striking root phenotype (ﬁg. 3b) although we did not detect expression of the CO gene in the root (data not shown). By contrast, the svp mutant did not display any root phenotype albeit the gene was highly expressed throughout the roots (ﬁg. 2c). The dormancy asso- ciated2 mutant had a signiﬁcant phenotype, including longer primary and secondary roots and an increased lateral root density. The same observations stand for the ipt3;5;7 triple mutant but not for the ipt3 single mutant. Because many ﬂowering time genes were found to be expressed in the roots, we analyzed the changes in gene expression occurring in the roots during the induction of ﬂowering. To do so, 7-week old vegetative plants grown in short days (SD) were induced to ﬂower by exposure to a single 22-h long day (LD). Roots were harvested during the photoperiod extension for transcriptomic analysis. We found that hundreds of genes were diﬀerentially expressed in the roots in LD vs SD (ﬁg. 2a). The biological signiﬁcance of these changes was addressed by recording whether loss of function mutants had a ﬂowering phenotype. Interestingly the cytokinin-biosynthesis genes IPT3, 5 & 7 (IPT; ISOPENTENYL TRANSFERASE) were all up-regulated in the roots during the during the induction of ﬂowering (ﬁg. 2b). According to the root map published by Brady et al. (2007), the expression of IPT3 and IPT5 is restricted to some tissues of the roots (ﬁg. 2c). We also looked at the expression pattern of well-characterized ﬂowering time genes detected in roots (ﬁg. 1b,c). Among them, we ob- served that SHORT VEGETATIVE PHASE (SVP) is expressed throughout the roots (ﬁg. 2c). FLORAL INDUCTION IMPACTS THE ROOT TRANSCRIPTOME FLOWERING TIME GENES ARE EXPRESSED IN ROOTS Plant Physiology ULg FLOWERING GOES UNDERGROUND F. Bouché, G. Lobet, M. D’Aloia, N. Detry, P. Tocquin, C. Périlleux. Laboratory of Plant Physiology, University of Liège, B22, Sart Tilman, B-4000 Liège, Belgium Corresponding author: f.bouche@ulg.ac.be In conclusion, complementary approaches based on published expression data, transcriptomic experiments and genetic analyses indicate that genes involved in ﬂowering time control are expressed in the roots and/or aﬀect root architecture. Further experiments are on the way to downregulate ﬂowering time genes in the roots by overexpressing artiﬁcial microRNAs in an organ-targeted manner. Acknowledgements : FB is grateful to the F.R.S.-FNRS for the award of a PhD fellowship. We thank Pr. Tatsuo Kakimoto (Osaka University, Japan) who kindly provided us with ipt3 and ipt3;5;7 seeds. This research is funded by the Interuniversity Attraction Poles Programme P7/29 initiated by the Belgian Science Policy Oﬃce. The genetic control of ﬂowering is complex : deepest knowledge has been accumulated on Arabidopsis where we identiﬁed 278 ﬂowering time genes from a littera- ture survey. We then crossed the list with transcriptomic data obtained from roots and found that 98 ﬂowering time genes were expressed in the roots of Arabidopsis plants grown in hydroponics, on soil, or in vitro (ﬁg. 1a,b). Among them, genes involved in photoperiodism or light perception were well represented whereas others – e.g. genes involved in ﬂower development - were not (ﬁg. 1c). References : Brady, S.M. et al., 2007. A high-resolution root spatiotemporal map reveals dominant expression patterns. Science, 318 ( 5851), 801-6. Lobet, G. et al., 2011. Novel Image Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture. Plant Physiology,157, 29-39. AT5G18840 Figure 1. Genes controlling ﬂowering time in Arabidopsis are expressed in the roots. (a) Root transcriptomic data were obtained from plants grown in hydropo


PhD Library Course Topics I´m a virtual librarian, ready to assist you with your PhD Library Course questions! Available 24/7 to assist PhD candidates with their coursework and research. Provides personalized feedback and real-time support. Helps students brainstorm keywords and formulate effective search queries. Guides users through citation styles and reference management using tools like Zotero. Facilitates understanding and implementation of Open Science practices. Enhances the overall research and learning experience for PhD candidates. Promotes engagement and active learning through interactive assistance. Demonstrates the potential of AI in transforming academic support services. 0% 10% 20% 30% 40% 50% I don't have access to full version of ChatGPT Consult dates and conditions of course Consult for deeper understanding of subject I don't like vi̶tual assistance Consult the assignments Archie Bookworm: Virtual Librarian for Advancing PhD Education PhD Library Course in Nutshell Blended learning format combining webinars, in-person workshops, e-learning, and practical assignments. Provides a platform for networking among PhD from different fields (over 90 participants attended this year). Focuses on developing core research competencies and practical skills. Encourages interdisciplinary collaboration and knowledge sharing. Regular feedback and personalized guidance enhance the learning experience (real-time support from the AI virtual librarian). Meet Archie Bookworm Feedback Highlights: How Archie Transformed Learning “Archie helped me formulate effective search queries, making my research process much smoother and more efficient.” “I found the use of AI in teaching through Archie inspiring. I'll be incorporating similar AI tools in my own teaching methods." “I'm not a fan of virtual assistants; I prefer human interaction. However, I can see the potential benefits for those who like using AI” Tereza Šímová Czech University of Life Sciences Prague www.terezasimova.com, simovat@lib.czu.cz


A Mixed-Mode Simulation Framework to Investigate Neuronal Signal Transduction and Sensing at Nanoelectrodes Federico Leva1*, Pierpaolo Palestri2, Luca Selmi1 1Dipartimento di Ingegneria ‘‘Enzo Ferrari’’, Università di Modena e Reggio Emilia, Modena, Italy 2Polytechnic department of Engineering and Architecture University of Udine, Udine, Italy *Corresponding author: federico.leva@unimore.it Overview Figure 1: Schematic representation of an intracellular (a) and extracellular (b) FET-based nanoelectrode integrated in CMOS technology, interfaced with a neuron and connected to a transimpedance readout circuit. Accurate physics-based numerical models of coupled neuron-sensor-readout CMOS-based systems are useful to: • design and optimize the sensing device and the readout, • interpret the measurements, • derive lumped-element descriptions of the recording systems related to geometrical and physical properties. A semiconductor-TCAD-based mixed-mode modeling environment is suited for such purposes. We exemplify its capabilities by analyzing relevant figures of merit (including SNR) for an active FET-based nanoelectrode envisioned for intra- and extracellular coupling to neurons (Fig. 1). This work has been financially supported by the European Union’s Horizon 2020 project “IN-FET” (Grant Agreement n. 862882) via the IUNET consortium. Methods The modelling framework consists of a FEM TCAD for semiconductors [1], which supports: • Mixed device-circuit simulations with user-defined physics and lumped-elements via PMI and CMI, respectively [1]. • Drift-diffusion transport in the intra- and extracellular electrolyte regions, implemented by mimicking anions and cations with electrons and holes, and suitably adjusting the semiconductor properties [2,3,4]. • Combined DC steady state, transient, AC small signal, and noise analysis. • Cellular membrane compartment description as (i) lossless insulator in TCAD (with parameters consistent to [5]), or (ii) lumped capacitor in the circuit portion. • Action potentials (APs) incorporation onto each membrane’s compartment as either: (i) voltage generator (Fig. 2.b), (ii) current generator (Fig. 2.c), or (iii) Hodgkin- Huxley (HH) [5] circuit model (Fig. 2.a), implemented via custom multi-port memristors described by CMIs. The CMIs set the (de)activation state-variables for the non- linear conductances of the K+ and Na+ ion-channels [5]. Results • Fig. 3 shows that our mixed-mode approach predicts the expected monophasic (a) and biphasic (b) waveforms of lumped-element circuit models (not shown) derived from state-of-art results [6] for intra- and extracellular contact. • Fig. 4 reports the neuron-to-readout transfer function (TF1) computed with AC small signal analysis. A band-pass behavior is observed for intracellular contact, whereas a derivative behavior for the extracellular case on the frequency range of the AP spectrum. The TF shapes are consistent with the time-domain profiles of Fig. 3. • Fig. 5 shows that the active FET-sensor SNR2 is not affected by the presence of the readout noise and only slightly affected by the coupling condition with the neuron, overall achieving adequately large values. • Extended results can be found in [7]. Figure 2: Different equivalent circuits to include the generation of action potentials across the passive neuron membrane: (a) Hodgkin-Huxley model; (b) external voltage boundary; (c) external current boundary. Figure 3: AP waveform comparison for TCAD and full L.E. Circuit descriptions of an active nanoelectrode in (a) intracellular and (b) extracellular contact (Fig. 1). Vm is the intracellular neuron signal, Vout is the output signal of the readout. Figure 4: Modulus of the system transfer function of the active intracellular and extracellular sensing systems (Fig. 1). Figure 5: SNR for the different access types, and in presence or absence of the readout noise. The readout gain has been set to provide recorded signals with 1 Vpp. References [1] Synopsys, I


Henrietta Swan Leavitt (7/4/1868 – 12/12/1921) 1 2 5 6 8 9 10 3 4 7 11 1) Henrietta Leavitt working at HCO, circa 1900. Measuring Variable Stars 2) Plate a2969. Leavitt studied changes in variable stars by inspecting photos of the same section of sky taken on different dates. Photos were imaged through tele scopes onto glass plate negatives coated in light-sensitive chemicals. (The bright er a star, the more photons reached the plate and the larger its dark dot.) She labeled each star, measuring diameters through a loupe (magnifying glass). 3) Leavitt kept her analyses in handwrit ten notebooks. For each plate, she would draw a detailed chart of the stars she was exam- ining as they appeared in the sky. (Mirror image to her markings on the back of the plate. See circled “u” and “v”.) 4) List of magnitudes for each labeled star on plate a2969. Stars were sometimes recalibrated. See 8. Comparing Plates 5) Detail from Plate b20650, exposed for 4 hours on October 20, 1897. Henrietta Swan Leavitt, a deaf American astronomer and graduate of Radcliffe College, worked at the Harvard College Observatory (HCO) as a “computer”, examining glass photographic plates in order to measure and catalog the bright- ness of stars. This work led her to discover the relation between the luminosity and the period of Cepheid variables. Though she received little recognition in her lifetime, Leavitt’s discovery later provided astronomers with the first “stand- ard candle” with which to measure the distance to faraway galaxies. 1 2 Williamina Fleming (5/15/1857 – 5/21/1911) c e a d f 4 5 6 8 9 7 new variable 10 11a 11b 1) Portrait, circa 1890s. Fleming orga nized the Draper Catalogue, classifying 10,498 stars, based on 28,266 spectra on 633 plates. By 1910, she had examined ~200,000 HCO photographic plates. 2) Orion Nebula in Glass Plate b10250 (de tail), September 8, 1893 with markings by Fleming. 3) b10250 (detail), in which Fleming dis covered the Horsehead Nebula. Fleming discovered 10 novae, 59 gaseous nebulae, ~ 300 variable stars, and was the first to recog nize the existence of white dwarfs. 4) Photo of Horsehead Nebula; Ken Craw ford, Rancho Del Sol Observatory. Note nebula color and position are reversed from negative in 3). Work With Variable Stars 5) Fleming’s notes. She would draw a chart with the new variable, as well as stars near it (red box), then document positions & known magni tudes (green). 6) Determining magnitude of new star (Plate i10491) using the “Pickering-Fleming Method” (cyan box): Compare variable star “v” with a known, slightly dimmer star. Note how many Williamina Patton Fleming was the most famous woman astronomer in America during her lifetime. She helped develop a common designation system for stars and showed that variable stars and novae could be identified by their spectra, discovering many. A founding member of the Harvard Computers, a group of female astronomers and analysts at Har vard College Observatory (HCO), she supervised other women astronomers and managed publications issued during her time there. A charter member of the Astronomical and Astrophysical Society, she advocated for women in astronomy. Read more about Williamina Fleming at https://library.cfa.harvard.edu/phaedra/fleming 3 The Project PHaEDRA Collection: An Anchor to Connect Modern Science With Historical Data Poster by: Peggy Wargelin, Project PHaEDRA, Wolbach Library, Center for Astrophysics | Harvard & Smithsonian Presented by: Edward Los, Harvard College Observatory, AAVSO Member ABSTRACT Project PHaEDRA (Preserving Harvard's Early Data and Research in Astronomy) is an initiative by the Wolbach Library, in collaboration with many partners, to catalog, digitize, transcribe, and enrich the metadata of over 2500 logbooks and notebooks produced by the Harvard Computers and early Harvard astronomers. Our goal is to ensure that this remarkable set of items, created by a remarkable group of people, is as accessible and useful as possi bl


On behalf of PID Network Germany Felix Burger (TIB), Andreas Czerniak (UB Bielefeld), Barbara Fischer (DNB), Stephanie Glagla-Dietz (DNB), Lena Messerschmidt (Helmholtz Open Science Office), Heinz Pampel (Helmholtz Open Science Office / Humboldt-Universität zu Berlin, IBI), Jochen Schirrwagen (UB Bielefeld), Antonia C. Schrader (Helmholtz Open Science Office), Paul Vierkant (DataCite), Frauke Ziedorn (TIB) This work, excluding logos, is licensed under a Creative Commons Attribution 4.0 International. Funder: Authors & license: Project partners: 10 PID use cases in the project’s focus About the project The goal of the project “PID Network Germany” is to build a network of existing and currently forming actors around Persistent Identifiers (short PIDs) in science and culture. The aim is to promote the application, implementation, standardization and interoperability of PID systems on a local, national and international level. The findings from the project will lead to recommendations in a national PID roadmap for Germany. The project started on March 01, 2023, and is funded by the German Research Foundation (DFG) scheduled to run for 36 months. The project website provides further insight into the goals of the project. Support & Contact • Website: www.pid-network.de • Contact: info.pidnetwork@listserv.dfn.de • Mailing list: PID Dialog Follow us on Social Media: • Mastodon: @PIDNetworkDE@openbiblio.social • Twitter: @PIDNetworkDE e. g. DataCite DOI, URN, Archival Resource Key (ARK) e. g. DataCite DOI, based on the metadata schema by the RDA WG PIDINST e. g. GND Why do we need PIDs? PIDs... • offer unique, universal, and permanent references to potentially any type of digital or non-digital entities in the research process. • enable linkage between entities. • contribute to the integrity of scholarly communication, its reusability and their reproducibility. • play a crucial role to make data FAIR. • provide a comprehensive overview of all entities in the research process. Netzwerk für die Förderung von persistenten Identifikatoren in Wissenschaft und Kultur e. g. ROR ID, ISNI, GND, or for funding information (Gepris or Crossref Funder Registry), and for projects RAiD e. g. ORCID iD and Integrated Authority File (GND) e. g. Research Resource Identifier (RRID) for biological and the International Generic Sample Number (IGSN) for samples from all scientific fields e. g. DOI using the Citation File Format (CFF) e. g. DOI and URN service of the German National Library e. g. DataCite DOI, as suggested by ConfIDent (DFG-funded project in Germany) Logos by Julian Kücklich (https://doi.org/10.5281/zenodo.5608845), licensed under CC 0 So far only few initiatives, such as re3data and FAIRsharing, are providing DOIs for research data repositories.


Lotte Wilms, Andreas Degkwitz, Caleb Derven, Marian Lefferts, Kirsty Lingstadt, Liam O’Dwyer, Demmy Verbeke & Digital Humanities and Digital Cultural Heritage WG Participants 56 participants - 54 institiutions - 20 countries Full report available at doi.org/10.5281/zenodo.3247286 3. Select youractivitieswisely Libraries are most active in data capture, creation and storage. Build on your (collection) strengths to decide what works best for you. 1. Createa goal or visionforyourlibrary A defined framework clarifies your goal and manages expectations of partners. Set up your organisation with enough resources to make sure you can also reach this goal. 2. Measureyourimpact Identify early on how you will measure your achievements and impact. This will help you define what works well and what needs to be re-evaluated. 4. Reflectthefull breadthof yourcollections By broadening your scope to the full width of your collection your DH offering can be strengthened. Work from your strenghts and make access as easy as possible. 5. Have confidencein yourexpertise As the creator of your digital collections, you are the expert. Your are therefore the ideal partner, as you know what has been digitised, how it’s been digitised, what licenses apply, what works well and what probably wouldn’t. Strengthening the position of libraries as partner in DH will be a a core theme for the WG for the next two years. 6. Involveallyourcolleagues, notjusttheobviousones DH activities are most succesful if they are supported by a large number of library staff. Work together to build your skills and ideas. 7. Collaborate, collaborate, collaborate! Building your network in DH is crucial, as collaboration is key. Once you have defined your goals and activities go out and disseminate your data, your team and you ideas. Special thanks to Friedel Grant for the design of all graphs, tables and the word cloud. We also wish to thank all contributors and our WG’s members for their input.


Genome Annotation using Nanopublications: An Approach to Interoperability of Genetic Data Rajaram Kaliyaperumal1, Peter A.C. ‘t Hoen1, Zuotian Tatum1, Mark Thompson1, Erik Schultes1, Andrew Gibson1, Ivo F.A. C. Fokkema1, Johan T. den Dunnen1, Jeroen F.J. Laros1, José Luis Oliveira2, Pedro Lopes2, Pedro Sernadela2, Marco Roos1 1 Department of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands, 2 DETI/IEETA, University of Aveiro, Aveiro, Portugal Nucleotide change Substitutions Deletions Duplications Indels Single 22 2 - - Multiple - 6 4 1 Variant DB-ID gChange No.of TSS deleted SGCB_00043 g. 52886872_52904485del 1 DYSF_00176 g.71707370_71838047del 9 LMNA_00209 g.156052975_156100408del 12 promoter TSS exon inton CAGE cluster peaks


HELSINGIN YLIOPISTO HELSINGFORS UNIVERSITET UNIVERSITY OF HELSINKI DMP PROCESS AT THE UNIVERSITY OF HELSINKI HELSINKI UNIVERSITY LIBRARY In 2020, the Research Council of Finland changed its DMP submission process: 1) The DMP has to be submitted only by those applicants who receive a positive funding decision. 2) The RPO is responsible for ensuring that the DMP can be implemented and that the measures taken are in line with good data management practice. The UH receives approximately 100-130 positive funding decisions in relation to the largest funding call of the year - how do we manage the DMP review process at the university level? Tuija Korhonen tuija.korhonen@helsinki.fi Soile Manninen soile.manninen@helsinki.fi HULib Data Team/UH Data Support 25 86 216 165 0 50 100 150 200 250 2016 2017 2018 2019 Year of the call Number of DMPs, RCF’s September call 2016– 2019 (DMPs in the application phase) 137 112 103 0 50 100 150 200 250 2020 2021 2022 Year of the call Number of DMPs, RCF’s September call 2020–2022 (DMPs after pos. funding decision)


Comparing two ways of generating 328 nm laser light for high-resolution spectroscopy of the S1/2 P3/2 transition in Ag Julius Wessolek1,2, Mitzi Urquiza3, Bram van den Borne4, Ruben de Groote4, Katerina Chrysalidis5, Kieran Flanagan1 and the CRIS Collaboration5 1) University of Manchester, 2) M Squared Lasers, 3) HÜBNER Photonics GmbH, 4) KU Leuven, 5) CERN Spectra of the 532 nm, 856 nm and 656 nm pulses were taken with a scanning FPI (Toptica FPI-100) and the linewidths extracted. The linewidths of the 328 nm beams can be calculated as quadratic sums of the components: ∆𝜈328𝑛𝑚 𝑠𝑢𝑚 𝑓𝑟𝑒𝑞𝑢𝑒𝑛𝑐𝑦= 177 𝑀𝐻𝑧 ∆𝜈328𝑛𝑚 𝑑𝑜𝑢𝑏𝑙𝑒𝑑 𝑃𝐷𝐴= 387 𝑀𝐻𝑧 High resolution spectroscopy of Ag has been conducted at the Collinear Resonance Ionization Spectroscopy (CRIS) experiment at CERN ISOLDE to measure nuclear properties of the ground- and isomeric states. For spectroscopy of the S1/2 -> P3/2 transition in Ag, nano-second pulsed narrow-band 328 nm laser light has been produced in two different ways: Fig. 1: Sum frequency generation of narrow-band Ti:sapphire light with pulsed 532 nm light to generate 328 nm. Fig. 2: Second harmonic generation of pulsed amplified light from a cw OPO to generate 328 nm. Fig. 3: Ionisation scheme of Ag. The measured pulse lengths show that the pulses are in no case Fourier limited. This is expected for the 532 nm laser which is only actively temperature stabilized against drifts down to minute timescales. The PDA was pumped by that same laser and showed a shorter pulse length. The pulses from an injection-locked Ti:sapphire laser are usually broadened by cavity mode pulling and refractive index variation of the active medium. This leads to an instantaneous frequency shift and chirp and the pulse is not Fourier limited. ∆𝜈𝑚𝑖𝑛= 90𝑀𝐻𝑧≪274𝑀𝐻𝑧 ∆𝜈𝑚𝑖𝑛= 51𝑀𝐻𝑧≪176𝑀𝐻𝑧 ∆𝜈𝑚𝑖𝑛= 9.7𝑀𝐻𝑧≪17.2𝑀𝐻𝑧 Fig. 5: Pulse lengths measured with a biased Si photodetector. The minimum spectral linewidths were calculated assuming Gaussian pulses and are all significantly smaller than the measured linewidths. Fig. 7: Spectra of the S1/2 -> P3/2 transition in 109Ag with 328 nm laser light produced in two different ways. The linewidths extracted from the spectra are ~ 250 MHz in both cases, contrary to the linewidths measured with the FPI. Figure from private communication with B. v. d. Borne. Spectra of stable 109Ag were taken with with both versions of the 328nm laser light at 6µW to minimize power broadening effects. The FWHM of the peaks is in the order of 250 MHz for both cases. This is contrary to the linewidth extracted from the FPI scans. For the summed light, small side peaks started to occur, suggesting not fully single mode operation. This could be caused by the implemented stabilization but it has to be investigated further. 109Ag with doubled PDA 109Ag with sum frequency generation Fig. 6: Scan of 109Ag with the 328 nm light from sum frequency generation. The regular side peaks are possibly from multimode operation. Fig. 4: Spectra of the different pulses, taken with a scanning FPI. The linewidth was extracted by fitting a Voigt profile to the peaks.


Drones above, Currents below: Using unmanned aerial systems for aerial systems to observe ocean surface current Take a closer look! Find supplementary details inside and a full copy of the poster on the back! The ocean surface measurement technique: UAS wave-based current mapping CONTACT INFO Vivek Bheeroo | Vbheeroo09@tamu.edu (603) 866-9406 A Mavic 2 Pro is deployed over the ocean surface. The drone is stabilized at an altitude of 120 m. The camera mounted to the drone records with a field of view of 55o. The resulting spatial dimensions of the acquired image sequence have approximate dimensions of 100 m x 75m. The image stack is divided into sub-windows of about 6 x 6 m. This procedure is shown in Fig. 1. A 3-dimensional Fast Fourier Transform (3D-FFT) is applied to the raw pixel intensities of the image stack in each sub-window. The 3D-FFT procedure is given by (1). Where I(x,y,t) is the intensity value at the point (x,y,t) in the spatio-temporal domain, F(kx,ky,ω) is the complex value at the point (kx,ky,ω) in the frequency-wavenumber domain, Nx, Ny, Nt are the dimensions of the 3D image data, kx and ky are the wavenumber vectors and ω is the angular wave frequency. The dispersion relation of a surface gravity wave describes the relationship between the wavenumber vector, k, and the angular wave frequency. This is shown in (2). For water waves that are influenced by an underlying current, U, the dispersion relation is expressed by (3). Fig. 1: Image acquisition and workflow breakdown Where h is the water depth and g is the acceleration due to gravity constant. For a wave field that does not experience interactions with an underlying current, (2) will form the dominant signal observed in the 3D FFT output in each sub- window. Typically, surface currents are present and influence the wave propagation. In these instances, (3) will manifest as the dominant signal in the 3D FFT output. To recover the ambient current in each sub-window, a fitting procedure is performed by applying a spectral energy-based maximization technique in the wavenumber-frequency domain. This is shown with a signal to noise ratio (SNR) optimization procedure in (4). Where Pw is the power related to surface waves, Pn is the power related to background noise, nw is the number of bins belonging to waves and nn is the number of bins belonging to noise. (1) 𝐹൫𝑘𝑥, 𝑘𝑦, ω൯= ෍෍෍𝐼(𝑥, 𝑦, 𝑡) ⋅e −2πi(𝑘𝑥𝑥 𝑁𝑥+𝑘𝑦𝑦 𝑁𝑦+𝜔𝑡 𝑁𝑡) 𝑁𝑡−1 𝑡=0 𝑁𝑦−1 𝑦=0 𝑁𝑥−1 𝑥=0 (2) 𝜔= ඥ𝑔𝒌𝑡𝑎𝑛ℎ(𝒌ℎ) (3) 𝜔= ඥ𝑔𝒌𝑡𝑎𝑛ℎ(𝒌ℎ) + 𝒌⋅𝐔 (4) 𝑆𝑁𝑅൫𝑈𝑥, 𝑈𝑦൯= ∑𝑃൫𝑘𝑥, 𝑘𝑦, 𝜔൯𝑤 ∑𝑃൫𝑘𝑥, 𝑘𝑦, 𝜔൯𝑛 𝑛𝑛 𝑛𝑤


KARMAN-HOWARTH-MONIN EQUATION FOR COMPRESSIBLE HALL MHD TURBULENCE VICTOR MONTAGUD-CAMPS1, PETR HELLINGER1, ANDREA VERDINI2, SIMONE LANDI2, LUCA FRANCI3, EMANUELE PAPINI2, LORENZO MATTEINI4 1Astronomical Institute , CAS, Prague, Czech Republic, 2Università di Firenze, Italy, 3Queen Mary University of London, UK, 4Imperial College, London, UK Contact e-mail: victor.montagud-camps@asu.cas.cz INTRODUCTION • The rate at which solar wind protons temperature decreases with heliospheric distance (Tp ∝ R−0.9[1]) is slower than the prediction for an ideal gas that expands adiabatically (Tp ∝R−4/3). • The energy from large scale ﬂuctuations driven by plasma turbulence towards smaller scales is one of the proposed mechanisms that could have a heating rate adequate to explain this difference. • The heating rate associated to turbulence is computed as the energy cascade rate, Q, that is, the net energy transfer rate between the scales at which turbulent non-linear interactions take place. • The Kármán-Howarth-Monin (KHM) equation is an accurate estimation of the energy cascade rate that can be directly derived from the compressible MHD equations using structure functions. • Our objective is to extend the estimation of the energy cascade rate given by the KHM equations to scales below the proton inertial length, di and assess the effect of turbulence anisotropy on the energy cascade rate estimation. VERIFICATION OF KHM FOR 2D COMPRESSIBLE HALL-MHD 10-1 100 101 102 -1.0 -0.5 0.0 0.5 1.0 l/di O = −∂S/∂t/4+KMHD+KHall+Ψ−D [Q] • Initial simulation set-up: Simulation box of size 2562d2 i , and 20482 grid-points resolution. B0 along z. Alfvénic ﬂuctuations δBrms/B0 = 0.17 for kdi < 0.2. Zero cross-helicity, turbulent Mach M = 0.26 and η = µ = 10−3. • KHM equations terms are normalized to Hall- MHD heating rate Q ≡⟨η∇B : ∇B + τ : ∇u⟩. • KHM equation holds, but non-linear terms do not show a clear inertial range, i.e., they are not con- stant over an extended range of scales. KHM ANISOTROPY ON 3D COMPRESSIBLE HALL-MHD • Initial simulations set-up: two simulation boxes of size 323d3 i , and 5123 grid-points resolution. B0 along x. One demagnetized |B0| = 0 (3D Iso) and the other one magnetized (3D ani) with B0 along z and Alfvénic ﬂuctuations δBrms/B0 = 0.2. Zero cross-helicity, turbulent Mach M = 0.1 and η = µ = 6 10−4. • Top row: averaging over all increments (top row), demagnetized case is qualitatively similar to the 2D magnetized one. Non constant contribution from non-linear terms. • Bottom row: KMHD and KHall gyrotropized about B0 axis and 1D cuts θ = 0o, 30o, 60o and 90o with respect to B0. Anisotropic behaviour of both terms for |B0| ̸= 0 run. REFERENCES [1] M. et al. Maksimovic. Anticorrelation between the Bulk Speed and the Electron Temperature in the Pristine Solar Wind: First Results from the Parker Solar Probe and Comparison with Helios. ApJS, 246(2):62, February 2020. [2] Petr Hellinger, Andrea Verdini, Simone Landi, Luca Franci, and Lorenzo Matteini. von Kármán-Howarth Equation for Hall Magnetohydrodynamics: Hybrid Simulations. ApJL, 857(2):L19, April 2018. [3] R. Ferrand, S. Galtier, F. Sahraoui, R. Meyrand, N. Andrés, and S. Banerjee. On Exact Laws in Incompressible Hall Magnetohydrodynamic Turbulence. ApJ, 881(1):50, August 2019. DISCUSSION AND CONCLUSIONS • KHM equation for compressible Hall-MHD holds true for 2D and 3D simulations. • Magnetized plasma and 3D non-linear interactions were necessary to develop clear range for constant KMHD. For the same case, B0-aligned KHall contribution is observed above di. Box size effect or inverse cascade? • Higher resolution and smaller dissipation are still needed to show signiﬁcant Hall contributions below di KHM EQUATION FOR COMPRESSIBLE HALL-MHD Derivation of KHM equation[2,3]: evaluate Hall-MHD equations at two different points x′ = x + l and x separated by an increment l. Subtract them and average over all possible increments. Hence, −1 4 ∂S ∂t + KMHD + KH + C + Ψ −D = 0 Second order st


Control of clathrin-mediated endocytosis by NIMA family kinases Braveen B. Joseph*, Yu Wang+, Phil Edeen*, Vladimir Lažetić*, Barth D. Grant+ and David S. Fay* *Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY 82071 +Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854 Abstract Suppressor screen NEKL kinases are highly conserved members of the NIMA-kinase family, which have been predominantly implicated in cell division and ciliogenesis. We previously reported, that NEKL-2/NEK8/9 and NEKL-3/NEK6/7 are required within the C. elegans epidermis, and that their knockdown causes molting defects that results in larval lethality. In addition, we discovered a conserved set of ankyrin repeat proteins, MLT-2/ANKS6, MLT-3/ANKS3, and MLT-4/INVS, that partner with the NEKLs to regulate their intracellular localization. To better understand the mechanistic functions of NEKL-MLTs we obtained genetic suppressors of molting defects in nekl-2; nekl-3 double mutants. Strikingly, our screen identified several mutations that directly affect the activity of AP2, a conserved heterotetrametric adaptor complex required for clathrin mediated endocytosis. Knockdown of individual AP2 subunits, or an allosteric activator of AP2, FCHO-1, strongly suppress molting defects in nekl mutants. Conversely, mutations that increase the levels of active AP2 strongly enhance nekl molting defects. In addition, inhibition of nekls suppress morphological defects associated with reduced AP2 function, attesting to the tight functional connection between the NEKLs and AP2. To determine the functions of NEKLs in endocytosis, while avoiding potential confounding effects caused by nekl- mutant larval arrest, we used auxin inducible degradation methods to deplete NEKLs specifically at the adult stage. Loss of NEKLs led to greatly elevated levels of clathrin at the epidermal apical membrane and to a profound reduction in apical clathrin mobility. Adult NEKL depletion also adversely affected uptake of LRP-1, an epidermal cargo critical for molting. These results are consistent with depletion of NEKLs leading to a defect in the ability of vesicles to release clathrin after scission and suggest that NEKLs promote clathrin uncoating. Notably, both defects were largely alleviated by a reduction in AP2 or FCHO-1 activities. These findings suggest that reduced AP2 activity may facilitate clathrin uncoating and indicate that reduced AP2 activity suppresses nekl molting defects through the restoration of normal trafficking. Lastly, we show that human NEK6 and NEK7, orthologs of NEKL-3, can rescue both molting and trafficking defects in NEKL-3 depleted strains, suggesting that the control of intracellular trafficking is an evolutionarily conserved function of NEK family kinases. Individual knock down of µ, a, and d subunits Model that NEKLs may promote closed AP2 Loss of NEKL changes epidermal clathrin localization Cargo trafficking is disrupted in NEKL-depleted adults ⍺-Flag ⍺-actin + + – – NEKL-2 ::AID NEKL-3 ::AID Auxin (20h) Auxin- Inducible Degron NEKL Auxin NEKL NEKL Ub Poly- ubiquitin TIR1 SCF Ub Ub Several suppressors connected to clathrin mediated endocytosis Dynamin Closed AP2 Open AP2 Cargo Clathrin Actin Auxilin Hsc70 Uncoating Plasma Membrane FCHO-1 FCHO-1 σ nekl-2; nekl-3; fcho-1(fd131) nekl-2; nekl-3; dpy-23(fd155) nekl-2(fd81); nekl-3(gk894345); Ex nekl-3+, GFP+ Allele nekl-2(fd81) nekl-2(fd90) nekl-2(fd91) nekl-2(gk839) nekl-3(gk894345) nekl-3(sv3) nekl-3(gk506) mlt-3(fd72) mlt-4(sv9) Change Y84L G88A Y84L G87A G88A Y84L G87A Deletion D228N P194L Deletion Deletion Splice Loss of function Weak Strong Moderate Null Weak Moderate Null Null Moderate MLT-4 Larval Molting MLT-3 NEKL-3 NEKL-2 MLT-2 Old Cuticle New Cuticle Shed Cuticle Synthesis α β σ μ NEKL-3 NEKL-2 NEKL-3 NEKL-2 μ α σ nekl molting defects are suppressed by decreased function of the AP2 clathrin-adapter comple


6th International Conference on Recent Trends in Bioengineering (ICRTB 2023), 20th January 2023 MIT School of Bioengineering Science and Research Molecular Docking and Dynamics Studies of CDK1 against Epithelial Ovarian Cancer Drugs Asmita Jagadale, Shama Mujawar and K. Venkateswara Swamy* *Corresponding author : venkateswara.swamy@mituniversity.edu.in Epithelial ovarian cancer has been researched to be the most common and an aggressive form of cancer. Owing to its ability to evade detection until stage 3, when the cancer has metastasized extensively, it is important and crucial to find an effective treatment. Keeping this concept in mind, we implemented in silico analyses in the form of molecular docking and dynamics. The gene CDK1, the encoder of the protein that is a member if the Ser/Thr protein kinase family, is a catalytic subunit of the M-phase promoting factor (MPF), and a key player in the eukaryotic cell cycle. The protein encoded by CDK1 was chosen as a target for molecular docking, due to its existence as a significant hub gene from literature reviews. The ligands chosen were imipramine, trazodone, propafenone, resveratrol, alpha estradiol, levonorgestrel, apigenine, doxazosin, rottlerin, nortriptyline, prochlorprazine, noretynodrel, chlomipramine, fluphenazine, amiodarone, medrysone, piperlongumine, daunorubicin, vironostat, methotrexate and scriptaid, based on their potential evaluated by drug databases. The active sites of the protein were analysed using PDBSUM, and their neighboring amino acids were evaluated. The amino acids were observed to be Tyrosine 15A, Glutamine 81, Isoleucine 10A and Leucine 83A. The grid was calculated based on the coordinates of isoleucine, glutamine and tyrosine residues. Grid formation was done based on this location of the active site, and molecular docking was carried out using AutoDock Vina. The highest docking score observed was the protein against Doxazosin, showing a binding affinity of -10.4 kcal/mol. The interactions within the complex were observed using ProteinsPlus and Discovery Studio, and the interactions seen were among The results will be analysed and the best docked complexes were chosen to carry out molecular dynamics simulations using DESMOND. Molecular Dynamics CDK1 Retrieval of protein structure Retrieval of receptor structure Molecular Docking and analysis Result and analysis Virtual Screening Abstract Methodology Result: M o l e c u l a r D o c k i n g Molecular Dynamics Doxazosin Fluphenazine Medrysone Background Conclusion: Acknowledgement: We would like to thank to our honorable director Prof. Vinayak Ghaisas and our HOD Dr. Renu Vyas for their guidance and infrastructure support. • Ovarian cancer caused by stromal or germ cell tumors have high survival rates as compared to epithelial ovarian cancer. • Ovarian cancer rates are highest in woman aged 55-64. 3,13,000 New cases per year 2,00,000 Deaths per year 2D view of the docked complex 3D view of the docked complex The molecular docking and dynamics studies of CDK1 and FDA approved 21 drugs reveals that doxazosin against ovarian cancer is more effective. The present research work supports doxazosin usage is more effective as compared to other 20 drugs as it has lowest binding energy with -10.4 kcal/mol against CDK1. The C-alpha backbone of CDK is more stable through out 100ns within range of RMSD 1.6 to 2.2 A0 in additional doxazosin ranging from 1.62 to 2.0 A0 also stable at TIP3P water model constructed with cubic box 10 A0 at NPT conditions with 300K with Desmond, Schrodinger software.


Liu-Liu Shen, Gui-Rong Zhang, Wei Li, Markus Biesalski, Bastian J.M. Etzold 50. Jahrestreffen Deutscher Katalytiker, 15th – 17th Mar. 2017, Weimar, Germany References: [1] P. Lodeiro, J. Barriada, R. Herrero, M.S. De Vicente, Environ. Pollut. 2006, 142, 264. [2] P. Apostoli, J. Chromatogr. B 2002, 778, 63. [3] Table of regulated drinking water contaminants. https://www.epa.gov/ [4] Guidelines for drinking water quality, 4th ed. World Health Organization: Geneva, 2011. [5] L. Shen, G. Zhang, W. Li, M. Biesalsiki, B. J. M. Etzold, ACS Omega in submission. Device fabrication: Modifier-Free Microfluidic Electrochemical Sensor for Heavy Metal Detection Heavy metals are hazard pollutants to the environment and impose severe risks to human health. Therefore, heavy metal detection is playing important role in environmental and clinical analysis. In this work, a simple, cost- effective and portable miniaturized electrochemical carbon-based sensor (µCS) is designed and proved to be highly sensitive towards Cd2+ and Pb2+ detection in aqueous solution. The µCS possess a novel 3D structure with working and reference electrodes directly facing each other but separated by the microfluidic paper channel. The electrodes in µCS are inexpensive graphite foil without any additional surface modifier such as mercury or bismuth. It is found that impressive low detection limits of 1.2 µg/L for Cd2+ and 1.8 µg/L for Pb2+ can be achieved on the µCS. The µCS also exhibits stable sensing performance up to 10 repetitive measurements, demonstrating the robustness of a sensing device for heavy metal detections. We believe that a proper design in the device configuration can completely eliminate the necessity to modify the working electrode by using additional surface modifier, which could provide new ideas for portable electroanalytical/sensing systems. Electrolyte: 0.1 M acetate buffer, pH=4.6 Individual detection of Cd2+ and Pb2+ § Deposition condition: Cd2+: -1.2 V, 60 s Pb2+: -1.1 V, 180 s § The limit of detection (LOD) are below the allowable limits in drinking water proposed by US Environmental Protection Agency (Cd: 5 µg/L, Pb: 15 µg/L) and World Health Organization (Cd: 3 µg/L, Pb: 10 µg/L). Stability and reproducibility of the µCS § The deposition condition for simultaneous detection is (-1.2 V, 180 s). § The detection limit is 6 µg/L for both Cd2+ and Pb2+. Conclusions: § A modifier-free, low cost, reusable, electrochemical microfluidic carbon-based sensor was developed for heavy metal detection. § High sensitivity and low detection limit at short detection time are obtained on the sensor during individual detection for Cd2+ and Pb2+. § The high sensitivity may originate from the combined microfluidic configuration and novel 3D electrode layout, which may provide some new ideas for other portable electroanalytical/sensing systems. Structure analysis of the graphite foil Simultaneous detection of Cd2+ and Pb2+ § Very good electrocatalytic stability was observed on µCS. Prof. Bastian J.M. Etzold (etzold@tc1.tu-darmstadt.de) Ernst-Berl-Institut für Technische und Makromolekulare Chemie Technische Universität Darmstadt 64287 Darmstadt Correspondence: This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement n° 681719) Electrochemical measurements 1. Metal deposition; 2. Square wave voltammetry Experimental Section Cd2+ Pb2+ LOD = 1.2 µg/L LOD = 1.8 µg/L § The electrodeposited Cd species are selectively located at the edge positions of graphite flakes. WE, CE & RE: graphite foil Paper channel: filter paper, pore size 15 µm


The Library Treasure Hunt – Reach for the Stars! Introducing first-year students to the landscape of scientific information Eva Jurlander, Lund Observatory and Carina Enestarre, Physics and Astronomy Library Cajsa Andersson, Library of Chemistry and Chemical Engineering, Kristina Holmin Verdozzi, Physics and Astronomy Library, Nina Reistad, Department of Physics The students gather in the library and meet the library staff. The librarians give a quick presentation of the library and an introduction to the treasure hunt. The students receive a stamp on the treasure map from the librarian. They get their next assignment and continue on with their quest. Mission accomplished! Each student evaluates the hunt via a short poll and receives a treasure. The librarians thank the students and hope to see them soon again in the library. The students are divided into smaller groups and given their first assignment and a treasure map. OBJECTIVE • To make the first encounter with the library useful, fun and memorable for the students • To provide all students with a minimum level of information literacy CHALLENGES • The library competes with many other introductory activities for the first-year student. • To find an amusing way to introduce the library. METHOD • Learning by doing • Hands-on excercises • On the spot assessment and evaluation • Reward system OUTCOME • All students receive a positive first encounter with the library. • They get to know essential aspects of the library resources. • It opens up for further development of the student’s information literacy. • The librarians get immediate input from the students. SUCCESS FACTORS • Close collaboration between librarians and teachers supported by the management • Making the library introduction an integrated and compulsory part of the course programme ADDED VALUE • Students practice team work • Interlibrary staff cooperation • Subject library profiling DEVELOPMENTS • Present new technology for example Ipads and e-readers to enhance the use of the digital collection. • The library should be an integrated part of all teachers’ planning at all levels. The students carry out the missions together in groups and discover the physical and digital library collections and services. The students communicate their findings directly to the librarian who gives instant feedback. . 1 Photo: Francois Polito CC BY-SA 3.0 4 4 4 3 2 5 6 Highlight of the hunt! A view from top of the Observatory tower Sweden www.fysik.lu.se/english/library/treasure


MIT Open Access Articles FEDERATED LEARNING FRAMEWORK FOR NLP IN HEALTHCARE: ASSESSING HOSPITAL READMISSION USING ELECTRONIC HEALTH RECORDS The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation: Nalawade, Sahil, Samineni, Soujanya, Chowdhury, Alex, Feng, Ling, Umeton, Renato et al. 2023. "FEDERATED LEARNING FRAMEWORK FOR NLP IN HEALTHCARE: ASSESSING HOSPITAL READMISSION USING ELECTRONIC HEALTH RECORDS." Conference Poster at Bio-IT World, Boston, 2023 (May). As Published: https://www.bio-itworldexpo.com/poster-presentations Persistent URL: https://hdl.handle.net/1721.1/151725 Version: Author's final manuscript: final author's manuscript post peer review, without publisher's formatting or copy editing Terms of Use: Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.