fairdataihub/poster-sentry-training-data huggingface dataset:
BD2K-LINCS DATA COORDINATION AND INTEGRATION CENTER Acknowledgements: This research was supported by grant U54HL127624 awarded by the National Heart, Lung, and Blood Institute through funds provided by the trans-NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program (http://www.lincsproject.org/) and the trans-NIH Big Data to Knowledge (BD2K) initiative (http://www.bd2k.nih.gov). Correspondence: s.schurer@miami.edu The LINCS Data Portal and FAIR LINCS Dataset Landing Pages Abstract The LINCS Data Portal (LDP) presents a unified interface to access LINCS datasets and metadata with mappings to several external resources. LDP provides various options to explore, query, and download LINCS dataset packages and reagents that have been described using the LINCS metadata standards. We recently introduced LINCS Dataset Landing Pages to provide integrated access to important content for each LINCS dataset. The landing pages provide deep metadata for each LINCS dataset including description of the assays, authors, data analysis pipelines, and standardized reagents such as small molecules cell lines, antibodies, etc, with rich annotations. The landing pages are a key component to make LINCS data persistent and reusable, by integrating LINCS datasets, data processing pipelines, analytes, perturbations, model systems and related concepts as uniquely identifiable digital research objects. LDP supports ontology-driven concept search, free text search, facet filtering, logical intersection of filters (AND, OR), and list, table, and matrix views. LDP enables download of LINCS dataset packages, which consist of released datasets and associated metadata. LDP also provides several specialized apps including small molecule compounds and cell lines. A landing page facilitates interactive exploration of all LINCS datasets via several classifications. LDP is built on a robust API and is integrated with the MetaData Registry and interfaces with other components of the Integrated Knowledge Environment (IKE) developed in our Center. All LINCS datasets are also indexed in bioCADDIE DataMed. Amar Koleti1, 5, Vasileios Stathias1, 2, 5, Raymond Terryn1, 2, 5, Michele Forlin1, 2, 5, Dušica Vidović1, 2, 5, Caty Chung1, 5, Wen Niu4, 5, Caroline Monteiro3, 5, Christopher Mader1, 5, Avi Ma’ayan3, 5, Mario Medvedovic4, 5, Stephan Schürer1, 2, 5 1Center for Computational Science and University of Miami, Miami, FL; 2Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL: 3Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1215, New York, NY; 4Division of Biostatistics and Bioinformatics, Environmental Health Department, University of Cincinnati; Cincinnati, OH; 5BD2K LINCS Data Coordination and Integration Center LINCS Data Portal (LDP) http://lincsportal.ccs.miami.edu LINCS Datasets Small Molecules EBI services cross-references LINCS Small Molecules IDs LINCS Datasets in DataMed CLO LINCS Cell Lines
Oct. Nov. Dec. Jan. Feb. Mar. Apr. May 10 20 30 40 50 60 70 80 409 665 220 504 646 265 310 354 Updates number : 2013 October – 2014 May Data volume increase (raw text format only, in Mo) 40% 54% 6% Regularly Occasionally Not at all Oct. Nov. Dec. Jan. Feb. Mar. Apr. May 1866 2613 982 2127 2813 1230 1512 1430 Number of requests : 2013 October – 2014 May Average 2013-2014 Average 2012-2013 TWiki : A collaborative space of internal documentation ~ An efficient way to work together ~ The documentalists at Strasbourg astronomical Data Center treat publications to create content for the SIMBAD and VizieR databases. The publication treatment is quite complex and the ingestion process needs to be described. This requires precise knowledge and mutual support among the documentalists in interaction with computer engineers and astronomers. Documentalists at CDS have thought of an adapted way to organize and enrich their internal documentation. The “TWiki” collaborative space, recently reorganized and enriched, regroups documents about agreed-upon procedures and methods, directions for use of the software and tools, shared problems/solutions. It is a tool for sharing, preserving and enriching the common knowledge of the whole staff. E. Son, A. Eisele, A. Schaaff, E. Perret, M. Brouty, C. Bruneau, C. Brunet, M. Buga, F. Genova, S. Guehenneux, S. Lesteven, C. Loup, L. Miguel, M. Neuville, A. Oberto, P. Vannier, P. Vonflie, F. Woelfel Observatoire Astronomique de Strasbourg, Université de Strasbourg/CNRS, UMR 7550 An organization per boxes : ●Staff organization ●SIMBAD and VizieR databases ●CDS Tools (DJIN and COSIM) ●SIMBAD Dictionnary of nomenclature ●Astrophysics ●Computer science ●Useful links What kind of information can we find in the Twiki space ? ●General information ●Updating commands ●Meetings reports ●PDF documents and web links ●Follow-up of the work progress Documentalists Computer scientists Astronomers Edition : everyone can easily add, complete, correct and refine data. Home Page Shortcuts To the most used pages Links to pages... Contents The Twiki space on a day to day basis Common knowledge : the information is available for the wole staff One place to find the good information : it's easy and accessible Preservation of information, common memory Added value Normalisation of work practices Training of new staff and keeping track of the knowledge of retiring staff Someone struggles, fines a solution and shares it with everybody Work monitoring in real time for complex and shared tasks Save time Improve productivity and efficiency Number of requests Updates and volume increase Attending the meeting (Mo) 14 573 requests /8 months 3 373 updates /8 months + 92% Text data /1 year Use by the CDS staff (34 people) 1082 1822 Updates average : 422 /month (vs 172 /month last year)
Start Here: On Ramps for the VIVO Project Mike Conlon, mconlon@duraspace.org; Julia Trimmer, julia.trimmer@duke.edu; Graham Triggs, gtriggs@duraspace.org Project Managers Ask Questions Join bit.ly/vivo-community and ask away! Read the Implementation Guide VIVO has a guide to implementation. See bit.ly/vivo-planning Work with Data Providers Speak with data providers about VIVO and your project. Share your interest in research discovery, open scholarship, and linked data Join Outreach and Engagement Calls Monthly calls for sharing outreach and engagement experiences bit.ly/vivo-oaeig Help us Grow The VIVO Registry bit.ly/vivo- registry lists all VIVO sites. Add your site. Developers Install VIVO github.com/vivo-project Read the Documentation bit.ly/vivo-docs Ask Questions Join bit.ly/vivo-tech and ask away! Join Developer Calls See bit.ly/vivo-dig Develop Ontology Ontologies used by VIVO are developed using open source processes. See github.com/openrif Review/Open JIRA tickets See bit.ly/vivo-jira Become a Committer See bit.ly/vivo-committers Faculty Learn about VIVO The VIVO Book is available here: bit.ly/vivo-book Join All Group Get VIVO Updates, a weekly summary of the VIVO news. bit.ly/vivo-all Advocate for VIVO Talk to fellow faculty members and administrators about VIVO and the case for open scholarship, research discovery, and linked data Participate in your VIVO Work with your local VIVO project to generate value for faculty. Ask us about your local project. mconlon@duraspace.org gtriggs@duraspace.org Participate in the VIVO Project The VIVO wiki bit.ly/vivo-wiki has more info Members Consider membership Financial support for VIVO comes from VIVO membership in Duraspace. See vivoweb.org/membership Become a member Not a member? Becoming a member is simple. See bit.ly/dura-join Join All Group Get VIVO Updates, a weekly summary of the VIVO news. bit.ly/vivo-all Attend the Summit Premium members are invited to the Duraspace Summit held in Washington DC each March. See bit.ly/dura-summit Participate in Governance Serve on Leadership and/or Steering. See VIVO charter bit.ly/vivo-charter Service Providers Learn About Registered Service Provider (RSP) Program See bit.ly/dura-rsp Join All Group Get VIVO Updates, a weekly summary of the VIVO news. bit.ly/vivo-all Become an RSP Questions? Contact Jonathan Markow (jjmarkow@duraspace.org) Help us Grow The VIVO Registry bit.ly/vivo-registry lists all VIVO sites. Add your sites. Ask Questions We want to hear from you. Drop us a note mconlon@duraspace.org, gtriggs@duraspace.org Participate in the VIVO Project The VIVO wiki bit.ly/vivo-wiki has more info VIVO has many on-line resources. Here are some suggestions to help you get started.
Double-Active Membranes for a sustainable CO2 cycle DAM4CO₂ develops a novel membrane technology for the simultaneous CO₂ separation and its photocatalytic conversion to C4-C9 molecules, as renewable fuels. The project will deliver a prototype, designed using the design-build-test-learn approach, for a proof-of-concept validation that will be tested in lab-conditions. The DBTL approach is inherent in each scientific/technological WP of the project. Our objective: Partners: This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement No 101115488. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Innovation Council and SMEs Executive Agency (EISMEA). Neither the European Union nor the granting authority can be held responsible for them. WP1: Coordination & Management WP2: Materials Synthesis WP3: Materials Characterization WP4: Membrane preparation & Characterization WP5: Capture with Membranes WP6: Conversion with Membranes WP7: Multiscale Modelling & Life Cycle Assessment WP8: Dissemination & Communication & Exploitation WP9: Portfolio Activities Contacts PROJECT COORDINATOR Dr. Alessio Fuoco, CNR – ITM E-mail: alessio.fuoco@cnr.it Website: www.dam4co2.eu E-mail: dam4co2@itm.cnr.it Project number: 101115488 Project title: Double-Active Membranes for a sustainable CO2 cycle Project Acronym: DAM4CO2 Granting authority: EISMEA and UKRI Start date: 01/11/2023 Duration: 36 months EU Contribution: 2 975 275.00 € UK Contribution: 823 176.00 £ • Use of non-critical raw materials at any stage of the project • Greener material and protocols for membrane production • Development of the next generation membranes for CO2 capture using advanced polymers and MOFs • Development of photocatalytic membranes using mono and bi-functional catalysts for CO2 conversion into C4-C9 molecules • Integration of the CO2 management and valorisation processes into a single device • Design of novel membrane modules CNR (IT) INSTM (IT) ME-SEP (PL) UEdin (UK) PRIMALCHIT (ES) UPV-ITQ (ES) USwan (UK) DAM4CO₂, responding to the call "EIC Pathfinder Challenge: Carbon dioxide and nitrogen management and valorisation", aims at changing the existing paradigm within separation and utilization of CO₂ by coupling membrane and catalytic technologies. https://www.instagram.com/dam4co2/ https://www.linkedin.com/company/dam4co2 https://www.youtube.com/@DAM4CO2_EIC https://twitter.com/dam4co2
GND in a Nutshell Ein Normdatensatz beschreibt regel- basiert eine bestimmte Entität. Die Datensätze enthalten Informationen, die die entsprechende Entitäten ex- plizit charakterisieren und so identifizieren. Die Gemeinsame Normdatei (GND) ist ein Dienst, um Normdaten kooperativ nutzen und verwalten zu können. Diese Normdaten reprä- sentieren und beschreiben Entitäten, wie Personen, Körperschaften, Kon- ferenzen, Geografika, Sachbegriffe und Werke, die in Bezug zu Kulturgut sowie kulturellen und wissenschaft- lichen Sammlungen stehen. Anforderungen sammeln Auf der Grundlage vorliegender Erfahrungen aus der Text+ Community, die zum Beispiel über die zahlreich eingereichten User Stories gesammelt wurden, werden Bedarfe an eine GND- Agentur ermittelt. Diese Aufgabe führen wir im Rahmen verschiedener Formate wie dem GND-Forum weiter, wobei ein Ergebnisbericht zum Dezember 2023 vorliegen wird. In Case Studies überführen Die ermittelten Bedarfe werden in Case Studies überführt. In der Datendomäne Editions schauen wir anhand von drei Editions- projekten an der SUB Göttingen, wie die Bedarfe an GND-Norm- datensätzen in konkreten Work- flows umgesetzt werden können. Ähnlich werden wir für die Datendomänen Collections und Lexical Resources verfahren. Die Workflows aus den Case Studies sollen in allgemeine, skalierbare Workflows bis April 2024 übertragen werden. Prototypische Strukturen testen Wir möchten die bereits vorhandenen und in Planung befindlichen Strukturen testen. Damit wollen wir gewährleisten, dass die technischen, administrativen und daten- theoretischen Strukturen der Agentur für die Text+ Community adäquat sind. Die Produktivnahme ist zum Juni 2025 geplant. Das NFDI-Konsortium Text+ wird gefördert durch die Deutsche Forschungsgemeinschaft (DFG) unter der Projektnummer 460033370. Text+ ist Teil der Hintergrund: „Frankfurt am Main“ im GND-Explorer. DNB 2022. CC BY-SA 3.0 Icon Nutshell: Tatyana. Noun Project. Icon Road: Sergey Krivoy. Noun Project. beide CC BY 3.0 https://gnd.network/Webs/gnd/DE/UeberGND/FAQ/faq_node.html Agenturaufgabenbaum. Jürgen Kett, DNB, Mai 2022. CC BY-SA 3.0 Task Area Infrastructure/Operations Ein Baum in der Roadmap Kontakt: gnd-info@dnb.de Poster: „Ein Baum in der GND – Gemeinsame Normdatei“ Inhalt: Text+ Infrastructure/Operations Verantwortlich: Marie Annisius , Barbara Fischer , Alexander Steckel Event: Text+ Plenary, 12-13. September 2022, Mannheim
libEnsemble: New capabilities for coordinating dynamic ensembles of calculations Stephen Hudson Jeffrey Larson John-Luke Navarro Stefan M. Wild Overview libEnsemble is a Python toolkit for coordinating dynamic, asynchronous ensembles of calculations on massively parallel resources. Worker processes launch simulation and generator functions. libEnsem- ble also provides: • Ad-hoc task generation • Dynamic Resource management • Application monitoring • Portability and ﬂexibility • Coordinating data-ﬂow between tasks • Low startup cost: pip install libensemble • Conﬁgure via Python scripts or yaml/toml/json Cross-System Ensembles libEnsemble can submit remote apps and user functions via the Balsam and funcX platforms. With Balsam: Remote applications With funcX: Remote simulation functions Multiﬁdelity optimization of a WarpX laser-plasma simulation Multi-ﬁdelity simulations have demon- strated 10x speedup over single ﬁdelity equivalents. Progress from ten replications of libEnsem- ble+WarpX with two multiﬁdelity meth- ods and a single (highest) ﬁdelity method. Objective value is computed from the highest ﬁdelity simulation. Variable Resource Management libEnsemble’s Resource Manager now divides resources into resource sets that can be assigned (and dynamically reas- signed) to workers. This enables easy support of multi-ﬁdelity simulations. Community Examples and Integrations The libEnsemble repository includes many simple exam- ple functions. Users can also now contribute to a separate growing library of functions and complete workﬂows, encouraging maximum code re-use. Example genera- tors include optimization, calibration, machine learn- ing, and many others. Libensemble/libe-community-examples All Workﬂows are Portable • Summit • Polaris • ThetaGPU • Perlmutter A New Pythonic Interface Download or Contribute Available through pip: pip install libensemble conda through conda-forge channel: conda install -c conda-forge libensemble Spack: spack install py-libensemble GitHub: http://github.com/Libensemble/libensemble Read the Docs: https://libensemble.readthedocs.io
Poster nr.: 421.08 −10 −5 0 5 10 value −10 −5 0 5 10 value -5 8 Natural History Placebo Video instructions and practice phase Placebo+Conditioning Standard task General Questionnaires Electrode preparation Waiting (10 min) Expectation Questionnaire 1 Standard task Manipulated task Experience Questionnaire 1 Sham tACS Expectation Questionnaire 2 Standard task Experience Questionnaire 2 Sham tACS Task 1 Task 2 Task 3 Block 2 Block 3 Anticipated (before) Experienced (after) decrease neutral improve decrease neutral improve 0 10 20 30 0 10 20 30 n Group NHG Placebo Placebo+Conditioning Expected and experienced changes in performance (forced choice) ● ● ● ● ● ● ● ● ● ● ● ● Anticipated (before) Experienced (after) 2 3 2 3 10 20 30 40 task value Group ● ● ● NHG Placebo Placebo+Conditioning Expected and experienced changes in performance (estimate) ● ● ● ● ● ● ● ● ● Total reward 1 2 3 200 300 400 task Reward Group ● ● ● NHG Placebo Placebo+Conditioning ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● alpha beta w NHG Placebo Placebo+conditioning −2 0 2 4 0.00 0.25 0.50 0.75 −0.5 0.0 0.5 1.0 1 2 3 1 2 3 1 2 3 val Task Task effects ● ● ●● ● ● ● ● ● ● 0.25 0.50 0.75 1.00 beta 0.25 0.50 0.75 1.00 alpha ● ● ●● ● ● ● ● ● ● 0.25 0.50 0.75 1.00 w 0.25 0.50 0.75 1.00 alpha ● ● ● ● ● ● ● ● ● ● 0.25 0.50 0.75 1.00 w 0.25 0.50 0.75 1.00 beta group 100 200 300 Expected Reward NHG Placebo Placebo+ Conditioning ● ● ● ● ● ● ● ● ● ● 0.1 0.2 0.3 0.4 beta 0.85 0.90 0.95 1.00 alpha ● ●● ● ● ● ● ● ● 0.3 0.4 0.5 0.6 0.7 w 0.85 0.90 0.95 1.00 alpha ● ● ● ● ● ● ● ● ● 0.4 0.5 0.6 0.7 w 0.1 0.2 0.3 0.4 beta q
@ F A C EITArcti c @ F A C EITArcti c @ fa c e _i t_arc tic @ The F A C E -IT Pro j e ct www.face-it-project.eu FACE-IT has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 869154. The Porsangerfjord in Northern Norway is a sub-arctic fjord with an inner arctic part and face an invasion by the red king crab Paralithodes camtschaticus since the end of the 1990’s. This offers the opportunity to study the dynamics of an Arctic ecosystem facing multiple stressors, i.e., climate change and invasive species. The Inner Fjord as a Refugium In the Porsangerfjord, fish species respond to climate change while bottom-living (= benthic) invertebrates are more threatened by invasive species such as the king crab. Fish diversity increases towards the inner fjord due to Arctic cold-adapted assemblages overlapping with newly arriving warm-adapted species. This effect was not observed in bottom- living invertebrates, yet the refuge function of the inner fjord might be unbalanced due to the red king crab’s predation on Arctic species. Red King Crab Paralithodes camtschaticus Climate Change Response in a Sub-Arctic Fjord: Fishes and Invertebrates Respond DifferentlyLaurène Mérillet1,2, Morten D. Skogen1,2, Frode Vikebø1,2, Lis LindalJørgensen3 1Institute of Marine Research, Bergen, Norway 2Bjerknes Centre for Climate Research, Bergen, Norway 3Institute of Marine Research, Tromsø, Norway Berengere.Husson@hi.no The main environmental changes in the fjord were: • freshening of the water • increase of the seabed current • decrease of the maximum sea ice extent. Species richness and diversity of fishes significantly increased into the fjord, due to the arrival of warm-water species over time that overlapped with cold-water species that have seen their biomass significantly reduced. No significant decrease in the biomass of the cold-water benthic (= sea floor associated) species was visible, which could indicate an efficient refugee effect of the inner fjord. Sampling areas between 2007 and 2019 Examples of bottom-living invertebrates Get Mérillet et al. 2022
Department of Computer Science, University of Helsinki Tommi Meskanen and Valtteri Niemi (tommi.meskanen@helsinki.fi, valtteri.niemi@helsinki.fi) Trust, Security and Privacy for HELIOS HELIOS is an EU Horizon 2020 project • duration of 3 years • budget 5 million euros • 15 partners around Europe, both industrial and academic HELIOS is a social media platform that is • modular • peer-to-peer • open-source • open for developers to build their apps on One of the main concepts of HELIOS platform is Trust. • Trust level is automatically calculated for other users the ego connects to. • Trust level is calculated based on the frequency and level of interactions between the ego and other users. No central authority. Security is based on encryption and authentication using the public keys that every user has and that are shared to their friends. For Privacy • all communication between users is end-to-end encrypted • all files on the users’ devices are encrypted HELIOS is able to identify the Context the user (Ego) is in. Based ot the context HELIOS decides which friends (Alters) or activities should have priority. The HELIOS platform enables users to create Ad Hoc groups • users can join and leave. • all communication in the group is again encrypted • people outside the group cannot read it
A Finite Element Study on the Biomechanics of Intracorneal Implants in Keratoconus Corneal Models Shima Bahramizadeh Sajadi1, Hamid Reza Katoozian2, Philippe Büchler3 1,2Department of Biomedical Engineering, Polytechnic of Tehran, Tehran, Iran 1,3Computational Bioengineering, ARTORG Center for Biomedical Engineering Research Introduction • Keratoconus (KC) is a progressive corneal disease characterized by thinning, weakening and steepening of the cornea. • KC progression is manifested by corneal protrusion, irregular astigmatism and severe unilateral and bilateral myopia. • The prevalence is 0.05% in Western countries but higher in the Middle East and Asia (0.76% - 3.30%). • KC-associated anatomical deviations strongly impact the patient’s vision and quality of life. • The etiology of KC is not well understood and there is no cure. • Corneal geometric alterations affect ophthalmic surgical plans. • Intracorneal ring segment (ICRS) implantation proved to be a clinically effective approach in retrieving the corneal curvature in more advanced stages of the disease. • Empirical nomograms are used by clinicians to define the surgical planning. Nomograms provide a homogenized view of the treatment. GOALS → Ring implant simulations in prediction of post-surgical deformation and internal stresses → To investigate geometrical features of ICRS surgeries to propose personalized sets of segments based on each patient’s corneal topographic maps Results and Discussion • Generic models Methods • A round, central KC cornea was modeled with physiological intraocular pressure. • Combination sets of ICRS implants were considered. References [1]. Flecha-Lescún, et al., Biomech Model Mechanobiol, 2018: pp. 1-16. [2]. Ariza-Gracia, 2020. Transl. Vis. Sci. Technol., 9(11), pp.26-26. [3]. Kling, S. and Marcos, S., Invest Ophthalmol Vis Sci, 2013. 54(1): pp. 881-889. [4]. nkcf.org, National Keratoconus Foundation Gallery. Ongoing/Future Work • Patient-specific models • Characterizing mechanical properties of corneas