cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Construction and use of medical devices for the selective removal of bacteria and endotoxins from biological fluids
Creators: name: Cappello, Giovanni
Publisher: name: Università di Siena
Year: 2023
Subjects: subject: medical devices, antimicrobial peptides, sepsis, lipopolysaccharides, bacterial infection
subject: BIO/10 BIOCHIMICA
subject: medical devices
subject: antimicrobial peptides
subject: sepsis
subject: lipopolysaccharides
subject: bacterial infection

description: Construction of a medical device, containing an antimicrobial peptide, for the removal of bacteria and endotoxins in sepsis patients
(500566) William Ayre
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-Modular Coupling
Creators: name: Wills, Peter R.
name: Popinga, Alex
name: Bouckaert, Remco
name: Carter, Charles W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: The role of aminoacyl-tRNA synthetases (aaRS) in the emergence and evolution of genetic coding poses challenging questions concerning their provenance. We seek evidence about their ancestry from curated structure-based multiple sequence alignments of a structurally invariant “scaffold” shared by all 10 canonical Class I aaRS. Three uncorrelated phylogenetic metrics—mutation frequency, its uniformity, and row-by-row cladistic congruence—imply that the Class I scaffold is a mosaic assembled from successive genetic sources. Metrics for different modules vary in accordance with their presumed functionality. Sequences derived from the ATP– and amino acid– binding sites exhibit specific two-way coupling to those derived from Connecting Peptide 1, a third module whose metrics suggest later acquisition. The data help validate: (i) experimental fragmentations of the canonical Class I structure into three partitions that retain catalytic activities in proportion to their length; and (ii) evidence that the ancestral Class I aaRS gene also encoded a Class II ancestor in frame on the opposite strand. A 46-residue Class I “protozyme” roots the Class I tree prior to the adaptive radiation of the Rossmann dinucleotide binding fold that refined substrate discrimination. Such rooting implies near simultaneous emergence of genetic coding and the origin of the proteome, resolving a conundrum posed by previous inferences that Class I aaRS evolved after the genetic code had been implemented in an RNA world. Further, pinpointing discontinuous enhancements of aaRS fidelity establishes a timeline for the growth of coding from a binary amino acid alphabet.
(500572) Joseph Millard
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
ReHyb: D11.5 Dissemination & Communication Plan and activity report 2
Creators: name: Endo, Satoshi
Publisher: name: Zenodo
Year: 2023
Subjects: Rehabilitation
Project visibility
Dissemination, Communication

description: This deliverable is the second iteration of the dissemination & communication plan and activity report, which describes the activities the project engaged in to increase its potential impact during Year 2 of the ReHyb project.
The Emerging Role of CAR T Cell Therapy in Relapsed/Refractory Hodgkin Lymphoma
Creators: name: Meier, Jeremy A.
name: Savoldo, Barbara
name: Grover, Natalie S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Treatment for Hodgkin lymphoma (HL) has evolved considerably from the time it was originally described in the 19th century with many patients now being cured with frontline therapy. Despite these advances, upwards of 10% of patients experience progressive disease after initial therapy with an even higher percentage relapsing. Until recently there had been limited therapeutic options for relapsed and/or refractory HL outside of highly intensive chemotherapy with stem cell rescue. Improved understanding of the pathophysiology of HL, coupled with the emergence of more targeted therapeutics, has reshaped how we view the treatment of relapsed/refractory HL and its prognosis. With this, there has been an increased focus on immunotherapies that can reprogram the immune system to better overcome the immunosuppressive milieu found in HL for improved cancer cell killing. In particular, chimeric antigen receptor (CAR) T cells are emerging as a valuable therapeutic tool in this area. Building on the success of antibody-drug conjugates directed against CD30, CAR T cells engineered to recognize the same antigen are now reaching patients. Though still in its infancy, CAR T therapy for relapsed/refractory HL has shown exceptional promise in early-stage clinical trials with the potential for durable responses even in patients who had progressed through multiple lines of prior therapy. Here we will review currently available data on the use of CAR T cells in HL, strategies to optimize their effectiveness, and how this therapy may fit into the treatment paradigm of HL going forward.
Annular Groove Phase Mask coronagraph in diamond for mid-IR wavelengths: manufacturing assessment and performance analysis
Creators: name: Delacroix, Christian
name: Forsberg, Pontus
name: Karlsson, Mikael
name: Mawet, Dimitri
name: Lenaerts, Cédric
name: Habraken, Serge
name: Hanot, Charles
name: Surdej, Jean
name: Boccaletti, Anthony
name: Baudrand, Jacques
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Phase-mask coronagraphs are known to provide high contrast imaging capabilities while preserving a small inner working angle, which allows searching for exoplanets or circumstellar disks with smaller telescopes or at longer wavelengths. The AGPM (Annular Groove Phase Mask, Mawet et al. 2005) is an optical vectorial vortex coronagraph (or vector vortex) induced by a rotationally symmetric subwavelength grating (i.e. with a period smaller than λ/n, λ being the observed wavelength and n the refractive index of the grating substrate). In this paper, we present our first mid- infrared AGPM prototypes imprinted on a diamond substrate. We firstly give an extrapolation of the expected coronagraph performances in the N-band (~10 μm), and prospects for down-scaling the technology to the most wanted L- band (~3.5 μm). We then present the manufacturing and measurement results, using diamond-optimized microfabrication techniques such as nano-imprint lithography (NIL) and reactive ion etching (RIE). Finally, the subwavelength grating profile metrology combines surface metrology (scanning electron microscopy, atomic force microscopy, white light interferometry) with diffractometry on an optical polarimetric bench and cross correlation with theoretical simulations using rigorous coupled wave analysis (RCWA).
description: 10 pages
(500575) William Woodman
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Expression of a Truncated Form of ODAD1 Associated with an Unusually Mild Primary Ciliary Dyskinesia Phenotype
Creators: name: Zariwala, Maimoona A.
name: Knowles, Michael R.
name: Bustamante-Marin, Ximena M.
name: Smith, Amanda J.
name: Dang, Hong
name: Yin, Weining
name: Capps, Nicole A.
name: Leigh, Margaret W.
name: Hildebrandt, Friedhelm
name: Sullivan, Kelli M.
name: Ostrowski, Lawrence E.
name: Daniels, Leigh Anne
name: Sears, Patrick R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Primary ciliary dyskinesia (PCD) is a rare lung disease caused by mutations that impair the function of motile cilia, resulting in chronic upper and lower respiratory disease, reduced fertility, and a high prevalence of situs abnormalities. The disease is genetically and phenotypically heterogeneous, with causative mutations in > 50 genes identified, and clinical phenotypes ranging from mild to severe. Absence of ODAD1 (CCDC114), a component of the outer dynein arm docking complex, results in a failure to assemble outer dynein arms (ODAs), mostly immotile cilia, and a typical PCD phenotype. We identified a female (now 34 years old) with an unusually mild clinical phenotype who has a homozygous non-canonical splice mutation (c.1502+5G>A) in ODAD1. To investigate the mechanism for the unusual phenotype, we performed molecular and functional studies of cultured nasal epithelial cells. We demonstrate that this splice mutation results in the expression of a truncated protein that is attached to the axoneme, indicating that the mutant protein retains partial function. This allows for the assembly of some ODAs and a significant level of ciliary activity that may result in the atypically mild clinical phenotype. The results also suggest that partial restoration of ciliary function by therapeutic agents could lead to significant improvement of disease symptoms.
Preliminary Acceptability of a Home-Based Peripheral Blood Collection Device for Viral Load Testing in the Context of Analytical Treatment Interruptions in HIV Cure Trials: Results from a Nationwide Survey in the United States
Creators: name: Lalley-Chareczko, Linden
name: Hiserodt, Emily
name: Montaner, Luis J.
name: Tebas, Pablo
name: Peterson, Beth
name: Taylor, Jeff
name: Shipley, Lisa
name: Carter, William B.
name: Howell, Bonnie J.
name: Anderson, Melanie
name: Dee, Lynda
name: Lynn, Kenneth M.
name: Rosenbloom, Daniel
name: Kim, Sukyung
name: Henley, Laney
name: Villa, Thomas J.
name: Campbell, Danielle M.
name: Hazuda, Daria J.
name: Hastie, Elizabeth
name: Bateman, Kevin
name: Mapp, Derrick
name: Evans, Brad R.
name: Roebuck, Christopher
name: Dubé, Karine
name: Eskaf, Shadi
name: Agarwal, Harsh
name: Mounzer, Karam
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Frequent viral load testing is necessary during analytical treatment interruptions (ATIs) in HIV cure-directed clinical trials, though such may be burdensome and inconvenient to trial participants. We implemented a national, cross-sectional survey in the United States to examine the acceptability of a novel home-based peripheral blood collection device for HIV viral load testing. Between June and August 2021, we distributed an online survey to people with HIV (PWH) and community members, biomedical HIV cure researchers and HIV care providers. We performed descriptive analyses to summarize the results. We received 73 survey responses, with 51 from community members, 12 from biomedical HIV cure researchers and 10 from HIV care providers. Of those, 51 (70%) were cisgender men and 50 (68%) reported living with HIV. Most (>80% overall) indicated that the device would be helpful during ATI trials and they would feel comfortable using it themselves or recommending it to their patients/participants. Of the 50 PWH, 42 (84%) indicated they would use the device if they were participating in an ATI trial and 27 (54%) also expressed a willingness to use the device outside of HIV cure studies. Increasing sensitivity of viral load tests and pluri-potency of the device (CD4 count, chemistries) would augment acceptability. Survey findings provide evidence that viral load home testing would be an important adjunct to ongoing HIV cure-directed trials involving ATIs. Survey findings may help inform successful implementation and uptake of the device in the context of personalized HIV care.
(500577) William Wilkinson
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Gravitational entropy of local cosmic voids
Creators: name: Sussman, Roberto A.
name: Larena, Julien
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We undertake a non-perturbative study of the evolution of the "gravitational entropy" proposed by Clifton, Ellis and Tavakol (CET) on local expanding cosmic CDM voids of $\sim 50-100$ Mpc size described as spherical under-dense regions with negative spatial curvature, whose dynamics is determined by Lemaitre-Tolman-Bondi (LTB) dust models asymptotic to three different types of FLRW background: $Λ$CDM, Einstein de Sitter and "open" FLRW with $Λ=0$ and negative spatial curvature. By assuming generic nearly spatially flat and linear initial conditions at the last scattering time, we examine analytically and numerically the CET entropy evolution into a fully non-linear regime in our present cosmic time and beyond. Both analytic and numerical analysis reveal that the late time CET entropy growth is determined by the amplitude of initial fluctuations of spatial curvature at the last scattering time. This entropy growth decays to zero in the late asymptotic time range for all voids, but at a faster rate in voids with $Λ$CDM and open FLRW backgrounds. However, only for voids in a $Λ$CDM background this suppression is sufficiently rapid for the CET entropy itself to reach a terminal equilibrium (or "saturation") value. The CET gravitational temperature vanishes asymptotically if $Λ=0$ and becomes asymptotically proportional to $Λ$ for voids in a $Λ$CDM background. In the linear regime of the LTB evolution our results coincide, qualitatively and quantitatively, with previous results based on linear perturbation theory.
description: 24 pages, 6 figures. Replaced to match the published version
Systemic and Lower Respiratory Tract Immunity to SARS-CoV-2 Omicron and Variants in Pediatric Severe COVID-19 and Mis-C
Creators: name: Novak, Tanya
name: Tang, Juanjie
name: Irby, Katherine
name: Randolph, Adrienne G.
name: Loftis, Laura L.
name: Walker, Tracie C.
name: Khurana, Surender
name: Zinter, Matt S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Mucosal immunity plays an important role in the control of viral respiratory infections like SARS-CoV-2. While systemic immune responses against the SARS-2-CoV-2 have been studied in children, there is no information on mucosal antibody response, especially in the lower respiratory tract of children coronavirus disease 2019 (COVID-19) and post-infectious multisystem inflammatory syndrome in children (MIS-C) against emerging SARS-CoV-2 variants. Therefore, we evaluated neutralizing antibody responses in paired plasma and endotracheal aspirates of pediatric severe, acute COVID-19 or MIS-C patients against SARS-CoV-2 WA1/2020, as well as against variants of concern (VOCs). Neutralizing antibody responses against the SARS-CoV-2 WA1/2020 strain in pediatric plasma were 2-fold or 35-fold higher compared with the matched endotracheal aspirate in COVID-19 or MIS-C patients, respectively. In contrast to plasma, neutralizing antibody responses against the VOCs and variants of interest (VOIs) in endotracheal aspirates were lower, with only one endotracheal aspirate demonstrating neutralizing titers against the Iota, Kappa, Beta, Gamma, and Omicron variants. In conclusion, our findings suggest that children and adolescents with severe COVID-19 or MIS-C have weak mucosal neutralizing antibodies in the trachea against circulating SARS-CoV-2 Omicron and other VOCs, which may have implications for recovery and for re-infection with emerging SARS-CoV-2 variants.
Machine Learning Approaches for Metalloproteins
Creators: name: Teo, Ruijie D.
name: Yu, Yue
name: Wang, Ruobing
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. Due to their ubiquity among biological systems, researchers have made immense efforts to predict the structural and functional roles of metalloproteins. Ultimately, having a comprehensive understanding of metalloproteins will lead to tangible applications, such as designing potent inhibitors in drug discovery. Recently, there has been an acceleration in the number of studies applying machine learning to predict metalloprotein properties, primarily driven by the advent of more sophisticated machine learning algorithms. This review covers how machine learning tools have consolidated and expanded our comprehension of various aspects of metalloproteins (structure, function, stability, ligand-binding interactions, and inhibitors). Future avenues of exploration are also discussed.
(500568) James Maitland
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Minimizers of the Landau-de Gennes energy around a spherical colloid particle
Creators: name: Alama, Stan
name: Bronsard, Lia
name: Lamy, Xavier
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We consider energy minimizing configurations of a nematic liquid crystal around a spherical colloid particle, in the context of the Landau-de Gennes model. The nematic is assumed to occupy the exterior of a ball of radius r_0, satisfy homeotropic weak anchoring at the surface of the colloid, and approach a uniform uniaxial state at infinity. We study the minimizers in two different limiting regimes: for balls which are small compared to the characteristic length scale r_0<>L. The relationship between the radius and the anchoring strength W is also relevant. For small balls we obtain a limiting quadrupolar configuration, with a "Saturn ring" defect for relatively strong anchoring, corresponding to an exchange of eigenvalues of the Q-tensor. In the limit of very large balls we obtain an axisymmetric minimizer of the Oseen-Frank energy, and a dipole configuration with exactly one point defect is obtained.
GitLab at the Socio-Economic Panel – A Roadshow
Creators: name: Wenzig, Knut
Publisher: name: Zenodo
Year: 2023

description: The Socio-Economic Panel (SOEP) relies heavily on a GitLab server for its data management and documentation needs. GitLab is a web-based Git repository manager that provides version control for source code, project management tools, and automation. At the SOEP, the GitLab server has been configured to provide several key features, including: Version control: GitLab provides a centralised repository for storing and managing source code, making it easier to track changes and collaborate with other team members. The SOEP uses this feature to manage scripts (Stata and R) and metadata. Issue tracking: GitLab's built-in issue tracker allows users to report and track bugs, defects, and other issues. At the SOEP, the issue tracker is used to report problems during data preparation, document issues, and track bug reports from data users. It is also used to manage teams or projects, complex internal processes with multiple stakeholders, and to organise weekly meetings. Service desks: GitLab's service desks feature enables users to create and manage support tickets. This feature can be used to centralise and distribute user requests to the relevant specialists, replacing email battles within the team. Automation: GitLab's pipeline feature allows the SOEP to automate the testing and deployment of metadata stored in CSV files. This feature has also been used to produce almost publication-ready PDF files. Wiki: GitLab's built-in wiki feature allows users to create and edit pages of content within the GitLab interface. The SOEP uses this feature to create internal documentation related to its data management activities. Overall, the GitLab server at the SOEP provides a range of features that support the organisation's research and data management needs. By using GitLab, the SOEP has been able to improve collaboration and streamline workflows.
Мобилизация данных о разнообразии сосудистых растений Среднего Поволжья
Creators: name: Степан Сенатор
Publisher: name: Zenodo
Year: 2020

description: Cообщается о системе Salix, которая хранит и обрабатывает информацию о флоре сосудистых растений Cреднего Поволжья. Gредставлена информация о создании электронного каталога гербария PVB.
Analyses of biomarker traits in diverse UK biobank participants identify associations missed by European-centric analysis strategies
Creators: name: Cheng, C.-Y.
name: Preuss, M.H.
name: Li, Y.
name: Avery, C.L.
name: Sim, X.
name: Chai, J.-F.
name: Haessler, J.
name: Franceschini, N.
name: Wen, J.
name: Rowland, B.
name: Kooperberg, C.
name: Cox, N.J.
name: Graff, M.
name: Lee, M.P.
name: Huang, L.
name: Miller-Fleming, T.W.
name: North, K.E.
name: Raffield, L.M.
name: Sun, Q.
Publisher: name: Springer Nature
Year: 2022

description: Despite the dramatic underrepresentation of non-European populations in human genetics studies, researchers continue to exclude participants of non-European ancestry, as well as variants rare in European populations, even when these data are available. This practice perpetuates existing research disparities and can lead to important and large effect size associations being missed. Here, we conducted genome-wide association studies (GWAS) of 31 serum and urine biomarker quantitative traits in African (n = 9354), East Asian (n = 2559), and South Asian (n = 9823) ancestry UK Biobank (UKBB) participants. We adjusted for all known GWAS catalog variants for each trait, as well as novel signals identified in a recent European ancestry-focused analysis of UKBB participants. We identify 7 novel signals in African ancestry and 2 novel signals in South Asian ancestry participants (p < 1.61E−10). Many of these signals are highly plausible, including a cis pQTL for the gene encoding gamma-glutamyl transferase and PIEZO1 and G6PD variants with impacts on HbA1c through likely erythrocytic mechanisms. This work illustrates the importance of using the genetic data we already have in diverse populations, with novel discoveries possible in even modest sample sizes.
Multi-ethnic genome-wide association analyses of white blood cell and platelet traits in the Population Architecture using Genomics and Epidemiology (PAGE) study
Creators: name: Blood Cell Consortium
name: Wojcik, G.L.
name: Thyagarajan, B.
name: Lettre, G.
name: Reiner, A.P.
name: Sun, Q.
name: Graff, M.
name: Li, Y.
name: Hindorff, L.A.
name: Hu, Y.
name: Loos, R.J.F.
name: Auer, P.L.
name: Nishimura, K.K.
name: Raffield, L.M.
name: Baldassari, A.R.
name: Hodonsky, C.J.
name: Chen, M.-H.
name: Qi, L.
name: Avery, C.L.
name: Tao, R.
name: Bien, S.A.
name: Huckins, L.M.
name: Highland, H.M.
name: Lin, D.
name: Fornage, M.
name: Haessler, J.
name: Kooperberg, C.
name: Mousas, A.
name: Sitlani, C.M.
name: Preuss, M.
name: Tang, W.
name: North, K.E.
name: Wang, Z.
name: Peters, U.
name: Buyske, S.
Publisher: name: BioMed Central Ltd
Year: 2021

description: Background: Circulating white blood cell and platelet traits are clinically linked to various disease outcomes and differ across individuals and ancestry groups. Genetic factors play an important role in determining these traits and many loci have been identified. However, most of these findings were identified in populations of European ancestry (EA), with African Americans (AA), Hispanics/Latinos (HL), and other races/ethnicities being severely underrepresented. Results: We performed ancestry-combined and ancestry-specific genome-wide association studies (GWAS) for white blood cell and platelet traits in the ancestrally diverse Population Architecture using Genomics and Epidemiology (PAGE) Study, including 16,201 AA, 21,347 HL, and 27,236 EA participants. We identified six novel findings at suggestive significance (P < 5E-8), which need confirmation, and independent signals at six previously established regions at genome-wide significance (P < 2E-9). We confirmed multiple previously reported genome-wide significant variants in the single variant association analysis and multiple genes using PrediXcan. Evaluation of loci reported from a Euro-centric GWAS indicated attenuation of effect estimates in AA and HL compared to EA populations. Conclusions: Our results highlighted the potential to identify ancestry-specific and ancestry-agnostic variants in participants with diverse backgrounds and advocate for continued efforts in improving inclusion of racially/ethnically diverse populations in genetic association studies for complex traits.
Exceptions to the Ne Bis in Idem principle in the context of Articles 54 and 55(1)(b) CISA and compatibility of declarations not to be bound by that principle with Articles 50 and 52(1) CFREU
Creators: name: Coffey, Ger
Publisher: name: University of Limerick
Year: 2024
Subjects: classificationCode: 480403
subject: Law and humanities

description: The judgment in Criminal proceedings against MR (Generalstaatsanwaltschaft Bamberg) Case C–365/21 was delivered on 23 March 2023 wherein the Court of Justice of the European Union (CJEU) examined the complex interrelated issues concerning Article 54 CISA interstate application of the ne bis in idem principle (in the context of free movement of persons), Article 55(1)(b) CISA exceptions to the application of that principle, Article 50 CFREU interstate application of the principle (in the context of a fundamental right), and Article 52(1) CFREU limitations to the application of that principle subject to the principle of proportionality. The CJEU examined the compatibility of declarations not to be bound by the application of Article 54 CISA commensurate with Article 55(1)(b) CISA in the context of a criminal organisation and financial crime, offences against national security or other equally essential interests, and the compatibility of such dec?larations with Article 50 and Article 52(1) CFREU. The CJEU ruled that Article 55(1)(b) CISA exception to the principle was compatible with Article 50 CFREU. This is the first CJEU judgment on exceptions to Article 54 CISA and compatibility of declarations not to be bound by that principle with Article 50 CFREU. This article examines the significance and implications of the judgment within the area of freedom, security and justice.
Future HPC Technologies
Creators: name: Lavignon, Jean-François
Publisher: name: Zenodo
Year: 2020
Subjects: EXDCI-2, HPC, HPDA, AI

description: The current technologies used for HPC systems will not be able to sustain the performance increase requested by the HPC/HPDA/AI1 application communities. Since the end of the Dennard scaling and with the approaching end of the Moore’s law, the standard CMOS2 technology has to be complemented by other approaches if we want to continue to deliver more performance.
 The three main HPC ecosystems beside Europe, namely US, China and Japan have undertaken significant research initiatives to work on these new approaches. The investigations include topics such as new materials that are more efficient than CMOS, new architecture, photonics, analogue system or quantum technologies. The level of investment is high in these three countries but we do not believe that they have already a competitive edge over Europe.
 This white paper presents first why is it mandatory to look for new HPC technologies. After a short presentation of the international landscape, we review the research options that could sustain the development of HPC. This analysis is the result of a work organized by EXDCI-2 to connect the HPC communities with the European electronics and photonics experts.
 The last section presents some recommendations for Europe to strengthen its position in technologies relevant for future HPC system. These recommendations could be implemented through EuroHPC actions and/or initiatives of the future Horizon Europe programme.
Semi-contact 3-body interaction for nuclear density functional theory
Creators: name: Lacroix, Denis
name: Bennaceur, Karim
Publisher: name: arXiv
Year: 2014
Subjects: subject: Nuclear Theory (nucl-th)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: To solve difficulties related to the use of nuclear density functional theory applied in its beyond mean-field version, we introduce a semi-contact 3-body effective interaction. We show that this interaction is a good candidate to replace the widely used density dependent effective interaction. The resulting new functionals are able to describe symmetric, neutron, polarized and neutron polarized nuclear matter as well as the effective mass properties simultaneously.
description: 5 pages, 3 figures, supplement material available upon request
All-optical magnetization switching in ferrimagnetic alloys: deterministic vs thermally activated dynamics
Creators: name: Guyader, L. Le
name: Moussaoui, S. El
name: Buzzi, M.
name: Savoini, M.
name: Tsukamoto, A.
name: Itoh, A.
name: Kirilyuk, A.
name: Rasing, Th.
name: Nolting, F.
name: Kimel, A. V.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Using photo-emission electron microscopy with X-ray magnetic circular dichroism as a contrast mechanism, new insights into the all-optical magnetization switching (AOS) phenomenon in GdFe based rare-earth transition metal ferrimagnetic alloys are provided. From a sequence of static images taken after single linearly polarized laser pulse excitation, the repeatability of AOS can be measured with a correlation coefficient. It is found that low coercivity enables thermally activated domain wall motion, limiting in turn the repeatability of the switching. Time-resolved measurement of the magnetization dynamics reveal that while AOS occurs below and above the magnetization compensation temperature $T_\text{M}$, it is not observed in GdFe samples where $T_\text{M}$ is absent. Finally, AOS is experimentally demonstrated against an applied magnetic field of up to 180 mT.
description: 18 pages, 4 figures
Gut Microbiota and Host Plasma Metabolites in Association with Blood Pressure in Chinese Adults
Creators: name: Zhang, B.
name: Wang, Y.
name: Wang, H.
name: Su, C.
name: Sun, S.
name: Zhang, J.
name: Howard, A.G.
name: Tsilimigras, M.C.B.
name: Avery, C.L.
name: Gordon-Larsen, P.
name: Sha, W.
name: Meyer, K.A.
name: Wang, Z.
name: Fodor, A.A.
Publisher: name: Lippincott Williams and Wilkins
Year: 2021

description: Animal studies have revealed gut microbial and metabolic pathways of blood pressure (BP) regulation, yet few epidemiological studies have collected microbiota and metabolomics data in the same individuals. In a population-based, Chinese cohort who did not report antihypertension medication use (30-69 years, 54% women), thus minimizing BP treatment effects, we examined multivariable-adjusted (eg, diet, physical activity, smoking, kidney function), cross-sectional associations between measures of gut microbiota (16S rRNA [ribosomal ribonucleic acid], N=1003), and plasma metabolome (liquid chromatography-mass spectrometry, N=434) with systolic (SBP, mean [SD]=126.0 [17.4] mm Hg) and diastolic BP (DBP [80.7 (10.7) mm Hg]). We found that the overall microbial community assessed by principal coordinate analysis varied by SBP and DBP (permutational multivariate ANOVA P<0.05). To account for strong correlations across metabolites, we first examined metabolite patterns derived from principal component analysis and found that a lipid pattern was positively associated with SBP (linear regression coefficient [95% CI] per 1 SD pattern score: 2.23 [0.72-3.74] mm Hg) and DBP (1.72 [0.81-2.63] mm Hg). Among 1104 individual metabolites, 34 and 39 metabolites were positively associated with SBP and DBP (false discovery rate-adjusted linear model P<0.05), respectively, including linoleate, palmitate, dihomolinolenate, 8 sphingomyelins, 4 acyl-carnitines, and 2 phosphatidylinositols. Subsequent pathway analysis showed that metabolic pathways of long-chain saturated acylcarnitine, phosphatidylinositol, and sphingomyelins were associated with SBP and DBP (false discovery rate-adjusted Fisher exact test P<0.05). Our results suggest potential roles of microbiota and metabolites in BP regulation to be followed up in prospective and clinical studies.
European Technology Research Projects
Creators: name: Lavignon, Jean-François
Publisher: name: Zenodo
Year: 2020
Subjects: FET, HPC

description: The objective of this white paper is to present the results or the on-going work of the first HPC technology projects initiated within the Horizon 2020 programme, namely within calls FET-HPC-2014, 2016 and 2017. We have also analysed the projects’ impact on the application domain. The results of these projects have been compiled (which has led to a database of project results) and analysed (with an objective to determine how their results can be re-used and what mechanisms are needed to achieve that).
 We have established that the FET-HPC projects have delivered a large set of IPs (intellectual property elements), which represents an important asset for the entire European HPC community. The impact of the work of the projects extends beyond the domain of technology onto applications and thus the work of the Centres of Excellence.
 This high-level, comprehensive analysis can be been used to: Increase the impact of the projects by creating synergies between the projects and by facilitating the reuse of project results; Understand the position of the European ecosystem in the international HPC landscape; Provide recommendations for shaping the future R&D HPC technology programme.
Obesity Duration, Severity, and Distribution Trajectories and Cardiovascular Disease Risk in the Atherosclerosis Risk in Communities Study
Creators: name: Seidelmann, S.
name: Yu, B.
name: Palta, P.
name: Demerath, E.
name: North, K.E.
name: Graff, M.
name: Gordon-Larsen, P.
name: Avery, C.L.
name: Lin, D.-Y.
name: Ndumele, C.
name: Cheng, S.
name: Rebholz, C.M.
name: Howard, A.G.
name: Raffield, L.M.
Publisher: name: American Heart Association Inc.
Year: 2021

description: BACKGROUND: Research examining the role of obesity in cardiovascular disease (CVD) often fails to adequately consider heterogeneity in obesity severity, distribution, and duration. METHODS AND RESULTS: We here use multivariate latent class mixed models in the biracial Atherosclerosis Risk in Communities study (N=14 514; mean age=54 years; 55% female) to associate obesity subclasses (derived from body mass index, waist circumference, self-reported weight at age 25, tricep skinfold, and calf circumference across up to four triennial visits) with total mortality, incident CVD, and CVD risk factors. We identified four obesity subclasses, summarized by their body mass index and waist circumference slope as decline (4.1%), stable/slow decline (67.8%), moderate increase (24.6%), and rapid increase (3.6%) subclasses. Compared with participants in the stable/slow decline subclass, the decline subclass was associated with elevated mortality (hazard ratio [HR] 1.45, 95% CI 1.31, 1.60, P<0.0001) and with heart failure (HR 1.41, 95% CI 1.22, 1.63, P<0.0001), stroke (HR 1.53, 95% CI 1.22, 1.92, P=0.0002), and coronary heart disease (HR 1.36, 95% CI 1.14, 1.63, P=0.0008), adjusting for baseline body mass index and CVD risk factor profile. The moderate increase latent class was not associated with any significant differences in CVD risk as compared to the stable/slow decline latent class and was associated with a lower overall risk of mortality (HR 0.85, 95% CI 0.80, 0.90, P<0.0001), despite higher body mass index at baseline. The rapid increase latent class was associated with a higher risk of heart failure versus the stable/slow decline latent class (HR 1.34, 95% CI 1.10, 1.62, P=0.004). CONCLUSIONS: Consideration of heterogeneity and longitudinal changes in obesity measures is needed in clinical care for a more precision-oriented view of CVD risk.
Recognizing and understanding user behaviors from screencasts
Creators: name: Zhao, Dehai
Publisher: name: The Australian National University
Year: 2022

description: User interacts with computers or mobile devices, leading to user behaviors on screen. In the context of software engineering, analyzing user behavior enables many applications such as intelligent bug fix, code completion and knowledge recommendation for developers. Such technique can be extended to more general knowledge worker environment, in which users have to manipulate devices according to specific guidelines. Existing works rely heavily on software instrumentation to obtain user actions from operation systems, which is hard to deploy and maintain. In addition, considering the security and privacy of some scenarios, non-intrusive is the major requirement to be included in the system. In this work, we leverage Computer Vision and Natural Language Processing techniques to recognize and understand user behaviors from screencasts, which is a non-intrusive and cross-platform method. We first recognize 10 categories of low level user actions such as mouse moving and type text, then summarize them to higher level abstractions (i.e. line-granularity coding steps). We also try to interpret user interaction with applications by multi-task learning and generate structured language descriptions (i.e. command, widget and location). Finally, unsupervised learning method is introduced for GUI linting problem, which is taken as a case study of user behavior analysis. To train the deep neural networks, we collect diverse video data from YouTube, Twitch and Bugzilla, and manually label them to build the dataset. The experiment results demonstrate the high performance of proposed method, and the user study validate the practical applications of many downstream tasks.
Rapid detection of identity-by-descent tracts for mega-scale datasets
Creators: name: Avery, C.L.
name: Shemirani, R.
name: Ambite, J.L.
name: Belbin, G.M.
name: Kenny, E.E.
name: Gignoux, C.R.
Publisher: name: Nature Research
Year: 2021

description: The ability to identify segments of genomes identical-by-descent (IBD) is a part of standard workflows in both statistical and population genetics. However, traditional methods for finding local IBD across all pairs of individuals scale poorly leading to a lack of adoption in very large-scale datasets. Here, we present iLASH, an algorithm based on similarity detection techniques that shows equal or improved accuracy in simulations compared to current leading methods and speeds up analysis by several orders of magnitude on genomic datasets, making IBD estimation tractable for millions of individuals. We apply iLASH to the PAGE dataset of ~52,000 multi-ethnic participants, including several founder populations with elevated IBD sharing, identifying IBD segments in ~3 minutes per chromosome compared to over 6 days for a state-of-the-art algorithm. iLASH enables efficient analysis of very large-scale datasets, as we demonstrate by computing IBD across the UK Biobank (~500,000 individuals), detecting 12.9 billion pairwise connections.
Regulating asymmetric information: legal form and economic theory
Creators: name: Downing, Gareth
Publisher: name: The Australian National University
Year: 2022

description: The regulation of asymmetric information is predicated on Akerlof's classic model which is entirely effects-based. This thesis sets aside the economic effects of asymmetric information to focus on a series of simple but critical questions concerning the origins and drivers of asymmetric information. The first of these questions, is why do information asymmetries exist? What factors drive the emergence of asymmetric information and its resolution? And how does an improved understanding of the origins and drivers of asymmetric information inform the selection of legal instruments and design of legal frameworks to address and ameliorate asymmetric information? In answering these questions, this thesis develops a novel, first generation model of asymmetric information that explains the emergence and resolution of information asymmetries by reference to information costs. The model is then applied to common regulatory and private law instruments to inform an original critical reappraisal of the classic model of asymmetric information. In re-examining the classic model of asymmetric information this thesis argues that it provides a narrow basis for regulation and must be revised and expanded to reflect regulatory practice and existing legal forms. In arguing for the revision of the classic theory of asymmetric information, this thesis argues that an improved understanding of the origins and drivers of asymmetric information provides a framework for analysing the efficiency trade-offs of different legal instruments to support instrument selection. Further, it is argued that an improved understanding of the origins and drivers of asymmetric information supports the development of normative guidance on when regulation may be merited based on a revised model of asymmetric information.
A New Paradigm For Environmental Data Management Technology
Creators: name: Jacques, Saulo Machado De Souza
Publisher: name: Zenodo
Year: 2020
Subjects: Environmental Data, Decentralization, Open Source, Privacy, Platform Capitalism, data sovereignty, Open Science

description: The technological infrastructures face a hyper-centralization with few companies controlling them. Coincidently, these companies are involved in different scandals related to user privacy, partnership with authoritarian governments, and the use of personal data for abusive economic exploitation. In this text, I bring an overview of the implications for environmental data and the basic principles that we take into account to develop the new approach of environmental data platform for its management, storage, and sharing.
Trends in US Cancer and Heart Disease Mortality, 1999-2018
Creators: name: Nichols, H.B.
name: Avery, C.L.
name: Howard, A.G.
Publisher: name: Lippincott Williams and Wilkins
Year: 2021

description: Since initial reports documenting an increase in midlife US mortality rates were first published, numerous studies have examined the resulting demographic, economic, and policy implications; however, fewer studies have examined trends for the 2 major drivers of US mortality: heart disease and cancer. Here, we used 2 decades (1999–2018) of death certificate data to further inform understanding of contemporary US cancer and heart disease mortality trends overall and by sex, race, ethnicity, and age group.
Hard Diffraction with Proton Tagging at the LHC
Creators: name: Trzebinski, Maciej
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The main parts of the LHC diffractive physics programme possible to be measured using a proton tagging technique are presented. The geometric acceptance of the ATLAS forward proton detectors: ALFA and AFP for various LHC optics settings are shown. The probabilities of observing a proton originating from a minimum-bias event in ALFA and AFP stations are given. The main properties of single diffractive and double Pomeron exchange production of dijets, photon+jet, jet-gap-jet and W/Z bosons are discussed. The possibility of measuring the jet production in exclusive (double proton tag) and semi-exclusive (single tag) mode is evaluated.