cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
>kj[kaM esa dks;yk m|ksx ds fodkl dk lkekftd] vkfFkZd vkSjij;kZo.kh; izHkko
Creators: name: Vkyksd Dqekj
Publisher: name: Zenodo
Year: 2022

description: yxHkx rhu lkS fefy;u o"kZ iwoZ i`Foh ij fupys tyh; {ks=ksa esa ?kus ou FksaA ck<+] Hkwdai tSls izkÑfrd vkinkvksa ds dkj.k Fks ou e`nk ds uhps nc x,A muds Åij vf/kd e`nk te tkus ds dkj.k os laihfM+r gks x;sA tSls&tSls os xgjs gksrs x;s mudk rki Hkh c<+rk x;kA mPp rki vkSj mPp nkc ds dkj.k i`Foh ds Hkhrj e`r isM+&ikS/ks /khjs&/khjs dks;ys esa ifjofrZr gks x;sA XyksIVksfjl vkSj fVyksQkbye eq[; ouLifr;k¡ Fkh ftuls dks;yk cukA dks;ys esa eq[; :i ls dkcZu gksrk gSA e`r ouLifr ds /khes izØe +}kjk dks;ys esa ifjorZu dks dkcZuhdj.k dgrs gS] D;ksafd og ouLifr ds vo'ks"kksa ls cuk gS] vr% dks;ys dks ^thok'e bZ/ku* Hkh dgrs gSA 40 ls 22-5 djksM+ o"kZ rd dk dky xksaM+okuk fu{ksi.k dks dky dgk tkrk gS tc lcls vkajHk esa nkeksnj Hkza'k dk fuekZ.k gksrk gS rFkk ckn esa dkcZuh ls ysdj Vªkbf,'kd dYi rd Øe'k% rkyphj] nkeqnk] iapsr] egknso la?kksa dk fu{ksi.k gksrk gS tks dks;ys ds fo'kky fu{ksi.k {ks= dk fuekZ.k djrs gSA1 xksaM+okuk lajpuk dk vkjafHkd dky nkeksnj Hkza'k dks fuekZ.k dk dky FkkA nkeksnj csflu {ks= esa fu{ksi.k dh 'kq:vkr dkcZuhQsjl dky ls gksus yxrh gS tks fØVsf'k;l ds vkjafHkd dky rd pyrh gSA bl nkeksnj csflu dk foLrkj if'pe esa gqVkj dks;yk {ks= ls iwjc esa >fj;k vkSj jkuhxat rd gSA ;gk¡ Hkkjr dk lcls mÙke dksfV dk dks;yk ik;k tkrk gSA vf/kdrj dks;yk lsy vksj ckyw iRFkjksa dh ijrksa esa fu{ksfir gSA
Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty
Creators: name: Moore S.
name: Rosenstrom E.T.
name: Mayorga M.E.
name: Truelove S.
name: Machi D.
name: Hill A.
name: Perkins A.
name: Porebski P.
name: Paul R.
name: Hochheiser H.
name: McKee C.D.
name: Vespignani A.
name: Klahn B.
name: Cadwell B.L.
name: Srivastava A.
name: Lessler J.
name: Karlen D.
name: Bents S.
name: Hurt B.
name: Venkatramanan S.
name: Galanti M.
name: Shin L.
name: Espino J.
name: Outten J.
name: Runge M.C.
name: Healy J.M.
name: Hulse J.D.
name: Jung S.-M.
name: Janies D.
name: Pei S.
name: Mortveit H.
name: Biggerstaff M.
name: Wilson A.
name: Rainwater-Lovett K.
name: van Panhuis W.G.
name: Thill J.-C.
name: Lee E.C.
name: Swann J.L.
name: Hladish T.
name: Chen J.
name: Pillai A.
name: España G.
name: Lachmann M.
name: Contamin L.
name: Davis J.T.
name: Howerton E.
name: Xiong X.
name: Viboud C.
name: Reich N.G.
name: Tallaksen K.
name: Shea K.
name: Slayton R.B.
name: Shaman J.
name: Fox S.J.
name: Mullany L.C.
name: Levander J.
name: Longini I., Jr.
name: Kaminsky J.
name: Smith C.P.
name: Mu K.
name: Bhattacharya P.
name: Wilson S.
name: Marathe M.
name: Pastore y Piontti A.
name: Chinazzi M.
name: Lewis B.
name: Kinsey M.
name: Chen S.
name: Johansson M.A.
name: Bi K.
name: Kerr J.
name: Loo S.L.
name: Lemaitre J.C.
name: Bouchnita A.
name: Hoops S.
name: Ben Toh K.
name: Cavany S.
name: Qin M.
name: Borchering R.K.
name: Ivy J.S.
name: Adiga A.
name: Meyers L.A.
name: Yamana T.
Publisher: name: Nature Research
Year: 2023

description: Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of critical epidemic drivers. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make months ahead projections of SARS-CoV-2 burden, totaling nearly 1.8 million national and state-level projections. Here, we find SMH performance varied widely as a function of both scenario validity and model calibration. We show scenarios remained close to reality for 22 weeks on average before the arrival of unanticipated SARS-CoV-2 variants invalidated key assumptions. An ensemble of participating models that preserved variation between models (using the linear opinion pool method) was consistently more reliable than any single model in periods of valid scenario assumptions, while projection interval coverage was near target levels. SMH projections were used to guide pandemic response, illustrating the value of collaborative hubs for longer-term scenario projections.
Additional file 2: of Benchmarking of alignment-free sequence comparison methods
Creators: name: Zielezinski, Andrzej
name: Girgis, Hani
name: Bernard, Guillaume
name: Chris-Andre Leimeister
name: Kujin Tang
name: Dencker, Thomas
name: Lau, Anna
name: RĂśhling, Sophie
name: Choi, Jae
name: Waterman, Michael
name: Comin, Matteo
name: Sung-Hou Kim
name: Vinga, Susana
name: Almeida, Jonas
name: Chan, Cheong
name: James, Benjamin
name: Fengzhu Sun
name: Morgenstern, Burkhard
name: Karlowski, Wojciech
Publisher: name: Figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S1. Comparison (tanglement) of test tree and reference tree of sulfatase modifying factor (SUMF) gene family in Eukaryotes. The test tree is inferred by 4 alignment-free measures in AFKS program (mismatch, markov, rre_k_r, kl_conditional). Reference phylogenetic tree was taken from SwissTree. Figure S2. Comparison (tanglement) of test tree and reference tree of complete mitochondrial genomes from 25 labroid fishes. The test tree is inferred by 9 alignment-free programs (AFKS, alfpy, CAFE, FSWM, jD2Stat, kmacs, mash, RTD-Phylogeny, and spaced). Reference phylogenetic tree was taken from [1]. Figure S3. Comparison (tanglement) of test and reference cladograms of complete genomes from 29 E. coli/Shigella species. Test tree was inferred by phylonium. Figure S4. Comparison (tanglement) of test and reference cladograms of complete genomes from 14 plant species. Test tree was inferred by co-phylog. Figure S5. Comparison (tanglement) of test and reference cladograms of complete genomes from 14 plant species. Test tree was inferred by mash. Figure S6. Comparison (tanglement) of test and reference cladograms of complete genomes from 14 plant species. Test tree was inferred by Multi-SpaM. Figure S7. Comparison (tanglement) of test and reference cladograms of complete genomes from 27 E.coli and Shigella species. Test tree was inferred by andi and co-phylog. Reference phylogenetic tree was constructed in [2â 4] from 5282 Bayesian protein trees. E. coli reference groups and Shigella (S) are indicated. Figure S8. Comparison (tanglement) of test and reference cladograms of complete genomes from 27 E. coli and Shigella species. Test tree was inferred by phylonium. Reference phylogenetic tree was constructed in [2â 4] from 5282 Bayesian protein trees. E. coli reference groups and Shigella (S) are indicated. Figure S9. Performance scores obtained by alfpy--canberra (dark gray) and AFKS--canberra (light gray) run on common word lengths across data sets. (PDF 1718 kb)
TREEcop - Entwicklung eines Sentineldatenbasierten Steuerungstools zur Ermittlung von Trockenstress des Stadtbaumbestandes in der Stadt Essen
Creators: name: Buddenbaum, Henning
Publisher: name: Zenodo
Year: 2023
Subjects: Treecop, Sentinel-2, Essen, City trees, drought stress

description: Presentation at the Symposium „Entwicklung und Implementierungsvorbereitung von Copernicus-Diensten für den öffentlichen Bedarf in Deutschland“, 23. Juni 2022, Allianz Forum Berlin.
Low-energy excitations and quasielastic contribution to electron-nucleus and neutrino-nucleus scattering in the continuum random phase approximation
Creators: name: Pandey, V.
name: Jachowicz, N.
name: Van Cuyck, T.
name: Ryckebusch, J.
name: Martini, M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We present a detailed study of a continuum random phase approximation approach to quasielastic electron-nucleus and neutrino-nucleus scattering. The formalism is validated by confronting ($e,e'$) cross-section predictions with electron scattering data for the nuclear targets $^{12}$C, $^{16}$O, and $^{40}$Ca, in the kinematic region where quasielastic scattering is expected to dominate. We examine the longitudinal and transverse contributions to $^{12}$C($e,e'$) and compare them with the available data. Further, we study the $^{12}$C($ν_μ,μ^{-}$) cross sections relevant for accelerator-based neutrino-oscillation experiments. We pay special attention to low-energy excitations which can account for non-negligible contributions in measurements, and require a beyond-Fermi-gas formalism.
description: 10 pages, 14 figures. Version published in Physical Review C
Evolution driven by a varying host environment selects for distinct HIV-1 entry phenotypes and other informative variants
Creators: name: Long, Nathan
name: Zhou, Shuntai
name: Swanstrom, Ronald
Publisher: name: Frontiers Media SA
Year: 2023

description: HIV-1 generates remarkable intra- and inter-host viral diversity during infection. In the response to the dynamic selective pressures of the host’s environment, HIV-1 evolves distinct phenotypes—biological features that provide fitness advantages. The transmitted form of HIV-1 has been shown to require a high density of CD4 on the target cell surface (as found on CD4+ T cells) and typically uses C–C chemokine receptor type 5 (CCR5) as a coreceptor during entry. This phenotype is referred to as R5T cell-tropic (or R5 T-tropic); however, HIV-1 can switch to a secondary coreceptor, C–X–C chemokine receptor type 4 (CXCR4), resulting in a X4T cell-tropic phenotype. Macrophage-tropic (or M-tropic) HIV-1 can evolve to efficiently enter cells expressing low densities of CD4 on their surface (such as macrophages/microglia). So far only CCR5-using M-tropic viruses have been found. M-tropic HIV-1 is most frequently found within the central nervous system (CNS), and infection of the CNS has been associated with neurologic impairment. It has been shown that interferon-resistant phenotypes have a selective advantage during transmission, but the underlying mechanism of this is still unclear. During untreated infection, HIV-1 evolves under selective pressure from both the humoral/antibody response and CD8+ T-cell killing. Sufficiently potent antiviral therapy can suppress viral replication, but if the antiviral drugs are not powerful enough to stop replication, then the replicating virus will evolve drug resistance. HIV-1 phenotypes are highly relevant to treatment efforts, clinical outcomes, vaccine studies, and cure strategies. Therefore, it is critical to understand the dynamics of the host environment that drive these phenotypes and how they affect HIV-1 pathogenesis. This review will provide a comprehensive discussion of HIV-1 entry and transmission, and drug-resistant phenotypes. Finally, we will assess the methods used in previous and current research to characterize these phenotypes.
Additional file 7 of Electroencephalographic features in patients undergoing extracorporeal membrane oxygenation
Creators: name: Peluso, Lorenzo
name: Rechichi, Serena
name: Franchi, Federico
name: Pozzebon, Selene
name: Scolletta, Sabino
name: Brasseur, Alexandre
name: Legros, Benjamin
name: Jean-Louis Vincent
name: Creteur, Jacques
name: Gaspard, Nicolas
name: Taccone, Fabio Silvio
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 7 Univariate and Multivariate analysis to hospital mortality.
Additional file 1: of Three years of follow-up of otodental syndrome in 3-year-old Chinese boy: a rare case report
Creators: name: Su, Ji-Mei
name: Zeng, Su-Juan
name: Ye, Xiao-Wei
name: Wu, Zhi-Fang
name: Huang, Xin-Wen
name: Janak Pathak
Publisher: name: Figshare
Year: 2019
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Developmental Biology
subject: Science Policy

description: Figure S1 Pure tone audiogram of the patientâ s mother (A and B). Air conduction (X, left ear; right ear) and bone conduction (>, left ear;
Bandakiopsis phaluti Panesar 2004
Creators: name: Pešić, Vladimir
name: Chatterjee, Tapas
name: Bordoloi, Sabitry
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Trombidiformes
Anisitsiellidae
Bandakiopsis
Bandakiopsis phaluti

description: Bandakiopsis phaluti Panesar, 2004
Records from the study area: West Bengal—Panesar (2004).
Habitat: Seepage area near a first order stream.
Distribution: India.
description: Published as part of Pešić, Vladimir, Chatterjee, Tapas & Bordoloi, Sabitry, 2010, A checklist of the water mites (Acari: Hydrachnidia) of India, with new records and description of one new species, pp. 1-54 in Zootaxa 2617 (1) on page 11, DOI: 10.11646/zootaxa.2617.1.1, http://zenodo.org/record/197964
Additional file 5: of Interventions to promote patients and familiesâ involvement in adult intensive care settings: a protocol for a mixed-method systematic review
Creators: name: Xyrichis, Andreas
name: Fletcher, Simon
name: Brearley, Sally
name: Philippou, Julia
name: Purssell, Ed
name: Terblanche, Marius
name: Rafferty, Anne
name: Reeves, Scott
Publisher: name: Figshare
Year: 2019
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Computational Biology

description: Draftâ qualitative quality assessment form. (DOCX 16 kb)
Exploring barriers and facilitators of implementing an at-home SARS-CoV-2 antigen self-testing intervention: The Rapid Acceleration of Diagnostics-Underserved Populations (RADx-UP) initiatives
Creators: name: Corbie G.
name: Cohen-Wolkowiez M.
name: Carilli C.
name: Dave G.
name: Cross L.M.
name: Yusuf B.
name: Richmond A.
name: Kibbe W.
name: Conserve D.
name: DeFosset A.
name: Anderson R.
Publisher: name: Public Library of Science
Year: 2023

description: BACKGROUND: Evaluating community-based programs provides value to researchers, funding entities, and community stakeholders involved in program implementation, and can increase program impact and sustainability. To understand factors related to program implementation, we aimed to capture the perspective of community partners engaged in organizing and executing community-engaged programs to distribute COVID-19 at-home tests in underserved communities. METHODS: We conducted semi-structured interviews and focus groups with community-based stakeholders informed by the Outcomes for Implementation Research framework. RESULTS: Findings describe how community-engaged communication and dissemination strategies drove program adoption among grassroots stakeholders. Establishing and sustaining trusted relationships was vital to engaging partners with aligned values and capacity. Respondents characterized the programs as generally feasible and appropriate, and community partners felt capable of delivering the program successfully. However, they also described an increased burden on their workforce and desired more significant support. Respondents recognized the programs' community engagement practices as a critical facilitator of acceptability and impact. DISCUSSION: Implementation evaluation aims to inform current and future community outreach and engagement efforts with best practices. As we continue to inform and advance community-engaged disaster response practice, a parallel reimagining of public health funding mechanisms and timelines could provide a foundation for trust, collaboration, and community resiliency that endures beyond a given crisis.
High Fat Diet-Induced Obesity Dysregulates Splenic B Cell Mitochondrial Activity
Creators: name: Benson, Emily
name: Lin, Chien-Te
name: Boykov, Ilya
name: Shaikh, Saame Raza
name: Neufer, P. Darrell
name: Kidd, Grahame
name: Pal, Anandita
name: Fisher-Wellman, Kelsey H.
Publisher: name: MDPI
Year: 2023

description: Diet-induced obesity impairs mitochondrial respiratory responses in tissues that are highly metabolically active, such as the heart. However, less is known about the impact of obesity on the respiratory activity of specific cell types, such as splenic B cells. B cells are of relevance, as they play functional roles in obesity-induced insulin resistance, inflammation, and responses to infection. Here, we tested the hypothesis that high-fat-diet (HFD)-induced obesity could impair the mitochondrial respiration of intact and permeabilized splenic CD19+ B cells isolated from C57BL/6J mice and activated ex vivo with lipopolysaccharide (LPS). High-resolution respirometry was used with intact and permeabilized cells. To reveal potential mechanistic targets by which HFD-induced obesity dysregulates B cell mitochondria, we conducted proteomic analyses and 3D serial block face scanning electron microscopy (SBFEM). High-resolution respirometry revealed that intact LPS-stimulated B cells of obese mice, relative to controls, displayed lower ATP-linked, as well as maximal uncoupled, respiration. To directly investigate mitochondrial function, we used permeabilized LPS-stimulated B cells, which displayed increased H2O2 emission and production with obesity. We also examined oxidative phosphorylation efficiency simultaneously, which revealed that oxygen consumption and ATP production were decreased in LPS-stimulated B cells with obesity relative to controls. Despite minimal changes in total respiratory complex abundance, in LPS-stimulated B cells of obese mice, three of the top ten most downregulated proteins were all accessory subunits of respiratory complex I. SBFEM showed that B cells of obese mice, compared to controls, underwent no change in mitochondrial cristae integrity but displayed increased mitochondrial volume that was linked to bioenergetic function. Collectively, these results establish a proof of concept that HFD-induced obesity dysregulates the mitochondrial bioenergetic metabolism of activated splenic B cells.
Weak error analysis for semilinear stochastic Volterra equations with additive noise
Creators: name: Andersson, Adam
name: Kovács, Mihály
name: Larsson, Stig
Publisher: name: arXiv
Year: 2014
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics
subject: 60H15, 60H07, 65C30, 65M60

description: We prove a weak error estimate for the approximation in space and time of a semilinear stochastic Volterra integro-differential equation driven by additive space-time Gaussian noise. We treat this equation in an abstract framework, in which parabolic stochastic partial differential equations are also included as a special case. The approximation in space is performed by a standard finite element method and in time by an implicit Euler method combined with a convolution quadrature. The weak rate of convergence is proved to be twice the strong rate, as expected. Our convergence result concerns not only functionals of the solution at a fixed time but also more complicated functionals of the entire path and includes convergence of covariances and higher order statistics. The proof does not rely on a Kolmogorov equation. Instead it is based on a duality argument from Malliavin calculus.
description: 23 pages
MOESM3 of Heterologous overexpression, purification and functional analysis of plant cellulose synthase from green bamboo
Creators: name: Hsuan-Yu Huang
name: Cheng, Yi-Sheng
Publisher: name: Figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology

description: Additional file 3:Â Figure S3. Immunoblot results of purification.
Learning the nonlinear geometry of high-dimensional data: Models and algorithms
Creators: name: Wu, Tong
name: Bajwa, Waheed U.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Machine Learning (stat.ML)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Modern information processing relies on the axiom that high-dimensional data lie near low-dimensional geometric structures. This paper revisits the problem of data-driven learning of these geometric structures and puts forth two new nonlinear geometric models for data describing "related" objects/phenomena. The first one of these models straddles the two extremes of the subspace model and the union-of-subspaces model, and is termed the metric-constrained union-of-subspaces (MC-UoS) model. The second one of these models---suited for data drawn from a mixture of nonlinear manifolds---generalizes the kernel subspace model, and is termed the metric-constrained kernel union-of-subspaces (MC-KUoS) model. The main contributions of this paper in this regard include the following. First, it motivates and formalizes the problems of MC-UoS and MC-KUoS learning. Second, it presents algorithms that efficiently learn an MC-UoS or an MC-KUoS underlying data of interest. Third, it extends these algorithms to the case when parts of the data are missing. Last, but not least, it reports the outcomes of a series of numerical experiments involving both synthetic and real data that demonstrate the superiority of the proposed geometric models and learning algorithms over existing approaches in the literature. These experiments also help clarify the connections between this work and the literature on (subspace and kernel k-means) clustering.
description: Extended version of the journal paper accepted for publication in IEEE Trans. Signal Processing (20 pages, 7 figures, 4 tables)
Additional file 8 of Electroencephalographic features in patients undergoing extracorporeal membrane oxygenation
Creators: name: Peluso, Lorenzo
name: Rechichi, Serena
name: Franchi, Federico
name: Pozzebon, Selene
name: Scolletta, Sabino
name: Brasseur, Alexandre
name: Legros, Benjamin
name: Jean-Louis Vincent
name: Creteur, Jacques
name: Gaspard, Nicolas
name: Taccone, Fabio Silvio
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 8 Characteristics of the study population, according to the ECMO configuration.
Additional file 9 of Electroencephalographic features in patients undergoing extracorporeal membrane oxygenation
Creators: name: Peluso, Lorenzo
name: Rechichi, Serena
name: Franchi, Federico
name: Pozzebon, Selene
name: Scolletta, Sabino
name: Brasseur, Alexandre
name: Legros, Benjamin
name: Jean-Louis Vincent
name: Creteur, Jacques
name: Gaspard, Nicolas
name: Taccone, Fabio Silvio
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 9 Characteristics of the study population, according to the occurrence of cardiac arrest.
Indigenous Peoples and research: self-determination in research governance
Creators: name: Carroll, Stephanie Russo
name: Sterling, Rogena
name: Hiraldo, Danielle
name: Curley, Caleigh
name: Garrison, Nanibaa' A.
name: David-Chavez, Dominique
name: Jennings, Lydia L.
name: Garba, Ibrahim
name: Cummins, Jewel
name: Yracheta, Joseph
name: Cordova-Marks, Felina M.
name: Plevel, Rebecca
name: Hudson, Maui
name: Carson, William
name: Jäger, Mary Beth
name: Fernandez, Adam
name: Martinez, Andrew
name: Hiratsuka, Vanessa
Publisher: name: Frontiers Media
Year: 2023

description: Indigenous Peoples are reimagining their relationship with research and researchers through greater self-determination and involvement in research governance. The emerging discourse around Indigenous Data Sovereignty has provoked discussions about decolonizing data practices and highlighted the importance of Indigenous Data Governance to support Indigenous decision-making and control of data. Given that much data are generated from research, Indigenous research governance and Indigenous Data Governance overlap. In this paper, we broaden the concept of Indigenous Data Sovereignty by using the CARE Principles for Indigenous Data Governance to discuss how research legislation and policy adopted by Indigenous Peoples in the US set expectations around recognizing sovereign relationships, acknowledging rights and interests in data, and enabling Indigenous Peoples' participation in research governance.
Holographic Entanglement Entropy Close to Quantum Phase Transitions
Creators: name: Ling, Yi
name: Liu, Peng
name: Niu, Chao
name: Wu, Jian-Pin
name: Xian, Zhuo-Yu
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We investigate the holographic entanglement entropy (HEE) of a strip geometry in four dimensional Q-lattice backgrounds, which exhibit metal-insulator transitions in the dual field theory. Remarkably, we find that the HEE always displays a peak in the vicinity of the quantum critical points. Our model provides the first direct evidence that the HEE can be used to characterize the quantum phase transition (QPT). We also conjecture that the maximization behavior of HEE at quantum critical points would be universal in general holographic models.
description: 10 pages, 4 figures
The PolarBase archive of stellar spectra
Creators: name: Petit, P.
name: Glorian, J.-M.
name: Stapel, H.
name: Mathias, P.
name: Paletou, F.
Publisher: name: Zenodo
Year: 2022

description: PolarBase is an online archive offering stellar data collected with the ESPaDOnS and NARVAL high-resolution spectropolarimeters, in their reduced form. All spectra feature a continuous coverage of the 370-1,000 nm spectral domain, at a spectral resolution of 65,000. As of 2022, observations of 4,700+ stellar objects throughout the Hertzsprung-Russell diagram are available for a total of more than 2x105 spectra. Intensity spectra are offered for all targets, and the majority of the observations also include simultaneous spectra in circular or linear polarization. Most observations are associated with a cross-correlation profile, significantly increasing the detectability of weak polarized signatures. Stokes V Zeeman signatures are detected for about 500 stars of all masses and evolutionary stages, and linear polarization is detected in a few dozen targets. This unique set of Zeeman detections offers the first opportunity to run homogeneous magnetometry studies throughout the H-R diagram. The web interface of PolarBase is available at http://polarbase.irap.omp.eu.
description: {"references": ["Petit, P., Louge, T., Th\u00e9ado, S., Paletou, F., Manset, N., Morin, J., Marsden, S. C., & Jeffers, S. V. (2014), PASP, 126, 469"]}
Additional file 1 of Prospective associations between ECG abnormalities and death or myocardial infarction in a cohort of 980 employed, middle-aged Swedish men
Creators: name: Dimberg, Lennart
name: Eriksson, Bo
name: Enqvist, Per
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 1: Appendix 1. The Renault-Volvo Coeur project group 1993-1998.
Irrotational-fluid cosmologies in fourth-order gravity
Creators: name: Abebe, Amare
name: Elmardi, Maye
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: In this paper, we explore classes of irrotational-fluid cosmological models in the context of f(R)-gravity in an attempt to put some theoretical and mathematical restrictions on the form of the f(R) gravitational Lagrangian. In particular, we investigate the consistency of linearised dust models for shear-free cases as well as in the limiting cases when either the gravito-magnetic or gravito-elecric components of the Weyl tensor vanish. We also discuss the existence and consistency of classes of non-expanding irrotational spacetimes in f(R)-gravity.
description: 17 pages, no figures, more comments and references added; matches published version
Spectroscopic analysis of roAp star HD 60435: Determination of the rotation axis inclination
Creators: name: Krüger, Joachim
name: Murphy, Simon J.
name: Wright, Duncan
Publisher: name: Zenodo
Year: 2024

description: We present a spectroscopic study of roAp star HD 60435, which ceased pulsating in the last few years. To accurately model a magnetic star’s pulsational behaviour, we need to determine the inclination of the rotational axis to constrain possible geometries. This study contains a detailed vsini analysis based on an extensive spectroscopic data set. HD 60435 was observed with the high-resolution (R=80,000) Veloce spectrograph on four nights across six months. Our observations indicate no evidence of binarity, as there are no double-line profiles, and the radial velocity remains constant. We determined vsini with MCMC profile fitting, including the intrinsic stellar profile (consisting of temperature, micro- and macroturbulence), instrumental broadening and rotational broadening. The fitting process was conducted on a single Fe I line at 543.45 nm, as it is well isolated, insensitive to magnetic broadening, and on a weighted average of LSD profiles. There is no significant difference between the two and no evidence for additional broadening mechanisms in LSD profiles, resulting in a determined value of 11.3 ± 0.5 km/s, with a standard deviation of 0.05 km/s for individual exposures. Further analysis of atmospheric parameters follows with T_eff, logg, and [Fe/H] determined from well-isolated iron lines. These parameters were used to proceed with the determination of individual abundances.
Metabolomic profiles associated with physical activity in White and African American adult men
Creators: name: Zhao L.-J.
name: Yin Z.
name: Fernadez R.
name: Qiu C.
name: Li Y.-Y.
name: Choi B.Y.
name: Deng H.-W.
name: Tian Q.
name: Shen H.
name: Du Y.
name: Wu L.
name: Qi L.
name: Luo Z.
name: Sharma K.
name: Su K.-J.
name: Zhao Q.
Publisher: name: Public Library of Science
Year: 2023

description: Background Physical activity (PA) is associated with various health benefits, especially in improving chronic health conditions. However, the metabolic changes in host metabolism in response to PA remain unclear, especially in racially/ethnically diverse populations. Objective This study is to assess the metabolic profiles associated with the frequency of PA in White and African American (AA) men. Methods Using the untargeted metabolomics data collected from 698 White and AA participants (mean age: 38.0±8.0, age range: 20-50) from the Louisiana Osteoporosis Study (LOS), we conducted linear regression models to examine metabolites that are associated with PA levels (assessed by self-reported regular exercise frequency levels: 0, 1-2, and ≥3 times per week) in White and AA men, respectively, as well as in the pooled sample. Covariates considered for statistical adjustments included race (only for the pooled sample), age, BMI, waist circumstance, smoking status, and alcohol drinking. Results Of the 1133 untargeted compounds, we identified 7 metabolites associated with PA levels in the pooled sample after covariate adjustment with a false discovery rate of 0.15. Specifically, compared to participants who did not exercise, those who exercised at a frequency ≥3 times/ week showed higher abundances in uracil, orotate, 1-(1-enyl-palmitoyl)-2-oleoyl-GPE (P-16:0/18:1) (GPE), threonate, and glycerate, but lower abundances in salicyluric glucuronide and adenine in the pooled sample. However, in Whites, salicyluric glucuronide and orotate were not significant. Adenine, GPE, and threonate were not significant in AAs. In addition, the seven metabolites were not significantly different between participants who exercised ≥3 times/week and 1-2 times/week, nor significantly different between participants with 1-2 times/week and 0/week in the pooled sample and respective White and AA groups. Conclusions Metabolite responses to PA are dose sensitive and may differ between White and AA populations. The identified metabolites may help advance our knowledge of guiding precision PA interventions. Studies with rigorous study designs are warranted to elucidate the relationship between PA and metabolites.
Differences between the globular cluster systems of the Virgo and Fornax Galaxy Clusters
Creators: name: Dabringhausen, J.
name: Fellhauer, M.
name: Mieske, S.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: It is well known that Globular cluster systems are different among galaxies. Here we test to which degree these differences remain on the scale of galaxy clusters by comparing the globular clusters (GCs) in optical surveys of the Virgo galaxy cluster (ACSVCS) and the Fornax galaxy cluster (ACSFCS) in Kolmogorov-Smirnoff Tests. Both surveys were obtained with the Advanced Camera for Surveys (ACS) on board the Hubble Space Telescope, and contain thousands of GCs in dozens of galaxies each. Also well over 100 point sources in the Chandra X-ray Observatory source catalogue were attributed to the GCs in both optical catalogues, and interpreted as low-mass X-ray binaries (LMXBs). Thus, the optical and X-ray data are as uniform as possible. Our main findings are as follows: (1) The spread in luminosities and half-light radii is larger in the ACSVCS than in the ACSFCS. (2) The ratio between the half-light radii for the F475W-passband and the F850LP-passband is on average smaller in the ACSVCS. (3) The distribution of the LMXBs with the luminosity of the GCs is different between both surveys. These findings are significant. The first finding could be a consequence of a wider spread in the distances of the GCs in the ACSVCS, but the others must have internal reasons in the GCs. Thus, the GC systems are also different on a galaxy cluster scale.
description: 24 pages, 13 figures, accepted to MNRAS
Additional file 10: of Elevated neoantigen levels in tumors with somatic mutations in the HLA-A, HLA-B, HLA-C and B2M genes
Creators: name: Castro, Andrea
name: Kivilcim Ozturk
name: Pyke, Rachel
name: Xian, Su
name: Zanetti, Maurizio
name: Carter, Hannah
Publisher: name: Figshare
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S9. HLA allele call comparison between Polysolver and xHLA. Barplot showing matched Polysolver HLA calls and calls with major and minor subtype differences. (PDF 337 kb)
Additional file 2 of Screening for sickle cell disease in newborns: a systematic review
Creators: name: Runkel, Britta
name: Klüppelholz, Birgit
name: Rummer, Anne
name: Sieben, Wiebke
name: Lampert, Ulrike
name: Bollig, Claudia
name: Markes, Martina
name: Paschen, Ulrike
name: Angelescu, Konstanze
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy
subject: Computational Biology

description: Additional file 2. Search strategy.
Analysis of Pivot Sampling in Dual-Pivot Quicksort
Creators: name: Wild, Sebastian
name: Nebel, Markus E.
name: Martínez, Conrado
Publisher: name: arXiv
Year: 2014
Subjects: subject: Data Structures and Algorithms (cs.DS)
subject: Probability (math.PR)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: The new dual-pivot Quicksort by Vladimir Yaroslavskiy - used in Oracle's Java runtime library since version 7 - features intriguing asymmetries. They make a basic variant of this algorithm use less comparisons than classic single-pivot Quicksort. In this paper, we extend the analysis to the case where the two pivots are chosen as fixed order statistics of a random sample. Surprisingly, dual-pivot Quicksort then needs more comparisons than a corresponding version of classic Quicksort, so it is clear that counting comparisons is not sufficient to explain the running time advantages observed for Yaroslavskiy's algorithm in practice. Consequently, we take a more holistic approach and give also the precise leading term of the average number of swaps, the number of executed Java Bytecode instructions and the number of scanned elements, a new simple cost measure that approximates I/O costs in the memory hierarchy. We determine optimal order statistics for each of the cost measures. It turns out that the asymmetries in Yaroslavskiy's algorithm render pivots with a systematic skew more efficient than the symmetric choice. Moreover, we finally have a convincing explanation for the success of Yaroslavskiy's algorithm in practice: Compared with corresponding versions of classic single-pivot Quicksort, dual-pivot Quicksort needs significantly less I/Os, both with and without pivot sampling.
description: This article is identical (up to typograhical details) to the Algorithmica version available from Springerlink (see DOI). It is an extended and improved version of our corresponding article at the AofA 2014 conference [arXiv:1403.6602]
Additional file 3 of Screening for sickle cell disease in newborns: a systematic review
Creators: name: Runkel, Britta
name: Klüppelholz, Birgit
name: Rummer, Anne
name: Sieben, Wiebke
name: Lampert, Ulrike
name: Bollig, Claudia
name: Markes, Martina
name: Paschen, Ulrike
name: Angelescu, Konstanze
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy
subject: Computational Biology

description: Additional file 3. Publications lists.
Metabolic syndrome and cognitive function in midlife
Creators: name: Foret, Janelle Caroline Thompson
name: 0000-0002-0463-2596
Publisher: name: The University of Texas at Austin
Year: 2020
Subjects: Neuropsychological assessment
Brain
Aging
Cognitive impairment
Metabolic syndrome
Executive function

description: Rates of dementia are expected to quadruple in the next 50 years. Interventions at late stages of the disease have been unsuccessful and early identification of individuals who are vulnerable to cognitive decline is a challenge. Declines likely begin decades before the onset of clinical symptoms. Metabolic Syndrome (MetS) identifies a cluster of risk factors associated with significant cardiovascular morbidity and mortality and cognitive decline in older age. In this study, we set out to test if changes in cognitive test performance in relation to MetS or its components can be detected with conventional neuropsychological tests in otherwise healthy middle-aged adults. Our study included 201 native English speakers (ages 40-60), free of neurological or psychiatric disorders. Global cognitive function was assessed with the Mini Mental State Examination and Wechsler Abbreviated Scale of Intelligence, 2nd Edition, Block Design and Vocabulary subtests. Executive function (EF) was assessed with the Stroop Color-Word, Digit Span Backward and Trails A and B tests. Memory was assessed with the California Verbal Learning Test, Second Edition. The presence of MetS was evaluated during a health assessment, based on consensus criteria established by Alberti et. al. (2009). We hypothesized that an increased number of MetS components will be associated with poorer performance on test of executive function as frontal lobe regions critical to EF are particularly vulnerable to the effects of cardiovascular disease. We found that the number of MetS components was related to EF. A similar relationship was detected for tests of memory. Our findings support prior research linking MetS components at midlife to executive dysfunction and demonstrate that MetS and its components are associated with poorer performance on assessments of memory function. This suggests that cognitive vulnerability can be detected at midlife. Interventions for MetS at midlife could alter cognitive outcomes
Additional file 1: of Elevated neoantigen levels in tumors with somatic mutations in the HLA-A, HLA-B, HLA-C and B2M genes
Creators: name: Castro, Andrea
name: Kivilcim Ozturk
name: Pyke, Rachel
name: Xian, Su
name: Zanetti, Maurizio
name: Carter, Hannah
Publisher: name: Figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Figure S1. MHC-I complex 3D structure.Â 3D crystal structure of MHC-I complex is displayed as B2M/HLA-A complex (PDB: 3bo8). Interface (blue and violet) and core (green and orange) regions of B2M and HLA-A proteins are highlighted, respectively. Transparent blue and violet regions correspond to the surface regions of B2M and HLA-A proteins, respectively. (PDF 1324 kb)
On the multiplicative form of the Lagrangian
Creators: name: Surawuttinack, Kittikun
name: Yoo-Kong, Sikarin
name: Tanasittikosol, Monsit
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: An alternative class of the Lagrangian called the multiplicative form is suc- cessfully derived for a system with one degree of freedom for both non-relativistic and relativistic cases. This new Lagrangian can be considered as a 1-parameter: λ extended class from the standard additive form of the Lagrangian since both yield the same equation of motion. Remarkably, the multiplicative form of the Lagrangian could be treated as a generating function to produce an infinite hierar- chy of Lagrangians which give the same equation of motion. This nontrivial set of Lagrangians confirms that indeed Lagrange function is not unique.
description: 21 pages
Additional file 7: of Elevated neoantigen levels in tumors with somatic mutations in the HLA-A, HLA-B, HLA-C and B2M genes
Creators: name: Castro, Andrea
name: Kivilcim Ozturk
name: Pyke, Rachel
name: Xian, Su
name: Zanetti, Maurizio
name: Carter, Hannah
Publisher: name: Figshare
Year: 2019
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: Figure S7. Allelic fraction percentile distribution for patients with B2M and HLA mutations accounting for aneuploidy, related to Fig. 4. Allelic fraction percentile distribution for expressed mutations in MSS patients with B2M and HLA mutations, excluding all mutations occurring in regions affected by CNVs. Patients that have both B2M and HLA mutations are excluded. (PDF 330 kb)
microBiomeGSM: the identification of taxonomic biomarkers from metagenomic data using grouping, scoring and modeling (G-S-M) approach
Creators: name: Wu, Di
name: Temiz, Mustafa
name: Yousef, Malik
name: Bakir-Gungor, Burcu
name: Jabeer, Amhar
Publisher: name: Frontiers Media
Year: 2023

description: Numerous biological environments have been characterized with the advent of metagenomic sequencing using next generation sequencing which lays out the relative abundance values of microbial taxa. Modeling the human microbiome using machine learning models has the potential to identify microbial biomarkers and aid in the diagnosis of a variety of diseases such as inflammatory bowel disease, diabetes, colorectal cancer, and many others. The goal of this study is to develop an effective classification model for the analysis of metagenomic datasets associated with different diseases. In this way, we aim to identify taxonomic biomarkers associated with these diseases and facilitate disease diagnosis. The microBiomeGSM tool presented in this work incorporates the pre-existing taxonomy information into a machine learning approach and challenges to solve the classification problem in metagenomics disease-associated datasets. Based on the G-S-M (Grouping-Scoring-Modeling) approach, species level information is used as features and classified by relating their taxonomic features at different levels, including genus, family, and order. Using four different disease associated metagenomics datasets, the performance of microBiomeGSM is comparatively evaluated with other feature selection methods such as Fast Correlation Based Filter (FCBF), Select K Best (SKB), Extreme Gradient Boosting (XGB), Conditional Mutual Information Maximization (CMIM), Maximum Likelihood and Minimum Redundancy (MRMR) and Information Gain (IG), also with other classifiers such as AdaBoost, Decision Tree, LogitBoost and Random Forest. microBiomeGSM achieved the highest results with an Area under the curve (AUC) value of 0.98% at the order taxonomic level for IBDMD dataset. Another significant output of microBiomeGSM is the list of taxonomic groups that are identified as important for the disease under study and the names of the species within these groups. The association between the detected species and the disease under investigation is confirmed by previous studies in the literature. The microBiomeGSM tool and other supplementary files are publicly available at: https://github.com/malikyousef/microBiomeGSM.